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Membrane-embedded structures now available!:
Mark Sansom's lab at Oxford has created the MemProtMD database of all known transmembrane proteins embedded in lipid membranes, described in Stansfeld et al. (2015) Structure 23:1350-1361. Links to the structures are now included in mpstruc. Click on the
icon, and you will be taken to the appropriate entry in MemProtMD.
Latest new protein entered: 03 Jul 2017 at 21:57 PDT.
Last database update: 03 Jul 2017 at 21:58 PDT
- Potassium-importing KdpFABC membrane complex: Escherichia coli, 2.9 Å
- Multidrug transporter ABCG2: Homo sapiens, 3.78 Å
- NarQ nitrate/nitrite sensor histidine kinase in symmetric holo state: Escherichia coli, 1.94 Å
- Activated glucagon (GLP-1) receptor in complex with a G protein: Oryctolagus cuniculus, 4.1 Å
- GLP-1 receptor in complex with PF-06372222: Homo sapiens, 2.7 Å
- Full-length glucagon receptor (GLP-1R) in complex with a truncated peptide: Homo sapiens, 3.7 Å
Unique proteins in database = 704
Coördinate files
in database = 2244
Published reports of membrane protein structures in database = 1254
(Counts do not include pre-publication structures)
A full list of pdb codes currently in the database is available here.
Unique proteins include proteins of same type from different species. For example, photosynthetic reaction centers from R. viridis and R. sphaeroides are considered unique. Structures of mutagenized versions of proteins already in the database are excluded as unique. Proteins that differ only by substrate bound or by physiological state are also excluded. Structures 'obsoleted' by the PDB are not included.
Total number of PDB coördinate files, including those for unique proteins. This number reflects the fact that published reports of structures often include several coördinate files describing, for example, the protein in different crystal forms, or with different bound substrates.
Pre-Publication Structures (link to mpstruc bulletin board page)
A word about the new interface to the protein table.
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Limit 32 characters. Special characters in the search text should be explicitly represented. You can cut-and-paste them into the search string (the easiest approach), or they can be composed: e.g., on a mac, Å can be composed with keyboard shift-option-A. See this page for more examples. |
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0: perfect match, 10: match everything. Recommended values from 0 to 5. A value of 0 forces a case-sensitive search. (What is fuzzy search?). |
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mpstruc database queries
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There are other ways of viewing the data in the mpstruc database besides the hierarchical view presented in the table on this page. The mpstruc database queries page (follow the above link) provides a list of queries on the database, some of which provide tables with sortable columns. Some of the queries may take a few moments. Query results are also available as XML data. Currently available queries include requesting a list of unique proteins, a list of all published reports, counting unique proteins by year, and counting all published reports by year. |
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XML Representations
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An XML representation provides a convenient machine or human readable format of the portion of the data table that has been made visible, and allows you to build software tools to consume it as you see fit. You can use the URLs adjacent to the buttons below to access the same view the corresponding button provides. |
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This button generates an XML representation of the currently visible portion of the table. |
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| http://blanco.biomol.uci.edu/mpstruc/listAll/mpstrucTblXml | |
| http://blanco.biomol.uci.edu/mpstruc/listAll/mpstrucMonotopicTblXml | |
| http://blanco.biomol.uci.edu/mpstruc/listAll/mpstrucBetaBrlTblXml | |
| http://blanco.biomol.uci.edu/mpstruc/listAll/mpstrucAlphaHlxTblXml | |
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If your browser doesn’t directly display a nicely formatted XML page, it should provide a "view page source" menu selection that will. It should also provide a "save page" option so that you can download the XML formatted data. If you’re not familiar with XML and how to use it, a good source of information is available here. NOTES:Generated XML uses the following Document Type Definition (DTD):
<!DOCTYPE mpstruc [
<!ELEMENT mpstruc (caption,groups*)>
<!ATTLIST mpstruc createdBy CDATA #REQUIRED>
<!ATTLIST mpstruc maintainedBy CDATA #REQUIRED>
<!ATTLIST mpstruc copyright CDATA #REQUIRED>
<!ATTLIST mpstruc url CDATA #REQUIRED>
<!ATTLIST mpstruc lastNewProteinDate CDATA #REQUIRED>
<!ATTLIST mpstruc lastDatabaseEditDate CDATA #REQUIRED>
<!ATTLIST mpstruc timeStamp CDATA #REQUIRED>
<!ELEMENT caption (#PCDATA)>
<!ELEMENT groups (group*)>
<!ELEMENT group (name,proteins,subgroups)>
<!ELEMENT subgroups (subgroup*)>
<!ELEMENT subgroup (name,proteins)>
<!ELEMENT name (#PCDATA)>
<!ELEMENT proteins (protein*)>
<!ELEMENT memberProteins (memberProtein*)>
<!ELEMENT protein (pdbCode,name,species,taxonomicDomain,expressedInSpecies,resolution,description,bibliography,
secondaryBibliographies,relatedPdbEntries,memberProteins)>
<!ELEMENT memberProtein (pdbCode,masterProteinPdbCode,name,species,expressedInSpecies,resolution,
description,bibliography,secondaryBibliographies,relatedPdbEntries)>
<!ELEMENT pdbCode (#PCDATA)>
<!ELEMENT masterProteinPdbCode (#PCDATA)>
<!ELEMENT species (#PCDATA)>
<!ELEMENT taxonomicDomain (#PCDATA)>
<!ELEMENT expressedInSpecies (#PCDATA)>
<!ELEMENT resolution (#PCDATA)>
<!ELEMENT description (#PCDATA)>
<!ELEMENT bibliography (pubMedId,authors,year,title,journal,volume,issue,pages,doi,notes)>
<!ELEMENT pubMedId (#PCDATA)>
<!ELEMENT authors (#PCDATA)>
<!ELEMENT year (#PCDATA)>
<!ELEMENT title (#PCDATA)>
<!ELEMENT journal (#PCDATA)>
<!ELEMENT volume (#PCDATA)>
<!ELEMENT issue (#PCDATA)>
<!ELEMENT pages (#PCDATA)>
<!ELEMENT doi (#PCDATA)>
<!ELEMENT notes (#PCDATA)>
<!ELEMENT secondaryBibliographies (bibliography*)>
<!ELEMENT relatedPdbEntries (pdbCode*)>
]>
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Links to the Protein Data Bank Site
Links to the Structural Biology Knowledgebase Site
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PDB Code | Links |
Reference
(links are to PubMed) |
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MONOTOPIC MEMBRANE PROTEINS
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Cyclooxygenases
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Ram Prostaglandin H2 synthase-1 (cyclooxygenase-1 or COX-1): Ovis aries E Eukaryota, 3.5 Å
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Picot et al. (1994).
Picot D, Loll PJ, & Garavito RM (1994). The x-ray crystal structure of the membrane protein prostaglandin H2synthase-1.
Nature 367 :243-249. PubMed Id: 8121489. |
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Ram Prostaglandin H2 synthase-1 (COX-1): Ovis aries E Eukaryota, 3.4 Å
In complex with bromoaspirin. |
Loll et al. (1995).
Loll PJ, Picot D, & Garavito RM (1995). The structural basis of aspirin activity inferred from the crystal structure of inactivated prostaglandin H2 synthase.
Nat Struct Biol 2 :637-643. PubMed Id: 7552725. |
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Ram Prostaglandin H2 synthase-1 (COX-1): Ovis aries E Eukaryota, 3.1 Å
In complex with flurbiprofen. |
Garavito et al. (1995).
Garavito RM, Picot D, & Loll PJ (1995). The 3.1 A X-ray crystal structure of the integral membrane enzyme prostaglandin H2 synthase-1.
Adv Prostaglandin Thromboxane Leukot Res 23 :99-103. PubMed Id: 7732912. |
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Selinsky et al. (2001).
Selinsky BS, Gupta K, Sharkey CT, Loll PJ (2001). Structural analysis of NSAID binding by prostaglandin H2 synthase: time-dependent and time-independent inhibitors elicit identical enzyme conformations.
Biochemistry 40 :5172-5180. PubMed Id: 11318639. |
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Ram Prostaglandin H2 synthase-1 (COX-1): Ovis aries E Eukaryota, 3.2 Å
In complex with O-actylsalicylhydroxamic acid. |
Loll et al. (2001).
Loll PJ, Sharkey CT, O'Connor SJ, Dooley CM, O'Brien E, Devocelle M, Nolan KB, Selinsky BS, & Fitzgerald DJ (2001). O-acetylsalicylhydroxamic acid, a novel acetylating inhibitor of prostaglandin H2 synthase: structural and functional characterization of enzyme-inhibitor interactions.
Mol Pharmacol 60 :1407-1413. PubMed Id: 11723249. |
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Ram Prostaglandin H2 synthase-1 (COX-1): Ovis aries E Eukaryota, 2.00 Å
In complex with alpha-methyl-4-biphenyl acetic acid. |
Gupta et al. (2004).
Gupta K, Selinsky BS, Kaub CJ, Katz AK, & Loll PJ (2004). The 2.0 Å resolution crystal structure of prostaglandin H2 synthase-1: structural insights into an unusual peroxidase.
J Mol Biol 335 :503-518. PubMed Id: 14672659. |
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Ram Prostaglandin H2 synthase-1 (COX-1): Ovis aries E Eukaryota, 2.00 Å
In complex with flurbiprofen + Mn(III) PPIX cofactor. |
Gupta et al. (2006).
Gupta K, Selinsky BS, & Loll PJ (2006). 2.0 angstroms structure of prostaglandin H2 synthase-1 reconstituted with a manganese porphyrin cofactor.
Acta Crystallogr D Biol Crystallogr 62 :151-156. PubMed Id: 16421446. |
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Ram Prostaglandin H2 synthase-1 (COX-1): Ovis aries E Eukaryota (expressed in Spodoptera frugiperda), 3.05 Å
3N8V is the unoccupied structure. R120Q/Native Heterodimer mutant in complex with Flurbiprofen, 2.75 Å: 3N8W COX-1 in complex with Nimesulide, 2.75 Å: 3N8X Aspirin Acetylated COX-1 in Complex with Diclofenac, 2.60 Å: 3N8Y COX-1 in Complex with Flurbiprofen, 2.90 Å: 3N8Z |
Sidhu et al. (2010).
Sidhu RS, Lee JY, Yuan C, & Smith WL (2010). Comparison of Cyclooxygenase-1 Crystal Structures: Cross-Talk between Monomers Comprising Cyclooxygenase-1 Homodimers.
Biochemistry 49 :7069-7079. PubMed Id: 20669977. |
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Cyclooxygenase-2: Mus musculus E Eukaryota, 3.0 Å
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Kurumbail et al. (1996).
Kurumbail RG, Stevens AM, Gierse JK, McDonald JJ, Stegeman RA, Pak JY, Gildehaus D, Miyashiro JM, Penning TD, Seibert, K et al (1996). Structural basis for selective inhibition of cyclooxygenase-2 by anti-inflammatory agents.
Nature 384 :644-648. PubMed Id: 8967954. |
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Fatty acid α-dioxygenase (α-DOX): Arabidopsis thaliana E Eukaryota (expressed in E. coli), 1.70 Å
First structure of a member of the α-DOX subfamily of cyclooxygenase-perixidase family of heme-containing proteins. With bound imidazole, 1.51 Å: 4HHR |
Goulah et al. (2013).
Goulah CC, Zhu G, Koszelak-Rosenblum M, & Malkowski MG (2013). The Crystal Structure of α-Dioxygenase Provides Insight into Diversity in the Cyclooxygenase-Peroxidase Superfamily.
Biochemistry 52 :1364-1372. PubMed Id: 23373518. doi:10.1021/bi400013k. |
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Lipoxygenases
Related to Cyclooxygenases Rather than being tethered by α-helices at the interface, they are tethered by N-terminal β-sheet C2-like domains |
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Arachidonic acid 15-lipoxygenase from soybeans: Glycine max E Eukaryota, 2.60 Å
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Boyington et al. (1993).
Boyington JC, Gaffney BJ, & Amzel LM (1993). The three-dimensional structure of an arachidonic acid 15-lipoxygenase.
Science 260 5113:1482-1486. PubMed Id: 8502991. doi:10.1126/science.8502991. |
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Lipoxygenase-L1 from soybeans: Glycine max E Eukaryota, 1.40 Å
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Minor et al. (1996).
Minor W, Steczko J, Stec B, Otwinowski Z, Bolin JT, Walter R, & Axelrod B (1996). Crystal structure of soybean lipoxygenase L-1 at 1.4 A resolution.
Biochemistry 35 33:10687-10701. PubMed Id: 8718858. doi:10.1021/bi960576u. |
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Lipoxygenase-L3 from soybeans: Glycine max E Eukaryota, 2.60 Å
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Skrzypczak-Jankun et al. (1997).
Skrzypczak-Jankun E, Amzel LM, Kroa BA, & Funk MO Jr (1997). Structure of soybean lipoxygenase L3 and a comparison with its L1 isoenzyme.
Proteins 29 1:15-31. PubMed Id: 9294864. doi:10.1002/(SICI)1097-0134(199709)29:1. |
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8R-Lipoxygenase from coral: Plexaura homomalla E Eukaryota (expressed in E. coli), 3.20 Å
2FNQ supersedes 1ZQ4 |
Oldham et al. (2005).
Oldham ML, Brash AR, & Newcomer ME (2005). Insights from the X-ray crystal structure of coral 8R-lipoxygenase: calcium activation via a C2-like domain and a structural basis of product chirality.
J Biol Chem 280 47:39545-39552. PubMed Id: 16162493. doi:10.1074/jbc.M506675200. |
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8R-Lipoxygenase from coral. Δ413-417 I805A mutant: Plexaura homomalla E Eukaryota (expressed in E. coli), 1.85 Å
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Neau et al. (2009).
Neau DB, Gilbert NC, Bartlett SG, Boeglin W, Brash AR, & Newcomer ME (2009). The 1.85 A structure of an 8R-lipoxygenase suggests a general model for lipoxygenase product specificity.
Biochemistry 48 33:7906-7915. PubMed Id: 19594169. doi:10.1021/bi900084m. |
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15-Lipoxygenase from rabbit reticulocytes: Oryctolagus cuniculus E Eukaryota, 2.40 Å
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Gillmor et al. (1997).
Gillmor SA, Villaseñor A, Fletterick R, Sigal E, & Browner MF (1997). The structure of mammalian 15-lipoxygenase reveals similarity to the lipases and the determinants of substrate specificity.
Nat Struct Mol Biol 4 12:1003-1009. PubMed Id: 9406550. doi:10.1038/nsb1297-1003 . |
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5-Lipoxygenase: Homo sapiens E Eukaryota (expressed in E. coli), 2.39 Å
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Gilbert et al. (2011).
Gilbert NC, Bartlett SG, Waight MT, Neau DB, Boeglin WE, Brash AR, & Newcomer ME (2011). The structure of human 5-lipoxygenase.
Science 331 :217-219. PubMed Id: 21233389. doi:10.1126/science.1197203. |
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15-Lipoxygenase-2 (15-LOX-2) with substrate mimic: Homo sapiens E Eukaryota (expressed in E. coli), 2.63 Å
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Kobe et al. (2014).
Kobe MJ, Neau DB, Mitchell CE, Bartlett SG, & Newcomer ME (2014). The structure of human 15-lipoxygenase-2 with a substrate mimic.
J Biol Chem 289 :8562-8569. PubMed Id: 24497644. doi:10.1074/jbc.M113.543777. |
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Squalene-Hopene Cyclases
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Squalene-hopene cyclase: Alicyclobacillus acidocaldarius B Bacteria, 2.0 Å
2SQC is space group P43212. 3SQC, 2.8 Å is P3221. |
Wendt et al. (1999).
Wendt KU, Lenhart A, & Schulz GE (1999). The structure of the membrane protein squalene-hopene cyclase at 2.0 Å resolution.
J. Mol. Biol. 286 :175-187. PubMed Id: 9931258. |
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Oxidases
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Monoamine Oxidase B: Homo sapiens (Human) mitochondrial outer membrane E Eukaryota (expressed in Pichia pastoris), 3.0 Å
NOTE: MAOB has a single transmembrane helix that anchors it to the outer membrane (residues 489-515). Nevertheless, we consider it monotopic because the bulk of the 520-residue protein, including the active site, is not located within the membrane core. |
Binda et al. (2002).
Binda C, Newton-Vinson P, Hubálek F, Edmondson DE, & Mattevi A (2002). Structure of human monoamine oxidase B, a drug target for the treatment of neurological disorders.
Nature Struct Biol 9 :22-26. PubMed Id: 11753429. |
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Monoamine Oxidase B with bound Isatin: Homo sapiens (Human) mitochondrial outer membrane E Eukaryota (expressed in Pichia pastoris), 1.70 Å
with bound Tranylcypromine, 2.20 Å: 1OJB with bound N-(2-aminoethyl)-p-chlorobenamide, 2.40 Å: 1OJC with bound Lauryldimethyl-amine N-Oxide, 3.10 Å: 1OJD with bound 1.4-Diphenyl-2-butene, 2.30 Å: 1OJ9 |
Binda et al. (2003).
Binda C, Li M, Hubálek F, Restelli N, Edmondson DE, & Mattevi A (2003). Insights into the mode of inhibition of human mitochondrial monoamine oxidase B from high-resolution crystal structures.
Proc Natl Acad Sci USA 100 :9750-9755. PubMed Id: 12913124. |
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Monoamine Oxidase A: Rattus norvegicus (Rat) mitochondrial outer membrane E Eukaryota (expressed in S. cerevisiae), 3.20 Å
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Ma et al. (2004).
Ma J, Yoshimura M, Yamashita E, Nakagawa A, Ito A, & Tsukihara T (2004). Structure of rat monoamine oxidase A and its specific recognitions for substrates and inhibitors.
J Mol Biol 338 :103-114. PubMed Id: 15050826. |
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De Colibus et al. (2005).
De Colibus L, Li M, Binda C, Lustig A, Edmondson DE, & Mattevi A (2005). Three-dimensional structure of human monoamine oxidase A (MAO A): relation to the structures of rat MAO A and human MAO B.
Proc Natl Acad Sci USA 102 :12684-12689. PubMed Id: 16129825. |
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Monoamine Oxidase A with bound Harmine: Homo sapiens (Human) mitochondrial outer membrane E Eukaryota (expressed in S. cerevisiae), 2.20 Å
G110A mutant with bound Harmine, 2.17 Å: 2Z5Y |
Son et al. (2008).
Son SY, Ma J, Kondou Y, Yoshimura M, Yamashita E, & Tsukihara T (2008). Structure of human monoamine oxidase A at 2.2-Å resolution: The control of opening the entry for substrates/inhibitors.
Proc Natl Acad Sci USA 105 :5739-5744. PubMed Id: 18391214. |
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Shiba et al. (2013).
Shiba T, Kido Y, Sakamoto K, Inaoka DK, Tsuge C, Tatsumi R, Takahashi G, Balogun EO, Nara T, Aoki T, Honma T, Tanaka A, Inoue M, Matsuoka S, Saimoto H, Moore AL, Harada S, & Kita K (2013). Structure of the trypanosome cyanide-insensitive alternative oxidase.
Proc Natl Acad Sci USA 110 :4580-4585. PubMed Id: 23487766. doi:10.1073/pnas.1218386110. |
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Hydrolases
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Fatty acid amide hydrolase: Rattus norvegicus E Eukaryota, 2.8 Å
NOTE: Like MAO, FAAH has a single TM segment. But the active site is external to the membrane, and many other residues on the protein surface contribute to membrane binding. Absence of the TM segment affects neither membrane association or function. |
Bracey et al. (2002).
Bracey MH, Hanson MA, Masuda KR, Stevens RC, & Cravatt BF (2002). Structural adaptations in a membrane enzyme that terminates endo cannabinoid signaling.
Science 298 :1793-1796. PubMed Id: 12459591. |
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Okada et al. (2016).
Okada C, Wakabayashi H, Kobayashi M, Shinoda A, Tanaka I, & Yao M (2016). Crystal structures of the UDP-diacylglucosamine pyrophosphohydrase LpxH from Pseudomonas aeruginosa.
Sci Rep 6 :32822. PubMed Id: 27609419. doi:10.1038/srep32822. |
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LpxI phosphodiester hydrolase for lipid A biosynthesis: Caulobacter crescentus B Bacteria (expressed in E. coli), 2.90 Å
D225A mutant, 2.52 Å: 4GGI |
Metzger et al. (2012).
Metzger LE 4th, Lee JK, Finer-Moore JS, Raetz CR, & Stroud RM (2012). LpxI structures reveal how a lipid A precursor is synthesized.
Nature Struc Mol Biol 19 :1132-1138. PubMed Id: 23042606. doi:10.1038/nsmb.2393. |
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Emptage et al. (2012).
Emptage RP, Daughtry KD, Pemble CW 4th, & Raetz CR (2012). Crystal structure of LpxK, the 4'-kinase of lipid A biosynthesis and atypical P-loop kinase functioning at the membrane interface.
Proc Natl Acad Sci USA 109 :12956-12961. PubMed Id: 22826246. doi:10.1073/pnas.1206072109. |
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N-acylphosphatidylethanolamine-hydrolyzing phospholipase D: Homo sapiens E Eukaryota (expressed in E. coli), 2.65 Å
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Magotti et al. (2015).
Magotti P, Bauer I, Igarashi M, Babagoli M, Marotta R, Piomelli D, & Garau G (2015). Structure of human N-acylphosphatidylethanolamine-hydrolyzing phospholipase D: regulation of Fatty Acid ethanolamide biosynthesis by bile acids.
Structure 23 3:598-604. PubMed Id: 25684574. doi:10.1016/j.str.2014.12.018. |
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PulA pullulanase: Klebsiella oxytoca B Bacteria (expressed in E. coli), 2.88 Å
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East et al. (2016).
East A, Mechaly AE, Huysmans GH, Bernarde C, Tello-Manigne D, Nadeau N, Pugsley AP, Buschiazzo A, Alzari PM, Bond PJ, & Francetic O (2016). Structural Basis of Pullulanase Membrane Binding and Secretion Revealed by X-Ray Crystallography, Molecular Dynamics and Biochemical Analysis.
Structure 24 :92-104. PubMed Id: 26688215. doi:10.1016/j.str.2015.10.023. |
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Acyltransferases
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LpxM lipid A acyltransferase: Acinetobacter baumannii B Bacteria (expressed in E. coli), 1.99 Å
The protein is anchored at the membrane interface by a single TM helix. E127A catalytic residue mutant, 1.9 Å: 5KNK |
Dovala et al. (2016).
Dovala D, Rath CM, Hu Q, Sawyer WS, Shia S, Elling RA, Knapp MS, & Metzger LE 4th (2016). Structure-guided enzymology of the lipid A acyltransferase LpxM reveals a dual activity mechanism.
Proc Natl Acad Sci USA 113 :E6064-E6071. PubMed Id: 27681620. doi:10.1073/pnas.1610746113. |
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Oxidoreductases (Monotopic)
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Sulfide:quinone oxidoreductase in complex with decylubiquinone: Aquifex aeolicus B Bacteria, 2.0 Å
"as-purified" protein, 2.30 Å: 3HYV in complex with aurachin C, 2.9 Å: 3HYX This monotopic membrane protein is thought to be buried about 12 Å in the bilayer interface. Listed under TRANSMEMBRANE PROTEINS: ALPHA-HELICAL : Oxidoreductases, MONOTOPIC MEMBRANE PROTEINS : Oxidoreductases (Monotopic). |
Marcia et al. (2009).
Marcia M, Ermler U, Peng G, & Michel H (2009). The structure of Aquifex aeolicus sulfide:quinone oxidoreductase, a basis to understand sulfide detoxification and respiration.
Proc Natl Acad Sci USA 106 :9625-9630. PubMed Id: 19487671. |
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Electron Transfer Flavoprotein-ubiquinone oxidoreductase (ETF-QO) with bound UQ: Sus scrofa E Eukaryota, 2.5 Å
UQ-free structure, 2.6 Å: 2GMJ. Because this is a mitochondrial respiratory chain protein, it is listed under TRANSMEMBRANE PROTEINS: ALPHA-HELICAL : Oxidoreductases and MONOTOPIC MEMBRANE PROTEINS : Oxidoreductases (Monotopic). |
Zhang et al. (2006).
Zhang J, Frerman FE, & Kim J-JP (2006). Structure of electron transfer flavoprotein-ubiquinone oxidoreductase and electron transfer to the mitochondrial ubiquinone pool.
Proc Natl Acad Sci U S A 103 :16212-16217. PubMed Id: 17050691. |
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Dehydrogenases
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Glycerol-3-phosphate dehydrogenase (GlpD, native): Escherichia coli B Bacteria, 1.75 Å
SeMet-GlpD, 1.95 Å: 2R4J GlpD-2-PGA, 2.3 Å: 2R45 GlpD-PEP, 2.1 Å: 2R46 GlpD-DHAP, 2.1 Å: 2R4E Listed under MONOTOPIC MEMBRANE PROTEINS : Dehydrogenases, TRANSMEMBRANE PROTEINS: ALPHA-HELICAL : Oxidoreductases. |
Yeh et al. (2008).
Yeh JI, Chinte U, & Du S (2008). Structure of glycerol-3-phosphate dehydrogenase, an essential monotopic membrane enzyme involved in respiration and metabolism.
Proc. Natl. Acad. Sci. USA 105 :3280-3285. PubMed Id: 18296637. |
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PutA proline utilization protein: Geobacter sulfurreducens B Bacteria (expressed in E. coli), 1.90 Å
in complex with L-tetrahydro-2-furoic acid, 2.10 Å: 4NMA in complex with L-lactate, 2.2 Å: 4NMB in complex with Zwittergent 3-12, 1.90 Å: 4NMC reduced with dithionite, 1.98 Å: 4NMD inactivated by N-propargylglycine, 2.09 Å: 4NME inactivated by N-propargylglycine and complexed with menadione bisulfite, 1.95 Å: 4NMF |
Singh et al. (2014).
Singh H, Arentson BW, Becker DF, & Tanner JJ (2014). Structures of the PutA peripheral membrane flavoenzyme reveal a dynamic substrate-channeling tunnel and the quinone-binding site.
Proc Natl Acad Sci USA 111 :3389-3394. PubMed Id: 24550478. doi:10.1073/pnas.1321621111. |
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Iwata et al. (2012).
Iwata M, Lee Y, Yamashita T, Yagi T, Iwata S, Cameron AD, & Maher MJ (2012). The structure of the yeast NADH dehydrogenase (Ndi1) reveals overlapping binding sites for water- and lipid-soluble substrates.
Proc Natl Acad Sci USA 109 :15247-15252. PubMed Id: 22949654. doi:10.1073/pnas.1210059109 . |
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Feng et al. (2012).
Feng Y, Li W, Li J, Wang J, Ge J, Xu D, Liu Y, Wu K, Zeng Q, Wu JW, Tian C, Zhou B, & Yang M (2012). Structural insight into the type-II mitochondrial NADH dehydrogenases.
Nature 491 :478-482. PubMed Id: 23086143. doi:10.1038/nature11541. |
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NDH-2 NADH dehydrogenase: Caldalkalibacillus thermarum B Bacteria (expressed in E. coli), 2.50 Å
NDH-2 is a non-proton pumping dehydrogenase. |
Heikal et al. (2014).
Heikal A, Nakatani Y, Dunn E, Weimar MR, Day CL, Baker EN, Lott JS, Sazanov LA, & Cook GM (2014). Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane protein with an essential role in energy generation.
Mol Microbiol 91 5:950-964. PubMed Id: 24444429. doi:10.1111/mmi.12507. |
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Glycosyltransferases
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Peptidoglycan Glycosyltransferase: Staphylococcus aureus B Bacteria, 2.8 Å
NOTE: The enzyme has a single TM segment, which is absent in the structure. The active site is external to the membrane, but the so-called Jaw Region contributes to membrane binding. 2OLV shows the enzyme complexed with moenomycin. 2OLU is the structure of the apoenzyme. |
Lovering et al. (2007).
Lovering AL, de Castro LH, Lim D, & Strynadka NCJ (2007). Structural insight into the transglycosylation step in bacterial cell-wall biosynthesis.
Science 315 :1402-1405. PubMed Id: 17347437. |
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Peptidoglycan Glycosyltransferase penicillin-binding protein 1a (PBP1a): Aquifex aeolicus B Bacteria (expressed in E. coli), 2.1 Å
NOTE: The enzyme has a single TM segment, which is absent in the structure. The active site is external to the membrane. |
Yuan et al. (2007).
Yuan Y, Barrett D, Zhang Y, Kahne D, Sliz P, & Walker S. (2007). Crystal structure of a peptidoglycan glycosyltransferase suggests a model for processive glycan chain synthesis.
Proc Natl Acad Sci USA 104 :5348-5353. PubMed Id: 17360321. |
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Peptidoglycan Glycosyltransferase penicillin-binding protein 1b (PBP1b): Escherichia coli B Bacteria, 2.16 Å
3VMA supersedes the original PDB entry 3FWM. NOTE: The single TM segment is present in this structure. The active site is external to the membrane. SeMet Protein, 3.09 Å: 3FWL |
Sung et al. (2009).
Sung MT, Lai YT, Huang CY, Chou LY, Shih HW, Cheng WC, Wong CH, & Ma C (2009). Crystal structure of the membrane-bound bifunctional transglycosylase PBP1b from Escherichia coli.
Proc Natl Acad Sci USA 106 :8824-8829. PubMed Id: 19458048. |
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Monofunctional glycosyltransferase WaaA, substrate free: Aquifex aeolicus B Bacteria (expressed in E. coli), 2.00 Å
WaaA catalyzes the transfer of Kdo to the lipid A precursor of lipopolysaccharide. Structure with substrate, 2.42 Å: 2XCU |
Schmidt et al. (2012).
Schmidt H, Hansen G, Singh S, Hanuszkiewicz A, Lindner B, Fukase K, Woodard RW, Holst O, Hilgenfeld R, Mamat U, & Mesters JR (2012). Structural and mechanistic analysis of the membrane-embedded glycosyltransferase WaaA required for lipopolysaccharide synthesis.
Proc Natl Acad Sci USA 109 :6253-6258. PubMed Id: 22474366. doi:10.1073/pnas.1119894109. |
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Monofunctional glycosyltransferase in complex with Lipid II analog: Staphylococcus aureus B Bacteria (expressed in E. coli), 2.30 Å
NOTE: The single TM segment is present in this structure. The active site is external to the membrane. Substrate-free protein, 2.52 Å: 3VMQ In complex with moenomycin, 3.69 Å: 3VMR In complex with NBD-Lipid II, 3.20 Å: 3VMS |
Huang et al. (2012).
Huang CY, Shih HW, Lin LY, Tien YW, Cheng TJ, Cheng WC, Wong CH, & Ma C (2012). Crystal structure of Staphylococcus aureus transglycosylase in complex with a lipid II analog and elucidation of peptidoglycan synthesis mechanism.
Proc Natl Acad Sci USA 109 :6496-6501. PubMed Id: 22493270. doi:10.1073/pnas.1203900109. |
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Peptidases
|
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LepB Signal Peptidase (SPase) in complex with a β-lactam inhibitor: Escherichia coli B Bacteria, 1.9 Å
Located in the periplasmic space, the SPase has two transmembrane segments (AAs 4-28 & 58-76), which are missing in this structure. The Ser-Lys catalytic site is part of a hydrophobic surface that interacts strongly with the membrane. |
Paetzel et al. (1998).
Paetzel M, Dalbey RE, & Strynadka NC (1998). Crystal structure of a bacterial signal peptidase in complex with a β-lactam inhibitor.
Nature 396 :186-190. PubMed Id: 9823901. |
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LepB Signal Peptidase (SPase), apoprotein: Escherichia coli B Bacteria, 2.40 Å
Δ2-75 protein lacking the two transmembrane helices |
Paetzel et al. (2002).
Paetzel M, Dalbey RE, & Strynadka NC (2002). Crystal structure of a bacterial signal peptidase apoenzyme
J Biol Chem 277 :9512-9519. PubMed Id: 11741964. |
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LepB Signal Peptidase (SPase) in complex with a lipopeptide inhibitor: Escherichia coli B Bacteria, 2.47 Å
This structure of the Δ2-75 protein reveals the likely position of the signal peptide in the active site. |
Paetzel et al. (2004).
Paetzel M, Goodall JJ, Kania M, Dalbey RE, & Page MG (2004). Crystallographic and biophysical analysis of a bacterial signal peptidase in complex with a lipopeptide-based inhibitor.
J Biol Chem 279 :30781-30790. PubMed Id: 15136583. |
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Ting et al. (2015).
Ting YT, Batot G, Baker EN, & Young PG (2015). Expression, purification and crystallization of a membrane-associated, catalytically active type I signal peptidase from Staphylococcus aureus.
Acta Crystallogr F Struct Biol Commun 71 :61-65. PubMed Id: 25615971. doi:10.1107/S2053230X1402603X. |
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Signal Peptide Peptidase (SppA), native protein: Escherichia coli B Bacteria, 2.55 Å
SeMet protein, 2.76 Å: 3BEZ. Long thought to be a transmembrane protein, the structure reveals a peripheral homotetramer that likely is buried in the membrane interface. Each monomer has a putative N-terminal transmembrane helix for anchoring to the membrane. This anchor was removed for crystallization. Listed under TRANSMEMBRANE PROTEINS: ALPHA-HELICAL : Intramembrane Proteases, MONOTOPIC MEMBRANE PROTEINS : Peptidases. |
Kim et al. (2008).
Kim AC, Oliver DC, & Paetzel M (2008). Crystal structure of a bacterial signal Peptide peptidase.
J Mol Biol 376 :352-366. PubMed Id: 18164727. |
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Signal Peptide Peptidase (SppA): Bacillus subtilis B Bacteria (expressed in E. coli), 2.37 Å
Each monomer of the homooctamer has a putative N-terminal transmembrane helix for anchoring to the membrane. This anchor was removed for crystallization. Listed under TRANSMEMBRANE PROTEINS: ALPHA-HELICAL : Intramembrane Proteases, MONOTOPIC MEMBRANE PROTEINS : Peptidases. |
Nam et al. (2012).
Nam SE, Kim AC, & Paetzel M (2012). Crystal Structure of Bacillus subtilis Signal Peptide Peptidase A.
J Mol Biol 419 :347-358. PubMed Id: 22472423. doi:10.1016/j.jmb.2012.03.020. |
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Signal Peptide Peptidase (SppA) K199A mutant showing C-terminal peptide bound in eight active sites: Bacillus subtilis B Bacteria (expressed in E. coli), 2.39 Å
Each monomer of the homooctamer has a putative N-terminal transmembrane helix for anchoring to the membrane. This anchor was removed for crystallization. Listed under TRANSMEMBRANE PROTEINS: ALPHA-HELICAL : Intramembrane Proteases, MONOTOPIC MEMBRANE PROTEINS : Peptidases. |
Nam & Paetzel (2013).
Nam SE, & Paetzel M (2013). Structure of Signal Peptide Peptidase A with C-Termini Bound in the Active Sites: Insights into Specificity, Self-Processing, and Regulation.
Biochemistry 52 :8811-8822. PubMed Id: 24228759. |
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Meprin β sheddase (metalloproteinase), pro-form: Homo sapiens E Eukaryota (expressed in Trichoplusia ni), 1.85 Å
Mature form, 3.00 Å: 4GWN |
Arolas et al. (2012).
Arolas JL, Broder C, Jefferson T, Guevara T, Sterchi EE, Bode W, Stöcker W, Becker-Pauly C, & Gomis-Rüth FX (2012). Structural basis for the sheddase function of human meprin β metalloproteinase at the plasma membrane.
Proc Natl Acad Sci USA 109 :16131-16136. PubMed Id: 22988105. doi:10.1073/pnas.1211076109. |
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Cytochromes P450
P450s are members of the CYP51 family involved in sterol biosynthesis |
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Lanosterol 14α-demethylase with bound lanosterol: Saccharomyces cerevisiae E Eukaryota, 1.90 Å
with bound itraconazole, 2.19 Å: 5EQB. Supersedes 4K0F. This is the first structure of a full-length single-span 'bitopic' membrane protein. Proteins of this structural type are anchored at the membrane surface by one or two TM segments, which are generally not seen in the structures. See, for example, 1B12. |
Monk et al. (2014).
Monk BC, Tomasiak TM, Keniya MV, Huschmann FU, Tyndall JD, O'Connell JD 3rd, Cannon RD, McDonald JG, Rodriguez A, Finer-Moore JS, & Stroud RM (2014). Architecture of a single membrane spanning cytochrome P450 suggests constraints that orient the catalytic domain relative to a bilayer.
Proc Natl Acad Sci USA 111 :3865-3870. PubMed Id: 24613931. doi:10.1073/pnas.1324245111. |
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Dihydroorotate Dehydrogenases (DHODH, class 2)
Class 1 DHODHs are soluble proteins. Class 2 are membrane associated proteins. |
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Dihydroorotate Dehydrogenase: Escherichia coli B Bacteria, 1.70 Å
|
Thoden et al. (2001).
Thoden JB, Phillips GN Jr, Neal TM, Raushel FM, & Holden HM (2001). Molecular structure of dihydroorotase: a paradigm for catalysis through the use of a binuclear metal center.
Biochemistry 40 :6989-6997. PubMed Id: 11401542. |
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Dihydroorotate Dehydrogenase: Escherichia coli B Bacteria, 1.90 Å
|
Lee et al. (2005).
Lee M, Chan CW, Mitchell Guss J, Christopherson RI, & Maher MJ (2005). Dihydroorotase from Escherichia coli: loop movement and cooperativity between subunits.
J Mol Biol 348 :523-533. PubMed Id: 15826651. |
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Dihydroorotate Dehydrogenase in complex with atovaquone: Rattus rattus E Eukaryota (expressed in E. coli), 2.30 Å
DHO in complex with brequinar, 2.40 Å: 1UUO |
Hansen et al. (2004).
Hansen M, Le Nours J, Johansson E, Antal T, Ullrich A, Löffler M, & Larsen S (2004). Inhibitor binding in a class 2 dihydroorotate dehydrogenase causes variations in the membrane-associated N-terminal domain.
Protein Sci 13 :1031-1042. PubMed Id: 15044733. |
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Walse et al. (2008).
Walse B, Dufe VT, Svensson B, Fritzson I, Dahlberg L, Khairoullina A, Wellmar U, & Al-Karadaghi S (2008). The structures of human dihydroorotate dehydrogenase with and without inhibitor reveal conformational flexibility in the inhibitor and substrate binding sites.
Biochemistry 47 :8929-8936. PubMed Id: 18672895. |
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Deng et al. (2009).
Deng X, Gujjar R, El Mazouni F, Kaminsky W, Malmquist NA, Goldsmith EJ, Rathod PK, & Phillips MA (2009). Structural plasticity of malaria dihydroorotate dehydrogenase allows selective binding of diverse chemical scaffolds.
J Biol Chem 284 :26999-27009. PubMed Id: 19640844. |
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Polymerases
|
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|
Lovering et al. (2010).
Lovering AL, Lin LY, Sewell EW, Spreter T, Brown ED, & Strynadka NC (2010). Structure of the bacterial teichoic acid polymerase TagF provides insights into membrane association and catalysis.
Nat Struct Mol Biol 17 :582-589. PubMed Id: 20400947. |
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ADP-Ribosylation Factors
|
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ADP-ribosylation factor (ARF1), myristoylated: Saccharomyces cerevisiae E Eukaryota (expressed in E. coli), NMR Structure
|
Liu et al. (2009).
Liu Y, Kahn RA, & Prestegard JH (2009). Structure and Membrane Interaction of Myristoylated ARF1.
Structure 17 :79-87. PubMed Id: 19141284. |
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ADP-ribosylation factor (ARF1*GTP), myristoylated: Saccharomyces cerevisiae E Eukaryota (expressed in E. coli), NMR Structure
|
Liu et al. (2010).
Liu Y, Kahn RA, & Prestegard JH (2010). Dynamic structure of membrane-anchored Arf*GTP.
Nature Struct Molec Biol 17 :876-881. PubMed Id: 20601958. |
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Isomerases
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RPE65 visual cycle retinoid isomerase: Bos taurus E Eukaryota, 2.14 Å
This retinal pigment epithelium (RPE) protein simultaneously cleaves and isomerizes all-trans-retinyl esters to 11-cis-retinol and a fatty acid. |
Kiser et al. (2009).
Kiser PD, Golczak M, Lodowski DT, Chance MR, Palczewski K (2009). Crystal structure of native RPE65, the retinoid isomerase of the visual cycle.
Proc Natl Acad Sci USA 106 :17325-17330. PubMed Id: 19805034. |
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Kiser et al. (2012).
Kiser PD, Farquhar ER, Shi W, Sui X, Chance MR, & Palczewski K (2012). Structure of RPE65 isomerase in a lipidic matrix reveals roles for phospholipids and iron in catalysis.
Proc Natl Acad Sci USA 109 :E2747-2756. PubMed Id: 23012475. |
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Phosphoinositide Kinases
|
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Phosphatidylinositol 4-kinase IIα: Homo sapiens E Eukaryota (expressed in E. coli), 2.77 Å
|
Baumlova et al. (2014).
Baumlova A, Chalupska D, Róźycki B, Jovic M, Wisniewski E, Klima M, Dubankova A, Kloer DP, Nencka R, Balla T, & Boura E (2014). The crystal structure of the phosphatidylinositol 4-kinase II?.
EMBO Rep 15 :1085-1092. PubMed Id: 25168678. doi:10.15252/embr.201438841. |
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TRANSMEMBRANE PROTEINS: BETA-BARREL
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Beta-Barrel Membrane Proteins: Porins and Relatives
|
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Porin: Rhodobacter capsulatus B Bacteria, 1.8 Å
|
Weiss & Schulz (1992).
Weiss MS & Schulz GE (1992). Structure of porin refined at 1.8 Å resolution.
J. Mol. Biol. 227 :493-509. PubMed Id: 1328651. |
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Porin: Rhodopeudomonas blastica B Bacteria, 1.96 Å
|
Kreusch & Schulz (1994).
Kreusch A & Schulz GE (1994). Refined structure of the porin from Rhodopseudomonas blastica. Comparison with the porin from Rhodobacter capsulatus.
J Mol Biol 243 :891-905. PubMed Id: 7525973. doi:10.1006/jmbi.1994.1690. See also: Kreusch et al. (1994). Kreusch A, Neubüser A, Schiltz E, Weckesser J, & Schulz GE (1994). Structure of the membrane channel porin from Rhodopseudomonas blastica at 2.0 Å resolution.
Protein Sci 3 :58-63. PubMed Id: 8142898. doi:10.1002/pro.5560030108. |
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Porin, E1M/A116K Mutant: Rhodopseudomonas blastica B Bacteria (expressed in E. coli), 2.19 Å
E1M/E99W/A116W mutant, 1.93 Å: 2PRN E1M/A104W mutant, 1.90 Å: 3PRN E1M/Y96W/S119W mutant, 2.00 Å: 5PRN E1M/K50A/R52A mutant, 2.04 Å: 6PRN E1M/D97A/E99A mutant, 2.25 Å: 7PRN E1M/K50A/R52A/D97A/E99A mutant, 2.30 Å: 8PRN |
Schmid et al. (1998).
Schmid B, Maveyraud L, Krömer M, & Schulz GE (1998). Porin mutants with new channel properties.
Protein Sci 7 :1603-1611. PubMed Id: 9684893. doi:10.1002/pro.5560070714. |
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Porin: Rhodopseudomonas blastica B Bacteria (expressed in E. coli), 3.00 Å
Positively charged peptide GGGGPKLAKMEKARGGGG inserted in periplasmic turn. |
Bannwarth & Schulz (2002).
Bannwarth M & Schulz GE (2002). Asymmetric conductivity of engineered porins.
Protein Eng 15 :799-804. PubMed Id: 12468713. doi:10.1093/protein/15.10.799. |
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OmpK36 osmoporin: Klebsiella pneumoniae B Bacteria, 3.2 Å
|
Dutzler et al. (1999).
Dutzler R, Rummel G, Alberti S, Hernandez-Alles S, Phale P, Rosenbusch J, Benedi V, & Schirmer T (1999). Crystal structure and functional characterization of OmpK36, the osmoporin of Klebsiella pneumoniae.
Structure Fold. Des 7 :425-434. PubMed Id: 10196126. |
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Omp32 anion-selective porin: Comamonas acidovorans B Bacteria, 2.1 Å
|
Zeth et al. (2000).
Zeth K, Diederichs K, Welte W, & Engelhardt H (2000). Crystal structure of Omp32, the anion-selective porin from Comamonas acidovorans, in complex with a periplasmic peptide at 2.1 A resolution.
Structure 8 :981-992. PubMed Id: 10986465. |
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Zachariae et al. (2006).
Zachariae U, Kluhspies T, De S, Engelhardt H, & Zeth K (2006). High resolution crystal structures and molecular dynamics studies reveal substrate binding in the porin omp32.
J Biol Chem 281 :7413-7420. PubMed Id: 16434398. |
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OmpF Porin: Escherichia coli B Bacteria, 2.4 Å
Note: Also see BtuB with bound colicin E3 R-domain, below. |
Cowan et al. (1992).
Cowan SW, Schirmer T, Rummel G, Steiert M, Ghosh R, Pauptit RA, Jansonius JN, & Rosenbusch JP (1992). Crystal structures explain functional properties of two Escherichia coli porins.
Nature 358 :727-733. PubMed Id: 1380671. |
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OmpF Porin from colicin-resistant E. coli: Escherichia coli B Bacteria, 3.00 Å
|
Jeanteur et al. (1994).
Jeanteur D, Schirmer T, Fourel D, Simonet V, Rummel G, Widmer C, Rosenbusch JP, Pattus F, & Pagès JM (1994). Structural and functional alterations of a colicin-resistant mutant of OmpF porin from Escherichia coli.
Proc Natl Acad Sci USA 91 :10675-10679. PubMed Id: 7524100. |
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OmpF Porin: Escherichia coli B Bacteria, 3.20 Å
Tetragonal crystal form. |
Cowan et al. (1995).
Cowan SW, Garavito RM, Jansonius JN, Jenkins JA, Karlsson R, König N, Pai EF, Pauptit RA, Rizkallah PJ, Rosenbusch JP, Rummel G, & Schirmer T (1995). The structure of OmpF porin in a tetragonal crystal form.
Structure 3 :1041-1050. PubMed Id: 8589999. doi:10.1016/S0969-2126(01)00240-4. |
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Lou et al. (1996).
Lou KL, Saint N, Prilipov A, Rummel G, Benson SA, Rosenbusch JP, & Schirmer T (1996). Structural and functional characterization of OmpF porin mutants selected for larger pore size. I. Crystallographic analysis.
J Biol Chem 271 :20669-20675. PubMed Id: 8702816. doi:10.1074/jbc.271.34.20669 . |
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OmpF Porin, D74A mutant: Escherichia coli B Bacteria (expressed in Escherichia coli B), 3.00 Å
|
Phale et al. (1998).
Phale PS, Philippsen A, Kiefhaber T, Koebnik R, Phale VP, Schirmer T, & Rosenbusch JP (1998). Stability of trimeric OmpF porin: the contributions of the latching loop L2.
Biochemistry 37 :15663-15670. PubMed Id: 9843370. doi:10.1021/bi981215c. |
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Phale et al. (2001).
Phale PS, Philippsen A, Widmer C, Phale VP, Rosenbusch JP, & Schirmer T (2001). Role of charged residues at the OmpF porin channel constriction probed by mutagenesis and simulation.
Biochemistry 40 :6319-6325. PubMed Id: 11371193. doi:10.1021/bi010046k. |
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OmpF Porin: Escherichia coli B Bacteria, 1.6 Å
With inserted 83 residue N-terminal peptide of colicin E3, 3.0 Å: 2ZLD |
Yamashita et al. (2008).
Yamashita E, Zhalnina MV, Zakharov SD, Sharma O, & Cramer WA (2008). Crystal structures of the OmpF porin: function in a colicin translocon.
EMBO J 27 :2171-2180. PubMed Id: 18636093. |
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OmpF porin with a synthetic dibenzo-18-crown-6: Escherichia coli B Bacteria, 3.40 Å
|
Reitz et al. (2009).
Reitz S, Cebi M, Reiss P, Studnik G, Linne U, Koert U, & Essen LO (2009). On the function and structure of synthetically modified porins.
Angew Chem Int Ed Engl 48 :4853-4857. PubMed Id: 19322865. doi:10.1002/anie.200900457. |
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OmpF Porin in complex with colicin peptide OBS1: Escherichia coli B Bacteria, 3.01 Å
Shows colicin bound within porin lumen spanning the membrane bilayer |
Housden et al. (2010).
Housden NG, Wojdyla JA, Korczynska J, Grishkovskaya I, Kirkpatrick N, Brzozowski AM, & Kleanthous C. (2010). Directed epitope delivery across the Escherichia coli outer membrane through the porin OmpF.
Proc Natl Acad Sci USA 107 :21412-21417. PubMed Id: 21098297. |
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OmpF Porin: Escherichia coli B Bacteria, 2.61 Å
Cation-selective pathway revealed by anomalous x-ray diffraction. Structure at 3.00 Å: 3HWB |
Dhakshnamoorthy et al. (2010).
Dhakshnamoorthy B, Raychaudhury S, Blachowicz L, & Roux B (2010). Cation-selective pathway of OmpF porin revealed by anomalous X-ray diffraction.
J Mol Biol 396 :293-300. PubMed Id: 19932117. doi:10.1016/j.jmb.2009.11.042. |
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OmpF Porin in presence of foscholine-12: Escherichia coli B Bacteria, 3.79 Å
Structure at 4.39 Å: 3K1B |
Kefala et al. (2010).
Kefala G, Ahn C, Krupa M, Esquivies L, Maslennikov I, Kwiatkowski W, & Choe S (2010). Structures of the OmpF porin crystallized in the presence of foscholine-12.
Protein Sci 19 :1117-1125. PubMed Id: 20196071. doi:10.1002/pro.369. |
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OmpF Porin: Escherichia coli B Bacteria, 3.5 Å
I2 space group |
Chaptal et al. (2016).
Chaptal V, Kilburg A, Flot D, Wiseman B, Aghajari N, Jault JM, & Falson P (2016). Two different centered monoclinic crystals of the E. coli outer-membrane protein OmpF originate from the same building block.
Biochim Biophy Acta 1858 :326-332. PubMed Id: 26620074. doi:10.1016/j.bbamem.2015.11.021. |
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OmpF Porin: Salmonella typhi B Bacteria (expressed in E. coli), 2.79 Å
|
Balasubramaniam et al. (2012).
Balasubramaniam D, Arockiasamy A, Kumar PD, Sharma A, & Krishnaswamy S (2012). Asymmetric pore occupancy in crystal structure of OmpF porin from Salmonella typhi.
J Struc Biol 178 :233-244. PubMed Id: 22525817. doi:10.1016/j.jsb.2012.04.005. |
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OmpC Osmoporin: Escherichia coli B Bacteria, 2.0 Å
|
Baslé et al. (2006).
Baslé A, Rummel G, Storici P, Rosenbusch J, & Schirmer T (2006). Crystal Structure of Osmoporin OmpC from E. coli at 2.0 Å.
J Mol Biol 362 :933-942. PubMed Id: 16949612. |
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Lou et al. (2011).
Lou H, Chen M, Black SS, Bushell SR, Ceccarelli M, Mach T, Beis K, Low AS, Bamford VA, Booth IR, Bayley H, & Naismith JH (2011). Altered antibiotic transport in OmpC mutants isolated from a series of clinical strains of multi-drug resistant E. coli.
PLoS One 6 :e25825. PubMed Id: 22053181. doi:10.1371/journal.pone.0025825. |
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OmpC homolog (OmpE36) with bound lipopolysaccharide (LPS): Enterobacter cloacae B Bacteria (expressed in E. coli), 1.45 Å
|
Arunmanee et al. (2016).
Arunmanee W, Pathania M, Solovyova AS, Le Brun AP, Ridley H, Baslé A, van den Berg B, & Lakey JH (2016). Gram-negative trimeric porins have specific LPS binding sites that are essential for porin biogenesis.
Proc Natl Acad Sci USA 113 34:E5034-E5043. PubMed Id: 27493217. doi:10.1073/pnas.1602382113. |
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OmpG *monomeric* porin: Escherichia coli B Bacteria, 2.3 Å
|
Subbarao and van den Berg (2006).
Subbarao GV & van den Berg B (2006). Crystal structure of the monomeric porin OmpG.
J Mol Biol 360 :750-759. PubMed Id: 16797588. |
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OmpG *monomeric* porin in open state: Escherichia coli B Bacteria, 2.3 Å
OmpG in closed state, 2.73 Å: 2IWW |
Yildiz et al. (2006).
Yildiz O, Vinothkumar KR, Goswami P, & Kuhlbrandt W (2006). Structure of the monomeric outer-membrane porin OmpG in the open and closed conformation.
EMBO J. 25 :3702-3713. PubMed Id: 16888630. |
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OmpG *monomeric* porin: Escherichia coli B Bacteria, NMR Structure (DPC micelles)
|
Liang & Tamm (2007).
Liang B & Tamm LK (2007). Structure of outer membrane protein G by solution NMR Spectroscopy.
Proc Natl Acad Sci USA 104 :16140-16145. PubMed Id: 17911261. |
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PhoE: Escherichia coli B Bacteria, 3.0 Å
|
Cowan et al. (1992).
Cowan SW, Schirmer T, Rummel G, Steiert M, Ghosh R, Pauptit RA, Jansonius JN, & Rosenbusch JP (1992). Crystal structures explain functional properties of two Escherichia coli porins.
Nature 358 :727-733. PubMed Id: 1380671. |
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LamB Maltoporin: Salmonella typhimurium B Bacteria, 2.4 Å
|
Meyer et al. (1997).
Meyer JEW, Hofnung M, & Schulz GE (1997). Structure of maltoporin from Salmonella typhimurium ligated with a nitrophenyl-maltotrioside.
J. Mol. Biol 266 :761-775. PubMed Id: 9102468. |
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LamB Maltoporin: Escherichia coli B Bacteria, 3.1 Å
|
Schirmer et al. (1995).
Schirmer T, Keller TA, Wang YF, & Rosenbusch JP (1995). Structural basis for sugar translocation through maltoporin channels at 3.1 Å resolution.
Science 267 :512-4. PubMed Id: 7824948. |
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Dutzler et al. (1996).
Dutzler R, Wang YF, Rizkallah P, Rosenbusch JP, Schirmer T (1996). Crystal structures of various maltooligosaccharides bound to maltoporin reveal a specific sugar translocation pathway.
Structure 4 :127-134. PubMed Id: 8805519. |
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LamB Maltoporin in complex with sucrose: Escherichia coli B Bacteria, 2.4 Å
In complex with trehalose, 3.0 Å: 1MPQ |
Wang et al. (1997).
Wang YF, Dutzler R, Rizkallah PJ, Rosenbusch JP, & Schirmer T (1997). Channel specificity: structural basis for sugar discrimination and differential flux rates in maltoporin.
J Mol Biol 272 :56-63. PubMed Id: 9299337. |
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ScrY sucrose-specific porin: Salmonella typhimurium B Bacteria, 2.4 Å
Complexed Form, 1A0T. Uncomplexed form, 1A0S. |
Forst et al. (1998).
Forst D, Welte W, Wacker T, & Diederichs K (1998). Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose.
Nature Structural Biol 5 :37-46. PubMed Id: 9437428. |
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MspA mycobacterial porin: Mycobacterium smegmatis B Bacteria, 2.5 Å
Homooctamer |
Faller et al. (2004).
Faller M, Niederweis M, & Schulz GE (2004). The structure of a mycobacterial outer-membrane channel.
Science 303 :1189-1192. PubMed Id: 14976314. |
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|
OprB carbohydrate-specific transporter at high pH: Pseudomonas putida B Bacteria (expressed in E. coli), 2.70 Å
low-pH structure, 3.10 Å: 4GF4 |
van den Berg (2012).
van den Berg B (2012). Structural basis for outer membrane sugar uptake in pseudomonads.
J Biol Chem 287 :41044-41052. PubMed Id: 23066028. doi:10.1074/jbc.M112.408518. |
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|
OprO diphosphate-specific transporter: Pseudomonas aeruginosa B Bacteria, 1.52 Å
F62Y/D114Y mutant, 1.54 Å: 4RJX |
Modi et al. (2015).
Modi N, Ganguly S, Bárcena-Uribarri I, Benz R, van den Berg B, & Kleinekathöfer U (2015). Structure, Dynamics, and Substrate Specificity of the OprO Porin from Pseudomonas aeruginosa.
Biophys J 109 :1429-1438. PubMed Id: 26445443. doi:10.1016/j.bpj.2015.07.035. |
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|
OprP phosphate-specific transporter: Pseudomonas aeruginosa B Bacteria, 1.9 Å
Contains a novel nine-residue arginine ladder |
Moraes et al. (2007).
Moraes TF, Bains M, Hancock REW & Strynadka NCJ (2007). An arginine ladder in OprP mediates phosphate-specific transfer across the outer membrane.
Nature Struc Mol Biol 14 :85-87. PubMed Id: 17187075. |
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|
PorB outer membrane protein, native structure: Neisseria meningitidis B Bacteria (expressed in E. coli), 2.30 Å
The second most common OMP of Neisseria, PorB is required for pathogenesis. Former 3A2R, 3A2T, and 3A2U superseded by 3VZT, 3VZW, and 3VZU, respectively. In complex with sucrose, 2.20 Å: 3A2S In complex with galactose, 3.20 Å: 3VZW In complex with AMP-PNP, 2.90 Å: 3ZVU |
Tanabe et al. (2010).
Tanabe M, Nimigean CM, & Iverson TM (2010). Structural basis for solute transport, nucleotide regulation, and immunological recognition of Neisseria meningitidis PorB.
Proc Natl Acad Sci USA 107 :6811-6816. PubMed Id: 20351243. |
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|
KdgM *monomeric* porin in complex with disordered oligogalacturonate: Dickeya dadantii B Bacteria (expressed in E. coli), 2.10 Å
|
Hutter et al. (2014).
Hutter CA, Lehner R, Wirth Ch, Condemine G, Peneff C, & Schirmer T (2014). Structure of the oligogalacturonate-specific KdgM porin.
Acta Crystallogr. D Biol. Crystallogr. 70 :1770-1778. PubMed Id: 24914987. doi:10.1107/S1399004714007147. |
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|
van den Berg et al. (2015).
van den Berg B, Prathyusha Bhamidimarri S, Dahyabhai Prajapati J, Kleinekathöfer U, & Winterhalter M (2015). Outer-membrane translocation of bulky small molecules by passive diffusion.
Proc Natl Acad Sci USA 112 :E2991-E2999. PubMed Id: 26015567. doi:10.1073/pnas.1424835112. |
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|
COG4313 outer membrane channel: Pseudomonas putida B Bacteria (expressed in E. coli), 2.30 Å
|
van den Berg et al. (2015).
van den Berg B, Bhamidimarri SP, & Winterhalter M (2015). Crystal structure of a COG4313 outer membrane channel.
Sci Rep 5 :11927. PubMed Id: 26149193. doi:10.1038/srep11927. |
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|
OprG outer membrane amino acid transporter: Pseudomonas aeruginosa B Bacteria (expressed in E. coli), NMR structure
P92A mutant, NMR structure: 2N6P |
Kucharska et al. (2015).
Kucharska I, Seelheim P, Edrington T, Liang B, & Tamm LK (2015). OprG Harnesses the Dynamics of its Extracellular Loops to Transport Small Amino Acids across the Outer Membrane of Pseudomonas aeruginosa.
Structure 23 :2234-2245. PubMed Id: 26655471. doi:10.1016/j.str.2015.10.009. |
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|
MOMP major outer membrane protein: Campylobacter jejuni (expressed in E. coli), 2.1 Å
expressed in C. jejuni, 2.88 Å: 5LDT |
Ferrara et al. (2016).
Ferrara LG, Wallat GD, Moynié L, Dhanasekar NN, Aliouane S, Acosta-Gutiérrez S, Pagès JM, Bolla JM, Winterhalter M, Ceccarelli M, & Naismith JH (2016). MOMP from Campylobacter jejuni Is a Trimer of 18-Stranded β-Barrel Monomers with a Ca2+ Ion Bound at the Constriction Zone.
J Mol Biol 428 :4528-4543. PubMed Id: 27693650. doi:10.1016/j.jmb.2016.09.021. |
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|
Outer Membrane Carboxylate Channels (Occ)
These outer membrane proteins require substrates to have a carboxyl group for efficient transport. OccD channels are selective for basic amino acids. OccK channels prefer cyclic substrates. See Eren et al. (2012). |
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OccD1 (OprD) basic amino acid uptake channel: Pseudomonas aeruginosa B Bacteria (expressed in E. coli), 2.9 Å
|
Biswas et al. (2007).
Biswas S, Mohammad MM, Patel DR, Movileanu L, & van den Berg B (2007). Structural insight into OprD substrate specificity.
Nature Struct Mol Biol 14 :1108-1109. PubMed Id: 17952093. |
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|
OccD1 (OprD) basic amino acid uptake channel: Pseudomonas aeruginosa B Bacteria (expressed in E. coli), 2.15 Å
|
Eren et al. (2012).
Eren E, Vijayaraghavan J, Liu J, Cheneke BR, Touw DS, Lepore BW, Indic M, Movileanu L, & van den Berg B (2012). Substrate Specificity within a Family of Outer Membrane Carboxylate Channels.
PLoS Biol 10 :e1001242. PubMed Id: 22272184. doi:10.1371/journal.pbio.1001242. |
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|
OccD2 (OpdC) basic amino acid uptake channel: Pseudomonas aeruginosa B Bacteria (expressed in E. coli), 2.80 Å
|
Eren et al. (2012).
Eren E, Vijayaraghavan J, Liu J, Cheneke BR, Touw DS, Lepore BW, Indic M, Movileanu L, & van den Berg B (2012). Substrate Specificity within a Family of Outer Membrane Carboxylate Channels.
PLoS Biol 10 :e1001242. PubMed Id: 22272184. doi:10.1371/journal.pbio.1001242. |
||
|
OccD3 (OpdP) basic amino acid uptake channel: Pseudomonas aeruginosa B Bacteria (expressed in E. coli), 2.70 Å
|
Eren et al. (2012).
Eren E, Vijayaraghavan J, Liu J, Cheneke BR, Touw DS, Lepore BW, Indic M, Movileanu L, & van den Berg B (2012). Substrate Specificity within a Family of Outer Membrane Carboxylate Channels.
PLoS Biol 10 :e1001242. PubMed Id: 22272184. doi:10.1371/journal.pbio.1001242. |
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|
OccK1 (OpdK) benzoate channel: Pseudomonas aeruginosa B Bacteria (expressed in E. coli), 2.8 Å
Binds vanillate. Forms labile trimer. |
Biswas et al. (2008).
Biswas S, Mohammad MM, Movileanu L, & van den Berg B (2008). Crystal structure of the outer membrane protein OpdK from Pseudomonas aeruginosa.
Structure 16 :1027-1035. PubMed Id: 18611376. |
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|
OccK1 (OpdK) benzoate channel: Pseudomonas aeruginosa B Bacteria (expressed in E. coli), 1.65 Å
|
Eren et al. (2012).
Eren E, Vijayaraghavan J, Liu J, Cheneke BR, Touw DS, Lepore BW, Indic M, Movileanu L, & van den Berg B (2012). Substrate Specificity within a Family of Outer Membrane Carboxylate Channels.
PLoS Biol 10 :e1001242. PubMed Id: 22272184. doi:10.1371/journal.pbio.1001242. |
||
|
OccK2 (OpdF) glucuronate channel: Pseudomonas aeruginosa B Bacteria (expressed in E. coli), 2.30 Å
|
Eren et al. (2012).
Eren E, Vijayaraghavan J, Liu J, Cheneke BR, Touw DS, Lepore BW, Indic M, Movileanu L, & van den Berg B (2012). Substrate Specificity within a Family of Outer Membrane Carboxylate Channels.
PLoS Biol 10 :e1001242. PubMed Id: 22272184. doi:10.1371/journal.pbio.1001242. |
||
|
OccK3 (OpdO) aromatic hydrocarbon channel: Pseudomonas aeruginosa B Bacteria (expressed in E. coli), 1.45 Å
|
Eren et al. (2012).
Eren E, Vijayaraghavan J, Liu J, Cheneke BR, Touw DS, Lepore BW, Indic M, Movileanu L, & van den Berg B (2012). Substrate Specificity within a Family of Outer Membrane Carboxylate Channels.
PLoS Biol 10 :e1001242. PubMed Id: 22272184. doi:10.1371/journal.pbio.1001242. |
||
|
OccK4 (OpdL) aromatic hydrocarbon channel: Pseudomonas aeruginosa B Bacteria (expressed in E. coli), 2.10 Å
|
Eren et al. (2012).
Eren E, Vijayaraghavan J, Liu J, Cheneke BR, Touw DS, Lepore BW, Indic M, Movileanu L, & van den Berg B (2012). Substrate Specificity within a Family of Outer Membrane Carboxylate Channels.
PLoS Biol 10 :e1001242. PubMed Id: 22272184. doi:10.1371/journal.pbio.1001242. |
||
|
OccK5 (OpdH) aromatic hydrocarbon channel: Pseudomonas aeruginosa B Bacteria (expressed in E. coli), 2.60 Å
|
Eren et al. (2012).
Eren E, Vijayaraghavan J, Liu J, Cheneke BR, Touw DS, Lepore BW, Indic M, Movileanu L, & van den Berg B (2012). Substrate Specificity within a Family of Outer Membrane Carboxylate Channels.
PLoS Biol 10 :e1001242. PubMed Id: 22272184. doi:10.1371/journal.pbio.1001242. |
||
|
OccK6 (OpdQ) aromatic hydrocarbon channel: Pseudomonas aeruginosa B Bacteria (expressed in E. coli), 2.35 Å
|
Eren et al. (2012).
Eren E, Vijayaraghavan J, Liu J, Cheneke BR, Touw DS, Lepore BW, Indic M, Movileanu L, & van den Berg B (2012). Substrate Specificity within a Family of Outer Membrane Carboxylate Channels.
PLoS Biol 10 :e1001242. PubMed Id: 22272184. doi:10.1371/journal.pbio.1001242. |
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|
BenF-like Porin (putative) benzoate channel: Pseudomonas fluorescens B Bacteria, 2.60 Å
Probably belongs to OccK subfamily |
Sampathkumar et al. (2010).
Sampathkumar P, Lu F, Zhao X, Li Z, Gilmore J, Bain K, Rutter ME, Gheyi T, Schwinn KD, Bonanno JB, Pieper U, Fajardo JE, Fiser A, Almo SC, Swaminathan S, Chance MR, Baker D, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Sali A, Sauder JM, &Burley SK (2010). Structure of a putative BenF-like porin from Pseudomonas fluorescens Pf-5 at 2.6 Å resolution.
Proteins 78 :3056-3062. PubMed Id: 20737437. |
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|
OccAB1 outer membrane channel: Acinetobacter baumannii B Bacteria (expressed in E. coli), 2.05 Å
|
Zahn et al. (2016).
Zahn M, Bhamidimarri SP, Baslé A, Winterhalter M, & van den Berg B (2016). Structural Insights into Outer Membrane Permeability of Acinetobacter baumannii.
Structure 24 :221-231. PubMed Id: 26805524. doi:10.1016/j.str.2015.12.009. |
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|
OccAB2 outer membrane channel: Acinetobacter baumannii B Bacteria (expressed in E. coli), 2.9 Å
|
Zahn et al. (2016).
Zahn M, Bhamidimarri SP, Baslé A, Winterhalter M, & van den Berg B (2016). Structural Insights into Outer Membrane Permeability of Acinetobacter baumannii.
Structure 24 :221-231. PubMed Id: 26805524. doi:10.1016/j.str.2015.12.009. |
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|
OccAB3 outer membrane channel: Acinetobacter baumannii B Bacteria (expressed in E. coli), 1.75 Å
|
Zahn et al. (2016).
Zahn M, Bhamidimarri SP, Baslé A, Winterhalter M, & van den Berg B (2016). Structural Insights into Outer Membrane Permeability of Acinetobacter baumannii.
Structure 24 :221-231. PubMed Id: 26805524. doi:10.1016/j.str.2015.12.009. |
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|
OccAB4 outer membrane channel: Acinetobacter baumannii B Bacteria (expressed in E. coli), 2.2 Å
|
Zahn et al. (2016).
Zahn M, Bhamidimarri SP, Baslé A, Winterhalter M, & van den Berg B (2016). Structural Insights into Outer Membrane Permeability of Acinetobacter baumannii.
Structure 24 :221-231. PubMed Id: 26805524. doi:10.1016/j.str.2015.12.009. |
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|
Beta-Barrel Membrane Proteins: Monomeric/Dimeric
|
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TolC outer membrane protein: Escherichia coli B Bacteria, 2.1 Å
NOTE: Functional protein is a homotrimer. Each monomer contributes 4 strands to a single barrel. |
Koronakis et al. (2000).
Koronakis V, Sharff A, Koronakis E, Luisi B, & Hughes C (2000). Crystal structure of the bacterial membrane protein TolC central to multidrug efflux and protein export.
Nature 405 :914-919. PubMed Id: 10879525. |
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|
TolC outer membrane protein, ligand blocked: Escherichia coli B Bacteria, 2.75 Å
|
Higgins et al. (2004).
Higgins MK, Eswaran J, Edwards P, Schertler GF, Hughes C, & Koronakis V (2004). Structure of the ligand-blocked periplasmic entrance of the bacterial multidrug efflux protein TolC.
J Mol Biol 342 :697-702. PubMed Id: 15342230. |
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|
TolC outer membrane protein (Y362F, R367E), partially open state: Escherichia coli B Bacteria, 3.2 Å
2VDE is P212121 form. C2 form, 3.30 Å: 2VDD |
Bavro et al. (2008).
Bavro VN, Pietras Z, Furnham N, Pérez-Cano L, Fernández-Recio J, Pei XY, Misra R, & Luisi B (2008). Assembly and channel opening in a bacterial drug efflux machine.
Mol Cell 30 :114-121. PubMed Id: 18406332. |
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|
CmeC bacterial multi-drug efflux transporter outer membrane channel: Campylobacter jejuni B Bacteria, 2.37 Å
|
Su et al. (2014).
Su CC, Radhakrishnan A, Kumar N, Long F, Bolla JR, Lei HT, Delmar JA, Do SV, Chou TH, Rajashankar KR, Zhang Q, & Yu EW (2014). Crystal structure of the Campylobacter jejuni CmeC outer membrane channel.
Protein Sci 23 7:954-961. PubMed Id: 24753291. doi:10.1002/pro.2478. |
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VceC outer membrane protein: Vibrio cholerae B Bacteria, 1.8 Å
NOTE: Functional protein is a homotrimer. Each monomer contributes 4 strands to a single barrel. |
Federici et al. (2005).
Federici L, Du D, Walas F, Matsumura H, Fernandez-Recio J, McKeegan KS, Borges-Walmsley MI, Luisi BF, & Walmsley AR (2005). The Crystal Structure of the Outer Membrane Protein VceC from the Bacterial Pathogen Vibrio cholerae at 1.8 A Resolution.
J Biol Chem 280 :15307-15314. PubMed Id: 15684414. |
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|
OprM drug discharge outer membrane protein: Pseudomonas aeruginosa B Bacteria, 2.56 Å
Functional protein is a homotrimer. Each monomer contributes 4 strands to a single barrel. H32 space group. OprM is the discharge channel for the tripartite efflux complex MexAB-OprM. The structures of MexB (the inner membrane efflux pump) and MexA (periplasmic fusion protein) are known. See 2V50 and 1T5E, respectively. |
Akama et al. (2004).
Akama H, Kanemaki M, Yoshimura M, Tsukihara T, Kashiwagi T, Yoneyama H, Narita S, Nakagawa A, & Nakae T (2004). Crystal structure of the drug discharge outer membrane protein, OprM, of Pseudomonas aeruginosa: dual modes of membrane anchoring and occluded cavity end.
J Biol Chem 279 :52816-52819. PubMed Id: 15507433. |
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|
OprM drug discharge outer membrane protein: Pseudomonas aeruginosa B Bacteria (expressed in E. coli), 2.40 Å
Structure of OprM in a non-symmetrical space group, P212121 |
Phan et al. (2010).
Phan G, Benabdelhak H, Lascombe MB, Benas P, Rety S, Picard M, Ducruix A, Etchebest C, & Broutin I (2010). Structural and dynamical insights into the opening mechanism of P. aeruginosa OprM channel.
Structure 18 :507-517. PubMed Id: 20399187. |
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OprN drug discharge outer membrane protein, I4 space group: Pseudomonas aeruginosa B Bacteria (expressed in E. coli), 1.69 Å
P321 space group, 2.70 Å: 5AZP |
Yonehara et al. (2016).
Yonehara R, Yamashita E, & Nakagawa A (2016). Crystal structures of OprN and OprJ, outer membrane factors of multidrug tripartite efflux pumps of Pseudomonas aeruginosa.
Proteins 84 6:759-769. PubMed Id: 26914226. doi:10.1002/prot.25022. |
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OprJ drug discharge outer membrane protein: Pseudomonas aeruginosa B Bacteria (expressed in E. coli), 3.10 Å
|
Yonehara et al. (2016).
Yonehara R, Yamashita E, & Nakagawa A (2016). Crystal structures of OprN and OprJ, outer membrane factors of multidrug tripartite efflux pumps of Pseudomonas aeruginosa.
Proteins 84 6:759-769. PubMed Id: 26914226. doi:10.1002/prot.25022. |
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|
ST50 discharge outer membrane protein: Salmonella enterica B Bacteria (expressed in E. coli), 2.98 Å
Functional protein is a homotrimer. Each monomer contributes 4 strands to a single barrel. |
Guan et al. (2015).
Guan HH, Yoshimura M, Chuankhayan P, Lin CC, Chen NC, Yang MC, Ismail A, Fun HK, & Chen CJ (2015). Crystal structure of an antigenic outer-membrane protein from Salmonella Typhi suggests a potential antigenic loop and an efflux mechanism.
Sci Rep 5 :16441. PubMed Id: 26563565. doi:10.1038/srep16441. |
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CusC heavy metal discharge outer membrane protein: Escherichia coli B Bacteria, 2.30 Å
NOTE: Functional protein is a homotrimer. Each monomer contributes 4 strands to a single barrel. H32 space group. |
Kulathila et al. (2011).
Kulathila R, Kulathila R, Indic M, & van den Berg B (2011). Crystal structure of Escherichia coli CusC, the outer membrane component of a heavy metal efflux pump.
PLoS One 6 :e15610. PubMed Id: 21249122. doi:10.1371/journal.pone.0015610. |
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|
Lei et al. (2014).
Lei HT, Bolla JR, Bishop NR, Su CC, & Yu EW (2014). Crystal Structures of CusC Review Conformational Changes Accompanying Folding and Transmembrane Channel Formation.
J Mol Biol 426 :403-411. PubMed Id: 24099674. doi:10.1016/j.jmb.2013.09.042. |
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|
Chimento et al. (2003).
Chimento DP, Mohanty AK, Kadner RJ, & Wiener MC (2003). Substrate-induced transmembrane signaling in the cobalamin transporter BtuB.
Nat Struct Biol. 10 :394-401. PubMed Id: 12652322. |
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BtuB with bound colicin E3 R-domain: Escherichia coli B Bacteria, 2.75 Å
NOTE: The 135-residue coiled-coil R-domain is believed to deliver the colicin to OmpF (above). |
Kurisu et al. (2003).
Kurisu G, Zakharov SD, Zhalnina MV, Bano S, Eroukova VY, Rokitskaya TI, Antonenko YN, Wiener MC, & Cramer WA (2003). The structure of BtuB with bound colicin E3 R-domain implies a translocon.
Nat. Struct. Biol. 10 :948-954. PubMed Id: 14528295. |
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|
apo BtuB by in meso crystallization: Escherichia coli B Bacteria, 1.95 Å
NOTE: Crystals were prepared from cubic phase lipids. This is the first β-barrel protein prepared by this method. |
Cherezov et al. (2006).
Cherezov V, Yamashita E, Liu W, Zhalnina M, Cramer WA & Caffrey M (2006). In meso structure of the cobalamin transporter, BtuB, at 1.95 Å resolution.
J Mol Biol 364 :716-734. PubMed Id: 17028020. |
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BtuB in complex with TonB: Escherichia coli B Bacteria, 2.1 Å
|
Shultis et al. (2006).
Shultis DD, Purdy MD, Banchs CN, & Wiener MC (2006). Outer membrane active transport: structure of the BtuB:TonB complex.
Science 312 :1396-1399. PubMed Id: 16741124. |
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BtuB with bound colicin E2 R-domain: Escherichia coli B Bacteria, 3.50 Å
|
Sharma et al. (2007).
Sharma O, Yamashita E, Zhalnina MV, Zakharov SD, Datsenko KA, Wanner BL, & Cramer WA (2007). Structure of the complex of the colicin E2 R-domain and its BtuB receptor. The outer membrane colicin translocon.
J Biol Chem 282 :23163-23170. PubMed Id: 17548346. |
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apo BtuB V10R1 spin-labeled: Escherichia coli B Bacteria, 2.44 Å
Spin-labeled BtuB V10R1 with bound calcium and cyanocobalamin, 2.44 Å: 3M8D |
Freed et al. (2010).
Freed DM, Horanyi PS, Wiener MC, & Cafiso DS (2010). Conformational exchange in a membrane transport protein is altered in protein crystals.
Biophys J 99 :1604-1610. PubMed Id: 20816073. doi:10.1016/j.bpj.2010.06.026. |
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Colicin I receptor Cir in complex with Colicin Ia binding domain: Escherichia coli B Bacteria, 2.5 Å
Cir Colicin I receptor alone, 2.65 Å: 2HDF |
Buchanan et al. (2007).
Buchanan S, Lukacik P, Grizot S, Ghirlando R, Ali MMU, Barnard TJ, Jakes S, Kienker PK, & Esser L. (2007). Structure of colicin I receptor bound to the R-domain of colicin Ia: Implications for protein import.
EMBO J 26 :2594-2604. PubMed Id: 17464289. |
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OmpA: Escherichia coli B Bacteria, 2.50 Å
|
Pautsch & Schulz (1998).
Pautsch A & Schulz GE (1998). Structure of the outer membrane protein A transmembrane domain.
Nature Struct Biol 5 :1013-1017. PubMed Id: 9808047. |
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|
OmpA: Escherichia coli B Bacteria, 1.60 Å
|
Pautsch & Schulz (2000).
Pautsch A & Schulz GE (2000). High-resolution structure of the OmpA membrane domain.
J Mol Biol 298 :273-282. PubMed Id: 10764596. |
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|
OmpA: Escherichia coli B Bacteria, NMR Structure
in DPC micelles |
Arora et al. (2001).
Arora A, Abildgaard F, Bushweller JH, & Tamm LK (2001). Structure of outer membrane protein A transmembrane domain by NMR spectroscopy.
Nature Structural Biol. 8 :334-338. PubMed Id: 11276254. |
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OmpA with four shortened loops: Escherichia coli B Bacteria, NMR Structure
DHPC micelles. Called β-barrel platform (BBP). |
Johansson et al. (2007).
Johansson MU, Alioth S, Hu K, Walser R, Koebnik R, & Pervushin K (2007). A minimal transmembrane β-barrel platform protein studied by nuclear magnetic resonance.
Biochemistry 46 :1128-1140. PubMed Id: 17260943. |
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|
OmpA: Klebsiella pneumoniae B Bacteria (expressed in E. coli), NMR Structure
DHPC micelles |
Renault et al. (2009).
Renault M, Saurel O, Czaplicki J, Demange P, Gervais V, Löhr F, Réat V, Piotto M, & Milon A (2009). Solution state NMR structure and dynamics of KpOmpA, a 210 residue transmembrane domain possessing a high potential for immunological applications
J Mol Biol 385 :117-130. PubMed Id: 18952100. doi:10.1016/j.jmb.2008.10.021. |
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|
OmpT outer membrane protease: Escherichia coli B Bacteria, 2.6 Å
|
Vandeputte-Rutten et al. (2001).
Vandeputte-Rutten L, Kramer RA, Kroon J, Dekker N, Egmond, MR, & Gros P (2001). Crystal structure of the outer membrane protease OmpT from Eschericia coli suggests a novel catalytic site.
EMBO J 20 :5033-5039. PubMed Id: 11566868. |
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|
Eren et al. (2010).
Eren E, Murphy M, Goguen J, & van den Berg B. (2010). An active site water network in the plasminogen activator Pla from Yersinia pestis.
Structure 18 :809-818. PubMed Id: 20637417. |
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OmpW outer membrane protein: Escherichia coli B Bacteria, 2.7 Å
2F1V is orthorhomibic form. Trigonal form, 3.0 Å: 2F1T |
Hong et al. (2006).
Hong H, Patel DR, Tamm LK, & van den Berg B (2006). The Outer Membrane Protein OmpW Forms an Eight-stranded beta-Barrel with a Hydrophobic Channel.
J Biol Chem 281 :7568-7577. PubMed Id: 16414958. |
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|
Zahn et al. (2015).
Zahn M, D'Agostino T, Eren E, Baslé A, Ceccarelli M, & van den Berg B (2015). Small-Molecule Transport by CarO, an Abundant Eight-Stranded β-Barrel Outer Membrane Protein from Acinetobacter baumannii.
J Mol Biol 427 :2329-2339. PubMed Id: 25846137. doi:10.1016/j.jmb.2015.03.016. |
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OprG outer membrane protein: Pseudomonas aeruginosa B Bacteria (expressed in E. coli), 2.4 Å
Potential channel for hydrophobic molecule transport |
Touw et al. (2010).
Touw DS, Patel DR, & van den Berg B (2010). The crystal structure of OprG from Pseudomonas aeruginosa, a potential channel for transport of hydrophobic molecules across the outer membrane.
PLoS One 5 :e15016. PubMed Id: 21124774. doi:10.1371/journal.pone.0015016. |
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|
OprH, outer membrane protein H: Pseudomonas aeruginosa B Bacteria (expressed in E. coli), NMR Structure
Structure determined in DHPC micelles. Eight strands. Chemical-shift measurements identify likely lipopolysaccharide interaction sites. |
Edrington et al. (2011).
Edrington TC, Kintz E, Goldberg JB, & Tamm LK (2011). Structural Basis for the Interaction of Lipopolysaccharide with Outer Membrane Protein H (OprH) from Pseudomonas aeruginosa
J Biol Chem 286 :39211-39223. PubMed Id: 21865172. doi:10.1074/jbc.M111.280933. |
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|
Vogt & Schulz (1999).
Vogt J & Schulz GE (1999). The structure of the outer membrane protein OmpX from Escherichia coli reveals possible mechanisms of virulence.
Structure Fold.Des. 7 :1301-1309. PubMed Id: 10545325. |
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|
OmpX: Escherichia coli B Bacteria, NMR (DHPC micelles)
|
Fernández et al. (2001).
Fernández C, Adeishvili K, & Wüthrich K (2001). Transverse relaxation-optimized NMR spectroscopy with the outer membrane protein OmpX in dihexanoyl phosphatidylcholine micelles.
Proc Natl Acad Sci USA 98 :2358-2363. PubMed Id: 11226244. |
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|
OmpX: Escherichia coli B Bacteria, NMR (DPC micelles, with H-bond constraints)
For structure without H-bond constraints, see 1Q9G |
Fernández et al. (2004).
Fernández C, Hilty C, Wider G, Guntert P, & Wüthrich K (2004). NMR structure of the integral membrane protein OmpX.
J Mol Biol. 336 :1211-1221. PubMed Id: 15037080. |
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|
OmpX in optimized nanodiscs: Escherichia coli B Bacteria, NMR Structure
In DPC micelles, NMR Structure: 2M07 |
Hagn et al. (2013).
Hagn F, Etzkorn M, Raschle T, & Wagner G (2013). Optimized phospholipid bilayer nanodiscs facilitate high-resolution structure determination of membrane proteins.
J Am Chem Soc 135 :1919-1925. PubMed Id: 23294159. doi:10.1021/ja310901f. |
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|
Ail adhesion protein: Yersinia pestis B Bacteria (expressed in E. coli), 1.80 Å
In complex with sucrose octasulfate (SOS), 1.85 Å: 3QRC |
Yamashita et al. (2011).
Yamashita S, Lukacik P, Barnard TJ, Noinaj N, Felek S, Tsang TM, Krukonis ES, Hinnebusch BJ, & Buchanan SK (2011). Structural Insights into Ail-Mediated Adhesion in Yersinia pestis.
Structure 19 :1672-1682. PubMed Id: 22078566. doi:10.1016/j.str.2011.08.010. |
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TtoA Outer Membrane Protein (OMP): Thermus thermophilus HB27 B Bacteria, 2.8 Å
First structure of an OMP from a thermophile |
Brosig et al. (2009).
Brosig A, Nesper J, Boos W, Welte W, & Diederichs K (2009). Crystal structure of a major outer membrane protein from Thermus thermophilus HB27.
J Mol Biol 385 :1445-1455. PubMed Id: 19101566. |
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OmpLA (PldA) outer membrane phospholipase A monomer: Escherichia coli B Bacteria, 2.17 Å
Dimer, 2.10 Å: 1QD6 |
Snijder et al. (1999).
Snijder HJ, Ubarretxena-Belandia I, Blaauw M, Kalk KH, Verheij HM, Egmond MR, Dekker N, & Dijkstra BW (1999). Structural evidence for dimerization-regulated activation of an integral membrane phospholipase.
Nature 401 :717-721. PubMed Id: 10537112. |
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OmpLA (PldA) outer membrane phospholipase A monomer with Ca++: Escherichia coli B Bacteria, 2.60 Å
Dimer, 2.80 Å: 1FW3 |
Snijder et al. (2001).
Snijder HJ, Kingma RL, Kalk KH, Dekker N, Egmond MR, & Dijkstra BW (2001). Structural investigations of calcium binding and its role in activity and activation of outer membrane phospholipase A from Escherichia coli.
J Mol Biol 309 :477-489. PubMed Id: 11371166. |
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|
Snijder et al. (2001).
Snijder HJ, Van Eerde JH, Kingma RL, Kalk KH, Dekker N, Egmond MR, & Dijkstra BW (2001). Structural investigations of the active-site mutant Asn156Ala of outer membrane phospholipase A: function of the Asn-His interaction in the catalytic triad.
Protein Sci 10 :1962-1969. PubMed Id: 11567087. |
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OpcA adhesin protein: Neisseria meningitidis B Bacteria, 2.0 Å
|
Prince et al. (2002).
Prince SM, Achtman M, & Derrick JP (2002). Crystal structure of the OpcA integral membrane adhesin from Neisseria meningitidis.
Proc. Natl. Acad. Sci. USA 99 :3417-3421. PubMed Id: 11891340. |
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OpcA adhesin protein: Neisseria meningitidis B Bacteria (expressed in E. coli), 1.95 Å
In meso crystallization |
Cherezov et al. (2008).
Cherezov V, Liu W, Derrick JP, Luan B, Aksimentiev A, Katritch V, & Caffrey M (2008). In meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the OpcA outer membrane adhesin.
Proteins 71 :24-34. PubMed Id: 18076035. doi:10.1002/prot.21841. |
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NspA surface protein: Neisseria meningitidis B Bacteria, 2.55 Å
|
Vandeputte-Rutten et al. (2003).
Vandeputte-Rutten L, Bos MP, Tommassen J, & Gros P (2003). Crystal structure of Neisserial surface protein A (NspA), a conserved outer membrane protein with vaccine potential.
J. Biol. Chem. 278 :24825-24830. PubMed Id: 12716881. |
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|
NanC Porin, model for KdgM porin family: Escherichia coli B Bacteria, 1.80 Å
H3 space group. See also 2WJQ, p6322 space group, 2.0 Å resolution. |
Wirth et al. (2009).
Wirth C, Condemine G, Boiteux C, Bernèche S, Schirmer T, & Peneff CM (2009). NanC Crystal Structure, a Model for Outer-Membrane Channels of the Acidic Sugar-Specific KdgM Porin Family.
J Mol Biol 394 :718-731. PubMed Id: 19796645. |
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PagL LPS 3-O-deacylase: Pseudomonas aeruginosa B Bacteria, 2.00 Å
|
Rutten et al. (2006).
Rutten L, Geurtsen J, Lambert W, Smolenaers JJ, Bonvin AM, de Haan A, van der Ley P, Egmond MR, Gros P, & Tommassen J (2006). Crystal structure and catalytic mechanism of the LPS 3-O-deacylase PagL from Pseudomonas aeruginosa.
Proc Natl Acad Sci USA 103 :7071-7076. PubMed Id: 16632613. doi:10.1073/pnas.0509392103. |
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LpxR lipid A deacylase: Salmonella typhimurium B Bacteria (expressed in E. coli), 1.90 Å
|
Rutten et al. (2009).
Rutten L, Mannie JP, Stead CM, Raetz CR, Reynolds CM, Bonvin AM, Tommassen JP, Egmond MR, Trent MS, & Gros P (2009). Active-site architecture and catalytic mechanism of the lipid A deacylase LpxR of Salmonella typhimurium.
Proc Natl Acad Sci USA 106 :1960-1964. PubMed Id: 19174515. doi:10.1073/pnas.0813064106 . |
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PagP outer membrane palimitoyl transferease: Escherichia coli B Bacteria, NMR
1MM4 is Structure in DPC micelles. Structure in OG micelles: 1MM5 |
Hwang et al. (2002).
Hwang PM, Choy WY, Lo EI, Chen L, Forman-Kay JD, Raetz CR, Privé GG, Bishop RE, Kay LE (2002). Solution structure and dynamics of the outer membrane enzyme PagP by NMR.
Proc Natl Acad Sci USA 99 :13560-13565. PubMed Id: 12357033. |
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PagP outer membrane palimitoyl transferease: Escherichia coli B Bacteria, 1.90 Å
|
Ahn et al. (2004).
Ahn VE, Lo EI, Engel CK, Chen L, Hwang PM, Kay LE, Bishop RE, & Prive GG (2004). A hydrocarbon ruler measures palmitate in the enzymatic acylation of endotoxin.
EMBO J. 23 :2931-2941. PubMed Id: 15272304. |
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PagP outer membrane palimitoyl transferease crystallized from SDS/Co-solvent: Escherichia coli B Bacteria, 1.40 Å
Reveals phospholipid access route (crenel between strands F and G) |
Cuesta-Seijo et al. (2010).
Cuesta-Seijo JA, Neale C, Khan MA, Moktar J, Tran CD, Bishop RE, Pomès R, & Privé GG (2010). PagP crystallized from SDS/cosolvent reveals the route for phospholipid access to the hydrocarbon ruler.
Structure 18 :1210-1219. PubMed Id: 20826347. |
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FadL long-chain fatty acid transporter: Escherichia coli B Bacteria, 2.6 Å
1T16 is from Monoclinic crystals. From hexagonal crystals, 2.8 Å: 1T1L |
van den Berg et al. (2004).
van den Berg B, Black PN, Clemons WM Jr, & Rapoport TA (2004). Crystal structure of the long-chain fatty acid transporter FadL.
Science 304 :1506-1509. PubMed Id: 15178802. |
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FadL long-chain fatty acid transporter A77E/S100R mutant: Escherichia coli B Bacteria, 2.5 Å
Mutants show that channel wall opening for passage of fatty acids into inner layer of outer membrane is likely. ΔS3 kink, 2.60 Å: 2R88 P34A mutant, 3.3 Å: 2R4L N33A mutant, 3.2 Å: 2R4N ΔNPA mutant, 3.6 Å: 2R4O G212E mutant, 2.9 Å: 2R4P |
Hearn et al. (2009).
Hearn EM, Patel DR, Lepore BW, Indic M, van den Berg B (2009). Transmembrane passage of hydrophobic compounds through a protein channel wall.
Nature 458 :367-370. PubMed Id: 19182779. |
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FadL long-chain fatty acid transporter D348R mutant: Escherichia coli B Bacteria, 2.60 Å
This and associated structures in conjunction with in vivo transport assays and Trp fluorescence demonstrate ligand gating of the β-barrel protein. delta N3 mutant, 3.40 Å: 2R89 D348A mutant, 2.70 Å: 3PF1 F3E mutant, 1.70 Å: 3PGU F3G mutant, 1.90 Å: 3PGS |
Lepore et al. (2011).
Lepore BW, Indic M, Pham H, Hearn EM, Patel DR, & van den Berg B (2011). Ligand-gated diffusion across the bacterial outer membrane
Proc Natl Acad Sci USA 108 :10121-10126. PubMed Id: 21593406. doi:10.1073/pnas.1018532108. |
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FadL homologue long-chain fatty acid transporter: Pseudomonas aeruginosa B Bacteria (expressed in E. coli), 2.2 Å
Shows break in channel wall for passage of fatty acids into inner layer of outer membrane in a species other than E. coli. Residues 22-463. |
Hearn et al. (2009).
Hearn EM, Patel DR, Lepore BW, Indic M, van den Berg B (2009). Transmembrane passage of hydrophobic compounds through a protein channel wall.
Nature 458 :367-370. PubMed Id: 19182779. |
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|
FauA alcaligin outer membrane transporter: Bordetella pertussis B Bacteria (expressed in E. coli), 2.3 Å
|
Brillet et al. (2009).
Brillet K, Meksem A, Lauber E, Reimmann & C, Cobessi D (2009). Use of an in-house approach to study the three-dimensional structures of various outer membrane proteins: structure of the alcaligin outer membrane transporter FauA from Bordetella pertussis.
Acta Crystallogr D Biol Crystallogr 65 :326-331. PubMed Id: 19307713. |
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TodX hydrocarbon transporter: Pseudomonas putida B Bacteria, 2.6 Å
3BS0 is P1 space group, 2 molecules in asymmetric unit. I222 space group, 3.2 Å: 3BRZ |
Hearn et al. (2008).
Hearn EM, Patel DR, & van den Berg BO (2008). Outer-membrane transport of aromatic hydrocarbons as a first step in biodegradation.
Proc Natl Acad Sci USA 105 :8601-8606. PubMed Id: 18559855. |
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TbuX hydrocarbon transporter: Ralstonia pickettii B Bacteria, 3.2 Å
|
Hearn et al. (2008).
Hearn EM, Patel DR, & van den Berg BO (2008). Outer-membrane transport of aromatic hydrocarbons as a first step in biodegradation.
Proc Natl Acad Sci USA 105 :8601-8606. PubMed Id: 18559855. |
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|
Ye and van den Berg (2004).
Ye J & van den Berg B (2004). Crystal structure of the bacterial nucleoside transporter Tsx.
EMBO J. 23 :3187-3195. PubMed Id: 15272310. |
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|
FhuA, Ferrichrome-iron receptor without ligand: Escherichia coli B Bacteria, 2.7 Å
With ligand: 1BY5 |
Locher et al. (1998).
Locher KP, Rees B, Koebnik R, Mitschler A, Moulinier L, Rosenbusch JP, & Moras D (1998). Transmembrane signaling across the ligand-gated FhuA receptor: crystal structures of free and ferrichrome-bound states reveal allosteric changes.
Cell 11 :771-8. PubMed Id: 9865695. |
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|
FhuA: Escherichia coli B Bacteria, 2.50 Å
Includes the structure of a bound lipopolysaccharide (LPS) molecule In complex with ferrichrome-iron, 2.70 Å: 1FCP |
Ferguson et al. (1998).
Ferguson AD, Hofmann E, Coulton JW, Diederichs K, & Welte W (1998). Siderophore-mediated iron transport: crystal structure of FhuA with bound lipopolysaccharide.
Protein Sci 9 :956-963. PubMed Id: 9856937. |
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FhuA-AW140-LPS: Escherichia coli B Bacteria, 2.5 Å
Structure of lipopolysaccharide (LPS) in complex with FhuA. FhuA-DL41-LPS-ferricrocin, 2.7 Å: 1QFF |
Ferguson et al. (2000).
Ferguson AD, Welte W, Hofmann E, Lindner B, Holst O, Coulton JW, & Diederichs K (2000). A conserved structural motif for lipopolysaccharide recognition by procaryotic and eucaryotic proteins.
Structure 8 :585-592. PubMed Id: 10873859. |
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|
FhuA in complex with albomycin: Escherichia coli B Bacteria, 3.10 Å
In complex with phenylferricrocin, 2.95 Å: 1QJQ |
Ferguson et al. (2000).
Ferguson AD, Braun V, Fiedler HP, Coulton JW, Diederichs K, & Welte W (2000). Crystal structure of the antibiotic albomycin in complex with the outer membrane transporter FhuA.
Science 282 :2215-2220. PubMed Id: 10850805. |
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FhuA in complex with lipopolysaccharide and rifamycin CGP4832: Escherichia coli B Bacteria, 2.90 Å
|
Ferguson et al. (2001).
Ferguson AD, Ködding J, Walker G, Bös C, Coulton JW, Diederichs K, Braun V, & Welte W (2001). Active transport of an antibiotic rifamycin derivative by the outer-membrane protein FhuA.
Structure 9 :707-716. PubMed Id: 11587645. |
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FhuA in complex withTonB: Escherichia coli B Bacteria, 3.3 Å
|
Pawelek et al. (2006).
Pawelek PD, Croteau N, Ng-Thow-Hing C, Khursigara CM, Moiseeva N, Allaire M, & Coulton JW (2006). Structure of TonB in complex with FhuA, E. coli outer membrane receptor.
Science 312 :1399-1402. PubMed Id: 16741125. |
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FepA, Ferric enterobactin receptor: Escherichia coli B Bacteria, 2.4 Å
|
Buchanan et al. (1999).
Buchanan S, Smith BS, Venkatramani L, Xia D, Esser L, Palnitkar M, Chakraborty R, van der Helm D, & Deisenhofer J. (1999). Crystal Structure of the outer membrane active transporter FepA from Escherichia coli.
Nature Structural Biol 6 :56-63. PubMed Id: 9886293. |
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|
Ferguson et al. (2002).
Ferguson AD, Chakraborty R, Smith BS, Esser L, van der Helm D, & Deisenhofer, J (2002). Structural basis of gating by the outer Membrane transporter FecA.
Science 295 :1715-1719. PubMed Id: 11872840. |
|||
|
Yue et al. (2003).
Yue WW, Grizot S, & Buchanan SK (2003). Structural evidence for iron-free citrate and ferric citrate binding to the TonB-dependent outer membrane transporter FecA.
J Mol Biol 332 :353-368. PubMed Id: 12948487. |
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FecA, siderophore transporter periplasmic signalling domain: Escherichia coli B Bacteria, NMR Structure
Shows the signalling domain not seen x-ray structures |
Garcia-Herrero & Vogel (2005).
Garcia-Herrero A & Vogel HJ (2005). Nuclear magnetic resonance solution structure of the periplasmic signalling domain of the TonB-dependent outer membrane transporter FecA from Escherichia coli.
Mol Microbiol 58 :1226-1237. PubMed Id: 16313612. |
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|
Krieg et al. (2009).
Krieg S, Huché F, Diederichs K, Izadi-Pruneyre N, Lecroisey A, Wandersman C, Delepelaire P, & Welte W. (2009). Heme uptake across the outer membrane as revealed by crystal structures of the receptor-hemophore complex.
Proc Natl Acad Sci USA 106 :1045-1050. PubMed Id: 19144921. |
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ShuA heme-uptake receptor in complex with HasA hemophore and heme: Shigella dysenteriae B Bacteria (expressed in E. coli), 2.6 Å
|
Cobessi et al. (2010).
Cobessi D, Meksem A, & Brillet K (2010). Structure of the heme/hemoglobin outer membrane receptor ShuA from Shigella dysenteriae: heme binding by an induced fit mechanism.
Proteins 78 :286-294. PubMed Id: 19731368. doi:10.1002/prot.22539. |
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FptA, pyochelin outer membrane receptor: Pseudomonas aeruginosa B Bacteria, 2.0 Å
|
Cobessi et al. (2005).
Cobessi D, Celia H, Pattus F (2005). Crystal structure at high resolution of ferric-pyochelin and its membrane receptor FptA from Pseudomonas aeruginosa.
J Mol Biol 352 :893-904. PubMed Id: 16139844. |
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FpvA, Pyoverdine receptor: Pseudomonas aeruginosa B Bacteria, 3.6 Å
|
Cobessi et al. (2005).
Cobessi D, Celia H, Folschweiller N, Schaik IJ, Abdallah MA, & Pattus F (2005). The crystal structure of the pyoverdine outer membrane receptor FpvA from Pseudomonas aeruginosa at 3.6 Å resolution.
J Mol Biol 347 :121-134. PubMed Id: 15733922. |
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FpvA, Pyoverdine receptor (apo form): Pseudomonas aeruginosa B Bacteria, 2.77 Å
|
Brillet et al. (2007).
Brillet K, Journet L, Célia H, Paulus L, Stahl A, Pattus F, & Cobessi D (2007). A β strand lock exchange for signal transduction in TonB-dependent transducers on the basis of a common structural motif.
Structure 15 :1383-1391. PubMed Id: 17997964. |
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|
FpvA, Full-length structure bound to iron-pyoverdine: Pseudomonas aeruginosa B Bacteria, 2.73 Å
|
Wirth et al. (2007).
Wirth C, Meyer-Klaucke W, Pattus F, & Cobessi D (2007). From the periplasmic signaling domain to the extracellular face of an outer membrane signal transducer of Pseudomonas aeruginosa: crystal structure of the ferric pyoverdine outer membrane receptor.
J Mol Biol 368 :398-406. PubMed Id: 17349657. |
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|
AlgE alginate export protein: Pseudomonas aeruginosa B Bacteria (expressed in E. coli), 2.30 Å
18-stranded β-barrel with a highly electropositive pore constriction that acts as a selectivity filter for negatively charged alginate. |
Whitney et al. (2011).
Whitney JC, Hay ID, Li C, Eckford PD, Robinson H, Amaya MF, Wood LF, Ohman DE, Bear CE, Rehm BH, & Lynne Howell P (2011). Structural basis for alginate secretion across the bacterial outer membrane.
Proc Natl Acad Sci USA 108 :13083-13088. PubMed Id: 21778407. doi:10.1073/pnas.1104984108. |
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|
Tan et al. (2014).
Tan J, Rouse SL, Li D, Pye VE, Vogeley L, Brinth AR, El Arnaout T, Whitney JC, Howell PL, Sansom MS, & Caffrey M (2014). A conformational landscape for alginate secretion across the outer membrane of Pseudomonas aeruginosa.
Acta Crystallogr D Biol Crystallogr 70 :2054-2068. PubMed Id: 25084326. doi:10.1107/S1399004714001850. |
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AlgE alginate export protein at 100 K: Pseudomonas aeruginosa B Bacteria (expressed in E. coli), 2.90 Å
data collected at 293 K, 2.80 Å: 4XNK Structures determined by serial x-ray crystallography |
Huang et al. (2015).
Huang CY, Olieric V, Ma P, Panepucci E, Diederichs K, Wang M, & Caffrey M (2015). In meso in situ serial X-ray crystallography of soluble and membrane proteins.
Acta Crystallogr D Biol Crystallogr 71 :1238-1256. PubMed Id: 26057665. doi:10.1107/S1399004715005210. |
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P pilus usher translocation domain, PapC130-640: Escherichia coli B Bacteria, 3.2 Å
|
Remaut et al. (2008).
Remaut H, Tang C, Henderson NS, Pinkner JS, Wang T, Hultgren SJ, Thanassi DG, Waksman G, & Li H (2008). Fiber formation across the bacterial outer membrane by the chaperone/usher pathway.
Cell 133 :640-652. PubMed Id: 18485872. |
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P pilus FimD usher bound to FimC:FimH substrate: Escherichia coli B Bacteria, 2.80 Å
FimD translocation domain, 3.01 Å: 3OHN |
Phan et al. (2011).
Phan G, Remaut H, Wang T, Allen WJ, Pirker KF, Lebedev A, Henderson NS, Geibel S, Volkan E, Yan J, Kunze MB, Pinkner JS, Ford B, Kay CW, Li H, Hultgren SJ, Thanassi DG, & Waksman G (2011). Crystal structure of the FimD usher bound to its cognate FimC-FimH substrate.
Nature 474 :49-53. PubMed Id: 21637253. doi:10.1038/nature10109. |
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P pilus FimD usher in complex with FimC:FimF:FimG:FimH: Escherichia coli B Bacteria, 3.80 Å
This is the complete structure of the tip complex assembly in which the FimC:FimF:FimG:FimH complex passes through FimD. |
Geibel et al. (2013).
Geibel S, Procko E, Hultgren SJ, Baker D, & Waksman G (2013). Structural and energetic basis of folded-protein transport by the FimD usher.
Nature 496 :243-246. PubMed Id: 23579681. doi:10.1038/nature12007. |
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Transferrin binding protein A (TbpA) in complex with human transferrin: Neisseria meningitidis serogroup b B Bacteria (expressed in E. coli), 2.60 Å
TbpA in complex with human transferrin C-lobe, 3.10 Å: 3V89 Diferric human transferrin, 2.10 Å: 3V83 Apo-human transferrin C-lobe with bound sulfate ions, 1.70 Å: 3SKP Transferrin binding protein B (TbpB), 2.40 Å: 3V8U |
Noinaj et al. (2012).
Noinaj N, Easley NC, Oke M, Mizuno N, Gumbart J, Boura E, Steere AN, Zak O, Aisen P, Tajkhorshid E, Evans RW, Gorringe AR, Mason AB, Steven AC, & Buchanan SK (2012). Structural basis for iron piracy by pathogenic Neisseria.
Nature 483 :53-58. PubMed Id: 22327295. doi:10.1038/nature10823. |
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Wzi outer-membrane lectin: Escherichia coli B Bacteria, 2.64 Å
Assists in the formation of the bacterial capsule via direct interaction with capsular polysaccharides. |
Bushell et al. (2013).
Bushell SR, Mainprize IL, Wear MA, Lou H, Whitfield C, & Naismith JH (2013). Wzi Is an Outer Membrane Lectin that Underpins Group 1 Capsule Assembly in Escherichia coli.
Structure 21 :844-853. PubMed Id: 23623732. doi:10.1016/j.str.2013.03.010. |
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Opa60 for receptor-mediated engulfment, EXPLOR refined: Neisseria gonorrhoeae B Bacteria, NMR strucuture
MD/EXPLOR refined structure, NMR structure: 2MAF |
Fox et al. (2014).
Fox DA, Larsson P, Lo RH, Kroncke BM, Kasson PM, & Columbus L (2014). Structure of the neisserial outer membrane protein opa60: loop flexibility essential to receptor recognition and bacterial engulfment.
J Am Chem Soc 136 :9938-9946. PubMed Id: 24813921. doi:10.1021/ja503093y. |
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CsgG bacterial amyloid secretion channel: Escherichia coli B Bacteria, 3.59 Å
Pre-pore conformation, 2.80 Å: 4UV2 |
Goyal et al. (2014).
Goyal P, Krasteva PV, Van Gerven N, Gubellini F, Van den Broeck I, Troupiotis-Tsaïlaki A, Jonckheere W, Péhau-Arnaudet G, Pinkner JS, Chapman MR, Hultgren SJ, Howorka S, Fronzes R, & Remaut H (2014). Structural and mechanistic insights into the bacterial amyloid secretion channel CsgG.
Nature 516 7530:250-253. PubMed Id: 25219853. doi:10.1038/nature13768. |
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CsgG bacterial amyloid secretion channel: Escherichia coli B Bacteria, 3.10 Å
|
Cao et al. (2014).
Cao B, Zhao Y, Kou Y, Ni D, Zhang XC, & Huang Y (2014). Structure of the nonameric bacterial amyloid secretion channel.
Proc Natl Acad Sci USA 111 50:E5439-E5444. PubMed Id: 25453093. doi:10.1073/pnas.1411942111. |
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FusA plant-ferredoxin receptor: Pectobacterium atrosepticum B Bacteria (expressed in E. coli), 3.2 Å
|
Grinter et al. (2016).
Grinter R, Josts I, Mosbahi K, Roszak AW, Cogdell RJ, Bonvin AM, Milner JJ, Kelly SM, Byron O, Smith BO, & Walker D (2016). Structure of the bacterial plant-ferredoxin receptor FusA.
Nat Commun 7 :13308. PubMed Id: 27796364. doi:10.1038/ncomms13308. |
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Outer Membrane Autotransporters
|
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NalP autotransporter translocator domain: Neisseria meningitidis B Bacteria (expressed in E. coli), 2.60 Å
p6122 space group. See also 1UYO, C2221 space group, 3.2 Å resolution. |
Oomen et al. (2004).
Oomen CJ, Van Ulsen P, Van Gelder P, Feijen M, Tommassen J, & Gros P (2004). Structure of the translocator domain of a bacterial autotransporter.
EMBO J 23 :1257-1266. PubMed Id: 15014442. |
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Hia1022-1098 trimeric autotransporter: Haemophilus influenzae B Bacteria (expressed in E. coli), 2.0 Å
Hia992-1098, 2.3 Å: 2GR7 |
Meng et al. (2006).
Meng G, Surana NK, St Geme JW 3rd, Waksman G (2006). Structure of the outer membrane translocator domain of the Haemophilus influenzae Hia trimeric autotransporter.
EMBO J 25 :2297-2304. PubMed Id: 16688217. |
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EspP autotransporter, post-cleavage state: Escherichia coli B Bacteria, 2.7 Å
|
Barnard et al. (2007).
Barnard TJ, Dautin N, Lukacik P, Bernstein HD, & Buchanan SK (2007). Autotransporter structure reveals intra-barrel cleavage followed by conformational changes.
Nature Struc Mol Biol 14 :1214-1220. PubMed Id: 17994105. |
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|
Barnard et al. (2012).
Barnard TJ, Gumbart J, Peterson JH, Noinaj N, Easley NC, Dautin N, Kuszak AJ, Tajkhorshid E, Bernstein HD, & Buchanan SK (2012). Molecular Basis for the Activation of a Catalytic Asparagine Residue in a Self-Cleaving Bacterial Autotransporter.
J Mol Biol 415 :128-142. PubMed Id: 22094314. doi:10.1016/j.jmb.2011.10.049. |
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|
EspP autotransporter passenger domain: Escherichia coli B Bacteria, 2.50 Å
Like a number of other auto-cleaved passengers, a parallel β-helix is a characteristic feature. |
Khan et al. (2011).
Khan S, Mian HS, Sandercock LE, Chirgadze NY, & Pai EF (2011). Crystal Structure of the Passenger Domain of the Escherichia coli Autotransporter EspP.
J Mol Biol 413 :985-1000. PubMed Id: 21964244. doi:10.1016/j.jmb.2011.09.028. |
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Hbp (hemoglobin protease) self-cleaving autotransporter with truncated passenger: Escherichia coli B Bacteria, 2.00 Å
The structure shows the pre-cleavage state. |
Tajima et al. (2010).
Tajima N, Kawai F, Park SY, & Tame JR (2010). A novel intein-like autoproteolytic mechanism in autotransporter proteins.
J Mol Biol 402 :645-656. PubMed Id: 20615416. doi:10.1016/j.jmb.2010.06.068. |
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|
Hbp (hemoglobin protease) full-length passenger domain: Escherichia coli B Bacteria, 2.20 Å
The passenger domain has a prominent β-helix domain. |
Otto et al. (2005).
Otto BR, Sijbrandi R, Luirink J, Oudega B, Heddle JG, Mizutani K, Park SY, & Tame JR (2005). Crystal structure of hemoglobin protease, a heme binding autotransporter protein from pathogenic Escherichia coli.
J Biol Chem 280 :17339-17345. PubMed Id: 15728184. doi:10.1074/jbc.M412885200. |
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EstA Autotransporter, full length: Pseudomonas aeruginosa B Bacteria (expressed in E. coli), 2.50 Å
This is the first full-length structure of an autotransporter. The passenger is not cleaved physiologically, but rather presents an esterase domain to the external world. |
van den Berg (2010).
van den Berg B (2010). Crystal Structure of a Full-Length Autotransporter.
J Mol Biol 396 :627-633. PubMed Id: 20060837. |
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IcsA autotransporter (autochaperone region only): Shigella flexneri B Bacteria (expressed in E. coli), 2.00 Å
|
Kühnel & Diezmann (2011).
Kühnel K & Diezmann D (2011). Crystal structure of the autochaperone region from the Shigella flexneri autotransporter IcsA.
J Bacteriol 193 :2042-2045 . PubMed Id: 21335457. doi:10.1128/JB.00790-10. |
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|
Intimin outer membrane β-domain: Escherichia coli B Bacteria, 1.86 Å
The C-terminal passenger domain, not present in this structure, is involved in adhesion to host cells. |
Fairman et al. (2012).
Fairman JW, Dautin N, Wojtowicz D, Liu W, Noinaj N, Barnard TJ, Udho E, Przytycka TM, Cherezov V, & Buchanan SK (2012). Crystal structures of the outer membrane domain of intimin and invasin from enterohemorrhagic E. coli and enteropathogenic Y. pseudotuberculosis.
Structure 20 :1233-1243. PubMed Id: 22658748. doi:10.1016/j.str.2012.04.011. |
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Intimin C-terminal passenger domain in complex with receptor: Escherichia coli B Bacteria, 2.90 Å
|
Luo et al. (2000).
Luo Y, Frey EA, Pfuetzner RA, Creagh AL, Knoechel DG, Haynes CA, Finlay BB, & Strynadka NC (2000). Crystal structure of enteropathogenic Escherichia coli intimin-receptor complex.
Nature 405 :1073-1077. PubMed Id: 10890451. doi:10.1038/35016618. See also: Batchelor et al. (2000). Batchelor M, Prasannan S, Daniell S, Reece S, Connerton I, Bloomberg G, Dougan G, Frankel G, & Matthews S (2000). Structural basis for recognition of the translocated intimin receptor (Tir) by intimin from enteropathogenic Escherichia coli.
EMBO J 19 :2452-2464. PubMed Id: 10835344. |
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|
Invasin outer membrane β-domain: Yersinia pseudotuberculosis B Bacteria (expressed in E. coli), 2.26 Å
The C-terminal passenger domain, not present in this structure, is involved in adhesion to host cells. |
Fairman et al. (2012).
Fairman JW, Dautin N, Wojtowicz D, Liu W, Noinaj N, Barnard TJ, Udho E, Przytycka TM, Cherezov V, & Buchanan SK (2012). Crystal structures of the outer membrane domain of intimin and invasin from enterohemorrhagic E. coli and enteropathogenic Y. pseudotuberculosis.
Structure 20 :1233-1243. PubMed Id: 22658748. doi:10.1016/j.str.2012.04.011. |
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|
Invasin C-terminal passenger domain: Yersinia pseudotuberculosis B Bacteria (expressed in E. coli), 2.30 Å
|
Hamburger et al. (1999).
Hamburger ZA, Brown MS, Isberg RR, & Bjorkman PJ (1999). Crystal structure of invasin: a bacterial integrin-binding protein.
Science 286 :291-295. PubMed Id: 10514372. |
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|
YadA trimeric adhesin autotransporter: Yersinia enterocolitica subsp. enterocolitica 8081 B Bacteria (expressed in E. coli), NMR Structure
Structure determined from microcrystals using solid-state NMR |
Shahid et al. (2012).
Shahid SA, Bardiaux B, Franks WT, Krabben L, Habeck M, van Rossum BJ, & Linke D (2012). Membrane-protein structure determination by solid-state NMR spectroscopy of microcrystals.
Nature Methods 9 :1212-1217. PubMed Id: 23142870. |
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|
TamA Autotransporter, full length: Escherichia coli B Bacteria, 2.25 Å
TamA POTRA domains 1-3, 1.84 Å: 4BZA |
Gruss et al. (2013).
Gruss F, Zähringer F, Jakob RP, Burmann BM, Hiller S, & Maier T (2013). The structural basis of autotransporter translocation by TamA.
Nat Struct Mol Biol 20 :1318-1320. PubMed Id: 24056943. doi:10.1038/nsmb.2689. |
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|
TibC dodecameric glycosyltransferase (type V secretion system): Escherichia coli ETEC H10407 B Bacteria (expressed in E. coli), 2.88 Å
in complex with ADP-D-beta-D-heptose, 3.88 Å: 4RB4 Cryo-EM structures of the TibC12-TibA6 are available in the EM Databank with accession numbers EMD-2755, -2756, -2757, and -2758. |
Yao et al. (2014).
Yao Q, Lu Q, Wan X, Song F, Xu Y, Hu M, Zamyatina A, Liu X, Huang N, Zhu P, & Shao F (2014). A structural mechanism for bacterial autotransporter glycosylation by a dodecameric heptosyltransferase family.
Elife 3 . PubMed Id: 25310236. doi:10.7554/eLife.03714. |
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Omp85-TpsB Outer Membrane Transporter Superfamily
|
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|
FhaC Filamentous Hemagglutinin Transporter: Bordetella pertussis B Bacteria (expressed in E. coli), 3.15 Å
The first outer membrane protein from the Omp85–two-partner secretion B (TpsB) superfamily. Supersedes 2QDZ. |
Clantin et al. (2007).
Clantin B, Delattre AS, Rucktooa P, Saint N, Meli AC, Locht C, Jacob-Dubuisson F, & Villeret V (2007). Structure of the membrane protein FhaC: a member of the Omp85-TpsB transporter superfamily.
Science 317 :957-961. PubMed Id: 17702945. |
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|
FhaC Filamentous Hemagglutinin Transporter, R450A mutant: Bordetella pertussis B Bacteria (expressed in E. coli), 3.50 Å
|
Delattre et al. (2010).
Delattre AS, Clantin B, Saint N, Locht C, Villeret V, & Jacob-Dubuisson F (2010). Functional importance of a conserved sequence motif in FhaC, a prototypic member of the TpsB/Omp85 superfamily.
FEBS J 277 :4755-4765. PubMed Id: 20955520. doi:10.1111/j.1742-4658.2010.07881.x. |
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TeOmp85-N POTRA domains: Thermosynechococcus elongatus B Bacteria (expressed in E. coli), 1.97 Å
Structure is of complete N-terminus containing three POTRA domains. The polypeptide transport-associated (POTRA) domains link to a transmembrane β-barrel, which is absent in this structure. |
Arnold et al. (2010).
Arnold T, Zeth K, & Linke D (2010). Omp85 from the thermophilic cyanobacterium thermosynechococcus elongatus differs from proteobacterial Omp85 in structure and domain composition.
J Biol Chem 285 :18003-18015. PubMed Id: 20351097. |
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|
anaOmp85-N POTRA domains (hexagonal crystals): Anabaena sp. PCC7120 B Bacteria (expressed in E. coli), 2.20 Å
Structure is of complete N-terminus containing three POTRA domains. The polypeptide transport-associated (POTRA) domains link to a transmembrane β-barrel, which is absent in this structure. Tetragonal crystals, 2.59 Å: 3MC8 |
Koenig et al. (2010).
Koenig P, Mirus O, Haarmann R, Sommer M, Sinning I, Schleiff E, & Tews I (2010). Conserved properties of POTRA domains derived from cyanobacterial OMP85.
J Biol Chem 285 :18016-18024. PubMed Id: 20348103. |
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|
BamA with POTRA domains 1 - 5: Neisseria gonorrhoeae B Bacteria (expressed in E. coli), 3.20 Å
This is the full-length BamA structure. |
Noinaj et al. (2013).
Noinaj N, Kuszak AJ, Gumbart JC, Lukacik P, Chang H, Easley NC, Lithgow T, & Buchanan SK (2013). Structural insight into the biogenesis of β-barrel membrane proteins.
Nature 501 :385-390. PubMed Id: 23995689. doi:10.1038/nature12521. |
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BamA with POTRA domains 4 & 5: Haemophilus ducreyi B Bacteria (expressed in E. coli), 2.91 Å
|
Noinaj et al. (2013).
Noinaj N, Kuszak AJ, Gumbart JC, Lukacik P, Chang H, Easley NC, Lithgow T, & Buchanan SK (2013). Structural insight into the biogenesis of β-barrel membrane proteins.
Nature 501 :385-390. PubMed Id: 23995689. doi:10.1038/nature12521. |
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|
BamA with POTRA domain 5: Escherichia coli B Bacteria, 3.00 Å
|
Albrecht et al. (2014).
Albrecht R, Schütz M, Oberhettinger P, Faulstich M, Bermejo I, Rudel T, Diederichs K, & Zeth K (2014). Structure of BamA, an essential factor in outer membrane protein biogenesis.
Acta Crystallogr D Biol Crystallogr 70 :1779-1789. PubMed Id: 24914988. doi:10.1107/S1399004714007482. |
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BamA21-351 POTRA domains (periplasmic fragment, P212121): Escherichia coli B Bacteria, 2.2 Å
BamA was formerly named YaeT. The polypeptide transport-associated (POTRA) domains link to a transmembrane β-barrel, which is absent in this structure. P21212 space group, 2.2 Å: 2QDF |
Kim et al. (2007).
Kim S, Malinverni JC, Sliz P, Silhavy TJ, Harrison SC, & Kahne D (2007). Structure and function of an essential component of the outer membrane protein assembly machine.
Science 317 :961-964. PubMed Id: 17702946. |
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BamA21-410 POTRA domains (periplasmic fragment): Escherichia coli B Bacteria, 3.3 Å
BamA was formerly named YaeT. The polypeptide transport-associated (POTRA) domains link to a transmembrane β-barrel, which is absent in this structure. Structure shows the first four POTRA domains in an extended conformation. |
Gatzeva-Topalova et al. (2008).
Gatzeva-Topalova PZ, Walton TA, & Sousa MC (2008). Crystal Structure of YaeT: Conformational flexibility and substrate recognition.
Structure 16 :1873-1881. PubMed Id: 19081063. |
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|
BamA21-174 POTRA domains 1 and 2: Escherichia coli B Bacteria, NMR Structure
BamA was formerly named YaeT. |
Knowles et al. (2008).
Knowles TJ, Jeeves M, Bobat S, Dancea F, McClelland D, Palmer T, Overduin M, & Henderson IR (2008). Fold and function of polypeptide transport-associated domains responsible for delivering unfolded proteins to membranes.
Mol Microbiol 68 :1216-1227. PubMed Id: 18430136. |
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BamA264-424 POTRA domains 4 and 5: Escherichia coli B Bacteria, 2.69 Å
BamA was formerly named YaeT. From this structure and earlier ones (above), Gatzeva-Topalova et al. have constructed a 'spliced' model for the complete POTRA1-5 structure. |
Gatzeva-Topalova et al. (2010).
Gatzeva-Topalova PZ, Warner LR, Pardi A, & Sousa MC (2010). Structure and Flexibility of the Complete Periplasmic Domain of BamA: The Protein Insertion Machine of the Outer Membrane.
Structure 18 :1492-1501. PubMed Id: 21070948. |
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BamA266-420 POTRA domains 4 and 5: Escherichia coli B Bacteria, 1.5 Å
BamA formerly named YaeT. |
Zhang et al. (2011).
Zhang H, Gao ZQ, Hou HF, Xu JH, Li LF, Su XD, & Dong YH (2011). High-resolution structure of a new crystal form of BamA POTRA4-5 from Escherichia coli.
Acta Crystallogr Sect F Struct Biol Cryst Commun F67 :734-738. PubMed Id: 21795783. doi:10.1107/S1744309111014254. |
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BamB component of the Bam β-barrel assembly machine: Escherichia coli B Bacteria, 1.80 Å
|
Heuck et al. (2011).
Heuck A, Schleiffer A, & Clausen T (2011). Augmenting β-Augmentation: Structural Basis of How BamB Binds BamA and May Support Folding of Outer Membrane Proteins.
J Mol Biol 406 :659-666. PubMed Id: 21236263. |
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BamB component of the Bam β-barrel assembly machine: Escherichia coli B Bacteria, 2.60 Å
|
Kim & Paetzel (2011).
Kim KH & Paetzel M (2011). Crystal Structure of Escherichia coli BamB, a Lipoprotein Component of the β-Barrel Assembly Machinery Complex.
J Mol Biol 406 :667-678. PubMed Id: 21168416. |
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|
Noinaj et al. (2011).
Noinaj N, Fairman JW, & Buchanan SK (2011). Crystal structures The Crystal Structure of BamB Suggests Interactions with BamA and Its Role within the BAM Complex.
J Mol Biol 407 :248-260. PubMed Id: 21277859. |
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BamB component of the Bam β-barrel assembly machine: Escherichia coli B Bacteria, 2.60 Å
|
Albrecht & Zeth (2011).
Albrecht R & Zeth K (2011). Structural basis of outer membrane protein biogenesis in bacteria.
J Biol Chem 286 :27792-27803. PubMed Id: 21586578. doi:10.1074/jbc.M111.238931. |
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BamB component of the Bam β-barrel assembly machine: Escherichia coli B Bacteria, 2.00 Å
|
Dong et al. (2012).
Dong C, Yang X, Hou HF, Shen YQ, & Dong YH (2012). Structure of Escherichia coli BamB and its interaction with POTRA domains of BamA.
Acta Crystallogr D Biol Crystallogr D68 :1134-1139. PubMed Id: 22948914. doi:10.1107/S0907444912023141. |
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BamB in complex with POTRA 3-4 domains of BamA: Escherichia coli B Bacteria, 2.15 Å
|
Chen et al. (2016).
Chen Z, Zhan LH, Hou HF, Gao ZQ, Xu JH, Dong C, & Dong YH (2016). Structural basis for the interaction of BamB with the POTRA3-4 domains of BamA.
Acta Crystallogr D Struct Biol 72 :236-244. PubMed Id: 26894671. doi:10.1107/S2059798315024729. |
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BamC component of the Bam β-barrel assembly machine: Escherichia coli B Bacteria, 1.55 Å
C-terminal domain, residues 101-212 |
Albrecht & Zeth (2011).
Albrecht R & Zeth K (2011). Structural basis of outer membrane protein biogenesis in bacteria.
J Biol Chem 286 :27792-27803. PubMed Id: 21586578. doi:10.1074/jbc.M111.238931. |
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|
BamC component of the Bam β-barrel assembly machine: Escherichia coli B Bacteria, 1.25 Å
N-terminal domain, residues 25-143 |
Albrecht & Zeth (2011).
Albrecht R & Zeth K (2011). Structural basis of outer membrane protein biogenesis in bacteria.
J Biol Chem 286 :27792-27803. PubMed Id: 21586578. doi:10.1074/jbc.M111.238931. |
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|
BamC component of the Bam β-barrel assembly machine (N-term, 101-212): Escherichia coli B Bacteria, NMR Structure
Structure obtained Using Rosetta with a limited NMR data set. C-term domain, 229-344: 2LAE |
Warner et al. (2011).
Warner LR, Varga K, Lange OF, Baker SL, Baker D, Sousa MC, & Pardi A (2011). Structure of the BamC two-domain protein obtained by Rosetta with a limited NMR data set.
J Mol Biol 411 :83-95. PubMed Id: 21624375. doi:10.1016/j.jmb.2011.05.022. |
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BamC component of the Bam β-barrel assembly machine (C-term, 224-343): Escherichia coli B Bacteria, 1.50 Å
|
Kim et al. (2011).
Kim KH, Aulakh S, Tan W, & Paetzel M (2011). Crystallographic analysis of the C-terminal domain of the Escherichia coli lipoprotein BamC.
Acta Crystallogr Sect F Struct Biol Cryst Commun 67 :1350-1358. PubMed Id: 22102230. doi:10.1107/S174430911103363X. |
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BamD component of the Bam β-barrel assembly machine: Rhodothermus marinus B Bacteria (expressed in E. coli), 2.15 Å
BamD associates with the membrane using a lipidated amino-terminal cysteine. BamE and BamC are thought to bind to the C-terminus of BamD. |
Sandoval et al. (2011).
Sandoval CM, Baker SL, Jansen K, Metzner SI, & Sousa MC (2011). Crystal Structure of BamD: An Essential Component of the β-Barrel Assembly Machinery of Gram-Negative Bacteria
J Mol Biol 409 :348-357. PubMed Id: 21463635. doi:10.1016/j.jmb.2011.03.035. |
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BamD component of the Bam β-barrel assembly machine: Escherichia coli B Bacteria, 1.80 Å
|
Albrecht & Zeth (2011).
Albrecht R & Zeth K (2011). Structural basis of outer membrane protein biogenesis in bacteria.
J Biol Chem 286 :27792-27803. PubMed Id: 21586578. doi:10.1074/jbc.M111.238931. |
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BamD component of the Bam β-barrel assembly machine: Escherichia coli B Bacteria, 2.60 Å
|
Dong et al. (2012).
Dong C, Hou HF, Yang X, Shen YQ, & Dong YH (2012). Structure of Escherichia coli BamD and its functional implications in outer membrane protein assembly.
Acta Crystallogr D68 :95-101. PubMed Id: 22281737. doi:10.1107/S0907444911051031. |
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BamE component of the Bam β-barrel assembly machine: Escherichia coli B Bacteria, NMR structure
|
Knowles et al. (2011).
Knowles TJ, Browning DF, Jeeves M, Maderbocus R, Rajesh S, Sridhar P, Manoli E, Emery D, Sommer U, Spencer A, Leyton DL, Squire D, Chaudhuri RR, Viant MR, Cunningham AF, Henderson IR, Overduin M (2011). Structure and function of BamE within the outer membrane and the β-barrel assembly machine.
EMBO Rep 12 :123-128. PubMed Id: 21212804. |
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BamE component of the Bam β-barrel assembly machine: Escherichia coli B Bacteria, 1.80 Å
|
Albrecht & Zeth (2011).
Albrecht R & Zeth K (2011). Structural basis of outer membrane protein biogenesis in bacteria.
J Biol Chem 286 :27792-27803. PubMed Id: 21586578. doi:10.1074/jbc.M111.238931. |
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BamCD complex of the Bam β-barrel assembly machine: Escherichia coli B Bacteria, 2.90 Å
The BamC component is the N-terminal domain, residues 26-217. The BamD component includes residues 32-240. |
Kim et al. (2011).
Kim KH, Aulakh S, & Paetzel M (2011). Crystal Structure of β-Barrel Assembly Machinery BamCD Protein Complex
J Biol Chem 286 :39116-39121. PubMed Id: 21937441. doi:10.1074/jbc.M111.298166. |
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BamACDE complex of the Bam β-barrel assembly machine: Escherichia coli B Bacteria, 3.4 Å
|
Bakelar et al. (2016).
Bakelar J, Buchanan SK, & Noinaj N (2016). The structure of the β-barrel assembly machinery complex.
Science 351 :180-186. PubMed Id: 26744406. doi:10.1126/science.aad3460. |
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BamA-POTRA4-5-BamD fusion complex of the Bam β-barrel assembly machine: Rhodothermus marinus B Bacteria (expressed in E. coli), 2.0 Å
|
Bergal et al. (2016).
Bergal HT, Hopkins AH, Metzner SI, & Sousa MC (2016). The Structure of a BamA-BamD Fusion Illuminates the Architecture of the β-Barrel Assembly Machine Core.
Structure 24 :243-251. PubMed Id: 26749448. doi:10.1016/j.str.2015.10.030. |
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BamABCDE complex of the Bam β-barrel assembly machine: Escherichia coli B Bacteria, 2.90 Å
BAM ACDE complex, 3.90 Å: 5D0Q |
Gu et al. (2016).
Gu Y, Li H, Dong H, Zeng Y, Zhang Z, Paterson NG, Stansfeld PJ, Wang Z, Zhang Y, Wang W, & Dong C (2016). Structural basis of outer membrane protein insertion by the BAM complex.
Nature 531 :64-69. PubMed Id: 26901871. doi:10.1038/nature17199. |
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BamABCDE complex of the Bam β-barrel assembly machine: Escherichia coli B Bacteria, 3.56 Å
|
Han et al. (2016).
Han L, Zheng J, Wang Y, Yang X, Liu Y, Sun C, Cao B, Zhou H, Ni D, Lou J, Zhao Y, & Huang Y (2016). Structure of the BAM complex and its implications for biogenesis of outer-membrane proteins.
Nat Struct Mol Biol 23 :192-196. PubMed Id: 26900875. doi:10.1038/nsmb.3181. |
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BamABCDE complex of the Bam β-barrel assembly machine: Escherichia coli B Bacteria, 4.9 Å
cryo-EM structure showing lateral opening of complex |
Iadanza et al. (2016).
Iadanza MG, Higgins AJ, Schiffrin B, Calabrese AN, Brockwell DJ, Ashcroft AE, Radford SE, & Ranson NA (2016). Lateral opening in the intact β-barrel assembly machinery captured by cryo-EM.
Nat Commun 7 :12865. PubMed Id: 27686148. doi:10.1038/ncomms12865. |
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Beta-Barrel Membrane Proteins: Mitochondrial Outer Membrane
|
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VDAC-1 voltage dependent anion channel: Homo sapiens E Eukaryota (expressed in E. coli), NMR structure
Structure determined in LDAO micelles. |
Hiller et al. (2008).
Hiller S, Garces RG, Malia TJ, Orekhov VY, Colombini M, & Wagner G (2008). Solution structure of the integral human membrane protein VDAC-1 in detergent micelles.
Science 321 :1206-1210. PubMed Id: 18755977. |
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VDAC-1 voltage dependent anion channel: Homo sapiens E Eukaryota (expressed in E. coli), 4 Å
Structure determined by combining x-ray and NMR data. |
Bayrhuber et al. (2008).
Bayrhuber M, Meins T, Habeck M, Becker S, Giller K, Villinger S, Vonrhein C, Griesinger C, Zweckstetter M, & Zeth K (2008). Structure of the human voltage-dependent anion channel.
Proc Natl Acad Sci USA 105 :15370-15375. PubMed Id: 18832158. |
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VDAC-1 voltage dependent anion channel: Mus musculus E Eukaryota (expressed in E. coli), 2.3 Å
Reveals the voltage-sensing N-terminal α-helix. |
Ujwal et al. (2008).
Ujwal R, Cascio D, Colletier JP, Faham S, Zhang J, Toro L, Ping P, & Abramson J (2008). The crystal structure of mouse VDAC1 at 2.3 Å resolution reveals mechanistic insights into metabolite gating.
Proc Natl Acad Sci USA 105 :17742-17747. PubMed Id: 18988731. |
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VDAC-1 voltage dependent anion channel with bound ATP: Mus musculus E Eukaryota (expressed in E. coli), 2.28 Å
|
Choudhary et al. (2014).
Choudhary OP, Paz A, Adelman JL, Colletier JP, Abramson J, & Grabe M (2014). Structure-guided simulations illuminate the mechanism of ATP transport through VDAC1.
Nat Struct Mol Biol 21 7:626-632. PubMed Id: 24908397. doi:10.1038/nsmb.2841. |
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VDAC-2 voltage dependent anion channel: Danio rerio E Eukaryota (expressed in E. coli), 2.80 Å
Double electron-electron resonance measurements indicate a population of oligomers. |
Schredelseker et al. (2014).
Schredelseker J, Paz A, López CJ, Altenbach C, Leung CS, Drexler MK, Chen JN, Hubbell WL, & Abramson J (2014). High-Resolution Structure and Double Electron-Electron Resonance of the Zebrafish Voltage Dependent Anion Channel 2 Reveal an Oligomeric Population.
J Biol Chem 289 :12566-12577. PubMed Id: 24627492. doi:10.1074/jbc.M113.497438. |
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Lipopolysaccharide (LPS) Transport Proteins
|
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LptD-LptE lipopolysaccharide transport complex: Salmonella enterica B Bacteria (expressed in E. coli), 2.80 Å
Structure provides the basis for LPS translocation across the outer membrane. LptD comprises residues 226-786. LptE comprises residues 19 - 169. |
Dong et al. (2014).
Dong H, Xiang Q, Gu Y, Wang Z, Paterson NG, Stansfeld PJ, He C, Zhang Y, Wang W, & Dong C (2014). Structural basis for outer membrane lipopolysaccharide insertion.
Nature 511 :52-56. PubMed Id: 24990744. doi:10.1038/nature13464. |
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LptD-LptE lipopolysaccharide transport complex: Shigella flexneri B Bacteria (expressed in E. coli), 2.39 Å
|
Qiao et al. (2014).
Qiao S, Luo Q, Zhao Y, Zhang XC, & Huang Y (2014). Structural basis for lipopolysaccharide insertion in the bacterial outer membrane.
Nature 511 :108-111. PubMed Id: 24990751. doi:10.1038/nature13484. |
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LptE lipopolysaccharide transport protein: Escherichia coli B Bacteria, 2.34 Å
|
Malojčić et al. (2014).
Malojčić G, Andres D, Grabowicz M, George AH, Ruiz N, Silhavy TJ, & Kahne D (2014). LptE binds to and alters the physical state of LPS to catalyze its assembly at the cell surface.
Proc. Natl. Acad. Sci. U.S.A. 111 26:9467-9472. PubMed Id: 24938785. doi:10.1073/pnas.1402746111. |
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LptD-LptE lipopolysaccharide transport complex: Yersinia pestis B Bacteria (expressed in E. coli), 2.75 Å
|
Botos et al. (2016).
Botos I, Majdalani N, Mayclin SJ, McCarthy JG, Lundquist K, Wojtowicz D, Barnard TJ, Gumbart JC, & Buchanan SK (2016). Structural and Functional Characterization of the LPS Transporter LptDE from Gram-Negative Pathogens.
Structure 24 :965-976. PubMed Id: 27161977. doi:10.1016/j.str.2016.03.026. |
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LptD-LptE lipopolysaccharide transport complex: Klebsiella pneumoniae B Bacteria (expressed in E. coli), 2.94 Å
full-length protein, 4.37 Å: 5IV9 |
Botos et al. (2016).
Botos I, Majdalani N, Mayclin SJ, McCarthy JG, Lundquist K, Wojtowicz D, Barnard TJ, Gumbart JC, & Buchanan SK (2016). Structural and Functional Characterization of the LPS Transporter LptDE from Gram-Negative Pathogens.
Structure 24 :965-976. PubMed Id: 27161977. doi:10.1016/j.str.2016.03.026. |
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|
LptD-LptE lipopolysaccharide transport complex: Pseudomonas aeruginosa B Bacteria (expressed in E. coli), 2.99 Å
|
Botos et al. (2016).
Botos I, Majdalani N, Mayclin SJ, McCarthy JG, Lundquist K, Wojtowicz D, Barnard TJ, Gumbart JC, & Buchanan SK (2016). Structural and Functional Characterization of the LPS Transporter LptDE from Gram-Negative Pathogens.
Structure 24 :965-976. PubMed Id: 27161977. doi:10.1016/j.str.2016.03.026. |
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Type II Secretion Systems
|
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|
GspD secretin: Escherichia coli B Bacteria, 3.04 Å
cryo-EM structure |
Yan et al. (2017).
Yan Z, Yin M, Xu D, Zhu Y, & Li X (2017). Structural insights into the secretin translocation channel in the type II secretion system.
Nat Struct Mol Biol 24 :177-183. PubMed Id: 28067918. doi:10.1038/nsmb.3350. |
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|
GspD secretin: Vibrio cholerae B Bacteria (expressed in E. coli), 3.26 Å
cryo-EM structure partially open state without the cap gate, 4.22 Å: 5WQ9 |
Yan et al. (2017).
Yan Z, Yin M, Xu D, Zhu Y, & Li X (2017). Structural insights into the secretin translocation channel in the type II secretion system.
Nat Struct Mol Biol 24 :177-183. PubMed Id: 28067918. doi:10.1038/nsmb.3350. |
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|
Type III Secretion Systems
|
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|
Worrall et al. (2016).
Worrall LJ, Hong C, Vuckovic M, Deng W, Bergeron JR, Majewski DD, Huang RK, Spreter T, Finlay BB, Yu Z, & Strynadka NC (2016). Near-atomic-resolution cryo-EM analysis of the Salmonella T3S injectisome basal body.
Nature 540 :597-601. PubMed Id: 27974800. doi:10.1038/nature20576. |
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Adventitious Membrane Proteins: Beta-sheet Pore-forming Toxins/Attack Complexes
|
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|
α-hemolysin: Staphylococcus aureus B Bacteria, 1.9 Å
|
Song et al. (1996).
Song L, Hobaugh MR, Shustak C, Cheley S, Bayley H, & Gouaux JE (1996). Structure of staphylococcal a -hemolysin, a heptameric transmembrane pore.
Science 274 :1859-1866. PubMed Id: 8943190. |
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Banerjee et al. (2010).
Banerjee A, Mikhailova E, Cheley S, Gu LQ, Montoya M, Nagaoka Y, Gouaux E, & Bayley H (2010). Molecular bases of cyclodextrin adapter interactions with engineered protein nanopores.
Proc Natl Acad Sci USA 107 :8165-8170. PubMed Id: 20400691. doi:10.1073/pnas.0914229107 . |
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α-hemolysin: Staphylococcus aureus B Bacteria (expressed in E. coli), 2.30 Å
Crystals were prepared using 2-methyl-2,4-pentanediol without detergent. |
Tanaka et al. (2011).
Tanaka Y, Hirano N, Kaneko J, Kamio Y, Yao M, & Tanaka I (2011). 2-Methyl-2,4-pentanediol induces spontaneous assembly of staphylococcal α-hemolysin into heptameric pore structure.
Protein Sci 20 :448-456. PubMed Id: 21280135. doi:10.1002/pro.579. |
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γ-hemolysin composed of LukF and Hlg2: Staphylococcus aureus B Bacteria (expressed in E. coli), 2.50 Å
|
Yamashita et al. (2011).
Yamashita K, Kawai Y, Tanaka Y, Hirano N, Kaneko J, Tomita N, Ohta M, Kamio Y, Yao M, & Tanaka I (2011). Crystal structure of the octameric pore of staphylococcal γ-hemolysin reveals the β-barrel pore formation mechanism by two components.
Proc Natl Acad Sci USA 108 :17314-17319. PubMed Id: 21969538. doi:10.1073/pnas.1110402108. |
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γ-hemolysin prepore: Staphylococcus aureus B Bacteria (expressed in E. coli), 2.99 Å
|
Yamashita et al. (2014).
Yamashita D, Sugawara T, Takeshita M, Kaneko J, Kamio Y, Tanaka I, Tanaka Y, & Yao M (2014). Molecular basis of transmembrane beta-barrel formation of staphylococcal pore-forming toxins.
Nat Commun 5 :4897. PubMed Id: 25263813. doi:10.1038/ncomms5897. |
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|
Olson et al. (1999).
Olson R, Nariya H, Yokota K, Kamio Y, & Gouaux E (1999). Crystal structure of Staphylococcal LukF delineates conformational changes accompanying formation of a transmembrane channel.
Nature Struc. Biol 6 :134-140. PubMed Id: 10048924. |
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LUK prepore formed from LukF & LukS: Staphylococcus aureus B Bacteria (expressed in E. coli), 2.40 Å
|
Yamashita et al. (2014).
Yamashita D, Sugawara T, Takeshita M, Kaneko J, Kamio Y, Tanaka I, Tanaka Y, & Yao M (2014). Molecular basis of transmembrane beta-barrel formation of staphylococcal pore-forming toxins.
Nat Commun 5 :4897. PubMed Id: 25263813. doi:10.1038/ncomms5897. |
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Perfringolysin O (PFO) protomer: Clostridium perfringens B Bacteria (expressed in E. coli), 2.20 Å
The protein is a thiol-activated cytolysin that uses membrane cholesterol as a receptor. 40 or more protomers assemble into a large pore anchored in the bilayer by the β-sheets of domain 4. Space group is C2221. P21212 space group, 3.0 Å: 1M3J. P31 space group, 2.90 Å: 1M3I. |
Rossjohn et al. (1997).
Rossjohn J, Feil SC, McKinstry WJ, Tweten RK, & Parker MW (1997). Structure of a cholesterol-binding, thiol-activated cytolysin and a model of its membrane form.
Cell 89 :685-692. PubMed Id: 9182756. |
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Anthrax Protective Antigen (PA) and Lethal Factor (LF) Prechannel Complex: Bacillus anthraciss B Bacteria (expressed in E. coli), 3.10 Å
The structure is the PA8LF4 prechannel. |
Feld et al. (2010).
Feld GK, Thoren KL, Kintzer AF, Sterling HJ, Tang II, Greenberg SG, Williams ER, & Krantz BA (2010). Structural basis for the unfolding of anthrax lethal factor by protective antigen oligomers.
Nat Struct Mol Biol 17 :1383-1390. PubMed Id: 21037566. |
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Anthrax protective antigen pore: Bacillus anthracis B Bacteria (expressed in E. coli), 2.9 Å
cryo-EM structure |
Jiang et al. (2015).
Jiang J, Pentelute BL, Collier RJ, & Zhou ZH (2015). Atomic structure of anthrax protective antigen pore elucidates toxin translocation.
Nature 521 :545-549. PubMed Id: 25778700. doi:10.1038/nature14247. |
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|
Lymphocyte preforin monomer: Mus musculus E Eukaryota (expressed in S. frugiperda), 2.75 Å
The multimeric pore structure has been visualized by cryo-EM. |
Law et al. (2010).
Law RH, Lukoyanova N, Voskoboinik I, Caradoc-Davies TT, Baran K, Dunstone MA, D'Angelo ME, Orlova EV, Coulibaly F, Verschoor S, Browne KA, Ciccone A, Kuiper MJ, Bird PI, Trapani JA, Saibil HR, & Whisstock JC (2010). The structural basis for membrane binding and pore formation by lymphocyte perforin.
Nature 468 :447-451. PubMed Id: 21037563. |
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Cytolysin pore-forming toxin: Vibrio cholerae B Bacteria (expressed in E. coli), 2.88 Å
Reveals the full structure of the assembled heptameric pore. The pore has a novel ring of tryptophan residues lining the narrowest constriction. |
De & Olson (2011).
De S & Olson R. (2011). Crystal structure of the Vibrio cholerae cytolysin heptamer reveals common features among disparate pore-forming toxins
Proc Natl Acad Sci USA 108 :7385-7390. PubMed Id: 21502531. doi:10.1073/pnas.1017442108. |
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Cytolysin pore-forming toxin protomer: Vibrio cholerae B Bacteria (expressed in E. coli), 2.30 Å
|
Olson & Gouaux (2005).
Olson R & Gouaux E (2005). Crystal structure of the Vibrio cholerae cytolysin (VCC) pro-toxin and its assembly into a heptameric transmembrane pore
J Mol Biol 350 :997-1016. PubMed Id: 15978620 . doi:10.1016/j.jmb.2005.05.045. |
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Streptolysin O pore-forming toxin: Streptococcus pyogenes B Bacteria (expressed in E. coli), 2.10 Å
|
Feil et al. (2014).
Feil SC, Ascher DB, Kuiper MJ, Tweten RK, & Parker MW (2014). Structural Studies of Streptococcus pyogenes Streptolysin O Provide Insights into the Early Steps of Membrane Penetration.
J Mol Biol 426 :785-792. PubMed Id: 24316049. doi:10.1016/j.jmb.2013.11.020. |
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Degiacomi et al. (2013).
Degiacomi MT, Iacovache I, Pernot L, Chami M, Kudryashev M, Stahlberg H, van der Goot FG, & Dal Peraro M (2013). Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism.
Nat Chem Biol 9 10:623-629. PubMed Id: 23912165. doi:10.1038/nchembio.1312. |
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Monalysin pore-forming toxin, cleaved form: Pseudomonas entomophila B Bacteria (expressed in E. coli), 1.70 Å
mutant deleted of the membrane-spanning domain, 2.65 Å: 4MKQ EM structure deposited in EMBD as EMD-2698. |
Leone et al. (2015).
Leone P, Bebeacua C, Opota O, Kellenberger C, Klaholz B, Orlov I, Cambillau C, Lemaitre B, & Roussel A (2015). X-ray and Cryo-electron Microscopy Structures of Monalysin Pore-forming Toxin Reveal Multimerization of the Pro-form.
J Biol Chem 290 :13191-13201. PubMed Id: 25847242. doi:10.1074/jbc.M115.646109. |
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|
poly-C9 component of the complement membrane attack Complex: Homo sapiens E Eukaryota, 8 Å
model from cryo-EM |
Dudkina et al. (2016).
Dudkina NV, Spicer BA, Reboul CF, Conroy PJ, Lukoyanova N, Elmlund H, Law RH, Ekkel SM, Kondos SC, Goode RJ, Ramm G, Whisstock JC, Saibil HR, & Dunstone MA (2016). Structure of the poly-C9 component of the complement membrane attack complex.
Nat Commun 7 . PubMed Id: 26841934. doi:10.1038/ncomms10588. See also: Serna et al. (2016). Serna M, Giles JL, Morgan BP, & Bubeck D (2016). Structural basis of complement membrane attack complex formation.
Nat Commun 7 :10587. PubMed Id: 26841837. doi:10.1038/ncomms10587. |
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|
Lysenin Pore complex: Eisenia fetida B Bacteria (expressed in E. coli), 3.1 Å
cryo-EM structure |
Bokori-Brown et al. (2016).
Bokori-Brown M, Martin TG, Naylor CE, Basak AK, Titball RW, & Savva CG (2016). Cryo-EM structure of lysenin pore elucidates membrane insertion by an aerolysin family protein.
Nat Commun 7 :11293. PubMed Id: 27048994. doi:10.1038/ncomms11293. |
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|
ILYml Cholesterol-dependent cytolysin, CD59-responsive: Streptococcus intermedius B Bacteria (expressed in E. coli), 2.89 Å
ILYml = monomer-locked via a disulfide. Bound to CD59D22A, 2.7 Å: 5IMT |
Lawrence et al. (2016).
Lawrence SL, Gorman MA, Feil SC, Mulhern TD, Kuiper MJ, Ratner AJ, Tweten RK, Morton CJ, & Parker MW (2016). Structural Basis for Receptor Recognition by the Human CD59-Responsive Cholesterol-Dependent Cytolysins.
Structure 24 :1488-1498. PubMed Id: 27499440. doi:10.1016/j.str.2016.06.017. |
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VLYml Cholesterol-dependent cytolysin, CD-59 responsive, bound to CD59D22A: Gardnerella vaginalis B Bacteria (expressed in E. coli), 2.4 Å
VLYml = monomer locked via a disulfide |
Lawrence et al. (2016).
Lawrence SL, Gorman MA, Feil SC, Mulhern TD, Kuiper MJ, Ratner AJ, Tweten RK, Morton CJ, & Parker MW (2016). Structural Basis for Receptor Recognition by the Human CD59-Responsive Cholesterol-Dependent Cytolysins.
Structure 24 :1488-1498. PubMed Id: 27499440. doi:10.1016/j.str.2016.06.017. |
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|
van Pee et al. (2017).
van Pee K, Neuhaus A, D'Imprima E, Mills DJ, Kühlbrandt W, & Yildiz Ö (2017). CryoEM structures of membrane pore and prepore complex reveal cytolytic mechanism of Pneumolysin.
Elife 6 :e23644. PubMed Id: 28323617. doi:10.7554/eLife.23644. |
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TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
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Adventitious Membrane Proteins: Alpha-helical Pore-forming Toxins.
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Cytolysin A (ClyA, aka HlyE): Escherichia coli B Bacteria, 3.29 Å
|
Mueller et al. (2009).
Mueller M, Grauschopf U, Maier T, Glockshuber R, & Ban N (2009). The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism.
Nature 459 :726-730. PubMed Id: 19421192. |
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Cry6Aa toxin: Bacillus thuringiensis B Bacteria (expressed in Pseudomonas fluorescens), 2.7 Å
trypsin-cleaved, 2.0 Å: 5KUC supersedes 5J65. |
Dementiev et al. (2016).
Dementiev A, Board J, Sitaram A, Hey T, Kelker MS, Xu X, Hu Y, Vidal-Quist C, Chikwana V, Griffin S, McCaskill D, Wang NX, Hung SC, Chan MK, Lee MM, Hughes J, Wegener A, Aroian RV, Narva KE, & Berry C (2016). The pesticidal Cry6Aa toxin from Bacillus thuringiensis is structurally similar to HlyE-family alpha pore-forming toxins.
BMC Biol 14 :71. PubMed Id: 27576487. doi:10.1186/s12915-016-0295-9. |
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FraC eukaryotic pore-forming toxin from sea anemone: Actinia fragacea E Eukaryota, 1.80 Å
|
Mechaly et al. (2011).
Mechaly AE, Bellomio A, Gil-Cartón D, Morante K, Valle M, González-Mañas JM, & Guérin DM (2011). Structural insights into the oligomerization and architecture of eukaryotic membrane pore-forming toxins.
Structure 19 :181-191. PubMed Id: 21300287. |
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FraC toxin pore with bound lipids: Actinia fragacea E Eukaryota (expressed in E. coli), 3.14 Å
Water soluble monomer (I), 1.70 Å: 3VWI Water soluble monomer (II), 2.10 Å: 3W9P Dimer with phosphorylcholine (I), 1.60 Å: 4TSL Dimer with phosphorylcholine (II), 1.57 Å: 4TSN Lipid (DHPC) bound (I), 2.30 Å: 4TSO Lipid (DHPC) bound (II), 2.15 Å: 4TSP Lipid (DHPC) bound (III), 1.60 Å: 4TSQ |
Tanaka et al. (2015).
Tanaka K, Caaveiro JM, Morante K, González-Mañas JM, & Tsumoto K (2015). Structural basis for self-assembly of a cytolytic pore lined by protein and lipid.
Nat Commun 6 :6337. PubMed Id: 25716479. doi:10.1038/ncomms7337. |
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Dermicidin hexameric anti-microbial peptide channel: Homo sapiens E Eukaryota (expressed in Synthetic construct), 2.49 Å
|
Song et al. (2013).
Song C, Weichbrodt C, Salnikov ES, Dynowski M, Forsberg BO, Bechinger B, Steinem C, de Groot BL, Zachariae U, & Zeth K (2013). Crystal structure and functional mechanism of a human antimicrobial membrane channel.
Proc Natl Acad Sci USA 110 :4586-4591. PubMed Id: 23426625. doi:10.1073/pnas.1214739110. |
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Tc Toxin, TcA prepore (TcdA1) subunit: Photorhabdus luminescens B Bacteria (expressed in E. coli), 3.50 Å
TcB-TcC (TcdB2-TccC3) subunits, 2.17 Å: 4O9X See also EM structures deposited in Electron Microscopy Data Bank under accession numbers EMD-2551 and EMD-2552. |
Meusch et al. (2014).
Meusch D, Gatsogiannis C, Efremov RG, Lang AE, Hofnagel O, Vetter IR, Aktories K, & Raunser S (2014). Mechanism of Tc toxin action revealed in molecular detail.
Nature 508 :61-65. PubMed Id: 24572368. doi:10.1038/nature13015. |
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Tc Toxin, TcA pore (TcdA1) embedded in lipid nanodiscs using flexible fitting: Photorhabdus luminescens B Bacteria (expressed in E. coli), 3.46 Å
cryo-EM structure. without flexible fitting, 3.46 Å: 5LKI |
Gatsogiannis et al. (2016).
Gatsogiannis C, Merino F, Prumbaum D, Roderer D, Leidreiter F, Meusch D, & Raunser S (2016). Membrane insertion of a Tc toxin in near-atomic detail.
Nat Struct Mol Biol 23 :884-890. PubMed Id: 27571177. doi:10.1038/nsmb.3281. |
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Listeriolysin O pore-forming toxin: Listeria monocytogenes B Bacteria, 2.15 Å
A model of the assembled pore contains 36 monomers. In that configuration, the membrane-spanning region of the toxin is a mix of α-helices and β-sheets |
Köster et al. (2014).
Köster S, van Pee K, Hudel M, Leustik M, Rhinow D, Kühlbrandt W, Chakraborty T, & Yildiz O (2014). Crystal structure of listeriolysin O reveals molecular details of oligomerization and pore formation.
Nat Commun 5 :3690. PubMed Id: 24751541. doi:10.1038/ncomms4690. |
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De novo Designed Membrane Proteins
Functional Proteins Designed from First Principles |
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Joh et al. (2014).
Joh NH, Wang T, Bhate MP, Acharya R, Wu Y, Grabe M, Hong M, Grigoryan G, & DeGrado WF (2014). De novo design of a transmembrane Zn2+-transporting four-helix bundle.
Science 346 6216:1520-1524. PubMed Id: 25525248. doi:10.1126/science.1261172. |
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Outer Membrane Proteins
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Wza translocon for capsular polysaccharides: Escherichia coli B Bacteria, 2.25 Å
The first outer membrane protein that penetrates the membrane as an alpha-helix bundle. The intact protein is comprised of eight monomers. |
Dong et al. (2006).
Dong C, Beis K, Nesper J, Brunkan-LaMontagne AL, Clarke BR JM, Whitfield C, & Naismith JH (2006). Wza the translocon for E. coli. capsular polysaccharides defines a new class of membrane protein.
Nature 444 :226-229. PubMed Id: 17086202. |
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Ziegler et al. (2008).
Ziegler K, Benz R, & Schulz GE (2008). A putative alpha-helical porin from Corynebacterium glutamicum.
J Mol Biol 379 :482-491. PubMed Id: 18462756. |
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Type IV outer membrane secretion complex: Escherichia coli B Bacteria, 2.60 Å
Comprised of 14 copies each of TraF, TraO, and TraN; 590 kDa. |
Chandran et al. (2009).
Chandran V, Fronzes R, Duquerroy S, Cronin N, Navaza J, & Waksman G (2009). Structure of the outer membrane complex of a type IV secretion system.
Nature 462 :1011-1015. PubMed Id: 19946264. |
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Bacterial Cell Divison Proteins
These proteins comprise the so-called 'divisome' |
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CrgA cell division structural & regulatory protein: Mycobacterium tuberculosis B Bacteria (expressed in E. coli), NMR Structure
Structure of protein determined using both oriented sample and magic-angle spinning NMR data from liquid-crystalline lipid bilayer preparation. |
Das et al. (2015).
Das N, Dai J, Hung I, Rajagopalan MR, Zhou HX, & Cross TA (2015). Structure of CrgA, a cell division structural and regulatory protein from Mycobacterium tuberculosis, in lipid bilayers.
Proc Natl Acad Sci USA 112 2:E119-E126. PubMed Id: 25548160. doi:10.1073/pnas.1415908112. |
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Bacterial and Algal Rhodopsins
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Bacteriorhodopsin (BR): Halobacterium salinarum A Archaea, 3.5 Å
Electron Diffraction. The first atomic-resolution structure of bacteriorhodopsin |
Grigorieff et al. (1996).
Grigorieff N, Ceska TA, Downing KH, Baldwin JM, & Henderson R (1996). Electron-crystallographic refinement of the structure of bacteriorhodopsin.
J Mol Biol 259 :393-421. PubMed Id: 8676377. |
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Bacteriorhodopsin (BR): Halobacterium salinarum A Archaea, 3.0 Å
Electron Diffraction |
Kimura et al. (1997).
Kimura Y, Vassylyev DG, Miyazawa A, Kidera A, Matsushima M, Mitsuok a K, Murata K, Hirai T, & Fujiyoshi Y (1997). Surface of bacteriorhodopsin revealed by high-resolution electron crystallography.
Nature 389 :206-211. PubMed Id: 8676377. |
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Bacteriorhodopsin (BR): Halobacterium salinarum A Archaea, 2.35 Å
The first x-ray structure of bacteriorhodopsin |
Pebay-Peyroula et al. (1997).
Pebay-Peyroula E, Rummel G, Rosenbusch JP, & Landau EM (1997). X-ray structure of bacteriorhodopsin at 2.5 Å from microcrystals grown in lipidic cubic phases.
Science 277 :1676-1681. PubMed Id: 9287223. |
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Bacteriorhodopsin (BR): Halobacterium salinarum A Archaea, 2.90 Å
|
Essen et al. (1998).
Essen L, Siegert R, Lehmann WD, & Oesterhelt D (1998). Lipid patches in membrane protein oligomers: crystal structure of the bacteriorhodopsin-lipid complex.
Proc Natl Acad Sci U S A 95 :11673-11678. PubMed Id: 9751724. |
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Bacteriorhodopsin (BR): Halobacterium salinarum A Archaea, 2.30 Å
|
Luecke et al. (1998).
Luecke H, Richter HT, & Lanyi JK (1998). Proton transfer pathways in bacteriorhodopsin at 2.3 Angstrom resolution.
Science 280 :1934-1937. PubMed Id: 9632391. |
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Bacteriorhodopsin (BR), K intermediate: Halobacterium salinarum A Archaea, 2.10 Å
R-free = O.255. R-free = 0.303, 2.1 Å: 1QKO |
Edman et al. (1999).
Edman K, Nollert P, Royant A, Belrhali H, Pebay-Peyroula E, Hajdu J, Neutze R, & Landau EM (1999). High-resolution X-ray structure of an early intermediate in the bacteriorhodopsin photocycle.
Nature 401 :822-826. PubMed Id: 10548112. |
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Bacteriorhodopsin (BR), K intermediate (illuminated): Halobacterium salinarum A Archaea, 1.43 Å
Non-illuminated, 1.47 Å: 1M0L |
Schobert et al. (2002).
Schobert B, Cupp-Vickery J, Hornak V, Smith S, & Lanyi J (2002). Crystallographic structure of the K intermediate of bacteriorhodopsin: conservation of free energy after photoisomerization of the retinal.
J. Mol. Biol. 321 :715-726. PubMed Id: 12206785. |
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Facciotti et al. (2001).
Facciotti MT, Rouhani S, Burkard FT, Betancourt FM, Downing KH, Rose RB, McDermott G, & Glaeser RM (2001). Structure of an early intermediate in the M-state phase of the bacteriorhodopsin photocycle
Biophys J 81 :3442-3455. PubMed Id: 11721006. doi:10.1016/S0006-3495(01)75976-0. |
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Bacteriorhodopsin (BR): Halobacterium salinarum A Archaea, 1.90 Å
|
Belrhali et al. (1999).
Belrhali H, Nollert P, Royant A, Menzel C, Rosenbusch JP, Landau EH, & Pebay-Peyroula E (1999). Protein, lipid, and water organization in bacteriorhodopsin crystals: A molecular view of the purple membrane at 1.9 Å resolution.
Structure 7 :909-917. PubMed Id: 10467143. |
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Bacteriorhodopsin (BR): Halobacterium salinarum A Archaea, 1.55 Å
|
Luecke et al. (1999).
Luecke H, Schobert B, Richter HT, Cartailler P, & Lanyi JK (1999). Structure of bacteriorhodopsin at 1.55 angstrom resolution.
J. Mol. Biol 291 :899-911. PubMed Id: 10452895. |
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Bacteriorhodopsin (BR), D96N in bR state: Halobacterium salinarum A Archaea, 1.80 Å
D96N in M-state, 2.00 Å: 1C8S. |
Luecke et al. (1999).
Luecke H, Schobert B, Richter HT, Cartailler P, & Lanyi JK (1999). Structural changes in bacteriorhodopsin during ion transport at 2 angstrom resolution.
Science 286 :255-260. PubMed Id: 10514362. |
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Bacteriorhodopsin in ground state: Halobacterium salinarum A Archaea, 1.78 Å
Ground state, after x-ray modification, 1.78 Å: 3NSB |
Borshchevskiy et al. (2011).
Borshchevskiy VI, Round ES, Popov AN, Büldt G, & Gordeliy VI (2011). X-ray-Radiation-Induced Changes in Bacteriorhodopsin Structure
J Mol Biol 409 :813-825. PubMed Id: 21530535. doi:10.1016/j.jmb.2011.04.038. |
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Bacteriorhodopsin phototaxis signalling mutant (A215T): Halobacterium sp. nrc-1 A Archaea (expressed in Halobacterium salinarum), 3.01 Å
This mutant enables BR's photochemical reactions to transmit signals to the transducer HtrII. |
Spudich et al. (2012).
Spudich EN, Ozorowski G, Schow EV, Tobias DJ, Spudich JL, & Luecke H (2012). A transporter converted into a sensor, a phototaxis signaling mutant of bacteriorhodopsin at 3.0 Å.
J Mol Biol 415 :455-463. PubMed Id: 22123198. doi:10.1016/j.jmb.2011.11.025. |
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Bacteriorhodopsin (BR); D96/F171C/F219L mutant: Halobacterium salinarum A Archaea, 2.65 Å
|
Wang et al. (2013).
Wang T, Sessions AO, Lunde CS, Rouhani S, Glaeser RM, Duan Y, & Facciotti MT (2013). Deprotonation of D96 in bacteriorhodopsin opens the proton uptake pathway.
Structure 21 :290-297. PubMed Id: 23394942. doi:10.1016/j.str.2012.12.018. |
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Bacteriorhodopsin (BR) determined using serial ms crystallography (SMX): Halobacterium salinarum A Archaea, 2.40 Å
Structure by conventional crystallography, 1.90 Å:4X32 |
Nogly et al. (2015).
Nogly P, James D, Wang D, White TA, Zatsepin N, Shilova A, Nelson G, Liu H, Johansson L, Heymann M, Jaeger K, Metz M, Wickstrand C, Wu W, Båth P, Berntsen P, Oberthuer D, Panneels V, Cherezov V, Chapman H, Schertler G, Neutze R, Spence J, Moraes I, Burghammer M, Standfuss J, & Weierstall U (2015). Lipidic cubic phase serial millisecond crystallography using synchrotron radiation.
IUCrJ 2 :168-176. PubMed Id: 25866654. doi:10.1107/S2052252514026487. |
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Bacteriorhodopsin (BR) native: Halobacterium salinarum A Archaea, 2.35 Å
Structure determind by XFEL. Crystallized from bicelles. Crystallized from Bicelles in Complex with Iodine-labeled Detergent HAD13a, 2.1 Å: 5B34 |
Nakane et al. (2016).
Nakane T, Hanashima S, Suzuki M, Saiki H, Hayashi T, Kakinouchi K, Sugiyama S, Kawatake S, Matsuoka S, Matsumori N, Nango E, Kobayashi J, Shimamura T, Kimura K, Mori C, Kunishima N, Sugahara M, Takakyu Y, Inoue S, Masuda T, Hosaka T, Tono K, Joti Y, Kameshima T, Hatsui T, Yabashi M, Inoue T, Nureki O, Iwata S, Murata M, & Mizohata E (2016). Membrane protein structure determination by SAD, SIR, or SIRAS phasing in serial femtosecond crystallography using an iododetergent.
Proc Natl Acad Sc. USA 113 :13039-13044. PubMed Id: 27799539. |
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Bacteriorhodopsin (BR) 3D movie, ground state: Halobacterium salinarum A Archaea, 2.0 Å
See the movie: http://science.sciencemag.org/content/sci/suppl/2016/12/21/354.6319.1552.DC1/aah3497s1.mp4 structure at: 16 nsec, 2.1 Å: 5B6W 40 nsec, 2.1 Å: 5H2H 110 nsec, 2.1 Å: 5H2I 290 nsec, 2.1 Å: 5H2J 760 nsec, 2.1 Å: 5B6X 2 μsec, 2.1 Å: 5H2K 5.25 μsec, 2.1 Å: 5H2L 13.8 μsec, 2.1 Å: 5H2M 36.2 μsec, 2.1 Å: 5B6Y 95.2 μsec, 2.1 Å: 5H2N 250 μsec, 2.1 Å: 5H2O 657 μsec, 2.1 Å: 5H2P 1.725 msec, 2.1 Å: 5B6Z |
Nango et al. (2016).
Nango E, Royant A, Kubo M, Nakane T, Wickstrand C, Kimura T, Tanaka T, Tono K, Song C, Tanaka R, Arima T, Yamashita A, Kobayashi J, Hosaka T, Mizohata E, Nogly P, Sugahara M, Nam D, Nomura T, Shimamura T, Im D, Fujiwara T, Yamanaka Y, Jeon B, Nishizawa T, Oda K, Fukuda M, Andersson R, Båth P, Dods R, Davidsson J, Matsuoka S, Kawatake S, Murata M, Nureki O, Owada S, Kameshima T, Hatsui T, Joti Y, Schertler G, Yabashi M, Bondar AN, Standfuss J, Neutze R, & Iwata S (2016). A three-dimensional movie of structural changes in bacteriorhodopsin.
Science 354 :1552-1557. PubMed Id: 28008064. doi:10.1126/science.aah3497. |
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|
Bacteriorhodopsin (BR), trimer in asymmetric unit: Haloquadratum walsbyi A Archaea (expressed in E. coli), 1.85 Å
This BR pumps protons efficiently under acid conditions. antiparallel dimer in asymmetric unit, 2.57 Å: 4QID |
Hsu et al. (2015).
Hsu MF, Fu HY, Cai CJ, Yi HP, Yang CS, & Wang AH (2015). Structural and Functional Studies of a Newly Grouped Haloquadratum walsbyi Bacteriorhodopsin Reveal the Acid-resistant Light-driven Proton Pumping Activity.
J Biol Chem 290 :29567-29577. PubMed Id: 26483542. doi:10.1074/jbc.M115.685065. |
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|
Bacteriorhodopsin (BR) crystallized from octylglucoside (OG) detergent micelles: Haloquadratum walsbyi A Archaea (expressed in E. coli), 2.18 Å
crystallized from styrene maleic acid (SMA) polymer nanodiscs, 2.0 Å: 5ITC |
Broecker et al. (2017).
Broecker J, Eger BT, & Ernst OP (2017). Crystallogenesis of Membrane Proteins Mediated by Polymer-Bounded Lipid Nanodiscs.
Structure 25 :384-392. PubMed Id: 28089451. doi:10.1016/j.str.2016.12.004. |
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|
Halorhodopsin (HR): Halobacterium salinarum A Archaea, 1.8 Å
|
Kolbe et al. (2000).
Kolbe M, Besir H, Essen L-O, & Oesterhelt D (2000). Structure of the light-driven chloride pump halorhodopsin at 1.8 Å.
Science 288 :1390-1396. PubMed Id: 10827943. |
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|
Halorhodopsin (HR): Natronomonas pharaonis A Archaea, 2.0 Å
|
Kouyama et al. (2010).
Kouyama T, Kanada S, Takeguchi Y, Narusawa A, Murakami M, Ihara K. (2010). Crystal Structure of the Light-Driven Chloride Pump Halorhodopsin from Natronomonas pharaonis.
J Mol Biol 396 :564-579. PubMed Id: 19961859. |
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|
Sensory Rhodopsin: Anabaena (Nostoc) sp. PCC7120 B Bacteria, 2.0 Å
|
Vogeley et al. (2004).
Vogeley L, Sineshchekov OA, Trivedi VD, Sasaki J, Spudich JL, & Luecke H (2004). Anabaena sensory rhodopsin: a photochromic color sensor at 2.0 Å.
Science 306 :1390-1393. PubMed Id: 15459346. |
||
|
Sensory Rhodopsin: Anabaena (Nostoc) sp. PCC7120 B Bacteria (expressed in E. coli), NMR Structure
|
Wang et al. (2013).
Wang S, Munro RA, Shi L, Kawamura I, Okitsu T, Wada A, Kim SY, Jung KH, Brown LS, & Ladizhansky V (2013). Solid-state NMR spectroscopy structure determination of a lipid-embedded heptahelical membrane protein.
Nat Methods 10 :1007-1012. PubMed Id: 24013819. doi:10.1038/nmeth.2635. |
||
|
Sensory Rhodopsin II (SRII): Natronomonas pharaonis A Archaea, 2.40 Å
|
Luecke et al. (2001).
Luecke H, Schobert B, Lanyi JK, Spudich EN, & Spudich JL (2001). Crystal structure of sensory rhodopsin II at 2.4 Å: Insights into color tuning and transducer interaction.
Science 293 :1499-1503. PubMed Id: 11452084. |
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|
Sensory Rhodopsin II (SRII): Natronomonas pharaonis A Archaea (expressed in E. coli), 2.10 Å
|
Royant et al. (2001).
Royant A, Nollert P, Edman K, Neutze R, Landau EM, & Pebay-Peyroula E. (2001). X-ray structure of sensory rhodopsin II at 2.1 Å resolution.
Proc Natl Acad Sci USA 98 :10131-10136. PubMed Id: 11504917. |
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|
Sensory Rhodopsin II (SRII) with transducer: Natronomonas pharaonis A Archaea (expressed in E. coli), 1.93 Å
|
Gordeliy et al. (2002).
Gordeliy VI, Labahn J, Moukhametzianov R, Efremov R, Granzin J, Schlesinger R, Büldt G, Savopol T, Scheidig AJ, Klare JP, & Engelhard M. (2002). Molecular basis of transmembrane signalling by sensory rhodopsin II-transducer complex.
Nature 419 :484-487. PubMed Id: 12368857. |
||
|
Sensory Rhodopsin II (SRII): Natronomonas pharaonis A Archaea (expressed in E. coli), NMR structure
|
Gautier et al. (2010).
Gautier A, Mott HR, Bostock MJ, Kirkpatrick JP, & Nietlispach D (2010). Structure determination of the seven-helix transmembrane receptor sensory rhodopsin II by solution NMR spectroscopy.
Nat Struct Mol Biol 17 :768-774. PubMed Id: 20512150. |
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|
Sensory Rhodopsin II (SRII) in active state: Natronomonas pharaonis A Archaea (expressed in E. coli), 2.50 Å
SR II in ground state, 1.90 Å: 3QAP |
Gushchin et al. (2011).
Gushchin I, Reshetnyak A, Borshchevskiy V, Ishchenko A, Round E, Grudinin S, Engelhard M, Büldt G, & Gordeliy V (2011). Active state of sensory rhodopsin II: structural determinants for signal transfer and proton pumping.
J Mol Biol 412 :591-600. PubMed Id: 21840321. doi:10.1016/j.jmb.2011.07.022. |
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|
Archaerhodopsin-1 (aR-1): Halorubrum sp. aus-1 A Archaea, 3.4 Å
|
Enami et al. (2006).
Enami N, Yoshimura K, Murakami M, Okumura H, Ihara K, & Kouyama T. (2006). Crystal Structures of Archaerhodopsin-1 and -2: Common Structural Motif in Archaeal Light-driven Proton Pumps.
J Mol Biol 356 :675-685. PubMed Id: 16540121. |
||
|
Archaerhodopsin-2 (aR-2): Haloroubrum sp. aus-2 A Archaea, 2.5 Å
|
Enami et al. (2006).
Enami N, Yoshimura K, Murakami M, Okumura H, Ihara K, & Kouyama T. (2006). Crystal Structures of Archaerhodopsin-1 and -2: Common Structural Motif in Archaeal Light-driven Proton Pumps.
J Mol Biol 356 :675-685. PubMed Id: 16540121. |
||
|
Archaerhodopsin-2 (aR-2): Haloroubrum sp. aus-2 A Archaea, 2.10 Å
Crystallized with the carotenoid bacterioruberin, space group P321. Space group P63, 2.50 Å: 2Z55. |
Yoshimura & Kouyama. (2008).
Yoshimura K & Kouyama T (2008). Structural role of bacterioruberin in the trimeric structure of archaerhodopsin-2.
J Mol Biol 375 :1267-1281. PubMed Id: 18082767. |
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|
Archaerhodopsin-2 (aR-2): Haloroubrum sp. aus-2 A Archaea, 1.80 Å
|
Kouyama et al. (2014).
Kouyama T, Fujii R, Kanada S, Nakanishi T, Chan SK, & Murakami M (2014). Structure of archaerhodopsin-2 at 1.8?Å resolution.
Acta Crystallogr D Biol Crystallogr 70 :2692-2701. PubMed Id: 25286853. doi:10.1107/S1399004714017313. |
||
|
Xanthorhodopsin: Salinibacter ruber B Bacteria, 1.9 Å
Contains bound carotenoid. |
Luecke et al. (2008).
Luecke H, Schobert B, Stagno J, Imasheva ES, Wang JM, Balashov SP, & Lanyi JK (2008). Crystallographic structure of xanthorhodopsin, the light-driven proton pump with a dual chromophore.
Proc Natl Acad Sci USA 105 :16561-16565. PubMed Id: 18922772. |
||
|
Acetabularia Rhodopsin II (ARII): Acetabularia acetabulum E Eukaryota (expressed in cell-free expression), 3.20 Å
This the first structure of a eukaryotic light-driven proton pump |
Wada et al. (2011).
Wada T, Shimono K, Kikukawa T, Hato M, Shinya N, Kim SY, Kimura-Someya T, Shirouzu M, Tamogami J, Miyauchi S, Jung KH, Kamo N, & Yokoyama S (2011). Crystal Structure of the Eukaryotic Light-Driven Proton-Pumping Rhodopsin, Acetabularia Rhodopsin II, from Marine Alga
J Mol Biol 411 :986-998. PubMed Id: 21726566. doi:10.1016/j.jmb.2011.06.028. |
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|
Channelrhodopsin (ChR) chimera between ChR1 & ChR2: Chlamydomonas reinhardtii E Eukaryota (expressed in S. frugiperda), 2.30 Å
First ChR structure. Reveals cation conduction pathway. |
Kato et al. (2012).
Kato HE, Zhang F, Yizhar O, Ramakrishnan C, Nishizawa T, Hirata K, Ito J, Aita Y, Tsukazaki T, Hayashi S, Hegemann P, Maturana AD, Ishitani R, Deisseroth K, & Nureki O (2012). Crystal structure of the channelrhodopsin light-gated cation channel.
Nature 482 :369-374. PubMed Id: 22266941. doi:10.1038/nature10870. |
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|
Channelrhodopsin (ChR) chimera between ChR1 & ChR2, T198G/G202A mutant: Chlamydomonas reinhardtii E Eukaryota (expressed in S. frugiperda), 2.50 Å
Blue-shifted mutant |
Kato et al. (2015).
Kato HE, Kamiya M, Sugo S, Ito J, Taniguchi R, Orito A, Hirata K, Inutsuka A, Yamanaka A, Maturana AD, Ishitani R, Sudo Y, Hayashi S, & Nureki O (2015). Atomistic design of microbial opsin-based blue-shifted optogenetics tools.
Nat Commun 6 :7177. PubMed Id: 25975962. doi:10.1038/ncomms8177. |
||
|
Proteorhodopsin (green-light absorbing) : Uncultured marine gamma proteobacterium ebac31a08 B Bacteria (expressed in E. coli-based cell-free expression system), NMR Structure
|
Reckel et al. (2011).
Reckel S, Gottstein D, Stehle J, Löhr F, Verhoefen MK, Takeda M, Silvers R, Kainosho M, Glaubitz C, Wachtveitl J, Bernhard F, Schwalbe H, Güntert P, Dötsch V (2011). Solution NMR structure of proteorhodopsin.
Angew Chem Int Ed Engl 50 :11942-11946. PubMed Id: 22034093. doi:10.1002/anie.201105648. |
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|
Proteorhodopsin: Exiguobacterium sibiricum B Bacteria (expressed in E. coli), 2.30 Å
Lysine is the proton donor in this novel proteorhodopsin |
Gushchin et al. (2013).
Gushchin I, Chervakov P, Kuzmichev P, Popov AN, Round E, Borshchevskiy V, Ishchenko A, Petrovskaya L, Chupin V, Dolgikh DA, Arseniev AA, Kirpichnikov M, & Gordeliy V (2013). Structural insights into the proton pumping by unusual proteorhodopsin from nonmarine bacteria.
Proc Natl Acad Sci USA 110 :12631-12636. PubMed Id: 23872846. doi:10.1073/pnas.1221629110. |
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|
Proteorhodopsin (blue-light absorbing), Med12BPR: uncultured bacterium B Bacteria (expressed in E. coli), 2.31 Å
Isolated from the Mediterranean Sea at a depth of 12 m. Oligomerizes as a hexameric ring. |
Ran et al. (2013).
Ran T, Ozorowski G, Gao Y, Sineshchekov OA, Wang W, Spudich JL, & Luecke H (2013). Cross-protomer interaction with the photoactive site in oligomeric proteorhodopsin complexes.
Acta Crystallogr D Biol Crystallogr 69 :1965-1980. PubMed Id: 24100316. |
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|
Proteorhodopsin (blue-light absorbing); HOT75BPR, D97N mutant: gamma proteobacterium B Bacteria (expressed in E. coli), 2.70 Å
Isolated from the Pacific Ocean near Hawaii at a depth of 75 m. Oligomerizes as a pentameric ring. D97N/Q105L mutant, 2.60 Å: 4KNF |
Ran et al. (2013).
Ran T, Ozorowski G, Gao Y, Sineshchekov OA, Wang W, Spudich JL, & Luecke H (2013). Cross-protomer interaction with the photoactive site in oligomeric proteorhodopsin complexes.
Acta Crystallogr D Biol Crystallogr 69 :1965-1980. PubMed Id: 24100316. |
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|
Cruxrhodopsin-3 (cR3), pH 5: Haloarcula vallismortis A Archaea (expressed in H. salinarum ), 2.10 Å
at pH 6, 2.30 Å: 4JR8 |
Chan et al. (2014).
Chan SK, Kitajima-Ihara T, Fujii R, Gotoh T, Murakami M, Ihara K, & Kouyama T (2014). Crystal Structure of Cruxrhodopsin-3 from Haloarcula vallismortis.
PLoS ONE 9 9:e108362. PubMed Id: 25268964. doi:10.1371/journal.pone.0108362. |
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|
KR2 light-driven Na+ pump, acidic conditions: Dokdonia eikasta B Bacteria (expressed in E. coli), 2.30 Å
basic conditions, 2.30 Å: 3X3C |
Kato et al. (2015).
Kato HE, Inoue K, Abe-Yoshizumi R, Kato Y, Ono H, Konno M, Hososhima S, Ishizuka T, Hoque MR, Kunitomo H, Ito J, Yoshizawa S, Yamashita K, Takemoto M, Nishizawa T, Taniguchi R, Kogure K, Maturana AD, Iino Y, Yawo H, Ishitani R, Kandori H, & Nureki O (2015). Structural basis for Na+ transport mechanism by a light-driven Na+ pump.
Nature 521 :48-53. PubMed Id: 25849775. doi:10.1038/nature14322. |
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|
Gushchin et al. (2015).
Gushchin I, Shevchenko V, Polovinkin V, Kovalev K, Alekseev A, Round E, Borshchevskiy V, Balandin T, Popov A, Gensch T, Fahlke C, Bamann C, Willbold D, Büldt G, Bamberg E, & Gordeliy V (2015). Crystal structure of a light-driven sodium pump.
Nat Struct Mol Biol 22 :390-395. PubMed Id: 25849142. doi:10.1038/nsmb.3002. |
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|
Thermophilic rhodopsin: Thermus thermophilus B Bacteria (expressed in E. coli), 2.8 Å
|
Tsukamoto et al. (2016).
Tsukamoto T, Mizutani K, Hasegawa T, Takahashi M, Honda N, Hashimoto N, Shimono K, Yamashita K, Yamamoto M, Miyauchi S, Takagi S, Hayashi S, Murata T, & Sudo Y (2016). X-ray Crystallographic Structure of Thermophilic Rhodopsin.
J Biol Chem 291 23:12223-12232. PubMed Id: 27129243. doi:10.1074/jbc.M116.719815. |
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|
Kim et al. (2016).
Kim K, Kwon SK, Jun SH, Cha JS, Kim H, Lee W, Kim JF, & Cho HS (2016). Crystal structure and functional characterization of a light-driven chloride pump having an NTQ motif.
Nat Commun 7 :12677. PubMed Id: 27554809. doi:10.1038/ncomms12677. |
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|
Novel Receptors
|
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|
Human sigma-1 (σ1) receptor, with bound PD144418: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.51 Å
with bound 4-IBP, 3.2 Å: 5HK2 |
Schmidt et al. (2016).
Schmidt HR, Zheng S, Gurpinar E, Koehl A, Manglik A, & Kruse AC (2016). Crystal structure of the human σ1 receptor.
Nature 532 :527-530. PubMed Id: 27042935. doi:10.1038/nature17391. |
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|
STRA6 retinol-uptake receptor in complex with calmodulin (CaM): Danio rerio E Eukaryota (expressed in sf9 cells), 3.9 Å
cryo-EM structure |
Chen et al. (2016).
Chen Y, Clarke OB, Kim J, Stowe S, Kim YK, Assur Z, Cavalier M, Godoy-Ruiz R, von Alpen DC, Manzini C, Blaner WS, Frank J, Quadro L, Weber DJ, Shapiro L, Hendrickson WA, & Mancia F (2016). Structure of the STRA6 receptor for retinol uptake.
Science 353 . PubMed Id: 27563101. doi:10.1126/science.aad8266. |
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|
Tetraspanins
Mediate essential functions in the immune, reproductive, genitourinary, and auditory systems |
|||
|
CD81 full-length tetraspanin: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.95 Å
|
Zimmerman et al. (2016).
Zimmerman B, Kelly B, McMillan BJ, Seegar TC, Dror RO, Kruse AC, & Blacklow SC (2016). Crystal Structure of a Full-Length Human Tetraspanin Reveals a Cholesterol-Binding Pocket.
Cell 167 4:1041-1051. PubMed Id: 27881302. doi:10.1016/j.cell.2016.09.056. |
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|
Adiponectin Receptors
7TM receptors with inverted topology relative to GPCR receptors Adiponectin is a protein hormone that is important in glucose & fatty acid metabolism |
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|
AdipoR1 adiponectin 1 receptor in complex with an Fv fragment: Homo sapiens E Eukaryota (expressed in Trichoplusia ni), 2.90 Å
This protein and AdipoR2 enclose a large cavity where 3 His residues coördinate a Zn ion. AdipoR2 adiponectin 2 receptor in complex with Fv fragment, 2.40 Å: 3WXW |
Tanabe et al. (2015).
Tanabe H, Fujii Y, Okada-Iwabu M, Iwabu M, Nakamura Y, Hosaka T, Motoyama K, Ikeda M, Wakiyama M, Terada T, Ohsawa N, Hato M, Ogasawara S, Hino T, Murata T, Iwata S, Hirata K, Kawano Y, Yamamoto M, Kimura-Someya T, Shirouzu M, Yamauchi T, Kadowaki T, & Yokoyama S (2015). Crystal structures of the human adiponectin receptors.
Nature 520 7547:312-316. PubMed Id: 25855295. doi:10.1038/nature14301. |
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|
AdipoR1 adiponectin 1 receptor in complex with an Fv fragment: Homo sapiens E Eukaryota (expressed in Trichoplusia ni), 2.73 Å
*5LXG supersedes 3WXV. AdipoR2 adiponectin 2 receptor in complex with Fv fragment, 2.4 Å: 5LWY *5LWY supersedes 3WXW AdipoR2 in complex with a C18 free fatty acid, 2.4 Å: 5LX9 AdipoR2 in complex with a C18 free fatty acid, 3.0 Å: 5LXA |
Vasiliauskaité-Brooks et al. (2017).
Vasiliauskaité-Brooks I, Sounier R, Rochaix P, Bellot G, Fortier M, Hoh F, De Colibus L, Bechara C, Saied EM, Arenz C, Leyrat C, & Granier S (2017). Structural insights into adiponectin receptors suggest ceramidase activity.
Nature 544 :120-123. PubMed Id: 28329765. doi:10.1038/nature21714. |
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|
Autonomously Folding "Membrane Proteins" (Sec-independent)
|
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|
Mistic membrane-integrating protein: Bacillus subtilis B Bacteria, NMR structure
Note: This is not a membrane protein. It is included here because of general interest. |
Roosild et al. (2005).
Roosild TP, Greenwald J, Vega M, Castronovo S, Riek R, & Choe S (2005). NMR structure of Mistic, a membrane-integrating protein for membrane protein expression.
Science 307 :1317-1321. PubMed Id: 15731457. |
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|
Virus Coat Proteins
|
|||
|
M13 Major Coat Protein in Dodecylphosphocholine micelles: Enterobacteria phage m13 V Viruses (expressed in E. coli), NMR Structure
In SDS micelles: 2CPS |
Papavoine et al. (1998).
Papavoine CH, Christiaans BE, Folmer RH, Konings RN, & Hilbers CW (1998). Solution structure of the M13 major coat protein in detergent micelles: a basis for a model of phage assembly involving specific residues.
J Mol Biol 282 :401-419. PubMed Id: 9735296. doi:10.1006/jmbi.1998.1860. |
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|
Pf1 Major Coat Protein: Pseudomonas phage Pf1 V Viruses, NMR Structure
The structure was determined by solid-state NMR using magnetically aligned bacteriophage particles. |
Thiriot et al. (2004).
Thiriot DS, Nevzorov AA, Zagyanskiy L, Wu CH, & Opella SJ (2004). Structure of the coat protein in Pf1 bacteriophage determined by solid-state NMR spectroscopy.
J Mol Biol 341 :869-879. PubMed Id: 15288792. doi:10.1016/j.jmb.2004.06.038. |
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Pf1 Major Coat Protein in lipid bilayers: Pseudomonas phage Pf1 V Viruses, NMR Structure
|
Park et al. (2010).
Park SH, Marassi FM, Black D, & Opella SJ (2010). Structure and dynamics of the membrane-bound form of Pf1 coat protein: implications of structural rearrangement for virus assembly.
Biophys J 99 :1465-1474. PubMed Id: 20816058. doi:10.1016/j.bpj.2010.06.009. |
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|
fd bacteriophage pVIII coat protein in lipid bilayers: Enterobacteria phage fd V Viruses, NMR Structure
|
Marassi & Opella (2003).
Marassi FM & Opella SJ (2003). Simultaneous assignment and structure determination of a membrane protein from NMR orientational restraints.
Protein Sci 12 :403-411. PubMed Id: 12592011. doi:10.1110/ps.0211503. |
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|
fd bacteriophage pVIII coat protein in SDS micelles: Enterobacteria phage fd V Viruses, NMR Structure
|
Almeida & Opella (1997).
Almeida FC & Opella SJ (1997). fd coat protein structure in membrane environments: structural dynamics of the loop between the hydrophobic trans-membrane helix and the amphipathic in-plane helix.
J Mol Biol 270 :481-495. PubMed Id: 9237913. doi:10.1006/jmbi.1997.1114. |
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|
HIV-1 Envelope spike (Env) protein: Human immunodeficiency virus 1 V Viruses (expressed in E. coli), NMR structure
Reconstituted in bicelles. Well-ordered trimer. |
Dev et al. (2016).
Dev J, Park D, Fu Q, Chen J, Ha HJ, Ghantous F, Herrmann T, Chang W, Liu Z, Frey G, Seaman MS, Chen B, & Chou JJ (2016). Structural basis for membrane anchoring of HIV-1 envelope spike.
Science 353 :172-175. PubMed Id: 27338706. doi:10.1126/science.aaf7066. |
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|
Glycoproteins
|
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|
Glycophorin A (GpA) transmembrane-domain dimer: Homo sapiens E Eukaryota (expressed in E. coli), NMR Structure
GpA in dodecylphosphocholine micelles. |
MacKenzie et al. (1997).
MacKenzie KR, Prestegard JH, & Engelman DM (1997). A transmembrane helix dimer: structure and implications.
Science 276 :131-133. PubMed Id: 9082985. |
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|
Glycophorin A (GpA) transmembrane-domain dimer: Homo sapiens E Eukaryota (expressed in E. coli), NMR structure
GpA in DMPC/DHPC bicelles. in DPC micelles, 2KPE |
Mineev et al. (2011).
Mineev KS, Bocharov EV, Volynsky PE, Goncharuk MV, Tkach EN, Ermolyuk YS, Schulga AA, Chupin VV, Maslennikov IV, Efremov RG, & Arseniev AS (2011). Dimeric structure of the transmembrane domain of glycophorin a in lipidic and detergent environments.
Acta Naturae 3 2:90-98. PubMed Id: 22649687. |
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|
Glycophorin A (GpA) transmembrane-domain dimer: Homo sapiens E Eukaryota (expressed in E. coli), 2.81 Å
Type 1 Lipidic cubic phase crystals showing GpA in bilayer environment |
Trenker et al. (2015).
Trenker R, Call ME, & Call MJ (2015). Crystal Structure of the Glycophorin A Transmembrane Dimer in Lipidic Cubic Phase.
J Am Chem Soc 137 50:15676-15679. PubMed Id: 26642914. doi:10.1021/jacs.5b11354. |
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Receptor Tyrosine Kinase (RTK) Family
Single-span TM proteins important in cellular signalling |
|||
|
Insulin receptor TM domain (AAs 940-980): Homo sapiens E Eukaryota (expressed in E. coli), NMR Structure
|
Li et al. (2014).
Li Q, Wong YL, & Kang C (2014). Solution structure of the transmembrane domain of the insulin receptor in detergent micelles.
Biochim Biophys Acta 1838 :1313-1321. PubMed Id: 24440425. doi:10.1016/j.bbamem.2014.01.005. |
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|
High-Density Lipoprotein (HDL) Receptors
|
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|
C-terminal transmembrane domain of scavenger receptor BI (SR-BI): Mus musculus E Eukaryota (expressed in E. coli), NMR structure
The C-terminal domain contains a leucine zipper dimerization motif |
Chadwick et al. (2017).
Chadwick AC, Jensen DR, Hanson PJ, Lange PT, Proudfoot SC, Peterson FC, Volkman BF, & Sahoo D (2017). NMR Structure of the C-Terminal Transmembrane Domain of the HDL Receptor, SR-BI, and a Functionally Relevant Leucine Zipper Motif.
Structure 25 :446-457. PubMed Id: 28162952. doi:10.1016/j.str.2017.01.001. |
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|
Tumor Necrosis Factor (TNF) Receptor Superfamily
|
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|
p75 neurotrophin receptor transmembrane domain: Rattus norvegicus E Eukaryota (expressed in E. coli), NMR structure
Structure determined in DPC micelles. The transmembrane domain includes residues 245-284 from the complete receptor. C257A mutant, 2MJO |
Nadezhdin et al. (2016).
Nadezhdin KD, García-Carpio I, Goncharuk SA, Mineev KS, Arseniev AS, & Vilar M (2016). Structural Basis of p75 Transmembrane Domain Dimerization.
J Biol Chem 291 23:12346-12357. PubMed Id: 27056327. doi:10.1074/jbc.M116.723585. |
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|
Erythropoietin-Producing Hepatocellular Receptors
Eph family of receptor tyrosine kinases (RTKs) |
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|
EphA1 transmembrane segment dimer, pH 6.3: Homo sapiens E Eukaryota (expressed in E. coli), NMR Structure
TM fragment 536-573 of EphA1 gene. Structure determined in DMPC/DHPC bicelles. Structure at pH 4.3: 2K1K |
Bocharov et al. (2008).
Bocharov EV, Mayzel ML, Volynsky PE, Goncharuk MV, Ermolyuk YS, Schulga AA, Artemenko EO, Efremov RG, & Arseniev AS (2008). Spatial structure and pH-dependent conformational diversity of dimeric transmembrane domain of the receptor tyrosine kinase EphA1.
J Biol Chem 283 :29385-29395. PubMed Id: 18728013. doi:10.1074/jbc.M803089200. |
||
|
EphA2 transmembrane segment dimer: Homo sapiens E Eukaryota (expressed in E. coli), NMR Structure
TM fragment 523-563 of EphA2 gene. Structure determined in DMPC/DHPC bicelles. |
Bocharov et al. (2010).
Bocharov EV, Mayzel ML, Volynsky PE, Mineev KS, Tkach EN, Ermolyuk YS, Schulga AA, Efremov RG, & Arseniev AS (2010). Left-handed dimer of EphA2 transmembrane domain: Helix packing diversity among receptor tyrosine kinases.
Biophys J 98 :881-889. PubMed Id: 20197042. doi:10.1016/j.bpj.2009.11.008. |
||
|
Fibroblast Growth Factor Receptors
FGFR family of receptor tyrosine kinases (RTKs) |
|||
|
FGFR3 Fibroblast growth factor receptor 3 transmembrane dimer: Homo sapiens E Eukaryota (expressed in E. coli), NMR Structure
|
Bocharov et al. (2013).
Bocharov EV, Lesovoy DM, Goncharuk SA, Goncharuk MV, Hristova K, & Arseniev AS (2013). Structure of FGFR3 Transmembrane Domain Dimer: Implications for Signaling and Human Pathologies.
Structure 21 :2087-2093. PubMed Id: 24120763. doi:10.1016/j.str.2013.08.026. |
||
|
Vascular Endothelial Growth Factor Receptors
VEGFR family of receptor tyrosine kinases (RTKs) |
|||
|
Manni et al. (2014).
Manni S, Mineev KS, Usmanova D, Lyukmanova EN, Shulepko MA, Kirpichnikov MP, Winter J, Matkovic M, Deupi X, Arseniev AS, & Ballmer-Hofer K (2014). Structural and functional characterization of alternative transmembrane domain conformations in VEGF receptor 2 activation.
Structure 22 8:1077-1089. PubMed Id: 24980797. doi:10.1016/j.str.2014.05.010. |
|||
|
Integrin Adhesion Receptors
|
|||
|
Human Integrin αIIbβ3 transmembrane-cytoplasmic heterodimer: Homo sapiens E Eukaryota (expressed in E. coli), NMR Structure
|
Yang et al. (2009).
Yang J, Ma YQ, Page RC, Misra S, Plow EF, & Qin J (2009). Structure of an integrin αIIbβ3 transmembrane-cytoplasmic heterocomplex provides insight into integrin activation.
Proc Natl Acad Sci U S A 106 :17729-17734. PubMed Id: 19805198. |
||
|
Histidine Kinase Receptors
|
|||
|
ArcB (1-115) Aerobic Respiration Control sensor membrane domain: Escherichia coli (cell-free expression) B Bacteria, NMR Structure
|
Maslennikov et al. (2010).
Maslennikov I, Klammt C, Hwang E, Kefala G, Okamura M, Esquivies L, Mörs K, Glaubitz C, Kwiatkowski W, Jeon YH, & Choe S (2010). Membrane domain structures of three classes of histidine kinase receptors by cell-free expression and rapid NMR analysis.
Proc Natl Acad Sci USA 107 :10902-10907. PubMed Id: 20498088. |
||
|
QseC (1-185) Sensor protein membrane domain: Escherichia coli (cell-free expression) B Bacteria, NMR Structure
|
Maslennikov et al. (2010).
Maslennikov I, Klammt C, Hwang E, Kefala G, Okamura M, Esquivies L, Mörs K, Glaubitz C, Kwiatkowski W, Jeon YH, & Choe S (2010). Membrane domain structures of three classes of histidine kinase receptors by cell-free expression and rapid NMR analysis.
Proc Natl Acad Sci USA 107 :10902-10907. PubMed Id: 20498088. |
||
|
KdpD (397-502) Sensor protein membrane domain: Escherichia coli (cell-free expression) B Bacteria, NMR Structure
|
Maslennikov et al. (2010).
Maslennikov I, Klammt C, Hwang E, Kefala G, Okamura M, Esquivies L, Mörs K, Glaubitz C, Kwiatkowski W, Jeon YH, & Choe S (2010). Membrane domain structures of three classes of histidine kinase receptors by cell-free expression and rapid NMR analysis.
Proc Natl Acad Sci USA 107 :10902-10907. PubMed Id: 20498088. |
||
|
Gushchin et al. (2017).
Gushchin I, Melnikov I, Polovinkin V, Ishchenko A, Yuzhakova A, Buslaev P, Bourenkov G, Grudinin S, Round E, Balandin T, Borshchevskiy V, Willbold D, Leonard G, Büldt G, Popov A, & Gordeliy V (2017). Mechanism of transmembrane signaling by sensor histidine kinases.
Science 356 :eaah6345. PubMed Id: 28522691. doi:10.1126/science.aah6345. |
||
|
Epidermal Growth Factor Receptors (EGFRs)
ErbB (or HER) family of receptor tyrosine kinases (RTKs) |
|||
|
ErbB2 transmembrane segment dimer: Homo sapiens E Eukaryota (expressed in E. coli), NMR Structure
TM fragment 641-684 of ErbB2 gene. Structure determined in DMPC/DHPC bicelles. |
Bocharov et al. (2008).
Bocharov EV, Mineev KS, Volynsky PE, Ermolyuk YS, Tkach EN, Sobol AG, Chupin VV, Kirpichnikov MP, Efremov RG, & Arseniev AS (2008). Spatial structure of the dimeric transmembrane domain of the growth factor receptor ErbB2 presumably corresponding to the receptor active state.
J Biol Chem 283 :6950-6956. PubMed Id: 18178548. doi:10.1074/jbcM709202200. |
||
|
ErbB2 (HER2) transmembrane segment dimer with juxtamembrane region: Homo sapiens E Eukaryota (expressed in E. coli), NMR structure
in DPC micelles |
Bragin et al. (2016).
Bragin PE, Mineev KS, Bocharova OV, Volynsky PE, Bocharov EV, & Arseniev AS (2016). HER2 Transmembrane Domain Dimerization Coupled with Self-Association of Membrane-Embedded Cytoplasmic Juxtamembrane Regions.
J Mol Biol 428 :52-61. PubMed Id: 26585403. doi:10.1016/j.jmb.2015.11.007. |
||
|
ErbB1/ErbB2 transmembrane segment heterodimer: Homo sapiens E Eukaryota (expressed in E. coli), NMR Structure
TM fragment 634-677 of ErbB1 gene. TM fragment 641-685 of ErbB2 gene. Structure determined in DMPC/DHPC bicelles. |
Mineev et al. (2010).
Mineev KS, Bocharov EV, Pustovalova YE, Bocharova OV, Chupin VV, & Arseniev AS (2010). Spatial structure of the transmembrane domain heterodimer of ErbB1 and ErbB2 receptor tyrosine kinases.
J Mol Biol 400 :231-243. PubMed Id: 20471394. doi:10.1016/j.jmb.2010.05.016. |
||
|
ErbB1 transmembrane segment homodimer: Homo sapiens E Eukaryota (expressed in E. coli), NMR structure
|
Bocharov et al. (2017).
Bocharov EV, Bragin PE, Pavlov KV, Bocharova OV, Mineev KS, Polyansky AA, Volynsky PE, Efremov RG, & Arseniev AS (2017). The Conformation of the Epidermal Growth Factor Receptor Transmembrane Domain Dimer Dynamically Adapts to the Local Membrane Environment.
Biochemistry 56 12:1697-1705. PubMed Id: 28291355. doi:10.1021/acs.biochem.6b01085. |
||
|
ErbB3 transmembrane segment dimer: Homo sapiens E Eukaryota (expressed in E. coli), NMR Structure
TM fragment 639-667 of ErbB3 gene. Structure determined in DPC micelles. |
Mineev et al. (2011).
Mineev KS, Khabibullina NF, Lyukmanova EN, Dolgikh DA, Kirpichnikov MP, & Arseniev AS (2011). Spatial structure and dimer--monomer equilibrium of the ErbB3 transmembrane domain in DPC micelles.
Biochim Biophys Acta 1808 :2081-2088. PubMed Id: 21575594. doi:10.1016/j.bbamem.2011.04.017. |
||
|
ErbB4 transmembrane segment dimer: Homo sapiens E Eukaryota (expressed in E. coli), NMR Structure
TM fragment 651-678 of ErbB4 gene. Structure determined in DMPC/DHPC bicelles. |
Bocharov et al. (2012).
Bocharov EV, Mineev KS, Goncharuk MV, & Arseniev AS (2012). Structural and thermodynamic insight into the process of "weak" dimerization of the ErbB4 transmembrane domain by solution NMR.
Biochim Biophys Acta 1818 :2158-2170. PubMed Id: 22579757. doi:10.1016/j.bbamem.2012.05.001. |
||
|
Immune Receptors
|
|||
|
Transmembrane ζ-ζ dimer of the TCR-CD3 complex: Homo sapiens E Eukaryota (expressed in E. coli), NMR Structure
|
Call et al. (2006).
Call ME, Schnell JR, Xu C, Lutz RA, Chou JJ, & Wucherpfennig KW (2006). The structure of the zetazeta transmembrane dimer reveals features essential for its assembly with the T cell receptor.
Cell 127 :355-368. PubMed Id: 17055436. |
||
|
DAP12 dimeric signaling domain in complex with activating receptor NKG2C: Homo sapiens E Eukaryota (expressed in E. coli), NMR Structure
DAP12 dimer: 2L34 |
Call et al. (2010).
Call ME, Wucherpfennig KW, & Chou JJ (2010). The structural basis for intramembrane assembly of an activating immunoreceptor complex.
Nature Immunol 11 :1023-1029. PubMed Id: 20890284. |
||
|
DAP12 signaling domain trimer: Homo sapiens E Eukaryota (expressed in E. coli), 1.77 Å
lipidic cubic phase crystallization DAP12 tetramer, 2.14Å: 4WO1 |
Knoblich et al. (2015).
Knoblich K, Park S, Lutfi M, van 't Hag L, Conn CE, Seabrook SA, Newman J, Czabotar PE, Im W, Call ME, & Call MJ (2015). Transmembrane Complexes of DAP12 Crystallized in Lipid Membranes Provide Insights into Control of Oligomerization in Immunoreceptor Assembly.
Cell Rep 11 :1184-1192. PubMed Id: 25981043. doi:10.1016/j.celrep.2015.04.045. |
||
|
SNARE Protein Family
|
|||
|
Syntaxin 1A/SNAP-25/Synaptobrevin-2 Complex with transmembrane regions: Rattus norvegicus E Eukaryota (expressed in E. coli), 3.4 Å
I212121 space group, 4.80 Å: 3HD9. |
Stein et al. (2009).
Stein A, Weber G, Wahl MC, & Jahn R (2009). Helical extension of the neuronal SNARE complex into the membrane.
Nature 460 :525-528. PubMed Id: 19571812. |
||
|
Synaptobrevin, lipid-bound : Rattus norvegicus E Eukaryota (expressed in E. coli), NMR Structure
Protein is in dodecylphosphocholine (DPC) micelles |
Ellena et al. (2009).
Ellena JF, Liang B, Wiktor M, Stein A, Cafiso DS, Jahn R, & Tamm LK (2009). Dynamic structure of lipid-bound synaptobrevin suggests a nucleation-propagation mechanism for trans-SNARE complex formation.
Proc Natl Acad Sci USA 106 :20306-20311. PubMed Id: 19918058. doi:10.1073/pnas.0908317106. |
||
|
Syntaxin 1A in prefusion state: Rattus norvegicus E Eukaryota (expressed in E. coli), NMR Structure
Structure in DPC micelles. |
Liang et al. (2013).
Liang B, Kiessling V, & Tamm LK (2013). Prefusion structure of syntaxin-1A suggests pathway for folding into neuronal trans-SNARE complex fusion intermediate.
Proc Natl Acad Sci USA 110 :19384-19389. PubMed Id: 24218570. doi:10.1073/pnas.1314699110. |
||
|
Claudins
Claudins form the backbone of tight junctions |
|||
|
Caludin-15: Mus musculus E Eukaryota (expressed in S. frugiperda), 2.61 Å
|
Suzuki et al. (2014).
Suzuki H, Nishizawa T, Tani K, Yamazaki Y, Tamura A, Ishitani R, Dohmae N, Tsukita S, Nureki O, & Fujiyoshi Y (2014). Crystal structure of a claudin provides insight into the architecture of tight junctions.
Science 344 :304-307. PubMed Id: 24744376. doi:10.1126/science.1248571. |
||
|
Claudin-19 in complex with Clostridium perfringens enterotoxin: Mus musculus E Eukaryota (expressed in S. frugiperda), 3.70 Å
|
Saitoh et al. (2015).
Saitoh Y, Suzuki H, Tani K, Nishikawa K, Irie K, Ogura Y, Tamura A, Tsukita S, & Fujiyoshi Y (2015). Tight junctions. Structural insight into tight junction disassembly by Clostridium perfringens enterotoxin.
Science 347 6223:775-778. PubMed Id: 25678664. doi:10.1126/science.1261833. |
||
|
TMEM16 Family Proteins
A functionally diverse family of proteins also known as Anoctamins |
|||
|
TMEM16 Ca2+-activated lipid scramblase, crystal form 1: Nectria haematococca E Eukaryota (expressed in S. cerevisiae), 3.30 Å
Crystal form 2, 3.40 Å: 4WIT |
Brunner et al. (2014).
Brunner JD, Lim NK, Schenck S, Duerst A, & Dutzler R (2014). X-ray structure of a calcium-activated TMEM16 lipid scramblase.
Nature 516 7530:207-212. PubMed Id: 25383531. doi:10.1038/nature13984. |
||
|
TMEM16A calcium-activated chloride channel: Mus musculus E Eukaryota (expressed in HEK293 cells), 6.6 Å
cryo-EM structure |
Paulino et al. (2017).
Paulino C, Neldner Y, Lam AK, Kalienkova V, Brunner JD, Schenck S, & Dutzler R (2017). Structural basis for anion conduction in the calcium-activated chloride channel TMEM16A.
Elife 6 :e26232. PubMed Id: 28561733. doi:10.7554/eLife.26232. |
||
|
Channels: Mechanosensitive
|
|||
|
MscL Mechanosensitive channel: Mycobacterium tuberculosis B Bacteria, 3.5 Å
This structure supersedes 1MSL. |
Chang et al. (1998).
Chang G, Spencer RH, Lee AT, Barclay MT, & Rees DC (1998). Structure of the MscL homolog from Mycobacterium tuberculosis: A gated mechanosensitive ion channel.
Science 282 :2220-2226. PubMed Id: 9856938. |
||
|
MscL Mechanosensitive channel, Δ95-120: Staphylococcus aureus B Bacteria, 3.8 Å
Shows MscL in an expanded intermediate state. |
Liu et al. (2009).
Liu Z, Gandhi CS, & Rees DC (2009). Structure of a tetrameric MscL in an expanded intermediate state.
Nature 461 :120-124. PubMed Id: 19701184. |
||
|
MscL mechanosensitive channel in closed state: Methanosarcina acetivorans A Archaea (expressed in E. coli), 3.5 Å
expanded intermediate state, 4.1 Å: 4Y7J |
Li et al. (2015).
Li J, Guo J, Ou X, Zhang M, Li Y, & Liu Z (2015). Mechanical coupling of the multiple structural elements of the large-conductance mechanosensitive channel during expansion.
Proc Natl Acad Sci USA 112 :10726-10731. PubMed Id: 26261325. doi:10.1073/pnas.1503202112. |
||
|
MscS voltage-modulated mechanosensitive channel: Escherichia coli B Bacteria, 3.70 Å
This structure supersedes 1MXM. |
Bass et al. (2002).
Bass RB, Strop P, Barclay M, & Rees DC (2002). Crystal Structure of Escherichia coli MscS, a Voltage-modulated and mechanosensitive channel.
Science 298 :1582-1587. PubMed Id: 12446901. |
||
|
MscS mechanosensitive channel in the open form: Escherichia coli B Bacteria, 3.45 Å
|
Wang et al. (2008).
Wang W, Black SS, Edwards MD, Miller S, Morrison EL, Bartlett W, Dong C, Naismith JH, & Booth IR (2008). The structure of an open form of an E. coli mechanosensitive channel at 3.45 Å resolution.
Science 321 :1179-1183. PubMed Id: 18755969. |
||
|
MscS voltage-modulated mechanosensitive channel, D67R1 mutant: Escherichia coli B Bacteria, 2.99 Å
|
Pliotas et al. (2015).
Pliotas C, Dahl AC, Rasmussen T, Mahendran KR, Smith TK, Marius P, Gault J, Banda T, Rasmussen A, Miller S, Robinson CV, Bayley H, Sansom MS, Booth IR, & Naismith JH (2015). The role of lipids in mechanosensation.
Nat Struct Mol Biol 22 :991-998. PubMed Id: 26551077. doi:10.1038/nsmb.3120. |
||
|
Piezo1 mechanosensitive channel by cryo-EM: Mus musculus E Eukaryota (expressed in HEK293 cells), 4.8 Å
C-terminal extracellular domain by x-ray, 1.45 Å: 4RAX |
Ge et al. (2015).
Ge J, Li W, Zhao Q, Li N, Chen M, Zhi P, Li R, Gao N, Xiao B, & Yang M (2015). Architecture of the mammalian mechanosensitive Piezo1 channel.
Nature 527 7576:64-69. PubMed Id: 26390154. doi:10.1038/nature15247. |
||
|
Channels: Potassium, Sodium, & Proton Ion-Selective
|
|||
|
KcsA Potassium channel, H+ gated: Streptomyces lividans B Bacteria (expressed in E. coli), 3.2 Å
|
Doyle et al. (1998).
Doyle DA, Cabral JM, Pfuetzner RA, Kuo AL, Gulbis JM, Cohen SL, Chait BT, & MacKinnon R (1998). The structure of the potassium channel: Molecular basis of K+conduction and selectivity.
Science 280 :69-77. PubMed Id: 9525859. |
||
|
KcsA Potassium channel, H+ gated. Complexed with Fab.: Streptomyces lividans B Bacteria (expressed in E. coli), 2.0 Å
R-free = 0.233. 1K4D, 2.3 Å, R-free = 0.235 |
Zhou et al. (2001).
Zhou Y, Morais-Cabral JH, Kaufman A, & MacKinnon R (2001). Chemistry of ion coordination and hydration revealed by a K+ channel-Fab complex at 2.0 Å.
Nature 414 :43-48. PubMed Id: 11689936. |
||
|
Full-length KcsA Potassium channel, H+ gated: Streptomyces lividans B Bacteria (expressed in E. coli), NMR structure
|
Cortes et al. (2001).
Cortes DM, Cuello LG, & Perozo E (2001). Molecular architecture of full-length KcsA: role of cytoplasmic domains in ion permeation and activation gating.
J Gen Physiol 117 2:165-180. PubMed Id: 11158168. doi:10.1085/jgp.117.2.165. |
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|
KcsA Potassium channel, H+ gated. Complexed with Fab, Tl, & Tetrabutylammonium (TBA): Streptomyces lividans B Bacteria (expressed in E. coli), 2.76 Å
In complex with tetraethylarsonium (TEAS) rather than TBA, 3.01 Å: 2BOC |
Lenaeus et al. (2005).
Lenaeus MJ, Vamvouka M, Focia PJ, & Gross A (2005). Structural basis of TEA blockade in a model potassium channel.
Nat Struc Mol Biol 12 :454-459. PubMed Id: 15852022. |
||
|
Lockless et al. (2007).
Lockless SW, Zhou M, & MacKinnon R (2007). Structural and thermodynamic properties of selective ion binding in a K+ channel.
PLoS Biol 5 :e121. PubMed Id: 17472437. doi:10.1371/journal.pbio.0050121. |
|||
|
Full-length KcsA Potassium channel, H+ gated: Streptomyces lividans B Bacteria (expressed in E. coli), 3.80 Å
Crystallized with synthetic Fab2 antibodies. C-terminal domain alone (residues 129-158) crystallized with synthetic Fab4 antibodies 3EFD, 2.60 Å |
Uysal et al. (2009).
Uysal S, Vásquez V, Tereshko V, Esaki K, Fellouse FA, Sidhu SS, Koide S, Perozo E, & Kossiakoff A (2009). Crystal structure of full-length KcsA in its closed conformation.
Proc Natl Acad Sci USA 106 :6644-6649. PubMed Id: 19346472. |
||
|
Full-length KcsA Potassium channel, H+ gated: Streptomyces lividans B Bacteria (expressed in E. coli), 3.80 Å
Open conformation of the full-length channel. Reveals that the activation gate expands about 20 Å |
Uysal et al. (2011).
Uysal S, Cuello LG, Cortes DM, Koide S, Kossiakoff AA, & Perozo E (2011). Mechanism of activation gating in the full-length KcsA K+ channel.
Proc Natl Acad Sci USA 108 :11896-11899. PubMed Id: 21730186. doi:10.1073/pnas.1105112108. |
||
|
KcsA Potassium channel in the presence of 150 mM Li+ and 3 mM K+: Streptomyces lividans B Bacteria (expressed in E. coli), 2.75 Å
KcsA in the presence of 150 mM Li+ and 0 mM K+, 2.85 Å: 3GB7 |
Thompson et al. (2009).
Thompson AN, Kim I, Panosian TD, Iverson TM, Allen TW, & Nimigean CM (2009). Mechanism of potassium-channel selectivity revealed by Na+and L+binding sites within the KcsA pore.
Nat Struct Mol Biol 16 :1321-1324. PubMed Id: 19946269. |
||
|
Cuello et al. (2010).
Cuello LG, Jogini V, Cortes DM, & Perozo E (2010). Structural mechanism of C-type inactivation in K+channels.
Nature 466 :203-208. PubMed Id: 20613835. |
|||
|
KcsA Potassium channel E71H-F103A inactivated-state mutant (closed state): Streptomyces lividans B Bacteria (expressed in E. coli), 3.20 Å
KcsA open-state in the presence of Rb+, 3.30 Å: 3FB7 |
Cuello et al. (2010).
Cuello LG, Jogini V, Cortes DM, Pan AC, Gagnon DG, Dalmas O, Cordero-Morales JF, Chakrapani S, Roux B, & Perozo E (2010). Structural basis for the coupling between activation and inactivation gates in K+channels.
Nature 466 :272-275. PubMed Id: 20613845. |
||
|
KcsA Potassium channel E71I modal-gating mutant: Streptomyces lividans B Bacteria (expressed in E. coli), 2.30 Å
E71Q mutant, 2.70 Å: 3OR6 |
Chakrapani et al. (2011).
Chakrapani S, Cordero-Morales JF, Jogini V, Pan AC, Cortes DM, Roux B, & Perozo E (2011). On the structural basis of modal gating behavior in K+channels.
Nat Struct Mol Biol 18 :67-74. PubMed Id: 21186363. |
||
|
KcsA Y82C with bound Cadmium : Streptomyces lividans B Bacteria (expressed in E. coli), 2.40 Å
with nitroxide spin label, 2.50 Å: 3STZ |
Raghuraman et al. (2012).
Raghuraman H, Cordero-Morales JF, Jogini V, Pan AC, Kollewe A, Roux B, & Perozo E (2012). Mechanism of Cd2+ Coordination during Slow Inactivation in Potassium Channels.
Structure 20 :1332-1342. PubMed Id: 22771214. doi:10.1016/j.str.2012.03.027. |
||
|
KcsA Potassium channel Y78 ester mutant in high K+: Streptomyces lividans B Bacteria (expressed in E. coli + semi-synthesis), 2.06 Å
|
Matulef et al. (2013).
Matulef K, Komarov AG, Costantino CA, & Valiyaveetil FI (2013). Using protein backbone mutagenesis to dissect the link between ion occupancy and C-type inactivation in K+ channels.
Proc Natl Acad Sci USA 110 44:17886-17891. PubMed Id: 24128761. doi:10.1073/pnas.1314356110. |
||
|
Lenaeus et al. (2014).
Lenaeus MJ, Burdette D, Wagner T, Focia PJ, & Gross A (2014). Structures of KcsA in Complex with Symmetrical Quaternary Ammonium Compounds Reveal a Hydrophobic Binding Site.
Biochemistry 53 :5365-5373. PubMed Id: 25093676. doi:10.1021/bi500525s. |
|||
|
Matulef et al. (2016).
Matulef K, Annen AW, Nix JC, & Valiyaveetil FI (2016). Individual Ion Binding Sites in the K+ Channel Play Distinct Roles in C-type Inactivation and in Recovery from Inactivation.
Structure 24 :750-761. PubMed Id: 27150040. doi:10.1016/j.str.2016.02.021. |
|||
|
Two-Pore Domain Potassium Channel K2P1.1 (TWIK-1): Homo sapiens E Eukaryota (expressed in Pichia pastoris), 3.40 Å
The protein is a homodimer. It is sensitive to temperature, pH, and membrane stretch. The channel becomes permeable to Na+ during hypokalemia. |
Miller & Long (2012).
Miller AN & Long SB (2012). Crystal structure of the human two-pore domain potassium channel K2P1.
Science 335 :432-436. PubMed Id: 22282804. doi:10.1126/science.121327. |
||
|
Two-Pore Domain Potassium Channel K2P4.1 (TRAAK): Homo sapiens E Eukaryota (expressed in Pichia pastoris), 3.80 Å
The protein is a homodimer. This channel is sensitive to temperature, pH, voltage, lipid interactions, and membrane stretch. |
Brohawn et al. (2012).
Brohawn SG, del Mármol J, & MacKinnon R (2012). Crystal structure of the human K2P TRAAK, a lipid- and mechano-sensitive K+ ion channel.
Science 335 :436-441. PubMed Id: 22282805. doi:10.1126/science.1213808. |
||
|
Two-Pore Domain Potassium Channel K2P4.1 (TRAAK): Homo sapiens E Eukaryota (expressed in Pichia pastoris), 2.75 Å
This structure reveals a domain-swapped chain connectivity enabled by the helical cap that exchanges two opposing outer helices 180° around the channel. |
Brohawn et al. (2013).
Brohawn SG, Campbell EB, & Mackinnon R (2013). Domain-swapped chain connectivity and gated membrane access in a Fab-mediated crystal of the human TRAAK K+ channel.
Proc Natl Acad Sci USA 110 :2129-2134. PubMed Id: 23341632. doi:10.1073/pnas.1218950110. |
||
|
Two-Pore Domain Potassium Channel K2P4.1 (TRAAK) in non-conductive state in the presence of K+: Homo sapiens E Eukaryota (expressed in Pichia pastoris), 2.50 Å
Non-conductive state in the presence of Tl+, 3.01 Å: 4WFH Conductive state in the presence of K+, 2.50 Å: 4WFE Conductive state in the presence of Tl+, 3.00 Å: 4WFG |
Brohawn et al. (2014).
Brohawn SG, Campbell EB, & MacKinnon R (2014). Physical mechanism for gating and mechanosensitivity of the human TRAAK K+ channel.
Nature 516 7529:126-130. PubMed Id: 25471887. doi:10.1038/nature14013. |
||
|
Dong et al. (2015).
Dong YY, Pike AC, Mackenzie A, McClenaghan C, Aryal P, Dong L, Quigley A, Grieben M, Goubin S, Mukhopadhyay S, Ruda GF, Clausen MV, Cao L, Brennan PE, Burgess-Brown NA, Sansom MS, Tucker SJ, & Carpenter EP (2015). K2P channel gating mechanisms revealed by structures of TREK-2 and a complex with Prozac.
Science 347 6227:1256-1259. PubMed Id: 25766236. doi:10.1126/science.1261512. |
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|
Two-pore channel TPC1: Arabidopsis thaliana E Eukaryota (expressed in S. cerevisiae), 2.87 Å
|
Kintzer & Stroud (2016).
Kintzer AF, & Stroud RM (2016). Structure, inhibition and regulation of two-pore channel TPC1 from Arabidopsis thaliana.
Nature 531 :258-262. PubMed Id: 26961658. doi:10.1038/nature17194. |
||
|
Two-pore channel TPC1: Arabidopsis thaliana E Eukaryota (expressed in Komagataella pastoris), 3.31 Å
|
Guo et al. (2016).
Guo J, Zeng W, Chen Q, Lee C, Chen L, Yang Y, Cang C, Ren D, & Jiang Y (2016). Structure of the voltage-gated two-pore channel TPC1 from Arabidopsis thaliana.
Nature 531 :196-201. PubMed Id: 26689363. doi:10.1038/nature16446. |
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|
Two-pore channel TPC1 mutant, Na+ selective: Arabidopsis thaliana E Eukaryota (expressed in Komagataella pastoris), 3.3 Å
|
Guo et al. (2017).
Guo J, Zeng W, & Jiang Y (2017). Tuning the ion selectivity of two-pore channels.
Proc Natl Acad Sci USA 114 :1009-1014. PubMed Id: 28096396. doi:10.1073/pnas.1616191114. |
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|
KvAP Voltage-gated potassium Channel in complex with Fab: Aeropyrum pernix A Archaea (expressed in E. coli), 3.2 Å
Voltage sensor domain, 1.9 Å: 1ORS |
Jiang et al. (2003).
Jiang Y, Lee A, Chen J, Ruta V, Cadene M, Chait BT, & MacKinnon R (2003). X-ray structure of a voltage-dependent K+channel.
Crystal structures.
Nature 423 :33-41. PubMed Id: 12721618. See also: Jiang et al. (2003). Jiang Y, Ruta V, Chen J, Lee A, & MacKinnon R (2003). The principle of gating charge movement in a voltage-dependent K+ channel.
Voltage sensor mechanism.
Nature 423 :42-48. PubMed Id: 12721619. |
||
|
KvAP Voltage-gated potassium Channel in complex with Fv fragments: Aeropyrum pernix A Archaea (expressed in E. coli), 3.9 Å
|
Lee et al. (2005).
Lee SY, Lee A, Chen J, & MacKinnon R (2005). Structure of the KvAP voltage-dependent K+ channel and its dependence on the lipid membrane.
Proc Natl Acad Sci USA 102 :15441-15446. PubMed Id: 16223877. |
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|
KvAP Voltage-Sensing Domain in phospholipid micelles: Aeropyrum pernix A Archaea (expressed in E. coli), NMR Structure
|
Butterwick & MacKinnon (2010).
Butterwick JA & MacKinnon R (2010). Solution structure and phospholipid interactions of the isolated voltage-sensor domain from KvAP.
J Mol Biol 403 :591-606. PubMed Id: 20851706. |
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|
Kv1.2 Voltage-gated potassium Channel: Rattus norvegicus E Eukaryota (expressed in Pichia pastoris), 2.9 Å
|
Long et al. (2005).
Long SB, Campbell EB, & Mackinnon R (2005). Crystal Structure of a Mammalian Voltage-Dependent Shaker Family K+ Channel.
Science 309 :897-903. PubMed Id: 16002581. See also: Long et al. (2005). Long SB, Campbell EB, & Mackinnon R (2005). Voltage Sensor of Kv1.2: Structural Basis of Electromechanical Coupling.
Science 309 :903-908. PubMed Id: 16002579. |
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|
Kv1.2 Voltage-gated potassium Channel (full length): Rattus norvegicus E Eukaryota (expressed in Pichia pastoris), 2.9 Å
Re-refinement of 2A79 above using normal-mode x-ray crystallographic refinement |
Chen et al. (2010).
Chen X, Wang Q, Ni F, & Ma J (2010). Structure of the full-length Shaker potassium channel Kv1.2 by normal-mode-based X-ray crystallographic refinement.
Proc Natl Acad Sci USA 107 :11352-11357. PubMed Id: 20534430. |
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|
Kv1.2/Kv2.1 Voltage-gated potassium channel chimera: Rattus norvegicus E Eukaryota (expressed in Pichia pastoris), 2.4 Å
First Kv channel with resolved lipids. |
Long et al. (2007).
Long SB, Tao X, Campbell EB, & Mackinnon R (2007). Atomic structure of a voltage-dependent K+channel in a lipid membrane-like environment.
Nature 450 :376-382. PubMed Id: 18004376. |
||
|
Kv1.2/Kv2.1 Voltage-gated potassium channel chimera: Rattus norvegicus E Eukaryota (expressed in Pichia pastoris), 2.9 Å
F233W Mutant. |
Tao et al. (2010).
Tao X, Lee A, Limapichat W, Dougherty DA, & MacKinnon R (2010). A gating charge transfer center in voltage sensors.
Science 328 :67-73. PubMed Id: 20360102. |
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|
Eag1 (KCNH1, Kv10.1) voltage-gated K+ channel with bound calmodulin (CaM): Rattus norvegicus E Eukaryota (expressed in SF9 cells), 3.78 Å
Cryo-EM structure |
Whicher & MacKinnon (2016).
Whicher JR, & MacKinnon R (2016). Structure of the voltage-gated K+ channel Eag1 reveals an alternative voltage sensing mechanism.
Science 353 :664-669. PubMed Id: 27516594. doi:10.1126/science.aaf8070. |
||
|
Wang & MacKinnon (2017).
Wang W, & MacKinnon R (2017). Cryo-EM Structure of the Open Human Ether-à-go-go-Related K+ Channel hERG.
Cell 169 3:422-430.e10. PubMed Id: 28431243. doi:10.1016/j.cell.2017.03.048. |
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|
KvLm voltaged-gated potassium channel: C-terminal pore module: Listeria monocytogenes B Bacteria (expressed in E. coli), 3.10 Å
Shows pore in transient conformation between closed and open. Crystallized under sodium condition, 3.35 Å: 4H37 |
Santos et al. (2012).
Santos JS, Asmar-Rovira GA, Han GW, Liu W, Syeda R, Cherezov V, Baker KA, Stevens RC, & Montal M (2012). Crystal Structure of a Voltage-gated K+ Channel Pore Module in a Closed State in Lipid Membranes.
J Biol Chem 287 :43063-43070. PubMed Id: 23095758. doi:10.1074/jbc.M112.415091. |
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|
MthK Potassium channel, Ca++ gated: Methanothermobacter thermautotrophicus A Archaea (expressed in E. coli), 3.3 Å
|
Jiang et al. (2002).
Jiang Y, Lee A, Chen J, Cadene M, Chait BT, MacKinnon R (2002). Crystal structure and mechanism of a calcium-gated potassium channel.
Crystal structure and mechanism.
Nature 417 :515-22. PubMed Id: 12037559. See also: Jiang et al. (2002). Jiang Y, Lee A, Chen J, Cadene M, Chait BT, MacKinnon R (2002). The open pore conformation of potassium channels.
Open pore conformation.
Nature 417 :523-6. PubMed Id: 12037560. |
||
|
Ye et al. (2010).
Ye S, Li Y, & Jiang Y (2010). Novel insights into K+selectivity from high-resolution structures of an open K+channel pore.
Nature Struct Molec Biol 17 :1019-1023. PubMed Id: 20676101. |
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MthK Potassium channel, Ca++ gated: Methanothermobacter thermautotrophicus A Archaea (expressed in E. coli), 3.40 Å
RCK domain D184N mutant, Ca2+-bound, 2.80 Å: 3RBX |
Pau et al. (2011).
Pau VP, Smith FJ, Taylor AB, Parfenova LV, Samakai E, Callaghan MM, Abarca-Heidemann K, Hart PJ, & Rothberg BS (2011). Structure and function of multiple Ca2+-binding sites in a K+ channel regulator of K+ conductance (RCK) domain.
Proc Natl Acad Sci USA 108 :17684-17689. PubMed Id: 21997217. doi:10.1073/pnas.1107229108. |
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|
MthK Potassium channel gating ring with bound Ba2+: Methanothermobacter thermautotrophicus A Archaea (expressed in E. coli), 3.10 Å
|
Smith et al. (2012).
Smith FJ, Pau VP, Cingolani G, Rothberg BS (2012). Crystal Structure of a Ba2+-Bound Gating Ring Reveals Elementary Steps in RCK Domain Activation.
Structure 20 :2038-2047. PubMed Id: 23085076. doi:10.1016/j.str.2012.09.014. |
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|
MthK Potassium channel pore (S68H,V77C mutant): Methanothermobacter thermautotrophicus A Archaea (expressed in E. coli), 1.65 Å
In the presence of TBSb, 1.65 Å 4HZ3 |
Posson et al. (2013).
Posson DJ, McCoy JG, & Nimigean CM (2013). The voltage-dependent gate in MthK potassium channels is located at the selectivity filter.
Nature Struc Mol Biol 20 :159-166. PubMed Id: 23262489. doi:10.1038/nsmb.2473. |
||
|
Smith et al. (2013).
Smith FJ, Pau VP, Cingolani G, & Rothberg BS (2013). Structural basis of allosteric interactions among Ca2+-binding sites in a K+ channel RCK domain.
Nat Commun 4 :2621. PubMed Id: 24126388. doi:10.1038/ncomms3621. |
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|
Slo1 (BK) calcium-activated K+ channel: Aplysia californica E Eukaryota (expressed in Trichoplusia ni), 3.5 Å
cryo-EM structure |
Tao et al. (2017).
Tao X, Hite RK, & MacKinnon R (2017). Cryo-EM structure of the open high-conductance Ca+2-activated K+ channel.
Nature 541 :46-51. PubMed Id: 27974795. doi:10.1038/nature20608. |
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|
Slo1 (BK) calcium-activated K+ channel with bound Ca2+: Aplysia californica E Eukaryota (expressed in Trichoplusia ni), 3.8 Å
cryo-EM structure |
Hite et al. (2017).
Hite RK, Tao X, & MacKinnon R (2017). Structural basis for gating the high-conductance Ca2+-activated K+ channel.
Nature 541 :52-57. PubMed Id: 27974801. doi:10.1038/nature20775. |
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|
Human BK (SLO1) Channel Ca2+-activation apparatus: Homo sapiens E Eukaryota (expressed in S. frugiperda), 3.0 Å
Consists of four BK subunits organized as a ring of 8 RCK (Regulator of K+ conductance) domains. Although not a transmembrane protein, it is an important accessory structure for regulating voltage-gated potassium channels. |
Yuan et al. (2010).
Yuan P, Leonetti MD, Pico AR, Hsiung Y, & MacKinnon R (2010). Structure of the human BK channel Ca2+-activation apparatus at 3.0 A resolution.
Science 329 :182-186. PubMed Id: 20508092. |
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|
Human BK (SLO1) Channel Ca2+-activation apparatus: Homo sapiens E Eukaryota (expressed in S. frugiperda), 3.1 Å
Consists of four BK subunits organized as a ring of 8 RCK (Regulator of K+ conductance) domains. Although not a transmembrane protein, it is an important accessory structure for regulating voltage-gated potassium channels. |
Wu et al. (2010).
Wu Y, Yang Y, Ye S, & Jiang Y (2010). Structure of the gating ring from the human large-conductance Ca2+-gated K(+) channel.
Nature 466 :393-397. PubMed Id: 20574420. |
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|
BK (SLO1) Channel Ca2+ gating ring from zebra fish in the open state: Danio rerio E Eukaryota (expressed in S. frugiperda), 3.61 Å
|
Yuan et al. (2012).
Yuan P, Leonetti MD, Hsiung Y, & Mackinnon R (2012). Open structure of the Ca2+ gating ring in the high-conductance Ca2+-activated K+ channel.
Nature 481 :94-97. PubMed Id: 22139424. doi:10.1038/nature10670. |
||
|
Hite et al. (2015).
Hite RK, Yuan P, Li Z, Hsuing Y, Walz T, & MacKinnon R (2015). Cryo-electron microscopy structure of the Slo2.2 Na(+)-activated K(+) channel.
Nature 527 :198-203. PubMed Id: 26436452. doi:10.1038/nature14958. |
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|
Slo2.2 Na+-activated K+ channel (complete), open conformation: Gallus gallus E Eukaryota (expressed in S. frugiperda), 3.8 Å
cryo-EM structure closed conformation, 4.3 Å: 5U76 |
Hite & MacKinnon (2017).
Hite RK, & MacKinnon R (2017). Structural Titration of Slo2.2, a Na+-Dependent K+ Channel.
Cell 168 :390-399. PubMed Id: 28111072. doi:10.1016/j.cell.2016.12.030. |
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|
SLO3 K+ Channel pH-sensitive Gating Ring: Homo sapiens E Eukaryota (expressed in S. frugiperda), 3.40 Å
Although not a transmembrane protein, it is an important accessory structure for regulating voltage-gated potassium channels. |
Leonetti et al. (2012).
Leonetti MD, Yuan P, Hsiung Y, & Mackinnon R (2012). Functional and structural analysis of the human SLO3 pH- and voltage-gated K+ channel.
Proc Natl Acad Sci USA 109 :19274-19279. PubMed Id: 23129643. doi:10.1073/pnas.1215078109. |
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|
GsuK multi-ligand gated K+ channel, L97D mutant: Geobacter sulfurreducens B Bacteria (expressed in E. coli), 2.60 Å
This a multi-ligand gated channel. Both ADP and NAD+ activate the channel, whereas Ca2+ serves as an allosteric inhibitor. L97D mutant with bound ADP, 2.80 Å: 4GX1 L97D mutant with bound NAD+, 3.20 Å: 4GX2 Wild-type channel, 3.70 Å: 4GX5 RCK domain, 3.00 Å: 4GVL |
Kong et al. (2012).
Kong C, Zeng W, Ye S, Chen L, Sauer DB, Lam Y, Derebe MG, & Jiang Y (2012). Distinct gating mechanisms revealed by the structures of a multi-ligand gated K+ channel.
eLife 1 :e00184. PubMed Id: 23240087. doi:10.7554/eLife.00184. |
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|
Kir2.2 Inward-Rectifier Potassium Channel (Complete): Gallus gallus E Eukaryota (expressed in Pichia pastoris), 3.1 Å
|
Tao et al (2009).
Tao X, Avalos JL, Chen J, & MacKinnon R (2009). Crystal structure of the eukaryotic strong inward-rectifier K+channel Kir2.2 at 3.1 Å resolution.
Science 326 :1668-1674. PubMed Id: 20019282. |
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Kir2.2 Inward-Rectifier Potassium Channel in complex with PIP2: Gallus gallus E Eukaryota (expressed in Pichia pastoris), 3.31 Å
In complex with dioctanoylglycerol pyrophosphate (DGPP), 2.45 Å: 3SPC I223L mutant in complex with PIP2, 3.00 Å: 3SPH I223L mutant, apo form, 3.31 Å: 3SPJ R186A mutant in complex with PIP2, 2.61 Å: 3SPG |
Hansen et al. (2011).
Hansen SB, Tao X, & Mackinnon R (2011). Structural basis of PIP2 activation of the classical inward rectifier K+ channel Kir2.2.
Nature 477 :495-498. PubMed Id: 21874019. doi:10.1038/nature10370. |
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|
Kir2.2 Inward-Rectifier Potassium Channel, K62W mutant (apo form): Gallus gallus E Eukaryota (expressed in Komagataella pastoris), 2.0 Å
in complex with PIP2, 2.8 Å: 5KUM |
Lee et al. (2016).
Lee SJ, Ren F, Zangerl-Plessl EM, Heyman S, Stary-Weinzinger A, Yuan P, & Nichols CG (2016). Structural basis of control of inward rectifier Kir2 channel gating by bulk anionic phospholipids.
J Gen Physiol 148 :227-237. PubMed Id: 27527100. doi:10.1085/jgp.201611616. |
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|
GIRK1 (Kir3.1) cytoplasmic domain: Mus musculus E Eukaryota (expressed in E. coli), 1.8 Å
GIRK = G-Protein-Gated Inward Rectifying Potassium Channel |
Nishida & MacKinnon (2002).
Nishida M & MacKinnon R (2002). Structural basis of inward rectification: cytoplasmic pore of the G protein-gated inward rectifier GIRK1 at 1.8 Å resolution.
Cell 111 :957-65. PubMed Id: 12507423. |
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Kir3.1-Prokaryotic Kir Chimera: Mus musculus & Burkholderia xenovornas E Eukaryota (expressed in Escherichia coli), 2.2 Å
|
Nishida et al (2007).
Nishida M, Cadene M, Chait, BT & MacKinnon R (2007). Crystal structure of a Kir3.1-prokaryotic Kir channel chimera.
EMBO J 26 :4005-4015. PubMed Id: 17703190. |
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|
Kir3.1 cytoplasmic domain: Mus musculus E Eukaryota (expressed in E. coli), 2.0 Å
|
Xu et al (2009).
Xu Y, Shin HG, Szép S, & Lu Z (2009). Physical determinants of strong voltage sensitivity of K+channel block.
Nat Struct Mol Biol 16 :1252-1258. PubMed Id: 19915587. |
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|
GIRK2 (Kir3.2) G-protein-gated K+ channel: Mus musculus E Eukaryota (expressed in Pichia pastoris), 3.60 Å
First complete structure of a G-protein-gated potassium-selective channel. Wild-type protein + PIP2, 3.00 Å: 3SYA D228N mutant, 3.4 Å: 3SYC R201A mutant, 3.1 Å: 3SYP R201A mutant + PIP2, 3.45 Å: 3SYQ |
Whorton & Mackinnon (2011).
Whorton MR & Mackinnon R (2011). Crystal Structure of the Mammalian GIRK2 K+ Channel and Gating Regulation by G Proteins, PIP2, and Sodium
Cell 147 :199-208. PubMed Id: 21962516. doi:10.1016/j.cell.2011.07.046. |
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GIRK2 (Kir3.2) G-protein-gated K+ channel in complex with βγ G-protein subunits: Mus musculus E Eukaryota (expressed in Pichia pastoris ), 3.45 Å
The β and γ subunits are from homo sapiens expressed in S. frugiperda |
Whorton & MacKinnon (2013).
Whorton MR & MacKinnon R (2013). X-ray structure of the mammalian GIRK2-βγ G-protein complex.
Nature 498 :190-197. PubMed Id: 23739333. doi:10.1038/nature12241. |
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KirBac1.1 Inward-Rectifier Potassium channel (closed state): Burkholderia pseudomallei B Bacteria, 3.65 Å
For re-refined structure, see 2WLL |
Kuo et al (2003).
Kuo A, Gulbis JM, Antcliff JF, Rahman T, Lowe ED, Zimmer J, Cuthbertson J, Ashcroft FM, Ezaki T, & Doyle DA (2003). Crystal structure of the potassium channel KirBac1.1 in the closed state.
Science 300 :1922-1926. PubMed Id: 12738871. |
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KirBac3.1 Inward-Rectifier Potassium channel (semi-latched): Magnetospirillum magnetotacticum B Bacteria (expressed in E. coli), 2.60 Å
(Re-refinement of 1XL4) Latched State, 2.80 Å: 2WLK (re-refinement of 1XL6) Semi-latched State, 3.09 Å: 2WLI Semi-latched State, 4.20 Å: 2WLO Semi-latched State, 3.61 Å: 2WLM Unlatched State, 3.44 Å: 2WLN Unlatched State, 3.28 Å: 2WLH Q170A mutant (stalled), 3.10 Å: 2X6A Q170A mutant (blocked with Ba++), 3.30 Å: 2X6B Q170A mutant (conductive), 2.70 Å: 2X6C |
Clarke et al. (2010).
Clarke OB, Caputo AT, Hill AP, Vandenberg JI, Smith BJ & Gulbis JM (2010). Domain reorientation and rotation of an intracellular assembly regulate conduction in Kir potassium channels.
Cell 141 :1018-1029. PubMed Id: 20564790. |
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KirBac3.1 Open-State Channel (S129R mutant): Magnetospirillum magnetotacticum B Bacteria (expressed in E. coli), 3.05 Å
|
Bavro et al. (2012).
Bavro VN, De Zorzi R, Schmidt MR, Muniz JR, Zubcevic L, Sansom MS, Vénien-Bryan C, & Tucker SJ (2012). Structure of a KirBac potassium channel with an open bundle crossing indicates a mechanism of channel gating.
Nature Struc Mol Biol 19 :158-163. PubMed Id: 22231399. doi:10.1038/nsmb.2208. |
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KirBac3.1 Open-State Channel (S129R/S205L mutant): Magnetospirillum magnetotacticum B Bacteria (expressed in E. coli), 2.46 Å
|
Zubcevic et al. (2014).
Zubcevic L, Bavro VN, Muniz JR, Schmidt MR, Wang S, De Zorzi R, Venien-Bryan C, Sansom MS, Nichols CG, & Tucker SJ (2014). Control of KirBac3.1 potassium channel gating at the interface between cytoplasmic domains.
J Biol Chem 289 :143-151. PubMed Id: 24257749. doi:10.1074/jbc.M113.501833 . |
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SUR1/Kir6.2 pancreatic ATP-sensitive K+ channel: Cricetus cricetus/Rattus norvegicus E Eukaryota (expressed in HEK293 cells), 6.3 Å
cryo-EM strucuture. Chimeric protein, SUR1 is from hamster (C. cricetus) and Kir6.2 from rat. |
Martin et al. (2017).
Martin GM, Yoshioka C, Rex EA, Fay JF, Xie Q, Whorton MR, Chen JZ, & Shyng SL (2017). Cryo-EM structure of the ATP-sensitive potassium channel illuminates mechanisms of assembly and gating.
Elife 6 :e2419. PubMed Id: 28092267. doi:10.7554/eLife.24149. |
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MlotiK1 cyclic nucleotide-regulated K+-channel: Mesorhizobium loti B Bacteria (expressed in E. coli), 3.1 Å
|
Clayton et al. (2008).
Clayton GM, Altieri S, Heginbotham L, Unger VM, & Morais-Cabral JH (2008). Structure of the transmembrane regions of a bacterial cyclic nucleotide-regulated channel.
Proc Natl Acad Sci U S A 105 :1511-1515. PubMed Id: 18216238. |
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NaK channel (Na+complex): Bacillus cereus B Bacteria (expressed in E. coli), 2.4 Å
K+ complex, 2.8 Å: 2AHZ. |
Shi et al. (2006).
Shi N, Ye S, Alam A, Chen L, & Jiang Y (2006). Atomic structure of a Na+- and K+-conducting channel.
Nature 440 :570-574. PubMed Id: 16467789. |
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|
Alam et al. (2007).
Alam A, Shi N, & Jiang Y (2007). Structural insight into Ca2+ specificity in tetrameric cation channels.
Proc Natl Acad Sci USA 104 :15334-15339. PubMed Id: 17878296. |
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NaK channel in open state (NΔ19 mutant): Bacillus cereus B Bacteria (expressed in E. coli), 1.60 Å
|
Alam & Jiang (2009).
Alam A & Jiang Y (2009). High-resolution structure of the open NaK channel.
Nat Struct Mol Biol 16 :30-34. PubMed Id: 19098917. |
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CNG-mimicking NaK channel mutant; NaK-ETPP/K+ complex: Bacillus cereus B Bacteria (expressed in E. coli), 1.95 Å
CNG-mimicking mutant; NaK-NTPP/K+ complex, 1.58 Å: 3K06 CNG-mimicking mutant; NaK-ETPP/Na+ complex, 1.95 Å: 3K0G CNG-mimicking mutant; NaK-DTPP/Na+ complex, 1.58 Å: 3K04 CNG-mimicking mutant; NaK-NTPP/Na+ complex, 1.62 Å: 3K08 |
Derebe et al. (2011).
Derebe MG, Zeng W, Li Y, Alam A, & Jiang Y (2011). Structural studies of ion permeation and Ca2+blockage of a bacterial channel mimicking the cyclic nucleotide-gated channel pore.
Proc Natl Acad Sci USA 108 :592-597. PubMed Id: 21187429. |
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|
Derebe et al. (2011).
Derebe MG, Sauer DB, Zeng W, Alam A, Shi N, & Jiang Y (2011). Tuning the ion selectivity of tetrameric cation channels by changing the number of ion binding sites.
Proc Natl Acad Sci USA 108 :598-602. PubMed Id: 21187421. |
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|
Sauer et al. (2011).
Sauer DB, Zeng W, Raghunathan S, & Jiang Y (2011). Protein interactions central to stabilizing the K+ channel selectivity filter in a four-sited configuration for selective K+ permeation.
Proc Natl Acad Sci USA 108 :16634-16639. PubMed Id: 21933962. doi:10.1073/pnas.1111688108. |
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NaK channel chimera with grafted C-terminal region of a NaV channel: Bacillus weihenstephanensis (NaK) and Sulfitobacter pontiacus (NaV) B Bacteria (expressed in E. coli), 3.20 Å
The NaVSulP C-terminal region grafted onto the C-terminus of NaK forms a four-helix bundle. |
Irie et al. (2012).
Irie K, Shimomura T, & Fujiyoshi Y (2012). The C-terminal helical bundle of the tetrameric prokaryotic sodium channel accelerates the inactivation rate.
Nature Commun 3 :793. PubMed Id: 22531178. doi:10.1038/ncomms1797. |
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|
Payandeh et al. (2011).
Payandeh J, Scheuer T, Zheng N, & Catterall WA (2011). The crystal structure of a voltage-gated sodium channel.
Nature 475 :353-358. PubMed Id: 21743477. doi:10.1038/nature10238. |
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Voltage-Gated Sodium Channel (NaV), wild-type: Arcobacter butzleri B Bacteria (expressed in Trichoplusia ni), 3.21 Å
Shows channel in two potentially inactivated states. |
Payandeh et al. (2012).
Payandeh J, Gamal El-Din TM, Scheuer T, Zheng N, & Catterall WA (2012). Crystal structure of a voltage-gated sodium channel in two potentially inactivated states.
Nature 486 :135-139. PubMed Id: 22678296. doi:10.1038/nature11077. |
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Voltage-Gated Sodium Channel (NaV) in closed state (NaVAb/FY): Arcobacter butzleri B Bacteria (expressed in Trichoplusia ni), 3.2 Å
in open state (NaVAb/1-226), 2.85 Å: 5VB8 |
Lenaeus et al. (2017).
Lenaeus MJ, Gamal El-Din TM, Ing C, Ramanadane K, Pomès R, Zheng N, & Catterall WA (2017). Structures of closed and open states of a voltage-gated sodium channel.
Proc Natl Acad Sci USA 114 :E3051-E3060. PubMed Id: 28348242. doi:10.1073/pnas.1700761114. |
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Voltage-Gated Sodium Channel (NaV): Alpha proteobacterium himb114 (Rickettsiales sp. HIMB114) B Bacteria (expressed in E. coli), 3.05 Å
Structure is probably of the channel in an inactivated state. |
Zhang et al. (2012).
Zhang X, Ren W, DeCaen P, Yan C, Tao X, Tang L, Wang J, Hasegawa K, Kumasaka T, He J, Wang J, Clapham DE, & Yan N (2012). Crystal structure of an orthologue of the NaChBac voltage-gated sodium channel.
Nature 486 :130-134. PubMed Id: 22678295. |
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Voltage-Gated Sodium Channel (NaV): Magnetococcus marinus B Bacteria (expressed in E. coli), 3.49 Å
Shows channel in an open conformation. |
McCusker et al. (2012).
McCusker EC, Bagnéris C, Naylor CE, Cole AR, D'Avanzo N, Nichols CG, & Wallace BA (2012). Structure of a bacterial voltage-gated sodium channel pore reveals mechanisms of opening and closing.
Nat Commun 3 :1102. PubMed Id: 23033078. doi:10.1038/ncomms2077. |
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Voltage-Gated Sodium Channel (NaV), complete structure with C-terminal domain: Magnetococcus marinus B Bacteria (expressed in E. coli), 2.92 Å
|
Bagnéris et al. (2013).
Bagnéris C, Decaen PG, Hall BA, Naylor CE, Clapham DE, Kay CW, & Wallace BA (2013). Role of the C-terminal domain in the structure and function of tetrameric sodium channels.
Nat Commun 4 :2465. PubMed Id: 24051986. doi:10.1038/ncomms3465. |
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Voltage-Gated Sodium Channel (NaV), apo open form: Magnetococcus marinus B Bacteria (expressed in E. coli), 2.66 Å
Wild-type with Pl1 blocker by soaking crystal, 2.89 Å: 4P9O Wild-type with Pl1 blocker co-crystallized, 3.43 Å: 4PA9 T207A/F214A apo mutant, 3.08 Å: 4P2Z T207A/F214A mutant with bound Pl1, 3.31 Å: 4P30 Wild-type with bound Pl2 blocker, 2.80 Å: 4OXS Wild-type with bound Pl3 blocker, 3.25 Å: 4PA3 Wild-type with bound Pl4 blocker, 3.02 Å: 4PA4 Wild-type with bound Pl5 blocker, 2.91 Å: 4P9P Wild-type with bound Pl6 blocker, 3.36 Å: 4PA6 Wild-type with bound Pl7 blocker, 3.02 Å: 4PA7 |
Bagnéris et al. (2014).
Bagnéris C, DeCaen PG, Naylor CE, Pryde DC, Nobeli I, Clapham DE, & Wallace BA (2014). Prokaryotic NavMs channel as a structural and functional model for eukaryotic sodium channel antagonism.
Proc Natl Acad Sci USA 111 :8428-8433. PubMed Id: 24850863. doi:10.1073/pnas.1406855111. |
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Voltage-Gated Sodium Channel (NaV) channel pore and C-terminal domain: Magnetococcus marinus B Bacteria (expressed in E. coli), 2.7 Å
E178D selectivity-filter mutant, 3.5 Å: 4X88 |
Naylor et al. (2016).
Naylor CE, Bagnéris C, DeCaen PG, Sula A, Scaglione A, Clapham DE, & Wallace BA (2016). Molecular basis of ion permeability in a voltage-gated sodium channel.
EMBO J 35 :820-830. PubMed Id: 26873592. doi:10.15252/embj.201593285. |
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FPC1 cockroach voltage-gated sodium channel (NaV): Periplaneta americana E Eukaryota (expressed in HEK293F), 3.8 Å
cryo-EM structure |
Shen et al. (2017).
Shen H, Zhou Q, Pan X, Li Z, Wu J, & Yan N (2017). Structure of a eukaryotic voltage-gated sodium channel at near-atomic resolution.
Science 355 :924. PubMed Id: 28183995. doi:10.1126/science.aal4326. Article summary. See Electronic Pub Id (doi) for full article |
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Shaya et al. (2014).
Shaya D, Findeisen F, Abderemane-Ali F, Arrigoni C, Wong S, Nurva SR, Loussouarn G, & Minor DL Jr (2014). Structure of a Prokaryotic Sodium Channel Pore Reveals Essential Gating Elements and an Outer Ion Binding Site Common to Eukaryotic Channels.
J Mol Biol 426 :467-483. PubMed Id: 24120938. doi:10.1016/j.jmb.2013.10.010. |
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Li et al. (2014).
Li Q, Wanderling S, Paduch M, Medovoy D, Singharoy A, McGreevy R, Villalba-Galea CA, Hulse RE, Roux B, Schulten K, Kossiakoff A, & Perozo E (2014). Structural mechanism of voltage-dependent gating in an isolated voltage-sensing domain.
Nat Struct Mol Biol 21 :244-252. PubMed Id: 24487958. doi:10.1038/nsmb.2768. |
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Hv1 chimeric (VSOP/Hv1) voltage-gated proton channel: Mus musculus E Eukaryota (expressed in S. frugiperda), 3.45 Å
|
Takeshita et al. (2014).
Takeshita K, Sakata S, Yamashita E, Fujiwara Y, Kawanabe A, Kurokawa T, Okochi Y, Matsuda M, Narita H, Okamura Y, & Nakagawa A (2014). X-ray crystal structure of voltage-gated proton channel.
Nat Struct Mol Biol 21 :352-357. PubMed Id: 24584463. doi:10.1038/nsmb.2783. |
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NaV1.7 VSD4 voltage dependent sodium channel: Homo sapiens E Eukaryota (expressed in Trichoplusia ni), 3.5 Å
Chimera: Portions of NaV1.7 on to the bacterial (Arcobacter butzleri) channel NaV |
Ahuja et al. (2015).
Ahuja S, Mukund S, Deng L, Khakh K, Chang E, Ho H, Shriver S, Young C, Lin S, Johnson JP Jr, Wu P, Li J, Coons M, Tam C, Brillantes B, Sampang H, Mortara K, Bowman KK, Clark KR, Estevez A, Xie Z, Verschoof H, Grimwood M, Dehnhardt C, Andrez JC, Focken T, Sutherlin DP, Safina BS, Starovasnik MA, Ortwine DF, Franke Y, Cohen CJ, Hackos DH, Koth CM, & Payandeh J (2015). Structural basis of Nav1.7 inhibition by an isoform-selective small-molecule antagonist.
Science 350 6267:1491. PubMed Id: 26680203. doi:10.1126/science.aac5464. |
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Trimeric intracellular cation (TRIC) channel, B1 isoform with bound Ca2+: Caenorhabditis elegans E Eukaryota (expressed in Komagataella pastoris), 3.3 Å
B2 isoform in absence of Ca2+, 2.3 Å: 5EIK |
Yang et al. (2016).
Yang H, Hu M, Guo J, Ou X, Cai T, & Liu Z (2016). Pore architecture of TRIC channels and insights into their gating mechanism.
Nature 538 :537-541. PubMed Id: 27698420. doi:10.1038/nature19767. |
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|
Su et al. (2017).
Su M, Gao F, Yuan Q, Mao Y, Li DL, Guo Y, Yang C, Wang XH, Bruni R, Kloss B, Zhao H, Zeng Y, Zhang FB, Marks AR, Hendrickson WA, & Chen YH (2017). Structural basis for conductance through TRIC cation channels.
Nat Commun 8 :15103. PubMed Id: 28524849. doi:10.1038/ncomms15103. |
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Trimeric intracellular cation (TRIC) channel: Colwellia psychrerythraea B Bacteria (expressed in E. coli), 2.40 Å
|
Su et al. (2017).
Su M, Gao F, Yuan Q, Mao Y, Li DL, Guo Y, Yang C, Wang XH, Bruni R, Kloss B, Zhao H, Zeng Y, Zhang FB, Marks AR, Hendrickson WA, & Chen YH (2017). Structural basis for conductance through TRIC cation channels.
Nat Commun 8 :15103. PubMed Id: 28524849. doi:10.1038/ncomms15103. |
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Cyclic-nucleotide-gated (CNG) channel: Caenorhabditis elegans E Eukaryota (expressed in Trichoplusia ni), 3.5 Å
cryo-EM structure. |
Li et al. (2017).
Li M, Zhou X, Wang S, Michailidis I, Gong Y, Su D, Li H, Li X, & Yang J (2017). Structure of a eukaryotic cyclic-nucleotide-gated channel.
Nature 7639:60-65. PubMed Id: 28099415. doi:10.1038/nature20819. |
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Cyclic-nucleotide-gated (CNG) channel: Leptospira licerasiae B Bacteria (expressed in E. coli), 4.2 Å
cryo-EM structure |
James et al. (2017).
James ZM, Borst AJ, Haitin Y, Frenz B, DiMaio F, Zagotta WN, & Veesler D (2017). CryoEM structure of a prokaryotic cyclic nucleotide-gated ion channel.
Proc Natl Acad Sci USA 114 :4430-4435. PubMed Id: 28396445. doi:10.1073/pnas.1700248114. |
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HCN1 hyperpolarization-activated channel: Homo sapiens E Eukaryota (expressed in HEK293S), 3.5 Å
cryo-EM structure with bound c-AMP, 3.51 Å: 5U6P |
Lee & MacKinnon (2017).
Lee CH, & MacKinnon R (2017). Structures of the Human HCN1 Hyperpolarization-Activated Channel.
Cell 168 :111-120.e11. PubMed Id: 28086084. doi:10.1016/j.cell.2016.12.023. |
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KCNQ1 cardiac slow-delayed rectifier K+ channel in complex with calmodulin: Xenopus laevis E Eukaryota (expressed in HEK293S cells), 3.7 Å
cryo-EM structure |
Sun & MacKinnon (2017).
Sun J, & MacKinnon R (2017). Cryo-EM Structure of a KCNQ1/CaM Complex Reveals Insights into Congenital Long QT Syndrome.
Cell 169 6:1042-1050.e9. PubMed Id: 28575668. doi:10.1016/j.cell.2017.05.019. |
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Channels: Calcium Ion-Selective
|
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Voltage-Gated Calcium Channel (CaV) created by mutation of the NaVAb channel: Arcobacter butzleri B Bacteria (expressed in Trichoplusia ni ), 2.75 Å
Mutation of the NaV pore motif 175TLESWSM181 to 175TLDDWSN181. [Ca+2] = 15 mM [Ca+2] = 0.5 mM, 3.20 Å: 4MTF [Ca+2] = 2.5 mM, 3.30 Å: 4MTG [Ca+2] = 5.0 mM, 3.40 Å: 4MTO [Ca+2] = 10.0 mM, 3.20 Å: 4MVM [Ca+2] = 15.0 mM, 3.30 Å: 4MVO [Ca+2] = 15.0 mM, 3.30 Å: 4MW3 [Ca+2] = 15.0 mM, 3.20 Å: 4MVU NaVAb mutants with 175TLESWSM181 to 175TLDDWSD181: [Ca+2] = 15.0 mM, 3.40 Å: 4MVQ [Mn+2] = 100 mM, 3.20 Å: 4MVR [Cd+2] = 100 mM, 3.30 Å: 4MVS [Ca+2] = 15.0 mM, 3.30 Å: 4MVZ NaVAb wild-type: [Ca+2] = 15.0 mM, 3.26 Å: 4MW8 |
Tang et al. (2014).
Tang L, Gamal El-Din TM, Payandeh J, Martinez GQ, Heard TM, Scheuer T, Zheng N, & Catterall WA (2014). Structural basis for Ca2+ selectivity of a voltage-gated calcium channel.
Nature 505 :56-61. PubMed Id: 24270805. doi:10.1038/nature12775. |
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Voltage-Gated Calcium Channel (CaV) created by mutation of the NaVAb channel: Arcobacter butzleri B Bacteria (expressed in Trichoplusia ni), 2.7 Å
[Ca2+] = 5mM W195Y mutant in complex with Br-dihydropyridine derivative UK-59811, 3.3 Å: 5KLG wild-type protein in complex with Br-dihydropyridine derivative UK-59811, 3.3 &Ariing;: 5KLS wild-type in complex with amlodipine, 3.2 Å: 5KMD wild-type in complex with nimodipine, 3.2 Å: 5KMF wild-type in complex with Br-verapamil, 3.2 Å: 5KMH |
Tang et al. (2016).
Tang L, El-Din TM, Swanson TM, Pryde DC, Scheuer T, Zheng N, & Catterall WA (2016). Structural basis for inhibition of a voltage-gated Ca2+ channel by Ca2+ antagonist drugs.
Nature 537 :117-121. PubMed Id: 27556947. doi:10.1038/nature19102. |
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CaV1.1 voltage-gated calcium channel: Oryctolagus cuniculus E Eukaryota (expressed in E. coli), 4.2 Å
cryo-EM structure |
Wu et al. (2015).
Wu J, Yan Z, Li Z, Yan C, Lu S, Dong M, & Yan N (2015). Structure of the voltage-gated calcium channel Cav1.1 complex.
Science 350 6267:1492. PubMed Id: 26680202. doi:10.1126/science.aad2395. |
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CaV1.1 voltage-gated calcium channel: Oryctolagus cuniculus E Eukaryota (expressed in E. coli), 3.6 Å
cryo-EM structure class II reconstruction map, 3.9 Å: 5GJW |
Wu et al. (2016).
Wu J, Yan Z, Li Z, Qian X, Lu S, Dong M, Zhou Q, & Yan N (2016). Structure of the voltage-gated calcium channel Cav1.1 at 3.6 Å resolution.
Nature 537 :191-196. PubMed Id: 27580036. doi:10.1038/nature19321. |
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Orai Calcium release-activated calcium (CRAC) channel: Drosophila melanogaster E Eukaryota (expressed in Pichia pastoris), 3.35 Å
K163W mutant, 3.35 Å: 4HKS |
Hou et al. (2012).
Hou X, Pedi L, Diver MM, & Long SB (2012). Crystal Structure of the Calcium Release-Activated Calcium Channel Orai.
Science 338 :1308-1313. PubMed Id: 23180775. doi:10.1126/science.1228757. |
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Chang et al. (2014).
Chang Y, Bruni R, Kloss B, Assur Z, Kloppmann E, Rost B, Hendrickson WA, & Liu Q (2014). Structural basis for a pH-sensitive calcium leak across membranes.
Science 344 :1131-1135. PubMed Id: 24904158. doi:10.1126/science.1252043. |
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RyR1 ryanodine receptor, closed state in complex with FKBP12. Cryo-EM structure: Oryctolagus cuniculus E Eukaryota, 3.8 Å
|
Yan et al. (2015).
Yan Z, Bai X, Yan C, Wu J, Li Z, Xie T, Peng W, Yin C, Li X, Scheres SH, Shi Y, & Yan N (2015). Structure of the rabbit ryanodine receptor RyR1 at near-atomic resolution.
Nature 517 :50-55. PubMed Id: 25517095. doi:10.1038/nature14063. |
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RyR1 ryanodine receptor, closed state in complex with FKBP12.6. Cryo-EM structure: Oryctolagus cuniculus E Eukaryota, 4.8 Å
|
Zalk et al. (2015).
Zalk R, Clarke OB, Georges AD, Grassucci RA, Reiken S, Mancia F, Hendrickson WA, Frank J, & Marks AR (2015). Structure of a mammalian ryanodine receptor.
Nature 517 :44-49. PubMed Id: 25470061. doi:10.1038/nature13950. |
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RyR1 ryanodine receptor Repeat12 domain: Oryctolagus cuniculus E Eukaryota (expressed in E. coli), 1.55 Å
|
Yuchi et al. (2015).
Yuchi Z, Yuen SM, Lau K, Underhill AQ, Cornea RL, Fessenden JD, & Van Petegem F (2015). Crystal structures of ryanodine receptor SPRY1 and tandem-repeat domains reveal a critical FKBP12 binding determinant.
Nat Commun 6 :7947. PubMed Id: 26245150. doi:10.1038/ncomms8947. |
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RyR2 ryanodine receptor SPRY1 domain critical in binding FKBP12: Mus musculus E Eukaryota (expressed in E. coli), 1.21 Å
|
Yuchi et al. (2015).
Yuchi Z, Yuen SM, Lau K, Underhill AQ, Cornea RL, Fessenden JD, & Van Petegem F (2015). Crystal structures of ryanodine receptor SPRY1 and tandem-repeat domains reveal a critical FKBP12 binding determinant.
Nat Commun 6 :7947. PubMed Id: 26245150. doi:10.1038/ncomms8947. |
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RyR2 ryanodine receptor, closed state: Sus scrofa E Eukaryota, 4.4 Å
Cryo-EM structure open-state structure, 4.2 Å: 5GOA |
Peng et al. (2016).
Peng W, Shen H, Wu J, Guo W, Pan X, Wang R, Chen SR, & Yan N (2016). Structural basis for the gating mechanism of the type 2 ryanodine receptor RyR2.
Science 354 :301. PubMed Id: 27708056. doi:10.1126/science.aah5324. One-page Research Article Summary on p. 301. For full article, follow the DOI. |
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InsP3R1 Inositol-1,4,5-trisphosphate receptor: Rattus norvegicus E Eukaryota, 4.7 Å
Cryo-EM structure |
Fan et al. (2015).
Fan G, Baker ML, Wang Z, Baker MR, Sinyagovskiy PA, Chiu W, Ludtke SJ, & Serysheva II (2015). Gating machinery of InsP3R channels revealed by electron cryomicroscopy.
Nature 527 :336-341. PubMed Id: 26458101. doi:10.1038/nature15249. |
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Mitochondrial calcium uniporter: Caenorhabditis elegans E Eukaryota (expressed in E. coli), NMR structure
|
Oxenoid et al. (2016).
Oxenoid K, Dong Y, Cao C, Cui T, Sancak Y, Markhard AL, Grabarek Z, Kong L, Liu Z, Ouyang B, Cong Y, Mootha VK, & Chou JJ (2016). Architecture of the mitochondrial calcium uniporter.
Nature 533 :269-273. PubMed Id: 27135929. doi:10.1038/nature17656. |
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Channels: Transient Receptor Potential (TRP)
Non-selective cation channels responding to a wide range of chemical and physical stimuli |
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TRPV1 transient receptor potential channel: Rattus norvegicus E Eukaryota (expressed in HEK293S GnTI- cells), 3.275 Å
Capsaicin Receptor. Not only is this the first structure of a TRP channel, it is the first membrane protein whose structure was determined at atomic-resolution using single-particle cryo-EM. |
Liao et al. (2013).
Liao M, Cao E, Julius D, & Cheng Y (2013). Structure of the TRPV1 ion channel determined by electron cryo-microscopy.
Nature 504 :107-112. PubMed Id: 24305160. doi:10.1038/nature12822. |
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TRPV1 transient receptor potential channel in complex with vanilloid agonist RTX: Rattus norvegicus E Eukaryota (expressed in HEK293S GnTI- cells), 3.8 Å
in complex with capsaicin, 4.2 Å: 3J5R |
Cao et al. (2013).
Cao E, Liao M, Cheng Y, & Julius D (2013). TRPV1 structures in distinct conformations reveal activation mechanisms.
Nature 504 :113-118. PubMed Id: 24305161. doi:10.1038/nature12823. |
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Gao et al. (2016).
Gao Y, Cao E, Julius D, & Cheng Y (2016). TRPV1 structures in nanodiscs reveal mechanisms of ligand and lipid action.
Nature 534 :347-351. PubMed Id: 27281200. doi:10.1038/nature17964. |
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TRPA1 transient receptor potential channel (wasabi receptor): Homo sapiens E Eukaryota (expressed in HEK293S GnTI-), 4.24 Å
Structure determined using single-particle cryo-EM. |
Paulsen et al. (2015).
Paulsen CE, Armache JP, Gao Y, Cheng Y, & Julius D (2015). Structure of the TRPA1 ion channel suggests regulatory mechanisms.
Nature 520 7548:511-517. PubMed Id: 25855297. doi:10.1038/nature14367. |
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TRPV2 transient receptor potential channel: Oryctolagus cuniculus E Eukaryota (expressed in S. frugiperda), 4 Å
cryo-EM structure |
Zubcevic et al. (2016).
Zubcevic L, Herzik MA Jr, Chung BC, Liu Z, Lander GC, & Lee SY (2016). Cryo-electron microscopy structure of the TRPV2 ion channel.
Nat Struct Mol Biol 23 :180-186. PubMed Id: 26779611. doi:10.1038/nsmb.3159. |
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TRPV2 channel, full-length: Rattus norvegicus E Eukaryota (expressed in S. cerevisiae), 4.4 Å
cryo-EM structure |
Huynh et al. (2016).
Huynh KW, Cohen MR, Jiang J, Samanta A, Lodowski DT, Zhou ZH, & Moiseenkova-Bell VY (2016). Structure of the full-length TRPV2 channel by cryo-EM.
Nat Commun 7 :11130. PubMed Id: 27021073. doi:10.1038/ncomms11130. |
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Saotome et al. (2016).
Saotome K, Singh AK, Yelshanskaya MV, & Sobolevsky AI (2016). Crystal structure of the epithelial calcium channel TRPV6.
Nature 534 :506-511. PubMed Id: 27296226. doi:10.1038/nature17975. |
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PKD2 polycystic kidney disease channel in lipid nanodiscs: Homo sapiens E Eukaryota (expressed in HEK293S cells), 3.0 Å
cryo-EM structure |
Shen et al. (2016).
Shen PS, Yang X, DeCaen PG, Liu X, Bulkley D, Clapham DE, & Cao E (2016). The Structure of the Polycystic Kidney Disease Channel PKD2 in Lipid Nanodiscs.
Cell 167 :763-773.e11. PubMed Id: 27768895. doi:10.1016/j.cell.2016.09.048. |
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PKD2 polycystic kidney disease channel in detergent: Homo sapiens E Eukaryota (expressed in S. frugiperda), 4.22 Å
cryo-EM structure |
Grieben et al. (2017).
Grieben M, Pike AC, Shintre CA, Venturi E, El-Ajouz S, Tessitore A, Shrestha L, Mukhopadhyay S, Mahajan P, Chalk R, Burgess-Brown NA, Sitsapesan R, Huiskonen JT, & Carpenter EP (2017). Structure of the polycystic kidney disease TRP channel Polycystin-2 (PC2).
Nat Struct Mol Biol 24 :114-122. PubMed Id: 27991905. doi:10.1038/nsmb.3343. |
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PKD2 polycystic kidney disease channel in complex with cations and lipids: Homo sapiens E Eukaryota (expressed in HEK293S cells), 4.3 Å
cryo-EM structure in complex with Ca2+ and lipids, 4.2 Å: 5MKF |
Wilkes et al. (2017).
Wilkes M, Madej MG, Kreuter L, Rhinow D, Heinz V, De Sanctis S, Ruppel S, Richter RM, Joos F, Grieben M, Pike AC, Huiskonen JT, Carpenter EP, Kühlbrandt W, Witzgall R, & Ziegler C (2017). Molecular insights into lipid-assisted Ca2+ regulation of the TRP channel Polycystin-2.
Nat Struct Mol Biol 24 :123-130. PubMed Id: 28092368. doi:10.1038/nsmb.3357. |
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Channels: Other Ion Channels
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GluA2 Glutamate receptor (AMPA-subtype): Rattus norvegicus E Eukaryota (expressed in sf9 cells), 3.60 Å
3KG2 is in complex with the competitive antagonist ZK 200775 GluA2 ligand-binding core complex with bound glutamate, 1.55 Å: 3KGC |
Sobolevsky et al. (2009).
Sobolevsky AI, Rosconi MP, & Gouaux E (2009). X-ray structure, symmetry and mechanism of an AMPA-subtype glutamate receptor.
Nature 462 :745-756. PubMed Id: 19946266. |
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GluA2 Glutamate receptor (AMPA-subtype) with competitive antagonist ZK 200775: Rattus norvegicus E Eukaryota (expressed in S. frugiperda), 4.49 Å
In complex with partial agonist (S)-5-nitrowillardiine (NOW), 4.79 Å: 4U4F |
Yelshanskaya et al. (2014).
Yelshanskaya MV, Li M, & Sobolevsky AI (2014). Structure of an agonist-bound ionotropic glutamate receptor.
Science 345 :1070-1074. PubMed Id: 25103407. |
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Meyerson et al. (2014).
Meyerson JR, Kumar J, Chittori S, Rao P, Pierson J, Bartesaghi A, Mayer ML, & Subramaniam S (2014). Structural mechanism of glutamate receptor activation and desensitization.
Nature 514 :328-334. PubMed Id: 25119039. doi:10.1038/nature13603. |
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GluA2 Glutamate receptor (AMPA-subtype), apo formA: Rattus norvegicus E Eukaryota (expressed in HEK293S cells), 3.24 Å
GluA2-kainate-(R,R)-2b complex crystal form A, 3.25 Å: 4U1W GluA2-kainate-(R,R)-2b complex crystal form B, 3.30 Å: 4U1X GluA2-FW-(R,R)-2b complex, 3.90 Å: 4U1Y GluA2 in complex with partial agonist kainate, 3.52 Å: 4U2Q |
Dürr et al. (2014).
Dürr KL, Chen L, Stein RA, De Zorzi R, Folea IM, Walz T, Mchaourab HS, & Gouaux E (2014). Structure and Dynamics of AMPA Receptor GluA2 in Resting, Pre-Open, and Desensitized States.
Cell 158 :778-792. PubMed Id: 25109876. doi:10.1016/j.cell.2014.07.023. |
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GluA2 Glutamate receptor (AMPA-subtype) A622T in complex with cone snail toxin, partial agonist KA, and postitive modulator (R,R)-2b: Rattus norvegicus E Eukaryota (expressed in HEK293 cells), 3.50 Å
T625G with cone snail toxin, partial agonist KA, and positive modulator (R,R)-2b, 3.51 Å: 4U5E With snail toxin, partial agonist KA and positive modulator (R,R)-2b, 3.58 Å: 4U5D With snail toxin, partial agonist FW and positive modulator (R,R)-2b complex, 3.69 Å: 4U5C With snail toxin, partial agonist KA and postitive modulator (R,R)-2b complex ( crystal form 2), 3.70 Å: 4U5F |
Chen et al. (2014).
Chen L, Dür KL, & Gouaux E (2014). X-ray structures of AMPA receptor-cone snail toxin complexes illuminate activation mechanism.
Science 345 :1021-1026. PubMed Id: 25103405. doi:10.1126/science.1258409. |
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Herguedas et al. (2016).
Herguedas B, García-Nafría J, Cais O, Fernández-Leiro R, Krieger J, Ho H, & Greger IH (2016). Structure and organization of heteromeric AMPA-type glutamate receptors.
Science 352 . PubMed Id: 26966189. doi:10.1126/science.aad3873. |
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GluA2 Glutamate receptor (AMPA-subtype) without bound stargazin (0-xSTZ) regulatory protein: Rattus norvegicus (GluA2) & Mus musculus (STZ) E Eukaryota (expressed in HEK293 cells), 8.7 Å
cryo-EM structures with 1 bound STZ (1xSTZ), 6.4 Å: 5KBT with 2 bound STZ (2xSTZ), 7.8 Å: 5KBU GluA2 with bound ZK200775, 6.8 Å: 5KBV |
Twomey et al. (2016).
Twomey EC, Yelshanskaya MV, Grassucci RA, Frank J, & Sobolevsky AI (2016). Elucidation of AMPA receptor-stargazin complexes by cryo-electron microscopy.
Science 353 :83-86. PubMed Id: 27365450. doi:10.1126/science.aaf8411. |
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GluA2 Glutamate receptor (AMPA-subtype) saturated with TARPγ2 subunits: Rattus norvegicus E Eukaryota (expressed in HEK293 cells), 7.3 Å
cryo-EM structure TARPγ2 is stargazin |
Zhao et al. (2016).
Zhao Y, Chen S, Yoshioka C, Baconguis I, & Gouaux E (2016). Architecture of fully occupied GluA2 AMPA receptor-TARP complex elucidated by cryo-EM.
Nature 536 :108-111. PubMed Id: 27368053. doi:10.1038/nature18961. |
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GluN1a/GluN2B NMDA receptor: Rattus norvegicus E Eukaryota (expressed in S. frugiperda), 3.96 Å
NMDA = N-methyl-D-aspartate |
Karakas et al. (2014).
Karakas E, & Furukawa H (2014). Crystal structure of a heterotetrameric NMDA receptor ion channel.
Science 344 :992-997. PubMed Id: 24876489. doi:10.1126/science.1251915. |
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GluN1a/GluN2B NMDA receptor: Xenopus laevis E Eukaryota (expressed in HEK293S GnTI-), 3.59 Å
The protein is the K216C mutant. Structure at 3.77 Å: 4TLM |
Lee et al. (2014).
Lee CH, Lü W, Michel JC, Goehring A, Du J, Song X, & Gouaux E (2014). NMDA receptor structures reveal subunit arrangement and pore architecture.
Nature 511 :191-197. PubMed Id: 25008524. doi:10.1038/nature13548. |
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GluN1a/GluN2B NMDA receptor: Xenopus laevis E Eukaryota (expressed in HEK293S), 7.0 Å
Cryo-EM structures. 5IOU is glutamate/glycine-bound. glutamate/glycine/Ro25-6981-bound conformation, 7.5 Å: 5IOV DCKA/D-APV-bound conformation, state 2, 13.5 Å: 5IPQ DCKA/D-APV-bound conformation, state 3, 14.1 Å: 5IPR DCKA/D-APV-bound conformation, state 4, 13.5 Å: 5IPS DCKA/D-APV-bound conformation, state 5, 14.1 Å: 5IPT DCKA/D-APV-bound conformation, state 6, 15.4 Å: 5IPU DCKA/D-APV-bound conformation, state 1, 9.25 Å: 5IPV |
Zhu et al. (2016).
Zhu S, Stein RA, Yoshioka C, Lee CH, Goehring A, Mchaourab HS, & Gouaux E (2016). Mechanism of NMDA Receptor Inhibition and Activation.
Cell 165 :704-714. PubMed Id: 27062927. doi:10.1016/j.cell.2016.03.028. |
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GluN1/GluN2A/GluN1/GluN2B heterotrimeric NMDA receptor in complex with Gly, Glu, & MK-801: Xenopus laevis E Eukaryota (expressed in HEK293S cells), 4.5 Å
cryo-EM structure additionally in complex with Ro 25-6981, 4.5 Å: 5UP2 |
Lü et al. (2017).
Lü W, Du J, Goehring A, & Gouaux E (2017). Cryo-EM structures of the triheteromeric NMDA receptor and its allosteric modulation.
Science 355 6331. PubMed Id: 28232581. doi:10.1126/science.aal3729. |
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GluR1 Glutamate receptor ligand binding domain with bound Glu: Adineta vaga E Eukaryota (expressed in E. coli), 1.37 Å
The structure does not include transmembrane domain. with bound Asp, 1.66 Å: 4IO3 with bound Ser, 1.94 Å: 4IO4 with bound Ala, 1.72 Å: 4IO5 with bound Met, 1.60 Å: 4IO6 with bound Phe, 1.92 Å: 4IO7 |
Lomash et al. (2013).
Lomash S, Chittori S, Brown P, & Mayer ML (2013). Anions Mediate Ligand Binding in Adineta vaga Glutamate Receptor Ion Channels.
Structure 21 :414-425. PubMed Id: 23434404. doi:10.1016/j.str.2013.01.006. |
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GluK2 Glutamate receptor (Kainate-subtype) in desensitized state with bound 2S,4R-4-methylglutamate: Rattus norvegicus E Eukaryota (expressed in S. frugiperda), 7.6 Å
|
Meyerson et al. (2014).
Meyerson JR, Kumar J, Chittori S, Rao P, Pierson J, Bartesaghi A, Mayer ML, & Subramaniam S (2014). Structural mechanism of glutamate receptor activation and desensitization.
Nature 514 :328-334. PubMed Id: 25119039. doi:10.1038/nature13603. |
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|
GluK2EM Glutamate receptor (Kainate-subtype) with bound 2S,4R-4-methylglutamate: Rattus norvegicus E Eukaryota (expressed in S. frugiperda), 3.8 Å
cryo-EM structure GluK2EM with LY66195, 11.6 Å: 5KUH GluK2EM dimer assembly complex with with bound 2S,4R-4-methylglutamate, x-ray 1.27 Å: 5CMM GluK2EM dimer assembly complex with LY66195, x-ray 1.8 Å: 5CMK |
Meyerson et al. (2016).
Meyerson JR, Chittori S, Merk A, Rao P, Han TH, Serpe M, Mayer ML, & Subramaniam S (2016). Structural basis of kainate subtype glutamate receptor desensitization.
Nature 537 :567-571. PubMed Id: 27580033. doi:10.1038/nature19352. |
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|
M2 proton channel (AM2): Influenza A (synthesized) V Viruses, 2.05 Å
with amantadine inhibitor, 3.50 Å: 3C9J |
Stouffer et al. (2008).
Stouffer AL, Acharya R, Salom D, Levine AS, Di Costanzo L, Soto CS, Tereshko V, Nanda V, Stayrook S, & DeGrado WF. (2008). Structural basis for the function and inhibition of an influenza virus proton channel.
Nature 451 :596-599. PubMed Id: 18235504. |
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|
M2 proton channel (AM2): Influenza A V Viruses (expressed in E. coli), NMR structure
with rimantadine inhibitor |
Schnell & Chou. (2008).
Schnell JR & Chou JJ (2008). Structure and mechanism of the M2 proton channel of influenza A virus.
Nature 451 :591-595. PubMed Id: 18235503. |
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|
M2 proton channel (AM2) in a hydrated lipid bilayer: Influenza A V Viruses (expressed in E. coli), NMR structure
|
Sharma et al. (2010).
Sharma M, Yi M, Dong H, Qin H, Peterson E, Busath DD, Zhou HX, & Cross TA (2010). Insight into the mechanism of the influenza A proton channel from a structure in a lipid bilayer.
Science 330 :509-512. PubMed Id: 20966252. |
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|
M2 proton channel (AM2), S31N mutant in complex with M2WJ332: Influenza A V Viruses (expressed in E. coli), NMR Structure
|
Wang et al. (2013).
Wang J, Wu Y, Ma C, Fiorin G, Wang J, Pinto LH, Lamb RA, Klein ML, & DeGrado WF (2013). Structure and inhibition of the drug-resistant S31N mutant of the M2 ion channel of influenza A virus.
Proc Natl Acad Sci USA 110 :1315-1320. PubMed Id: 23302696. doi:10.1073/pnas.1216526110. |
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|
M2 proton channel (AM2): Influenza A V Viruses (expressed in Synthesized), 1.65 Å
|
Acharya et al. (2010).
Acharya R, Carnevale V, Fiorin G, Levine BG, Polishchuk AL, Balannik V, Samish I, Lamb RA, Pinto LH, DeGrado WF, & Klein ML (2010). Structure and mechanism of proton transport through the transmembrane tetrameric M2 protein bundle of the influenza A virus.
Proc Natl Acad Sci USA 107 :15075-15080. PubMed Id: 20689043. doi:10.1073/pnas.1007071107. |
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|
M2 proton channel (AM2) at low pH: Influenza A V Viruses (expressed in Synthesized), 1.10 Å
at high pH, 1.10 Å: 4QK7 |
Thomaston et al. (2015).
Thomaston JL, Alfonso-Prieto M, Woldeyes RA, Fraser JS, Klein ML, Fiorin G, & DeGrado WF (2015). High-resolution structures of the M2 channel from influenza A virus reveal dynamic pathways for proton stabilization and transduction.
Proc Natl Acad Sci USA 112 :14260-14265. PubMed Id: 26578770. doi:10.1073/pnas.1518493112. |
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|
M2 proton channel (BM2): Influenza B V Viruses (expressed in Escherichia coli), NMR Structure
Cytoplasmic domain, NMR Structure: 2KJ1 |
Wang et al. (2009).
Wang J, Pielak RM, McClintock MA, & Chou JJ (2009). Solution structure and functional analysis of the influenza B proton channel.
Nat Struct Mol Biol 16 :1267-1271. PubMed Id: 19898475. |
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|
M2A-M2B chimeric proton channel (AM2-BM2): Influenza A/Influenza B V Viruses (expressed in E. coli), NMR Structure
With rimantadine inhibitor, NMR structure: 2LJC |
Pielak et al. (2011).
Pielak RM, Oxenoid K, & Chou JJ (2011). Structural Investigation of Rimantadine Inhibition of the AM2-BM2 Chimera Channel of Influenza Viruses.
Structure 19 :1655-1663. PubMed Id: 22078564. doi:10.1016/j.str.2011.09.003. |
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|
p7 hexamer channel: Hepatitis C virus (isolate EUH1480) V Viruses (expressed in E. coli), NMR Structure
|
OuYang et al. (2013).
OuYang B, Xie S, Berardi MJ, Zhao X, Dev J, Yu W, Sun B, & Chou JJ (2013). Unusual architecture of the p7 channel from hepatitis C virus.
Nature 498 :521-525. PubMed Id: 23739335. doi:10.1038/nature12283. |
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ASIC1 Acid-Sensing Ion Channel (ΔASIC1; N- and C-term deletions): Gallus gallus E Eukaryota (expressed in S. frugiperda), 1.9 Å
Construct does not exhibit proton-dependent gating |
Jasti et al. (2007).
Jasti J, Furukawa H, Gonzales EB, & Gouaux E (2007). Structure of acid-sensing ion channel 1 at 1.9 Å resolution and low pH.
Nature 449 :316-323. PubMed Id: 17882215. |
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|
ASIC1 Acid-Sensing Ion Channel (ASIC1mfc; minimal functional channel): Gallus gallus E Eukaryota (expressed in S. frugiperda), 3.0 Å
Desensitized State |
Gonzales et al. (2009).
Gonzales EB, Kawate T, & Gouaux E (2009). Pore architecture and ion sites in acid-sensing ion channels and P2X receptors.
Nature 460 :599-604. PubMed Id: 19641589. |
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|
ASIC1 Acid-Sensing Ion Channel in complex with psalmotoxin 1 (PcTx1): Gallus gallus E Eukaryota (expressed in S. frugiperda), 2.99 Å
Apo protein, 2.60 Å: 3S3W |
Dawson et al. (2012).
Dawson RJ, Benz J, Stohler P, Tetaz T, Joseph C, Huber S, Schmid G, Hügin D, Pflimlin P, Trube G, Rudolph MG, Hennig M, & Ruf A (2012). Structure of the Acid-sensing ion channel 1 in complex with the gating modifier Psalmotoxin 1.
Nature Commun 3 :936. PubMed Id: 22760635. doi:10.1038/ncomms1917. |
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|
ASIC1 Acid-Sensing Ion Channel in complex with psalmotoxin 1 (PcTx1), pH 5.5: Gallus gallus E Eukaryota (expressed in S. frugiperda), 2.80 Å
13 AA removed from N-terminus, 63 AA removed from C-terminus (referred to as Δ13) at pH 7.25, 3.36 Å: 4FZ1 |
Baconguis & Gouaux (2012).
Baconguis I & Gouaux E (2012). Structural plasticity and dynamic selectivity of acid-sensing ion channel-spider toxin complexes.
Nature 489 :400-405. PubMed Id: 22842900. doi:10.1038/nature11375. |
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|
Baconguis et al. (2014).
Baconguis I, Bohlen CJ, Goehring A, Julius D, & Gouaux E (2014). X-Ray Structure of Acid-Sensing Ion Channel 1-Snake Toxin Complex Reveals Open State of a Na(+)-Selective Channel.
Cell 156 :717-729. PubMed Id: 24507937. doi:10.1016/j.cell.2014.01.011. |
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|
Hattori et al. (2007).
Hattori M, Tanaka Y, Fukai S, Ishitani R, & Nureki O (2007). Crystal structure of the MgtE Mg2+transporter.
Nature 448 :1072-1075. PubMed Id: 17700703. |
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|
MgtE Mg2+ Transporter: Thermus thermophilus B Bacteria (expressed in E. coli), 2.9 Å
|
Hattori et al. (2009).
Hattori M, Iwase N, Furuya N, Tanaka Y, Tsukazaki T, Ishitani R, Maguire ME, Ito K, Maturana A, & Nureki O (2009). Mg(2+)-dependent gating of bacterial MgtE channel underlies Mg(2+) homeostasis.
EMBO J 28 :3602-3612. PubMed Id: 19798051. |
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|
Takeda et al. (2014).
Takeda H, Hattori M, Nishizawa T, Yamashita K, Shah ST, Caffrey M, Maturana AD, Ishitani R, & Nureki O (2014). Structural basis for ion selectivity revealed by high-resolution crystal structure of Mg2+ channel MgtE.
Nat Commun 5 :5374. PubMed Id: 25367295. doi:10.1038/ncomms6374. |
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|
Chen et al. (2010).
Chen YH, Hu L, Punta M, Bruni R, Hillerich B, Kloss B, Rost B, Love J, Siegelbaum SA, & Hendrickson WA (2010). Homologue structure of the SLAC1 anion channel for closing stomata in leaves.
Nature 467 :1074-1080. PubMed Id: 20981093. |
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|
SLAC1 anion channel, TehA homolog (wild-type) at room temperature.: Haemophilus influenzae B Bacteria (expressed in E. coli), 2.30 Å
|
Axford et al. (2015).
Axford D, Foadi J, Hu NJ, Choudhury HG, Iwata S, Beis K, Evans G, & Alguel Y (2015). Structure determination of an integral membrane protein at room temperature from crystals in situ.
Acta Crystallogr D Biol Crystallogr 71 :1228-1237. PubMed Id: 26057664. doi:10.1107/S139900471500423X. |
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ATP-gated P2X4 ion channel (apo protein; ΔP2X4-B construct): Danio rerio (zebra fish) E Eukaryota (expressed in S. frugiperda), 3.1 Å
Closed state. ΔP2X4-A construct, 3.5 Å: 3I5D |
Kawate et al. (2009).
Kawate T, Michel JC, Birdsong WT, & Gouaux E (2009). Crystal structure of the ATP-gated P2X4ion channel in the closed state.
Nature 460 :592-598. PubMed Id: 19641588. |
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|
ATP-gated P2X4 ion channel with bound ATP in open-pore conformation: Danio rerio (zebra fish) E Eukaryota (expressed in S. frugiperda ), 2.80 Å
Structure without bound ATP, 2.90 Å: 4DW0 |
Hattori & Gouaux (2012).
Hattori M & Gouaux E (2012). Molecular mechanism of ATP binding and ion channel activation in P2X receptors.
Nature 485 :207-2112. PubMed Id: 22535247. doi:10.1038/nature11010. |
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|
ATP-gated P2X3 ion channel, closed apo state: Homo sapiens E Eukaryota (expressed in HEK293S), 2.98 Å
ATP-bound, open state, 2.77 Å: 5SVK ATP-bound, closed(desensitized) state, 2.9 Å: 5SVL bound to agonist 2-methylthio-ATP in the desensitized state, 3.09 Å: 5SVM agonist 2-methylthio-ATP bound in desensitized state, 3.3 Å: 5SVP bound to competitive antagonist TNP-ATP, 3.25 Å: 5SVQ bound to competitive antagonist A-317491, 3.13 Å: 5SVR Mn2+ divalent cation-binding site, 4.03 Å: 5SVS Cs+ at Na+ entry site, 3.79 Å: 5SVT |
Mansoor et al. (2016).
Mansoor SE, Lü W, Oosterheert W, Shekhar M, Tajkhorshid E, & Gouaux E (2016). X-ray structures define human P2X3 receptor gating cycle and antagonist action.
Nature 538 :66-71. PubMed Id: 27626375. doi:10.1038/nature19367. |
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|
Bestrophin-1 (BEST1) Ca2+-activated Cl- channel: Gallus gallus E Eukaryota (expressed in Pichia pastoris), 2.85 Å
|
Kane Dickson et al. (2014).
Kane Dickson V, Pedi L, & Long SB (2014). Structure and insights into the function of a Ca2+-activated Cl- channel.
Nature 516 7530:213-218. PubMed Id: 25337878. doi:10.1038/nature13913. |
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|
Bestrophin-1 (BEST1) Ca2+-activated Cl- channel I76A, F80A, F84A mutant: Gallus gallus E Eukaryota (expressed in Pichia pastoris), 3.1 Å
|
Vaisey et al. (2016).
Vaisey G, Miller AN, & Long SB (2016). Distinct regions that control ion selectivity and calcium-dependent activation in the bestrophin ion channel.
Proc Natl Acad Sci USA 113 :E7399–E7408. PubMed Id: 27821745. doi:10.1073/pnas.1614688113. |
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|
KpBest Bestrophin homolog of the BEST1 Ca2+-activated Cl- channel (ΔC7): Klebsiella pneumoniae B Bacteria (expressed in E. coli), 2.90 Å
This homolog is not Ca2+ activated and conducts cations rather than anions. ΔC11, 2.30 Å: 4WD8 |
Yang et al. (2014).
Yang T, Liu Q, Kloss B, Bruni R, Kalathur RC, Guo Y, Kloppmann E, Rost B, Colecraft HM, & Hendrickson WA (2014). Structure and selectivity in bestrophin ion channels.
Science 346 :355-359. PubMed Id: 25324390. doi:10.1126/science.1259723. |
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ExbB/ExbD complex associated with TonB complex, pH 7.0: Escherichia coli B Bacteria, 2.6 Å
ExbB/ExbD complex at pH 4.5, 3.5 Å: 5SV1 |
Celia et al. (2016).
Celia H, Noinaj N, Zakharov SD, Bordignon E, Botos I, Santamaria M, Barnard TJ, Cramer WA, Lloubes R, & Buchanan SK (2016). Structural insight into the role of the Ton complex in energy transduction.
Nature 538 :60-65. PubMed Id: 27654919. doi:10.1038/nature19757. |
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|
CLC-K chloride ion channel, class 1: Bos taurus E Eukaryota (expressed in S. frugiperda), 3.76 Å
cryo-EM structure class 2, 3.95 Å: 5TR1 |
Park et al. (2017).
Park E, Campbell EB, & MacKinnon R (2017). Structure of a CLC chloride ion channel by cryo-electron microscopy.
Nature 541 :500-505. PubMed Id: 28002411. doi:10.1038/nature20812. |
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Channels: Fluc Family
These are F--selective channels |
|||
|
Stockbridge et al. (2015).
Stockbridge RB, Kolmakova-Partensky L, Shane T, Koide A, Koide S, Miller C, & Newstead S (2015). Crystal structures of a double-barrelled fluoride ion channel.
Nature 525 7570:548-551. PubMed Id: 26344196. doi:10.1038/nature14981. |
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Fluc F- ion channel homolog in complex Ec2-S9 monobody F801 mutant: Escherichia coli B Bacteria, 2.48 Å
F831 mutant, 2.69 Å: 5KOM |
Last et al. (2016).
Last NB, Kolmakova-Partensky L, Shane T, & Miller C (2016). Mechanistic signs of double-barreled structure in a fluoride ion channel.
Elife 5 :e18767. PubMed Id: 27449280. doi:10.7554/eLife.18767. |
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Cys-Loop Receptor Family
Cation-selective and Anion-selective Ligand-gated Channels Cation-selective include nicotinic acetylcholine and serotonin 5-HT3 receptors. Anion-selective include γ-aminobutyric, glycine, and invertebrate glutamate-gated chloride channels (GluCl) |
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|
Nicotinic Acetylcholine Receptor Pore (closed state): Torpedo marmorata E Eukaryota, 4.0 Å
Electron Diffraction |
Miyazawa et al. (2003).
Miyazawa A, Fujiyoshi Y, & Unwin N (2003). Structure and gating mechanism of the acetylcholine receptor pore.
Nature 423 :949-955. PubMed Id: 12827192. |
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|
Nicotinic Acetylcholine Receptor, refined structure: Torpedo marmorata E Eukaryota, 4.0 Å
Electron Diffraction |
Unwin (2005).
Unwin N. (2005). Refined structure of the nicotinic acetylcholine receptor at 4 Å resolution.
J Mol Biol 346 :967-989. PubMed Id: 15701510. |
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Acetylcholine receptor analysed by time-resolved electron cryo-microscopy (closed class): Torpedo marmorata E Eukaryota, 6.2 Å
Open class, 6.5 Å: 4AQ9 |
Unwin & Fujiyoshi (2012).
Unwin N & Fujiyoshi Y (2012). Gating movement of acetylcholine receptor caught by plunge-freezing.
J Mol Biol 422 :617-634. PubMed Id: 22841691. doi:10.1016/j.jmb.2012.07.010. |
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|
Nicotinic Acetylcholine α4β2 Receptor: Homo sapiens E Eukaryota (expressed in HEK293S), 3.94 Å
|
Morales-Perez et al. (2016).
Morales-Perez CL, Noviello CM, & Hibbs RE (2016). X-ray structure of the human α4β2 nicotinic receptor.
Nature 538 :411-415. PubMed Id: 27698419. doi:10.1038/nature19785. |
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|
Prokaryotic pentameric ligand-gated ion channel (ELIC): Erwinia chrysanthemi B Bacteria (expressed in E. coli), 3.3 Å
First high-resolution x-ray structure of an AChR-like channel. |
Hilf & Dutzler (2008).
Hilf RJC & Dutzler R (2008). X-ray structure of a prokaryotic pentameric ligand-gated ion channel.
Nature 452 :375-379. PubMed Id: 18322461. |
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|
Prokaryotic pentameric ligand-gated ion channel (ELIC) in complex with acetylcholine: Erwinia chrysanthemi B Bacteria (expressed in E. coli), 2.91 Å
Apo protein, 3.09 Å: 3RQU |
Pan et al. (2012).
Pan J, Chen Q, Willenbring D, Yoshida K, Tillman T, Kashlan OB, Cohen A, Kong XP, Xu Y, & Tang P (2012). Structure of the pentameric ligand-gated ion channel ELIC cocrystallized with its competitive antagonist acetylcholine.
Nature Commun 3 :714. PubMed Id: 22395605. doi:10.1038/ncomms1703. |
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|
Prokaryotic pentameric ligand-gated ion channel (ELIC) in complex with bromoform: Erwinia chrysanthemi B Bacteria (expressed in E. coli), 3.65 Å
|
Spurny et al. (2013).
Spurny R, Billen B, Howard RJ, Brams M, Debaveye S, Price KL, Weston DA, Strelkov SV, Tytgat J, Bertrand S, Bertrand D, Lummis SC, & Ulens C (2013). Multi-Site Binding Of A General Anesthetic To The Prokaryotic Pentameric Ligand-Gated Ion Channel ELIC.
J Biol Chem 288 :8355-8364. PubMed Id: 23364792. doi:10.1074/jbc.M112.424507. |
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Prokaryotic pentameric ligand-gated ion channel (ELIC) in complex with Br-memantine: Dickeya chrysanthemi B Bacteria (expressed in E. coli), 3.20 Å
note: species formerly Erwinia chrysanthemi, now renamed as Dickeya dadantii, although the PDB designates it as Dickeya chrysanthemi. complexed with memantine, 3.90 Å: 4TWF apo form, 3.60 Å: 4TWH |
Ulens et al. (2014).
Ulens C, Spurny R, Thompson AJ, Alqazzaz M, Debaveye S, Han L, Price K, Villalgordo JM, Tresadern G, Lynch JW, & Lummis SC (2014). The Prokaryote Ligand-Gated Ion Channel ELIC Captured in a Pore Blocker-Bound Conformation by the Alzheimer's Disease Drug Memantine.
Structure 22 :1399-1407. PubMed Id: 25199693. doi:10.1016/j.str.2014.07.013. |
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Prokaryotic pentameric ligand-gated ion channel (GLIC): Gloeobacter violaceus B Bacteria (expressed in E. coli), 3.1 Å
Related to ELIC (above), this pentameric channel is apparently in an open state. E221A mutant, 3.50 Å: 3EI0 |
Hilf & Dutzler (2009).
Hilf RJC & Dutzler R (2009). Structure of a potentially open state of a proton-activated pentameric ligand-gated ion channel.
Nature 457 :115-118. PubMed Id: 18987630. |
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Prokaryotic pentameric ligand-gated ion channel (GLIC): Gloeobacter violaceus B Bacteria (expressed in E. coli), 2.9 Å
Related to ELIC (above), this pentameric channel is apparently in an open state. |
Bocquet et al. (2009).
Bocquet N, Nury H, Baaden M, Le Poupon C, Changeux JP, Delarue M, & Corringer PJ (2009). X-ray structure of a pentameric ligand-gated ion channel in an apparently open conformation.
Nature 457 :111-114. PubMed Id: 18987633. |
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|
Prokaryotic pentameric ligand-gated ion channel (GLIC), wildtype-TBSb complex: Gloeobacter violaceus B Bacteria (expressed in E. coli), 3.70 Å
Wildtype-TEAs complex, 3.50 Å: 2XQ5 E221D-TEAs complex, 3.20 Å: 2XQ9 Wildtype-TMAs complex, 3.60 Å: 2XQ4 Wildtype-bromo-lidocaine complex, 3.50 Å: 2XQ3 Wildtype-Cd2+ complex, 3.40 Å: 2XQ7 Wildtype-Zn2+ complex, 3.60 Å: 2XQ8 Wildtype-Cs+ complex, 3.70 Å: 2XQ6 |
Hilf et al. (2010).
Hilf RJ, Bertozzi C, Zimmermann I, Reiter A, Trauner D, & Dutzler R (2010). Structure of a potentially open state of a proton-activated pentameric ligand-gated ion channel.
Nat Struct Mol Biol 17 :1330-1336. PubMed Id: 21037567. |
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|
Prokaryotic pentameric ligand-gated ion channel (GLIC): Gloeobacter violaceus B Bacteria (expressed in E. coli), 2.40 Å
Channel is in the open state. Selenium-derived DDM, 3.30 Å: 4IL4 With sulfates, 3.00 Å: 4ILC A237F mutant + CsCl, 3.50 Å: 4ILA A237F mutant + NaBr, 2.83 Å: 4IL9 A237F mutant + RbCl, 3.15 Å: 4ILB |
Sauguet et al. (2013).
Sauguet L, Poitevin F, Murail S, Van Renterghem C, Moraga-Cid G, Malherbe L, Thompson AW, Koehl P, Corringer PJ, Baaden M, & Delarue M. (2013). Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels.
EMBO J 32 :728-741. PubMed Id: 23403925. doi:10.1038/emboj.2013.17. |
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|
Prokaryotic "pentameric" ligand-gated ion channel (GLIC) with hexameric quaternary structure: Gloeobacter violaceus B Bacteria (expressed in E. coli), 2.3 Å
|
Nury et al. (2010).
Nury H, Bocquet N, Le Poupon C, Raynal B, Haouz A, Corringer PJ, & Delarue M (2010). Crystal structure of the extracellular domain of a bacterial ligand-gated ion channel.
J Mol Biol 395 :1114-1127. PubMed Id: 19917292. |
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Prokaryotic pentameric ligand-gated ion channel (GLIC) in complex with propofol anesthetic: Gloeobacter violaceus B Bacteria (expressed in E. coli), 3.30 Å
In complex with desflurane, 3.20 Å: 3P4W |
Nury et al. (2011).
Nury H, Van Renterghem C, Weng Y, Tran A, Baaden M, Dufresne V, Changeux JP, Sonner JM, Delarue M, & Corringer PJ (2011). X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channe.
Nature 469 :428-431. PubMed Id: 21248852. |
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|
Prokaryotic pentameric ligand-gated ion channel (GLIC) in complex with ketamine anesthetic: Gloeobacter violaceus B Bacteria (expressed in E. coli), 2.99 Å
|
Pan et al. (2012).
Pan J, Chen Q, Willenbring D, Mowrey D, Kong XP, Cohen A, Divito CB, Xu Y, & Tang P (2012). Structure of the Pentameric Ligand-Gated Ion Channel GLIC Bound with Anesthetic Ketamine.
Structure 20 :1463-1469. PubMed Id: 22958642. doi:10.1016/j.str.2012.08.009. |
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|
Prokaryotic pentameric ligand-gated ion channel (GLIC), pH 4: Gloeobacter violaceus B Bacteria (expressed in D. melanogaster), 3.35 Å
Neutral pH, 4.35 Å: 4NPQ |
Sauguet et al. (2014).
Sauguet L, Shahsavar A, Poitevin F, Huon C, Menny A, Nemecz A, Haouz A, Changeux JP, Corringer PJ, & Delarue M (2014). Crystal structures of a pentameric ligand-gated ion channel provide a mechanism for activation.
Proc Natl Acad Sci USA 111 3:966-971. PubMed Id: 24367074. doi:10.1073/pnas.1314997111. |
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Prokaryotic pentameric ligand-gated ion channel (GLIC): Gloeobacter violaceus B Bacteria (expressed in E. coli), 3.00 Å
complex with bromoacetate, 3.40 Å: 4QH1 |
Fourati et al. (2015).
Fourati Z, Sauguet L, & Delarue M (2015). Genuine open form of the pentameric ligand-gated ion channel GLIC.
Acta Crystallogr D Biol Crystallogr 71 :454-460. PubMed Id: 25760595. doi:10.1107/S1399004714026698. |
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Prokaryotic pentameric ligand-gated ion channel (GLIC), Bromoform bound, K33C-L246C mutant: Gloeobacter violaceus B Bacteria (expressed in E. coli), 2.95 Å
K33C-N245C cross-linked mutant, bromoform bound, 3.15 Å: 5HCM |
Laurent et al. (2016).
Laurent B, Murail S, Shahsavar A, Sauguet L, Delarue M, & Baaden M (2016). Sites of Anesthetic Inhibitory Action on a Cationic Ligand-Gated Ion Channel.
Structure 24 :595-605. PubMed Id: 27021161. doi:10.1016/j.str.2016.02.014. |
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|
Fourati et al. (2017).
Fourati Z, Ruza RR, Laverty D, Drège E, Delarue-Cochin S, Joseph D, Koehl P, Smart T, & Delarue M (2017). Barbiturates Bind in the GLIC Ion Channel Pore and Cause Inhibition by Stabilizing a Closed State.
J Biol Chem 292 :1550-1558. PubMed Id: 27986812. doi:10.1074/jbc.M116.766964. |
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Prokaryotic pentameric ligand-gated ion channel (GLIC) in complex with DHA: Gloeobacter violaceus B Bacteria, 3.25 Å
DHA: docosahexaenoic acid |
Basak et al. (2017).
Basak S, Schmandt N, Gicheru Y, & Chakrapani S (2017). Crystal structure and dynamics of a lipid-induced potential desensitized-state of a pentameric ligand-gated channel.
Elife 6 :e23886. PubMed Id: 28262093. doi:10.7554/eLife.23886. |
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Human glycine receptor (hGlyR-α1) transmembrane domain monomer: Homo sapiens E Eukaryota (expressed in E. coli), NMR Structure
Pentameric open-channel structure (putative): 2M6I |
Mowrey et al. (2013).
Mowrey DD, Cui T, Jia Y, Ma D, Makhov AM, Zhang P, Tang P, & Xu Y (2013). Open-Channel Structures of the Human Glycine Receptor ?1 Full-Length Transmembrane Domain.
Structure 21 :1897-1904. PubMed Id: 23994010. doi:10.1016/j.str.2013.07.014. |
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Human glycine receptor (hGlyR-α3) in complex with strychnine: Homo sapiens E Eukaryota (expressed in S. frugiperda), 3.04 Å
|
Huang et al. (2015).
Huang X, Chen H, Michelsen K, Schneider S, & Shaffer PL (2015). Crystal structure of human glycine receptor-α3 bound to antagonist strychnine.
Nature 526 7572:277-280. PubMed Id: 26416729. doi:10.1038/nature14972. |
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Human glycine receptor (hGlyR-α3) N38Q mutant in complex with AM-3607: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.61 Å
wildtype w. bound AM-3607, 3.25 Å: 5TIO |
Huang et al. (2017).
Huang X, Shaffer PL, Ayube S, Bregman H, Chen H, Lehto SG, Luther JA, Matson DJ, McDonough SI, Michelsen K, Plant MH, Schneider S, Simard JR, Teffera Y, Yi S, Zhang M, DiMauro EF, & Gingras J (2017). Crystal structures of human glycine receptor α3 bound to a novel class of analgesic potentiators.
Nat Struct Mol Biol 24 :108-113. PubMed Id: 27991902. doi:10.1038/nsmb.3329. |
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Human glycine receptor (hGlyR-α3) in complex with Gly and ivermectin: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.85 Å
N38Q mutant with bound AM-3607, 3.1 Å: 5VDI |
Huang et al. (2017).
Huang X, Chen H, & Shaffer PL (2017). Crystal Structures of Human GlyRα3 Bound to Ivermectin.
Structure 25 :945-950.e2. PubMed Id: 28479061. doi:10.1016/j.str.2017.04.007. |
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Du et al. (2015).
Du J, Lü W, Wu S, Cheng Y, & Gouaux E (2015). Glycine receptor mechanism elucidated by electron cryo-microscopy.
Nature 526 7572:224-229. PubMed Id: 26344198. doi:10.1038/nature14853. |
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|
Hibbs & Gouaux (2011).
Hibbs RE & Gouaux E (2011). Principles of activation and permeation in an anion-selective Cys-loop receptor
Nature 474 :54-60. PubMed Id: 21572436. doi:10.1038/nature10139. |
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α7 neuronal ACh recptor TM domain: Homo sapiens E Eukaryota (expressed in E. coli), NMR Structure
|
Bondarenko et al. (2014).
Bondarenko V, Mowrey DD, Tillman TS, Seyoum E, Xu Y, & Tang P (2014). NMR structures of the human α7 nAChR transmembrane domain and associated anesthetic binding sites.
Biochim. Biophys. Acta 1838 :1389-1395. PubMed Id: 24384062. doi:10.1016/j.bbamem.2013.12.018. |
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GABAAR receptor (β3 homopentamer): Homo sapiens E Eukaryota (expressed in HEK293F cells), 2.97 Å
|
Miller et al. (2014).
Miller PS, & Aricescu AR (2014). Crystal structure of a human GABAA receptor.
Nature 512 :270-275. PubMed Id: 24909990. doi:10.1038/nature13293. |
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|
Serotonin 5-HT3 receptor: Mus musculus E Eukaryota (expressed in HEK293F cells), 3.50 Å
|
Hassaine et al. (2014).
Hassaine G, Deluz C, Grasso L, Wyss R, Tol MB, Hovius R, Graff A, Stahlberg H, Tomizaki T, Desmyter A, Moreau C, Li XD, Poitevin F, Vogel H, & Nury H (2014). X-ray structure of the mouse serotonin 5-HT3 receptor.
Nature 512 :276-281. PubMed Id: 25119048. doi:10.1038/nature13552. |
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Channels: Aquaporins and Glyceroporins
|
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AQP0 aquaporin water channel: Bos taurus (Bovine) lens E Eukaryota, 2.24 Å
|
Harries et al. (2004).
Harries WE, Akhavan D, Miercke LJ, Khademi S, & Stroud RM (2004). The channel architecture of aquaporin 0 at a 2.2 Å resolution.
Proc Natl Acad Sci U S A 101 :14045-14050. PubMed Id: 15377788. |
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AQP0 aquaporin water channel from sheep lens.: Ovis aries E Eukaryota, 3.0 Å
AQP0 reconstituted with dimyristoylphosphatidylcholine and organized as a membrane junction. Electron Diffraction. Resolution: 3 Å in membrane plane, 3.5 Å normal to membrane plane. |
Gonen et al. (2004).
Gonen T, Sliz P, Kistler J, Cheng Y, & Walz T (2004). Aquaporin-0 membrane junctions reveal the structure of a closed water pore.
Nature 429 :193-197. PubMed Id: 15141214. |
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AQP0 aquaporin sheep lens junction: Ovis aries E Eukaryota, 1.90 Å
Electron Diffraction Non-junctional form, 2.4 Å: 2B6P |
Gonen et al. (2005).
Gonen T, Cheng Y, Sliz P, Hiroaki Y, Fujiyoshi Y, Harrison SC, & Walz T (2005). Lipid-protein interactions in double-layered two-dimensional AQP0 crystals.
Nature 438 :633-638. PubMed Id: 16319884. |
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AQP0 aquaporin sheep lens junction: Ovis aries E Eukaryota, 2.5 Å
Electron Diffraction. AQP0 reconstituted with E. coli polar lipids and organized as a membrane junction |
Hite et al. (2010).
Hite RK, Li Z, & Walz T. (2010). Principles of membrane protein interactions with annular lipids deduced from aquaporin-0 2D crystals.
EMBO J 29 :1652-1658. PubMed Id: 20389283. |
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AQP1 red blood cell aquaporin water channel: Homo sapiens E Eukaryota, 3.8 Å
Electron Diffraction. Resolution shown is in-plane. |
Murata et al. (2000).
Murata K, Mitsuoka K, Hirai T, Walz T, Agre P, Heymann J B, Engel A, & Fujiyoshi Y (2000). Structural determinants of water permeation through aquaporin-1.
Nature 407 :599-605. PubMed Id: 11034202. |
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AQP1 red blood cell aquaporin water channel: Homo sapiens E Eukaryota, 3.7 Å
Electron Diffraction. Protein in vitreous ice. |
Ren et al. (2001).
Ren G, Reddy VS, Cheng A, Melnyk P, & Mitra AK (2001). Visualization of a water-selective pore by electron crystallography in vitreous ice.
Proc Natl Acad Sci USA 98 :1398-1403. PubMed Id: 11171962. |
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AQP1 red blood cell aquaporin water channel: Homo sapiens E Eukaryota (expressed in S. frugiperda), 3.28 Å
|
Ruiz Carrillo et al. (2014).
Ruiz Carrillo D, To Yiu Ying J, Darwis D, Soon CH, Cornvik T, Torres J, & Lescar J (2014). Crystallization and preliminary crystallographic analysis of human aquaporin 1 at a resolution of 3.28 Å.
Acta Crystallogr F Struct Biol Commun 70 :1657-1663. PubMed Id: 25484221. doi:10.1107/S2053230X14024558. |
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AQP1 aquaporin red blood cell water channel: Bos taurus E Eukaryota, 2.20 Å
X-ray Diffraction |
Sui et al. (2001).
Sui H, Han BG, Lee JK, Walian P, & Jap BK (2001). Structural basis of water-specific transport through the AQP1 water channel.
Nature 414 :872-8. PubMed Id: 11780053. |
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AQP2 Aquaporin from kidney: Homo sapiens E Eukaryota (expressed in Pichia pastoris), 2.75 Å
|
Frick et al. (2014).
Frick A, Eriksson UK, de Mattia F, Oberg F, Hedfalk K, Neutze R, de Grip WJ, Deen PM, & Törnroth-Horsefield S (2014). X-ray structure of human aquaporin 2 and its implications for nephrogenic diabetes insipidus and trafficking.
Proc Natl Acad Sci USA 111 :6305-6310. PubMed Id: 24733887. doi:10.1073/pnas.1321406111. |
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AQP4 aquaporin rat glial cell water channel: Rattus norvegicus E Eukaryota (expressed in S. frugiperda), 3.2 Å
Electron Diffraction. |
Hiroaki et al. (2005).
Hiroaki Y, Tani K, Kamegawa A, Gyobu N, Nishikawa K, Suzuki H, Walz T, Sasaki S, Mitsuoka K, Kimura K, Mizoguchi A, & Fujiyoshi Y (2005). Implications of the Aquaporin-4 Structure on Array Formation and Cell Adhesion.
J Mol Biol 355 :628-639. PubMed Id: 16325200. |
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AQP4 aquaporin rat glial cell water channel: Rattus norvegicus E Eukaryota (expressed in S. frugiperda), 2.80 Å
Electron Diffraction. S180D mutant. Structure reveals five lipids associated with AQP4. |
Tani et al. (2009).
Tani K, Mitsuma T, Hiroaki Y, Kamegawa A, Nishikawa K, Tanimura Y, & Fujiyoshi Y (2009). Mechanism of aquaporin-4's fast and highly selective water conduction and proton exclusion.
J Mol Biol 389 :694-706. PubMed Id: 19406128. |
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AQP4 aquaporin water channel: Homo sapiens E Eukaryota (expressed in Pichia pastoris), 1.8 Å
|
Ho et al. (2009).
Ho JD, Yeh R, Sandstrom A, Chorny I, Harries WE, Robbins RA, Miercke LJ, & Stroud RM (2009). Crystal structure of human aquaporin 4 at 1.8 A and its mechanism of conductance.
Proc Natl Acad Sci USA 106 :7437-74422. PubMed Id: 19383790. |
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AQP5 aquaporin water channel (HsAQP5): Homo sapiens E Eukaryota (expressed in Pichia pastoris), 2.0 Å
|
Horsefield et al. (2008).
Horsefield R, Nordén K, Fellert M, Backmark A, Törnroth-Horsefield S, Terwisscha van Scheltinga AC, Kvassman J, Kjellbom P, Johanson U, & Neutze R. (2008). High-resolution x-ray structure of human aquaporin 5.
Proc Natl Acad Sci USA 105 :13327-13332. PubMed Id: 18768791. |
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AqpM aquaporin water channel: Methanothermobacter marburgensis A Archaea (expressed in E. coli), 1.68 Å
Initial structure, 2.3 Å: 2EVU |
Lee et al. (2005).
Lee JK, Kozono D, Remis J, Kitagawa Y, Agre P, & Stroud RM (2005). Structural basis for conductance by the archaeal aquaporin AqpM at 1.68 Å.
Proc Natl Acad Sci USA 102 :18932-18937. PubMed Id: 16361443. |
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AqpZ aquaporin water channel: Escherichia coli B Bacteria, 2.5 Å
|
Savage et al. (2003).
Savage DF, Egea PF, Robles-Colmenares Y, Iii JD, & Stroud RM (2003). Architecture and Selectivity in Aquaporins: 2.5 Å X-Ray Structure of Aquaporin Z.
PLoS Biol 1 :334-340. PubMed Id: 14691544. |
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AqpZ aquaporin showing two conformations of Arg-189: Escherichia coli B Bacteria, 3.2 Å
|
Jiang et al. (2006).
Jiang J, Daniels BV, & Fu D (2006). Crystal structure of AqpZ tetramer reveals two distinct R189 conformations associated with water permeation through the narrowest constriction of the water-conducting channel.
J Biol Chem 281 :454-460. PubMed Id: 16239219. |
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Savage & Stroud (2007).
Savage DF & Stroud RM (2007). Structural basis of aquaporin inhibition by mercury.
J Mol Biol 368 :607-617. PubMed Id: 17376483. |
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Savage et al. (2010).
Savage DF, O'Connell JD 3rd, Miercke LJ, Finer-Moore J, & Stroud RM (2010). Structural context shapes the aquaporin selectivity filter.
Proc Natl Acad Sci USA 107 :17164-17169. PubMed Id: 20855585. |
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SoPIP2;1 plant aquaporin (closed conformation): Spinacia oleracea E Eukaryota (expressed in Pichia pastoris), 2.10 Å
Open conformation, 3.90 Å: 2B5F |
Törnroth-Horsefield et al. (2006).
Törnroth-Horsefield S, Wang Y, Hedfalk K, Johanson U, Karlsson M, Tajkhorshid E, Neutze R, & Kjellbom P (2006). Structural mechanism of plant aquaporin gating.
Nature 439 :688-694. PubMed Id: 16340961. |
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Nyblom et al. (2009).
Nyblom M, Frick A, Wang Y, Ekvall M, Hallgren K, Hedfalk K, Neutze R, Tajkhorshid E, & Törnroth-Horsefield S (2009). Structural and functional analysis of SoPIP2;1 mutants adds insight into plant aquaporin gating.
J Mol Biol 387 :653-668. PubMed Id: 19302796. doi:10.1016/j.jmb.2009.01.065. |
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GlpF glycerol facilitator channel: Escherichia coli B Bacteria, 2.2 Å
|
Fu et al. (2000).
Fu D, Libson A, Miercke LJW, Weitzman C, Nollert P, Krucinski J, & Stroud RM (2000). Structure of a glycerol-conducting channel and the basis for its selectivity.
Science 290 :481-486. PubMed Id: 11039922. |
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Tajkhorshid et al. (2002).
Tajkhorshid E, Nollert P, Jensen MØ, Miercke LJ, O'Connell J, Stroud RM, & Schulten K (2002). Control of the selectivity of the aquaporin water channel family by global orientational tuning.
Science 296 :525-530. PubMed Id: 11964478. |
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PfAQP aquaglyceroporin: Plasmodium falciparum E Eukaryota, 2.05 Å
Transports water and glycerol equally well. |
Newby et al. (2008).
Newby ZE, O'Connell J 3rd, Robles-Colmenares Y, Khademi S, Miercke LJ, & Stroud RM (2008). Crystal structure of the aquaglyceroporin PfAQP from the malarial parasite Plasmodium falciparum.
Nature Struc Mol Biol 15 :619-625. PubMed Id: 18500352. |
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Fischer et al. (2009).
Fischer G, Kosinska-Eriksson U, Aponte-Santamaría C, Palmgren M, Geijer C, Hedfalk K, Hohmann S, de Groot BL, Neutze R, & Lindkvist-Petersson K. (2009). Crystal structure of a yeast aquaporin at 1.15 Å reveals a novel gating mechanism.
PLoS Bio 7 6:e1000130. PubMed Id: 19529756. doi:10.1371/journal.pbio.1000130. |
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Aqy1 yeast aquaporin (pH 8.0): Pischia pastoris E Eukaryota, 0.88 Å
|
Kosinska Eriksson et al. (2013).
Kosinska Eriksson U, Fischer G, Friemann R, Enkavi G, Tajkhorshid E, & Neutze R (2013). Subangstrom resolution X-ray structure details aquaporin-water interactions.
Science 340 :1346-1349. PubMed Id: 23766328. doi:10.1126/science.1234306. |
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TIP2;1 ammonia-permeable aquaporin: Arabidopsis thaliana E Eukaryota (expressed in Komagataella pastoris), 1.18 Å
|
Kirscht et al. (2016).
Kirscht A, Kaptan SS, Bienert GP, Chaumont F, Nissen P, de Groot BL, Kjellbom P, Gourdon P, & Johanson U (2016). Crystal Structure of an Ammonia-Permeable Aquaporin.
PLoS Biol 14 3. PubMed Id: 27028365. doi:10.1371/journal.pbio.1002411. |
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Channels : Formate/Nitrite Transporter (FNT) Family
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FocA, pentameric aquaporin-like formate transporter: Escherichia coli B Bacteria, 2.20 Å
3KCU structure is for P212121 space group. P32 space group: 3KCV, 3.2 Å |
Wang et al. (2009).
Wang Y, Huang Y, Wang J, Cheng C, Huang W, Lu P, Xu YN, Wang P, Yan N, & Shi Y (2009). Structure of the formate transporter FocA reveals a pentameric aquaporin-like channel.
Nature 462 :467-472. PubMed Id: 19940917. |
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FocA formate transporter without formate: Vibrio cholerae B Bacteria (expressed in E. coli), 2.10 Å
FocA with bound formate: 3KLZ, 2.50 Å |
Waight et al. (2010).
Waight AB, Love J, & Wang DN (2010). Structure and mechanism of a pentameric formate channel.
Nat Struct Mol Biol 17 :31-37. PubMed Id: 20010838. |
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FocA formate transporter at pH 4.0: Salmonella typhimurium B Bacteria, 2.80 Å
Three different conformations are observed in the asymmetric unit: Open, Intermediate, & closed |
Lü et al. (2011).
Lü W, Du J, Wacker T, Gerbig-Smentek E, Andrade SL, & Einsle O (2011). pH-dependent gating in a FocA formate channel
Science 332 :352-354. PubMed Id: 21493860. doi:10.1126/science.1199098. |
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Czyzewski & Wang (2012).
Czyzewski BK & Wang DN (2012). Identification and characterization of a bacterial hydrosulphide ion channel.
Nature 483 :494-497. PubMed Id: 22407320. doi:10.1038/nature10881. |
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Channels: Urea Transporters
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Urea transporter: Desulfovibrio vulgaris B Bacteria (expressed in E. coli), 2.30 Å
Structure with bound dimethyl urea: 3K3G, 2.40 Å |
Levin et al. (2009).
Levin EJ, Quick M, & Zhou MG (2009). Crystal structure of a bacterial homologue of the kidney urea transporter.
Nature 462 :757-761. PubMed Id: 19865084. |
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UT-B Urea Transporter: Bos taurus E Eukaryota (expressed in S. frugiperda), 2.36 Å
First structure of a mammalian urea transporter. Bound to Selenourea, 2.50 Å: 4EZD |
Levin et al. (2012).
Levin EJ, Cao Y, Enkavi G, Quick M, Pan Y, Tajkhorshid E, & Zhou M (2012). Structure and permeation mechanism of a mammalian urea transporter.
Proc Natl Acad Sci USA 109 :11194-11199. PubMed Id: 22733730. doi:10.1073/pnas.1207362109. |
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UreI proton-gated inner membrane urea channel: Helicobacter pylori B Bacteria (expressed in E. coli), 3.26 Å
Formed from six protomers with a two-helix hairpin motif. |
Strugatsky et al. (2013).
Strugatsky D, McNulty R, Munson K, Chen CK, Soltis SM, Sachs G, & Luecke H (2013). Structure of the proton-gated urea channel from the gastric pathogen Helicobacter pylori.
Nature 493 :255-258. PubMed Id: 23222544. doi:10.1038/nature11684. |
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Channels: Gap Junctions
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Connexin 26 (Cx26; GJB2) gap junction: Homo sapiens E Eukaryota (expressed in Sf9 cells), 3.5 Å
|
Maeda et al. (2009).
Maeda S, Nakagawa S, Suga M, Yamashita E, Oshima A, Fujiyoshi Y, & Tsukihara T (2009). Structure of the connexin 26 gap junction channel at 3.5 Å resolution.
Nature 458 :597-602. PubMed Id: 19340074. |
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Innexin-6 gap junction channel: Caenorhabditis elegans E Eukaryota (expressed in Spodoptera frugiperda), 3.6 Å
cryo-EM structure hemichannel, 3.3 Å: 5H1Q |
Oshima et al. (2016).
Oshima A, Tani K, & Fujiyoshi Y (2016). Atomic structure of the innexin-6 gap junction channel determined by cryo-EM.
Nat Commun 7 :13681. PubMed Id: 27905396. doi:10.1038/ncomms13681. |
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Channels: Intercellular
Channels found in sporulating bacteria that connect mother cell to forespore |
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SpoIIQ-SpoIIIAH Complex: Bacillus subtilis B Bacteria (expressed in E. coli), 2.26 Å
This is the protomer structure. Modeling studies suggest that the pore is formed from 12 protomers to form a channel with a diameter of 60 Å. |
Levdikov et al. (2012).
Levdikov VM, Blagova EV, McFeat A, Fogg MJ, Wilson KS, & Wilkinson AJ (2012). Structure of components of an intercellular channel complex in sporulating Bacillus subtilis.
Proc Natl Acad Sci USA 109 :5441-5445. PubMed Id: 22431604. doi:10.1073/pnas.1120087109. |
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SpoIIQ-SpoIIIAH Complex: Bacillus subtilis B Bacteria (expressed in E. coli), 2.82 Å
The structure is of the protomer. Modeling studies suggest that the pore is formed from 15 or 18 protomers to form a channel with a diameter of 82 or 116 Å. |
Meisner et al. (2012).
Meisner J, Maehigashi T, André I, Dunham CM, & Moran CP Jr (2012). Structure of the basal components of a bacterial transporter.
Proc Natl Acad Sci USA 109 :5446-5451. PubMed Id: 22431613. doi:10.1073/pnas.1120113109. |
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Channels: Amt/Mep/Rh proteins
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Khademi et al. (2004).
Khademi S, O'Connell J 3rd, Remis J, Robles-Colmenares Y, Miercke LJ, & Stroud RM (2004). Mechanism of ammonia transport by Amt/MEP/Rh: structure of AmtB at 1.35 Å.
Science 305 :1587-1594. PubMed Id: 15361618. |
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AmtB ammonia channel (wild-type): Escherichia coli B Bacteria, 1.8 Å (P63 crystal form)
R3 crystal form: 1XQE, 2.1 Å resolution |
Zheng et al. (2004).
Zheng L, Kostrewa D, Berneche S, Winkler FK, & Li XD (2004). The mechanism of ammonia transport based on the crystal structure of AmtB of Escherichia coli.
Proc Natl Acad Sci U S A 101 :17090-17095. PubMed Id: 15563598. |
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AmtB ammonia channel (wild-type): Escherichia coli B Bacteria, 2.1 Å
Wild-type in the presence of ammonium with imidazole: 2NOP, 2.0 Å H168E mutant in the presence of ammonium: 2NOW, 2.2 Å H168A mutant in the presence of ammonium with imidazole: 2NPC, 2.1 Å H168F mutant in the presence of ammonium with imidazole: 2NPD, 2.1 Å H318A mutant in the absence of ammonium: 2NPE, 2.1 Å H318F mutant in the presence of ammonium: 2NPG, 2.0 Å H318F mutant in the presence of ammonium with imidazole: 2NPJ, 2.0 Å H168A/H318A mutant in the presence of ammonium with imidazole: 2NPK, 2.0 Å |
Javelle et al. (2006).
Javelle A, Lupo D, Zheng L, Li XD, Winkler FK, & Merrick M (2006). An unusual twin-his arrangement in the pore of ammonia channels is essential for substrate conductance.
J Biol Chem 281 :39492-39498. PubMed Id: 17040913. |
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AmtB ammonia channel in complex with GlnK: Escherichia coli B Bacteria, 2.5 Å
|
Conroy et al. (2007).
Conroy MJ, Durand A, Lupo D, Li X-D, Bullough PA, Winkler FK, & Merrick M (2007). The crystal structure of the Escherichia coli AmtB-GlnK complex reveals how GlnK regulates the ammonia channel.
Proc Natl Acad Sci USA 104 :1213-1218. PubMed Id: 17220269. |
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AmtB ammonia channel in complex with inhibitory GlnK: Escherichia coli B Bacteria, 1.96 Å
|
Gruswitz et al. (2007).
Gruswitz F, O'Connell III J, & Stroud RM (2007). Inhibitory complex of the transmembrane ammonia channel, AmtB, and the cytosolic regulatory protein, GlnK, at 1.96 Å.
Proc Natl Acad Sci USA 104 :42-47. PubMed Id: 17190799. |
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AmtB ammonia channel in complex with phosphatidylglycerol: Escherichia coli B Bacteria, 2.30 Å
Structure reveals distinct conformational changes that re-position AmtB residues to interact with the lipid bilayer. |
Laganowsky et al. (2014).
Laganowsky A, Reading E, Allison TM, Ulmschneider MB, Degiacomi MT, Baldwin AJ, & Robinson CV (2014). Membrane proteins bind lipids selectively to modulate their structure and function.
Nature 510 :172-175. PubMed Id: 24899312. doi:10.1038/nature13419. |
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Andrade et al. (2005).
Andrade SL, Dickmanns A, Ficner R, & Einsle O (2005). Crystal structure of the archaeal ammonium transporter Amt-1 from Archaeoglobus fulgidus.
Proc Natl Acad Sci U S A 102 :14994-14999. PubMed Id: 16214888. |
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Rh protein, possible ammonia or CO2 channel: Nitrosomonas europaea B Bacteria (expressed in Methylococcus capsulatus), 1.85 Å
CO2 pressurized protein, 1.85 Å: 3B9Z |
Li et al. (2007).
Li X, Jayachandran S, Nguyen HH, & Chan MK (2007). Structure of the Nitrosomonas europaea Rh protein.
Proc Natl Acad Sci U S A 104 :19279-19284. PubMed Id: 18040042. |
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Rh protein, possible ammonia or CO2 channel: Nitrosomonas europaea B Bacteria (expressed in E. coli), 1.30 Å
|
Lupo et al. (2007).
Lupo D, Li XD, Durand A, Tomizaki T, Cherif-Zahar B, Matassi G, Merrick M, & Winkler FK (2007). The 1.3-Å resolution structure of Nitrosomonas europaea Rh50 and mechanistic implications for NH3transport by Rhesus family proteins.
Proc Natl Acad Sci U S A 104 :19303-19308. PubMed Id: 18032606. |
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Human Rh C glycoprotein ammonia transporter: Homo sapiens E Eukaryota (expressed in HEK293s cells), 2.10 Å
|
Gruswitz et al. (2010).
Gruswitz F, Chaudhary S, Ho JD, Schlessinger A, Pezeshki B, Ho CM, Sali A, Westhoff CM, & Stroud RM (2010). Function of human Rh based on structure of RhCG at 2.1 Å.
Proc Natl Acad Sci USA 107 :9638-9643. PubMed Id: 20457942. |
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Mep2 ammonium transceptor: Saccharomyces cerevisiae E Eukaryota, 3.2 Å
|
van den Berg et al. (2016).
van den Berg B, Chembath A, Jefferies D, Basle A, Khalid S, & Rutherford JC (2016). Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
Nat Commun 7 :11337. PubMed Id: 27088325. doi:10.1038/ncomms11337. |
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van den Berg et al. (2016).
van den Berg B, Chembath A, Jefferies D, Basle A, Khalid S, & Rutherford JC (2016). Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
Nat Commun 7 :11337. PubMed Id: 27088325. doi:10.1038/ncomms11337. |
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G Protein-Coupled Receptors (GPCRs)
GPCRdb Home Page GPCR Network Home Page |
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Rhodopsin: Bos taurus (Bovine) Rod Outer Segment E Eukaryota, 2.80 Å
See also 1HZX and RPE65 retinoid isomerase |
Palczewski et al. (2000).
Palczewski K, Kumasaka T, Hori T, Behnke CA, Motoshima H, Fox BA, Le Trong I, Teller DC, Okada T, Stenkamp RE, Yamamoto M, & Miyano M (2000). Crystal structure of rhodopsin: A G protein-coupled receptor.
Science 289 :739-745. PubMed Id: 10926528. |
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Rhodopsin: Bos taurus (Bovine) Rod Outer Segment E Eukaryota, 2.6 Å
|
Okada et al. (2002).
Okada T, Fujiyoshi Y, Silow M, Navarro J, Landau EM, & Shichida Y (2002). Functional role of internal water molecules in rhodopsin revealed by X-ray crystallography.
Proc Natl Acad Sci U S A 99 :5982-5987. PubMed Id: 11972040. |
||
|
Rhodopsin: Bos taurus (Bovine) Rod Outer Segment E Eukaryota, 2.65 Å
|
Li et al. (2004).
Li J, Edwards PC, Burghammer M, Villa C, & Schertler GF (2004). Structure of bovine rhodopsin in a trigonal crystal form.
J Mol Biol. 343 :511-521. PubMed Id: 15491621. |
||
|
Rhodopsin: Bos taurus E Eukaryota, 2.65 Å
Alternative model for 1GZM. Described using spacegroup P64 |
Stenkamp (2008).
Stenkamp RE (2008). Alternative models for two crystal structures of bovine rhodopsin.
Acta Crystallogr D Biol Crystallogr D64 :902-904. PubMed Id: 18645239. doi:10.1107/S0907444908017162. |
||
|
Rhodopsin: Bos taurus (Bovine) Rod Outer Segment E Eukaryota, 2.2 Å
|
Okada et al. (2004).
Okada T, Sugihara M, Bondar AN, Elstner M, Entel P, & Buss V (2004). The retinal conformation and its environment in rhodopsin in light of a new 2.2 Å crystal structure.
J Mol Biol 342 :571-583. PubMed Id: 15327956. |
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|
Rhodopsin: Bos taurus (Bovine) Rod Outer Segment E Eukaryota (expressed in COS cells), 3.4 Å
Recombinant rhodopsin mutant, N2C/D282C |
Standfuss et al. (2007).
Standfuss J, Xie G, Edwards PC, Burghammer M, Oprian DD, & Schertler GF (2007). Crystal structure of a thermally stable rhodopsin mutant.
J Mol Biol 372 :1179-1188. PubMed Id: 17825322. |
||
|
Rhodopsin: Bos taurus E Eukaryota, 3.40 Å
Recombinant rhodopsin mutant, N2C/D282C. Refinement of 2J4Y using P64 subgroup. |
Stenkamp (2008).
Stenkamp RE (2008). Alternative models for two crystal structures of bovine rhodopsin.
Acta Crystallogr D Biol Crystallogr D64 :902-904. PubMed Id: 18645239. doi:10.1107/S0907444908017162. |
||
|
Salom et al. (2006).
Salom D, Ladowski DT, Stenkamp RE, Trong IL, Golczak M, Jastrzebska B, Harris T, Ballesteros JA & Palczewski K (2006). Crystal structure of a photoactivated deprotonated intermediate of rhodopsin.
Proc Natl Acad Sci USA 103 :16123-16128. PubMed Id: 17060607. |
|||
|
Rhodopsin in ligand-free state (opsin): Bos taurus (Bovine) Rod Outer Segment E Eukaryota, 2.9 Å
2 molecules in asymmetric unit. |
Park et al. (2008).
Park JH, Scheerer P, Hofmann KP, Choe HW, & Ernst OP (2008). Crystal structure of the ligand-free G-protein-coupled receptor opsin.
Nature 454 :183-187. PubMed Id: 18563085. |
||
|
Rhodopsin in ligand-free state (opsin): Bos taurus E Eukaryota, 2.65 Å
with bound GαCT2 peptide |
Park et al. (2013).
Park JH, Morizumi T, Li Y, Hong JE, Pai EF, Hofmann KP, Choe HW, & Ernst OP (2013). Opsin, a structural model for olfactory receptors?
Angew Chem Int Ed Engl 52 :11021-11024. PubMed Id: 24038729. doi:10.1002/anie.201302374. |
||
|
Rhodopsin in ligand-free state (opsin): Bos taurus E Eukaryota, 2.29 Å
with bound GαCT2 peptide. |
Blankenship et al. (2015).
Blankenship E, Vahedi-Faridi A, & Lodowski DT (2015). The High-Resolution Structure of Activated Opsin Reveals a Conserved Solvent Network in the Transmembrane Region Essential for Activation.
Structure 23 :2358-2364. PubMed Id: 26526852. doi:10.1016/j.str.2015.09.015. |
||
|
Rhodopsin in ligand-free state (opsin) in complex with ArrFL-1: Bos taurus E Eukaryota, 2.75 Å
|
Szczepek et al. (2014).
Szczepek M, Beyrière F, Hofmann KP, Elgeti M, Kazmin R, Rose A, Bartl FJ, von Stetten D, Heck M, Sommer ME, Hildebrand PW, & Scheerer P (2014). Crystal structure of a common GPCR-binding interface for G protein and arrestin.
Nat Comms 5 :4801. PubMed Id: 25205354. doi:10.1038/ncomms5801. |
||
|
Rhodopsin, Ops*-GαCT peptide complex: Bos taurus (Bovine) Rod Outer Segment E Eukaryota, 3.2 Å
|
Scheerer et al. (2008).
Scheerer P, Park JH, Hildebrand PW, Kim YJ, Krauss N, Choe HW, Hofmann KP, & Ernst OP (2008). Crystal structure of opsin in its G-protein-interacting conformation.
Nature 455 :497-502. PubMed Id: 18818650. |
||
|
Rhodopsin in Meta II state: Bos taurus (Bovine) Rod Outer Segment E Eukaryota, 3.00 Å
Metarhodopsin II in complex with C-terminal fragment of Gα (GαCT2), 2.85 Å: 3PQR |
Choe et al. (2011).
Choe HW, Kim YJ, Park JH, Morizumi T, Pai EF, Krauß N, Hofmann KP, Scheerer P, & Ernst OP (2011). Crystal structure of metarhodopsin II.
Nature 471 :651-655. PubMed Id: 21389988. |
||
|
Rhodopsin in constitutively active meta-II state: Bos taurus E Eukaryota (expressed in HEK2935-GnTl- cells), 3.30 Å
M257Y mutant in complex with GαCT. |
Deupi et al. (2012).
Deupi X, Edwards P, Singhal A, Nickle B, Oprian D, Schertler G, & Standfuss J (2012). Stabilized G protein binding site in the structure of constitutively active metarhodopsin-II.
Proc Natl Acad Sci USA 109 :119-124. PubMed Id: 22198838. doi:10.1073/pnas.1114089108. |
||
|
Rhodopsin in agonist-induced active state: Bos taurus E Eukaryota, 3.00 Å
|
Standfuss et al. (2011).
Standfuss J, Edwards PC, D'Antona A, Fransen M, Xie G, Oprian DD, & Schertler GF (2011). The structural basis of agonist-induced activation in constitutively active rhodopsin
Nature 471 7340:656-660. PubMed Id: 21389983. doi:10.1038/nature09795. |
||
|
Rhodopsin, Squid: Todarodes pacificus E Eukaryota, 2.50 Å
|
Murakami & Kouyama (2008).
Murakami M & Kouyama T (2008). Crystal structure of squid rhodopsin.
Nature 453 :363-367. PubMed Id: 18480818. |
||
|
Rhodopsin, Squid: Todarodes pacificus E Eukaryota, 3.7 Å
Shows intracellularly extended cytoplasmic region. |
Shimamura et al. (2008).
Shimamura T, Hiraki K, Takahashi N, Hori T, Ago H, Masuda K, Takio K, Ishiguro M, & Miyano M. (2008). Crystal structure of squid rhodopsin with intracellularly extended cytoplasmic region.
J Biol Chem 283 :17753-17756. PubMed Id: 18463093. |
||
|
Rhodopsin, Squid; 9-cis isorhodopsin (Iso): Todarodes pacificus E Eukaryota, 2.70 Å
Batho intermediate state, 2.80 Å: 3AYM |
Murakami & Kouyama (2011).
Murakami M & Kouyama T (2011). Crystallographic analysis of the primary photochemical reaction of squid rhodopsin.
J Mol Biol 413 :615-627. PubMed Id: 21906602. doi:10.1016/j.jmb.2011.08.044. |
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|
Human rhodopsin with bound mouse visual arrestin: Homo sapiens E Eukaryota (expressed in HEK293S cells), 3.30 Å
Engineered protein. T4 lysozyme (Cys-free) fused to N-terminus of rhodopsin and arrestin fused to C-terminus with a 15-residue linker. Structure determined by fS x-ray laser. |
Kang et al. (2015).
Kang Y, Zhou XE, Gao X, He Y, Liu W, Ishchenko A, Barty A, White TA, Yefanov O, Han GW, Xu Q, de Waal PW, Ke J, Tan MH, Zhang C, Moeller A, West GM, Pascal BD, Van Eps N, Caro LN, Vishnivetskiy SA, Lee RJ, Suino-Powell KM, Gu X, Pal K, Ma J, Zhi X, Boutet S, Williams GJ, Messerschmidt M, Gati C, Zatsepin NA, Wang D, James D, Basu S, Roy-Chowdhury S, Conrad CE, Coe J, Liu H, Lisova S, Kupitz C, Grotjohann I, Fromme R, Jiang Y, Tan M, Yang H, Li J, Wang M, Zheng Z, Li D, Howe N, Zhao Y, Standfuss J, Diederichs K, Dong Y, Potter CS, Carragher B, Caffrey M, Jiang H, Chapman HN, Spence JC, Fromme P, Weierstall U, Ernst OP, Katritch V, Gurevich VV, Griffin PR, Hubbell WL, Stevens RC, Cherezov V, Melcher K, & Xu HE (2015). Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser.
Nature 523 :561-567. PubMed Id: 26200343. doi:10.1038/nature14656. |
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|
OX1 orexin receptor with bound suvorexant: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.75 Å
with bound SB-674042, 2.83 Å: 4ZJC |
Yin et al. (2016).
Yin J, Babaoglu K, Brautigam CA, Clark L, Shao Z, Scheuermann TH, Harrell CM, Gotter AL, Roecker AJ, Winrow CJ, Renger JJ, Coleman PJ, & Rosenbaum DM (2016). Structure and ligand-binding mechanism of the human OX1 and OX2 orexin receptors.
Nat Struct Mol Biol 23 :293-299. PubMed Id: 26950369. doi:10.1038/nsmb.3183. |
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|
OX2 orexin receptor with bound suvorexant: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.50 Å
4S0V supersedes 4RNB. Engineered protein: Pyrococcus abysii glycogen synthase replaced 39 residues of the 3rd intracellular loop. |
Yin et al. (2015).
Yin J, Mobarec JC, Kolb P, & Rosenbaum DM (2015). Crystal structure of the human OX2 orexin receptor bound to the insomnia drug suvorexant.
Nature 519 7542:247-250. PubMed Id: 25533960. doi:10.1038/nature14035. |
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|
β1 adrenergic receptor (engineered): Meleagris gallopavo (turkey) E Eukaryota (expressed in Trichoplusia ni), 2.7 Å
|
Warne et al. (2008).
Warne T, Serrano-Vega MJ, Baker JG, Moukhametzianov R, Edwards PC, Henderson R, Leslie AG, Tate CG, & Schertler GF (2008). Structure of a β1-adrenergic G-protein-coupled receptor.
Nature 454 :486-491. PubMed Id: 18594507. |
||
|
Warne et al. (2011).
Warne T, Moukhametzianov R, Baker JG, Nehmé R, Edwards PC, Leslie AG, Schertler GF, & Tate CG (2011). The structural basis for agonist and partial agonist action on a β1-adrenergic G-protein-coupled receptor.
Nature 469 :241-244. PubMed Id: 21228877. |
|||
|
Moukhametzianov et al. (2011).
Moukhametzianov R, Warne T, Edwards PC, Serrano-Vega MJ, Leslie AG, Tate CG, & Schertler GF (2011). Two distinct conformations of helix 6 observed in antagonist-bound structures of a β1-adrenergic receptor
Proc Natl Acad Sci USA 108 :8228-8232. PubMed Id: 21540331. doi:10.1073/pnas.1100185108. |
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|
β1 adrenergic receptor (engineered) with bound carvedilol: Meleagris gallopavo (turkey) E Eukaryota (expressed in Trichoplusia ni), 2.30 Å
With bound bucindolol, 3.20 Å:4AMI |
Warne et al. (2012).
Warne T, Edwards PC, Leslie AG, & Tate CG (2012). Crystal Structures of a Stabilized ?1-Adrenoceptor Bound to the Biased Agonists Bucindolol and Carvedilol.
Structure 20 :841-849. PubMed Id: 22579251. doi:10.1016/j.str.2012.03.014. |
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|
β1 adrenergic receptor oligomer, basal state: Meleagris gallopavo E Eukaryota (expressed in Trichoplusia ni), 3.50 Å
|
Huang et al. (2013).
Huang J, Chen S, Zhang JJ, & Huang XY (2013). Crystal structure of oligomeric β1-adrenergic G protein-coupled receptors in ligand-free basal state.
Nature Struc Mol Biol 20 :419-425. PubMed Id: 23435379. doi:10.1038/nsmb.2504. |
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|
β2 adrenergic receptor: Homo sapiens E Eukaryota (expressed in S. frugiperda), 3.4/3.7 Å
from β2AR365-Fab5 complex. From β2AR24/365-Fab5 complex: 2R4S |
Rasmussen et al. (2007).
Rasmussen SG, Choi HJ, Rosenbaum DM, Kobilka TS, Thian FS, Edwards PC, Burghammer M, Ratnala VR, Sanishvili R, Fischetti RF, Schertler GF, Weis WI, & Kobilka BK (2007). Crystal structure of the human β2adrenergic G-protein-coupled receptor.
Nature 450 :383-387. PubMed Id: 17952055. |
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|
Methylated β2 adrenergic receptor: Homo sapiens E Eukaryota (expressed in S. frugiperda), 3.4 Å
from β2AR365-Fab5 complex. |
Bokoch et al. (2010).
Bokoch MP, Zou Y, Rasmussen SG, Liu CW, Nygaard R, Rosenbaum DM, Fung JJ, Choi HJ, Thian FS, Kobilka TS, Puglisi JD, Weis WI, Pardo L, Prosser RS, Mueller L, & Kobilka BK (2010). Ligand-specific regulation of the extracellular surface of a G-protein-coupled receptor.
Nature 463 :108-112. PubMed Id: 20054398. |
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|
β2 adrenergic receptor (engineered): Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.4 Å
T4 lysozyme replaces third intracellular loop. Reveals close association with cholesterol. |
Cherezov et al. (2007).
Cherezov V, Rosenbaum DM, Hanson MA, Rasmussen SG, Thian FS, Kobilka TS, Choi HJ, Kuhn P, Weis WI, Kobilka BK, & Stevens RC (2007). High-resolution crystal structure of an engineered human β2-adrenergic G protein-coupled receptor.
Science 318 :1258-1265. PubMed Id: 17962520. |
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|
β2 adrenergic receptor (engineered): Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.8 Å
T4 lysozyme replaces third intracellular loop. Reveals specific cholesterol binding site. |
Hanson et al. (2008).
Hanson MA, Cherezov V, Griffith MT, Roth CB, Jaakola VP, Chien EY, Velasquez J, Kuhn P, & Stevens RC (2008). A Specific Cholesterol Binding Site Is Established by the 2.8 Å Structure of the Human β2-Adrenergic Receptor.
Structure 16 :897-905. PubMed Id: 18547522. |
||
|
Wacker et al. (2010).
Wacker D, Fenalti G, Brown MA, Katritch V, Abagyan R, Cherezov V, & Stevens RC (2010). Conserved binding mode of human β2 adrenergic receptor inverse agonists and antagonist revealed by X-ray crystallography.
J Am Chem Soc 132 :11443-11445. PubMed Id: 20669948. doi:10.1021/ja105108q. |
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|
β2 adrenergic receptor (engineered) in nanobody-stabilized active state: Homo sapiens E Eukaryota (expressed in S. frugiperda), 3.50 Å
T4 lysozyme replaces third intracellular loop. The nanobody Nb80 is an intact antigen-binding domain of a camelid heavy-chain antibody. |
Rasmussen et al. (2011).
Rasmussen SG, Choi HJ, Fung JJ, Pardon E, Casarosa P, Chae PS, Devree BT, Rosenbaum DM, Thian FS, Kobilka TS, Schnapp A, Konetzki I, Sunahara RK, Gellman SH, Pautsch A, Steyaert J, Weis WI, & Kobilka BK (2011). Crystal structure of the human β2adrenergic G-protein-coupled receptor.
Nature 469 :175-180. PubMed Id: 21228869. |
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|
β2 adrenergic receptor (engineered) with irreversibly-bound agonist: Homo sapiens E Eukaryota (expressed in S. frugiperda), 3.50 Å
T4 lysozyme replaces third intracellular loop. The agonist is covalently linked to the receptor by a disulphide bond. |
Rosenbaum et al. (2011).
Rosenbaum DM, Zhang C, Lyons JA, Holl R, Aragao D, Arlow DH, Rasmussen SG, Choi HJ, Devree BT, Sunahara RK, Chae PS, Gellman SH, Dror RO, Shaw DE, Weis WI, Caffrey M, Gmeiner P, Kobilka BK (2011). Structure and function of an irreversible agonist-β2adrenoceptor complex.
Nature 469 :236-240. PubMed Id: 21228876. |
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β2 adrenergic receptor-Gs protein complex: Homo sapiens E Eukaryota (expressed in S. frugiperda), 3.20 Å
The receptor is engineered; T4 lysozyme at the N-terminus. Nanobody-stabilized active state. |
Rasmussen et al. (2011).
Rasmussen SG, Devree BT, Zou Y, Kruse AC, Chung KY, Kobilka TS, Thian FS, Chae PS, Pardon E, Calinski D, Mathiesen JM, Shah ST, Lyons JA, Caffrey M, Gellman SH, Steyaert J, Skiniotis G, Weis WI, Sunahara RK, & Kobilka BK (2011). Crystal structure of the β2 adrenergic receptor-Gs protein complex.
Nature 477 :549-555. PubMed Id: 21772288. doi:10.1038/nature10361. |
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β2 adrenergic receptor (engineered): Homo sapiens E Eukaryota (expressed in S. frugiperda), 3.99 Å
T4 lysozyme fused at N-terminal. |
Zou et al. (2012).
Zou Y, Weis WI, & Kobilka BK (2012). N-terminal T4 lysozyme fusion facilitates crystallization of a G protein coupled receptor.
PLoS ONE 7 10:e46039. PubMed Id: 23056231. doi:10.1371/journal.pone.0046039. |
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A1 adenosine receptor: Homo sapiens E Eukaryota (expressed in S. frugiperda), 3.2 Å
Engineered protein. b562 (BRIL) inserted into the third intracellular loop between residues 211 & 220. |
Glukhova et al. (2017).
Glukhova A, Thal DM, Nguyen AT, Vecchio EA, Jörg M, Scammells PJ, May LT, Sexton PM, & Christopoulos A (2017). Structure of the Adenosine A1 Receptor Reveals the Basis for Subtype Selectivity.
Cell 168 :867-877.e13. PubMed Id: 28235198. doi:10.1016/j.cell.2017.01.042. |
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A2A adenosine receptor: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.6 Å
In complex with a high-affinity subtype-selective antagonist ZM241385. Engineered protein: T4 lysozyme inserted between TM helices V and VI. |
Jaakola et al. (2008).
Jaakola VP, Griffith MT, Hanson MA, Cherezov V, Chien EY, Lane JR, Ijzerman AP, & Stevens RC (2008). The 2.6 Angstrom Crystal Structure of a Human A2AAdenosine Receptor Bound to an Antagonist.
Science 322 :1211-1217. PubMed Id: 18832607. |
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|
A2A adenosine receptor with bound agonist (UK-432097): Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.71 Å
Reveals structural changes in helices III, V, & VI relative to inactive, antagonist-bound form. Engineered protein: T4 lysozyme inserted between TM helices V and VI. |
Xu et al. (2011).
Xu F, Wu H, Katritch V, Han GW, Jacobson KA, Gao ZG, Cherezov V, & Stevens RC (2011). Structure of an agonist-bound human A2A adenosine receptor
Science 332 :322-327. PubMed Id: 21393508. doi:10.1126/science.1202793. |
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A2A adenosine receptor (engineered) with bound adenosine: Homo sapiens E Eukaryota (expressed in Trichoplusia ni), 3.00 Å
With synthetic agonist NECA, 2.6 Å:2YDV |
Lebon et al. (2011).
Lebon G, Warne T, Edwards PC, Bennett K, Langmead CJ, Leslie AG, & Tate CG (2011). Agonist-bound adenosine A2A receptor structures reveal common features of GPCR activation
Nature 474 :521-525. PubMed Id: 21593763. doi:10.1038/nature10136. |
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|
Doré et al. (2011).
Doré AS, Robertson N, Errey JC, Ng I, Hollenstein K, Tehan B, Hurrell E, Bennett K, Congreve M, Magnani F, Tate CG, Weir M, & Marshall FH (2011). Structure of the Adenosine A2A Receptor in Complex with ZM241385 and the Xanthines XAC and Caffeine.
Structure 19 :1283-1293. PubMed Id: 21885291. doi:10.1016/j.str.2011.06.014. |
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A2A adenosine receptor in complex inverse-agonist antibody: Homo sapiens E Eukaryota (expressed in Pichia pastoris), 2.70 Å
The structure was determined with bound mouse Fab2838 in the presence of the antagonist ZM241385. High-occupancy ZM241385 structure, 3.10 Å: 3VGA |
Hino et al. (2012).
Hino T, Arakawa T, Iwanari H, Yurugi-Kobayashi T, Ikeda-Suno C, Nakada-Nakura Y, Kusano-Arai O, Weyand S, Shimamura T, Nomura N, Cameron AD, Kobayashi T, Hamakubo T, Iwata S, & Murata T (2012). G-protein-coupled receptor inactivation by an allosteric inverse-agonist antibody.
Nature 482 :237-240. PubMed Id: 22286059. doi:10.1038/nature10750. |
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|
A2A adenosine receptor in complex with ZM241385: Homo sapiens E Eukaryota (expressed in S. frugiperda), 1.80 Å
Engineered protein: Apocytochrome b562 replaces loop 3 of wild-type protein. Structure reveals stabilizing cholesterol molecules, 23 ordered lipids, and 57 ordered waters. |
Liu et al. (2012).
Liu W, Chun E, Thompson AA, Chubukov P, Xu F, Katritch V, Han GW, Roth CB, Heitman LH, IJzerman AP, Cherezov V, & Stevens RC (2012). Structural basis for allosteric regulation of GPCRs by sodium ions.
Science 337 :232-236. PubMed Id: 22798613. doi:10.1126/science.1219218. |
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|
A2A adenosine receptor (engineered) with bound CGS21680 (P21): Homo sapiens E Eukaryota (expressed in Trichoplusia ni), 2.60 Å
P212121 space group, 2.60 Å: 4UG2 |
Lebon et al. (2015).
Lebon G, Edwards PC, Leslie AG, & Tate CG (2015). Molecular Determinants of CGS21680 Binding to the Human Adenosine A2A Receptor.
Mol Pharmacol 87 :907-915. PubMed Id: 25762024. doi:10.1124/mol.114.097360. |
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A2A adenosine receptor with bound engineered G protein: Homo sapiens E Eukaryota (expressed in Trichoplusia ni), 3.4 Å
|
Carpenter et al. (2016).
Carpenter B, Nehmé R, Warne T, Leslie AG, & Tate CG (2016). Structure of the adenosine A2A receptor bound to an engineered G protein.
Nature 536 :104-107. PubMed Id: 27462812. doi:10.1038/nature18966. |
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CXCR1 chemokine receptor in phospholipid bilayers: Homo sapiens E Eukaryota (expressed in E. coli), NMR Structure
|
Park et al. (2012).
Park SH, Das BB, Casagrande F, Tian Y, Nothnagel HJ, Chu M, Kiefer H, Maier K, De Angelis AA, Marassi FM, & Opella SJ (2012). Structure of the chemokine receptor CXCR1 in phospholipid bilayers.
Nature 491 :779-783. PubMed Id: 23086146. doi:10.1038/nature11580. |
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CCR2 Chemokine receptor with ortho- and allosteric antagonists: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.81 Å
Engineered protein: T4 lysozyme inserted between TM helices V and VI. |
Zheng et al. (2016).
Zheng Y, Qin L, Zacarías NV, de Vries H, Han GW, Gustavsson M, Dabros M, Zhao C, Cherney RJ, Carter P, Stamos D, Abagyan R, Cherezov V, Stevens RC, IJzerman AP, Heitman LH, Tebben A, Kufareva I, & Handel TM (2016). Structure of CC chemokine receptor 2 with orthosteric and allosteric antagonists.
Nature 540 :458-461. PubMed Id: 27926736. doi:10.1038/nature20605. |
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|
CXCR4 chemokine receptor complexed with IT1t antagonist: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.5 Å
Engineered protein: T4 lysozyme inserted between TM helices V and VI. P21 space group. CXCR4 with IT1t (P1 space group), 3.10 Å: 3OE8 CXCR4 with IT1t (P1 space group), 3.10 Å: 3OE9 CXCR4 with IT1t (I222 space group), 3.20 Å: 3OE6 CXCR4 with cyclic peptide antagonist CVX15 (C2 space group), 2.90 Å: 3OE0 |
Wu et al. (2010).
Wu B, Chien EY, Mol CD, Fenalti G, Liu W, Katritch V, Abagyan R, Brooun A, Wells P, Bi FC, Hamel DJ, Kuhn P, Handel TM, Cherezov V, & Stevens RC (2010). Structures of the CXCR4 Chemokine GPCR with Small-Molecule and Cyclic Peptide Antagonists.
Science 330 :1066-1071. PubMed Id: 20929726. |
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CXCR4 chemokine receptor complexed with viral chemokine antagonist vMIP-II: Homo sapiens E Eukaryota (expressed in S. frugiperda), 3.10 Å
Engineered protein: T4 lysozyme inserted between TM helices V and VI. |
Qin et al. (2015).
Qin L, Kufareva I, Holden LG, Wang C, Zheng Y, Zhao C, Fenalti G, Wu H, Han GW, Cherezov V, Abagyan R, Stevens RC, & Handel TM (2015). Structural biology. Crystal structure of the chemokine receptor CXCR4 in complex with a viral chemokine.
Science 347 6226:1117-1122. PubMed Id: 25612609. doi:10.1126/science.1261064. |
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CCR5 chemokine receptor with bound Maraviroc: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.71 Å
Engineered protein: Met1-Glu54 of rubredoxin were inserted between Arg223 & Glu227 after deletion of Cys224-Asn226 in intracellular loop 3 (ICL3). |
Tan et al. (2013).
Tan Q, Zhu Y, Li J, Chen Z, Han GW, Kufareva I, Li T, Ma L, Fenalti G, Li J, Zhang W, Xie X, Yang H, Jiang H, Cherezov V, Liu H, Stevens RC, Zhao Q, & Wu B (2013). Structure of the CCR5 chemokine receptor-HIV entry inhibitor maraviroc complex.
Science 341 :1387-1390. PubMed Id: 24030490. doi:10.1126/science.1241475. |
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Chemokine receptor CCR9 in complex with vercirnon: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.8 Å
|
Oswald et al. (2016).
Oswald C, Rappas M, Kean J, Doré AS, Errey JC, Bennett K, Deflorian F, Christopher JA, Jazayeri A, Mason JS, Congreve M, Cooke RM, & Marshall FH (2016). Intracellular allosteric antagonism of the CCR9 receptor.
Nature 540 :462-465. PubMed Id: 27926729. doi:10.1038/nature20606. |
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Human cytomeglovirius US28 GPCR with bound human cytokine CX3CL1: Cytomeglovirus V Viruses (expressed in HEK cells), 2.89 Å
Additional structure, 3.80 Å: 4XT3 |
Burg et al. (2015).
Burg JS, Ingram JR, Venkatakrishnan AJ, Jude KM, Dukkipati A, Feinberg EN, Angelini A, Waghray D, Dror RO, Ploegh HL, & Garcia KC (2015). Structural biology. Structural basis for chemokine recognition and activation of a viral G protein-coupled receptor.
Science 347 6226:1113-1117. PubMed Id: 25745166. doi:10.1126/science.aaa5026. |
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|
endothelin ETB receptor with bound endothelin-1: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.8 Å
Engineered protein: T4 lysozyme inserted between TM helices V and VI. Thermostabilized. without bound endothelin-1, 2.5 Å: 5GLI |
Shihoya et al. (2016).
Shihoya W, Nishizawa T, Okuta A, Tani K, Dohmae N, Fujiyoshi Y, Nureki O, & Doi T (2016). Activation mechanism of endothelin ETB receptor by endothelin-1.
Nature 537 :363-368. PubMed Id: 27595334. doi:10.1038/nature19319. |
||
|
Dopamine D3 receptor complexed with D2/D3-selective antagonist: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.89 Å
Engineered protein: T4 lysozyme inserted between TM helices V and VI. |
Chien et al. (2010).
Chien EY, Liu W, Zhao Q, Katritch V, Han GW, Hanson MA, Shi L, Newman AH, Javitch JA, Cherezov V, & Stevens RC (2010). Structure of the human dopamine D3 receptor in complex with a D2/D3 selective antagonist.
Science 330 :1091-1095. PubMed Id: 21097933. |
||
|
Histamine H1 receptor, complexed with doxepin: Homo sapiens E Eukaryota (expressed in Pichia pastoris), 3.10 Å
|
Tsujimoto et al. (2011).
Shimamura T, Shiroishi M, Weyand S, Tsujimoto H, Winter G, Katritch V, Abagyan R, Cherezov V, Liu W, Han GW, Kobayashi T, Stevens RC, & Iwata S (2011). Structure of the human histamine H1 receptor complex with doxepin.
Nature 475 :65-70. PubMed Id: 21697825. doi:10.1038/nature10236. |
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|
Sphingosine 1-phosphate receptor: Homo sapiens E Eukaryota (expressed in S. frugiperda), 3.35 Å
Engineered protein: T4 lysozyme inserted between TM helices V and VI. Structure determined using microdiffraction data assembly, 2.80 Å: 3V2Y |
Hanson et al. (2012).
Hanson MA, Roth CB, Jo E, Griffith MT, Scott FL, Reinhart G, Desale H, Clemons B, Cahalan SM, Schuerer SC, Sanna MG, Han GW, Kuhn P, Rosen H, & Stevens RC (2012). Crystal structure of a lipid G protein-coupled receptor.
Science 335 :851-855. PubMed Id: 22344443. doi:10.1126/science.1215904. |
||
|
M1 human muscarinic acetylcholine receptor with bound tiotropium: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.7 Å
Engineered protein: T4 lysozyme inserted between TM helices V and VI |
Thal et al. (2016).
Thal DM, Sun B, Feng D, Nawaratne V, Leach K, Felder CC, Bures MG, Evans DA, Weis WI, Bachhawat P, Kobilka TS, Sexton PM, Kobilka BK, & Christopoulos A (2016). Crystal structures of the M1 and M4 muscarinic acetylcholine receptors.
Nature 531 :335-340. PubMed Id: 26958838. doi:10.1038/nature17188. |
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|
M2 human muscarinic acetylcholine receptor bound to an antagonist: Homo sapiens E Eukaryota (expressed in S. frugiperda), 3.00 Å
Engineered protein: T4 lysozyme inserted between TM helices V and VI. |
Haga et al. (2012).
Haga K, Kruse AC, Asada H, Yurugi-Kobayashi T, Shiroishi M, Zhang C, Weis WI, Okada T, Kobilka BK, Haga T, & Kobayashi T (2012). Structure of the human M2 muscarinic acetylcholine receptor bound to an antagonist.
Nature 482 :547-551. PubMed Id: 22278061. doi:10.1038/nature10753. |
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|
M2 muscarinic acetylcholine receptor bound to the agonist iperoxo: Homo sapiens E Eukaryota (expressed in S. frugiperda), 3.50 Å
Stabilized by camelid antibody fragment. with bound iperoxo and allosteric modulator LY2119620, 3.70 Å: 4MQT |
Kruse et al. (2013).
Kruse AC, Ring AM, Manglik A, Hu J, Hu K, Eitel K, Hübner H, Pardon E, Valant C, Sexton PM, Christopoulos A, Felder CC, Gmeiner P, Steyaert J, Weis WI, Garcia KC, Wess J, & Kobilka BK (2013). Activation and allosteric modulation of a muscarinic acetylcholine receptor.
Nature 504 :101-106. PubMed Id: 24256733. doi:10.1038/nature12735. |
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|
M3 muscarinic acetylcholine receptor: Rattus norvegicus E Eukaryota (expressed in S. frugiperda), 3.40 Å
Engineered protein: T4 lysozyme inserted between TM helices V and VI. |
Kruse et al. (2012).
Kruse AC, Hu J, Pan AC, Arlow DH, Rosenbaum DM, Rosemond E, Green HF, Liu T, Chae PS, Dror RO, Shaw DE, Weis WI, Wess J, & Kobilka BK (2012). Structure and dynamics of the M3 muscarinic acetylcholine receptor.
Nature 482 :552-556. PubMed Id: 22358844. doi:10.1038/nature10867. |
||
|
M4 human muscarinic acetylcholine receptor with bound tiotropium: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.6 Å
Engineered protein: T4 lysozyme inserted between TM helices V and VI. |
Thal et al. (2016).
Thal DM, Sun B, Feng D, Nawaratne V, Leach K, Felder CC, Bures MG, Evans DA, Weis WI, Bachhawat P, Kobilka TS, Sexton PM, Kobilka BK, & Christopoulos A (2016). Crystal structures of the M1 and M4 muscarinic acetylcholine receptors.
Nature 531 :335-340. PubMed Id: 26958838. doi:10.1038/nature17188. |
||
|
κ-opioid receptor in complex with JDTic: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.90 Å
Engineered protein: T4 lysozyme inserted between TM helices V and VI. |
Wu et al. (2012).
Wu H, Wacker D, Mileni M, Katritch V, Han GW, Vardy E, Liu W, Thompson AA, Huang XP, Carroll FI, Mascarella SW, Westkaemper RB, Mosier PD, Roth BL, Cherezov V, & Stevens RC (2012). Structure of the human κ-opioid receptor in complex with JDTic.
Nature 485 :327-332. PubMed Id: 22437504. doi:10.1038/nature10939. |
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|
μ-opioid receptor bound to a morphinan antagonist: Mus musculus E Eukaryota (expressed in S. frugiperda), 2.80 Å
Engineered protein: T4 lysozyme inserted between TM helices V and VI. |
Manglik et al. (2012).
Manglik A, Kruse AC, Kobilka TS, Thian FS, Mathiesen JM, Sunahara RK, Pardo L, Weis WI, Kobilka BK, & Granier S (2012). Crystal structure of the μ-opioid receptor bound to a morphinan antagonist.
Nature 485 :321-326. PubMed Id: 22437502. doi:10.1038/nature10954. |
||
|
μ-opioid receptor bound to a morphinan antagonist BU72: Mus musculus E Eukaryota (expressed in S. frugiperda), 2.10 Å
|
Huang et al. (2015).
Huang W, Manglik A, Venkatakrishnan AJ, Laeremans T, Feinberg EN, Sanborn AL, Kato HE, Livingston KE, Thorsen TS, Kling RC, Granier S, Gmeiner P, Husbands SM, Traynor JR, Weis WI, Steyaert J, Dror RO, & Kobilka BK (2015). Structural insights into µ-opioid receptor activation.
Nature 524 :315-321. PubMed Id: 26245379. doi:10.1038/nature14886. |
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|
δ-opioid receptor in complex with naltrindol: Mus musculus E Eukaryota (expressed in S. frugiperda), 3.40 Å
Engineered protein: T4 lysozyme inserted between TM helices V and VI. |
Granier et al. (2012).
Granier S, Manglik A, Kruse AC, Kobilka TS, Thian FS, Weis WI, & Kobilka BK (2012). Structure of the δ-opioid receptor bound to naltrindole.
Nature 485 :400-404. PubMed Id: 22596164. doi:10.1038/nature11111. |
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|
δ-opioid receptor in complex with naltrindol: Homo sapiens E Eukaryota (expressed in S. frugiperda), 1.80 Å
Engineered Protein: apocytochrome b562 RIL (BRIL) fused at amino terminal of truncated receptor (residues 36-338). |
Fenalti et al. (2014).
Fenalti G, Giguere PM, Katritch V, Huang XP, Thompson AA, Cherezov V, Roth BL, & Stevens RC (2014). Molecular control of δ-opioid receptor signalling.
Nature 506 :191-196. PubMed Id: 24413399. doi:10.1038/nature12944. |
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|
δ-opioid receptor with bound antagonist/agonist tetrapeptide DIPP-NH2: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.70 Å
Free electron laser (XFEL) structure. Engineered Protein: apocytochrome b562 RIL (BRIL) fused at amino terminal of truncated receptor (residues 39-338). Synchrotron structure, 3.28 Å: 4RWA |
Fenalti et al. (2015).
Fenalti G, Zatsepin NA, Betti C, Giguere P, Han GW, Ishchenko A, Liu W, Guillemyn K, Zhang H, James D, Wang D, Weierstall U, Spence JC, Boutet S, Messerschmidt M, Williams GJ, Gati C, Yefanov OM, White TA, Oberthuer D, Metz M, Yoon CH, Barty A, Chapman HN, Basu S, Coe J, Conrad CE, Fromme R, Fromme P, Tourwé D, Schiller PW, Roth BL, Ballet S, Katritch V, Stevens RC, & Cherezov V (2015). Structural basis for bifunctional peptide recognition at human ?-opioid receptor.
Nat Struct Mol Biol 22 3:265-268. PubMed Id: 25686086. doi:10.1038/nsmb.2965. |
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CB1 cannabinoid receptor complexed with stabilizing antagonist AM6538: Homo sapiens E Eukaryota (expressed in HEK293F cells), 2.80 Å
Engineered protein: Y98W Flavodoxin fused to third intracellular loop. |
Hua et al. (2016).
Hua T, Vemuri K, Pu M, Qu L, Han GW, Wu Y, Zhao S, Shui W, Li S, Korde A, Laprairie RB, Stahl EL, Ho JH, Zvonok N, Zhou H, Kufareva I, Wu B, Zhao Q, Hanson MA, Bohn LM, Makriyannis A, Stevens RC, & Liu ZJ (2016). Crystal Structure of the Human Cannabinoid Receptor CB1.
Cell 167 :750-762.e14. PubMed Id: 27768894. doi:10.1016/j.cell.2016.10.004. |
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|
CB1 cannabinoid receptor with bound inhibitor taranabant: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.6 Å
Engineered protein: Pyrococcus abysii glycogen synthase replaced the 3rd intracellular loop. N-terminal 89 residues deleted. T210A point mutation. |
Shao et al. (2016).
Shao Z, Yin J, Chapman K, Grzemska M, Clark L, Wang J, & Rosenbaum DM (2016). High-resolution crystal structure of the human CB1 cannabinoid receptor.
Nature 540 :602-606. PubMed Id: 27851727. doi:10.1038/nature20613. |
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Nociceptin/orphanin FQ (N/OFQ) receptor with bound peptide: Homo sapiens E Eukaryota (expressed in S. frugiperda), 3.01 Å
Engineered protein: T4 lysozyme inserted between TM helices V and VI. |
Thompson et al. (2012).
Thompson AA, Liu W, Chun E, Katritch V, Wu H, Vardy E, Huang XP, Trapella C, Guerrini R, Calo G, Roth BL, Cherezov V, & Stevens RC (2012). Structure of the nociceptin/orphanin FQ receptor in complex with a peptide mimetic.
Nature 485 :395-399. PubMed Id: 22596163. doi:10.1038/nature11085. |
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Nociceptin/orphanin FQ (N/OFQ) receptor with bound C-35: Homo sapiens E Eukaryota (expressed in S. frugiperda), 3.0 Å
Engineered protein: T4 lysozyme inserted between TM helices V and VI. with bound SB-612111, 3.0 Å: 5DHH |
Miller et al. (2015).
Miller RL, Thompson AA, Trapella C, Guerrini R, Malfacini D, Patel N, Han GW, Cherezov V, Caló G, Katritch V, & Stevens RC (2015). The Importance of Ligand-Receptor Conformational Pairs in Stabilization: Spotlight on the N/OFQ G Protein-Coupled Receptor.
Structure 23 :2291-2299. PubMed Id: 26526853. doi:10.1016/j.str.2015.07.024. |
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NTS1 neurotensin receptor in complex with neurotensin: Rattus norvegicus E Eukaryota (expressed in Trichoplusia ni), 2.80 Å
Engineered protein: T4 lysozyme inserted between TM helices V and VI. |
White et al. (2012).
White JF, Noinaj N, Shibata Y, Love J, Kloss B, Xu F, Gvozdenovic-Jeremic J, Shah P, Shiloach J, Tate CG, & Grisshammer R (2012). Structure of the agonist-bound neurotensin receptor.
Nature 490 :508-513. PubMed Id: 23051748. doi:10.1038/nature11558. |
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|
NTS1 neurotensin receptor produced by direct evolution, agonist bound (TM86V-ΔIC3B mutant): Rattus norvegicus E Eukaryota (expressed in E. coli), 2.75 Å
These proteins are not stabilized by a T4 lysozyme insertion. TM86V-ΔIC3A mutant, 3.00 Å: 3ZEV OGG7-ΔIC3A mutant, 3.10 Å: 4BV0 HTHGH4-ΔIC3 mutant, 3.57 Å: 4BWB |
Egloff et al. (2014).
Egloff P, Hillenbrand M, Klenk C, Batyuk A, Heine P, Balada S, Schlinkmann KM, Scott DJ, Schütz M, & Plückthun A (2014). Structure of signaling-competent neurotensin receptor 1 obtained by directed evolution in Escherichia coli.
Proc Natl Acad Sci USA 111 :E655–E662. PubMed Id: 24453215. doi:10.1073/pnas.1317903111. |
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NTS1 neurotensin receptor in active-like state: Rattus norvegicus E Eukaryota (expressed in Trichoplusia ni), 2.90 Å
Engineered protein: T4 lysozyme inserted between TM helices V and VI, 2.60 Å: 4XES |
Krumm et al. (2015).
Krumm BE, White JF, Shah P, & Grisshammer R (2015). Structural prerequisites for G-protein activation by the neurotensin receptor.
Nat Commun 6 :7895. PubMed Id: 26205105. doi:10.1038/ncomms8895. |
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NTS1 neurotensin receptor, NTSR1-EL constitutively active mutant: Rattus norvegicus E Eukaryota (expressed in Trichoplusia ni), 3.3 Å
Engineered protein: T4 lysozyme inserted between TM helices V and VI plus six thermostabilizing mutations. |
Krumm et al. (2016).
Krumm BE, Lee S, Bhattacharya S, Botos I, White CF, Du H, Vaidehi N, & Grisshammer R (2016). Structure and dynamics of a constitutively active neurotensin receptor.
Sci Rep 6 :38564. PubMed Id: 27924846. doi:10.1038/srep38564. |
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Protease-activated receptor 1 (PAR1) bound with antagonist vorapaxar: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.20 Å
Engineered protein: T4 lysozyme inserted between TM helices V and VI. |
Zhang et al. (2012).
Zhang C, Srinivasan Y, Arlow DH, Fung JJ, Palmer D, Zheng Y, Green HF, Pandey A, Dror RO, Shaw DE, Weis WI, Coughlin SR, & Kobilka BK (2012). High-resolution crystal structure of human protease-activated receptor 1.
Nature 492 :387-392. PubMed Id: 23222541. doi:10.1038/nature11701. |
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|
Langelaan et al. (2013).
Langelaan DN, Reddy T, Banks AW, Dellaire G, Dupré DJ, & Rainey JK (2013). Structural features of the apelin receptor N-terminal tail and first transmembrane segment implicated in ligand binding and receptor trafficking.
Biochim Biophys Acta 1828 :1471-1483. PubMed Id: 23438363. doi:10.1016/j.bbamem.2013.02.005. |
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Apelin receptor (angiotensin II protein J receptor [APJR]) in complex with apelin-17 mimetic peptide: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.6 Å
|
Ma et al. (2017).
Ma Y, Yue Y, Ma Y, Zhang Q, Zhou Q, Song Y, Shen Y, Li X, Ma X, Li C, Hanson MA, Han GW, Sickmier EA, Swaminath G, Zhao S, Stevens RC, Hu LA, Zhong W, Zhang M, & Xu F (2017). Structural Basis for Apelin Control of the Human Apelin Receptor.
Structure 25 :858-866.e4. PubMed Id: 28528775. doi:10.1016/j.str.2017.04.008. |
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5-HT1B serotonin receptor with bound ergotamine: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.70 Å
Engineered Protein: apocytochrome b562 RIL (BRIL) replaces cytoplasmic loop 3 (L240-M305). With bound dihydroergotamine, 2.80 Å: 4IAQ |
Wang et al. (2013).
Wang C, Jiang Y, Ma J, Wu H, Wacker D, Katritch V, Han GW, Liu W, Huang XP, Vardy E, McCorvy JD, Gao X, Zhou XE, Melcher K, Zhang C, Bai F, Yang H, Yang L, Jiang H, Roth BL, Cherezov V, Stevens RC, & Xu HE (2013). Structural basis for molecular recognition at serotonin receptors.
Science 340 :610-614. PubMed Id: 23519210. doi:10.1126/science.1232807. |
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5-HT2B serotonin receptor with bound ergotamine: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.70 Å
Engineered Protein: apocytochrome b562 RIL (BRIL) replaces cytoplasmic loop 3 (Y249-V313). |
Wacker et al. (2013).
Wacker D, Wang C, Katritch V, Han GW, Huang XP, Vardy E, McCorvy JD, Jiang Y, Chu M, Siu FY, Liu W, Xu HE, Cherezov V, Roth BL, & Stevens RC (2013). Structural features for functional selectivity at serotonin receptors.
Science 340 :615-619. PubMed Id: 23519215. doi:10.1126/science.1232808. |
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5-HT2B serotonin receptor: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.80 Å
Structure determined by serial femtosecond crystallography. Engineered Protein: apocytochrome b562 RIL (BRIL) replaces cytoplasmic loop 3 (Y249-V313). |
Liu et al. (2013).
Liu W, Wacker D, Gati C, Han GW, James D et al. (2013). Serial femtosecond crystallography of G protein-coupled receptors.
Science 342 :1521-1524. PubMed Id: 24357322. doi:10.1126/science.1244142. |
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5-HT2B serotonin receptor with bound LSD: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.9 Å
Engineered Protein: apocytochrome b562 RIL (BRIL) replaces cytoplasmic loop 3 (Y249-V312) |
Wacker et al. (2017).
Wacker D, Wang S, McCorvy JD, Betz RM, Venkatakrishnan AJ, Levit A, Lansu K, Schools ZL, Che T, Nichols DE, Shoichet BK, Dror RO, & Roth BL (2017). Crystal Structure of an LSD-Bound Human Serotonin Receptor.
Cell 168 :377-389. PubMed Id: 28129538. doi:10.1016/j.cell.2016.12.033. |
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Smoothened (SMO) receptor with bound antagonist, LY2940680: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.45 Å
Engineered Protein: apocytochrome b562 RIL (BRIL) fused to truncated N-terminus at S190. C-terminus truncated at Q555. |
Wang et al. (2013).
Wang C, Wu H, Katritch V, Han GW, Huang XP, Liu W, Siu FY, Roth BL, Cherezov V, & Stevens RC (2013). Structure of the human smoothened receptor bound to an antitumour agent.
Nature 497 :338-343. PubMed Id: 23636324. doi:10.1038/nature12167. |
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P2Y12 receptor in complex with an antithrombotic drug: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.62 Å
Engineered Protein: apocytochrome b562 RIL (BRIL) replaces cytoplasmic loop 3 |
Zhang et al. (2014).
Zhang K, Zhang J, Gao ZG, Zhang D, Zhu L, Han GW, Moss SM, Paoletta S, Kiselev E, Lu W, Fenalti G, Zhang W, Müller CE, Yang H, Jiang H, Cherezov V, Katritch V, Jacobson KA, Stevens RC, Wu B, & Zhao Q (2014). Structure of the human P2Y12 receptor in complex with an antithrombotic drug.
Nature 509 :115-118. PubMed Id: 24670650. doi:10.1038/nature13083. |
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P2Y12 receptor with bound agonist 2MeSADP: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.50 Å
Engineered Protein: apocytochrome b562 RIL (BRIL) replaces cytoplasmic loop 3 with bound 2MeSATP, 3.10 Å: 4PY0 |
Zhang et al. (2014).
Zhang J, Zhang K, Gao ZG, Paoletta S, Zhang D, Han GW, Li T, Ma L, Zhang W, Müller CE, Yang H, Jiang H, Cherezov V, Katritch V, Jacobson KA, Stevens RC, Wu B, & Zhao Q (2014). Agonist-bound structure of the human P2Y12 receptor.
Nature 509 :119-122. PubMed Id: 24784220. doi:10.1038/nature13288. |
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P2Y1 receptor in complex with BPTU: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.20 Å
Engineered protein. Rubredoxin inserted into the ICL3 domain between residues 247K and 253P, replacing residues 248N to 252S. in complex with MRS2500, 2.70 Å: 4XNW |
Zhang et al. (2015).
Zhang D, Gao ZG, Zhang K, Kiselev E, Crane S, Wang J, Paoletta S, Yi C, Ma L, Zhang W, Han GW, Liu H, Cherezov V, Katritch V, Jiang H, Stevens RC, Jacobson KA, Zhao Q, & Wu B (2015). Two disparate ligand-binding sites in the human P2Y1 receptor.
Nature 520 7547:317-321. PubMed Id: 25822790. doi:10.1038/nature14287. |
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Class B GPCR corticotropin-releasing factor receptor 1 in complex with CP-376395 small-molecule antagonist: Homo sapiens E Eukaryota (expressed in Trichoplusia ni), 2.98 Å
Engineered protein: T4 lysozyme inserted between TM helices III and IV. Lacks the N-terminal extracellular domain. |
Hollenstein et al. (2013).
Hollenstein K, Kean J, Bortolato A, Cheng RK, Doré AS, Jazayeri A, Cooke RM, Weir M, & Marshall FH (2013). Structure of class B GPCR corticotropin-releasing factor receptor 1.
Nature 499 7459:438-443. PubMed Id: 23863939. doi:10.1038/nature12357. |
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Class B GPCR glucagon receptor: Homo sapiens E Eukaryota (expressed in S. frugiperda), 3.30 Å
Engineered Protein: E. coli apocytochrome b562 RIL (BRIL) fused at residue 123. C-terminus truncated at residue 432. |
Siu et al. (2013).
Siu FY, He M, de Graaf C, Han GW, Yang D, Zhang Z, Zhou C, Xu Q, Wacker D, Joseph JS, Liu W, Lau J, Cherezov V, Katritch V, Wang MW, & Stevens RC (2013). Structure of the human glucagon class B G-protein-coupled receptor.
Nature 499 7459:444-449. PubMed Id: 23863937. doi:10.1038/nature12393. |
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Class B GPCR glucagon receptor, full length. XFEL structure: Homo sapiens E Eukaryota (expressed in S. frugiperda), 3.0 Å
synchrotron structure, 3.19 Å: 5XF1 |
Zhang et al. (2017).
Zhang H, Qiao A, Yang D, Yang L, Dai A, de Graaf C, Reedtz-Runge S, Dharmarajan V, Zhang H, Han GW, Grant TD, Sierra RG, Weierstall U, Nelson G, Liu W, Wu Y, Ma L, Cai X, Lin G, Wu X, Geng Z, Dong Y, Song G, Griffin PR, Lau J, Cherezov V, Yang H, Hanson MA, Stevens RC, Zhao Q, Jiang H, Wang MW, & Wu B (2017). Structure of the full-length glucagon class B G-protein-coupled receptor.
Nature 546 :259-264. PubMed Id: 28514451. doi:10.1038/nature22363. |
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Full-length glucagon receptor (GLP-1R) in complex with a truncated peptide: Homo sapiens E Eukaryota (expressed in S. frugiperda), 3.7 Å
|
Jazayeri et al. (2017).
Jazayeri A, Rappas M, Brown AJH, Kean J, Errey JC, Robertson NJ, Fiez-Vandal C, Andrews SP, Congreve M, Bortolato A, Mason JS, Baig AH, Teobald I, Doré AS, Weir M, Cooke RM, & Marshall FH (2017). Crystal structure of the GLP-1 receptor bound to a peptide agonist.
Nature 546 :254-258. PubMed Id: 28562585. doi:10.1038/nature22800. |
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GLP-1 receptor in complex with PF-06372222: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.7 Å
in complex with NNC0640, 3.0 Å: 5VEX |
Song et al. (2017).
Song G, Yang D, Wang Y, de Graaf C, Zhou Q, Jiang S, Liu K, Cai X, Dai A, Lin G, Liu D, Wu F, Wu Y, Zhao S, Ye L, Han GW, Lau J, Wu B, Hanson MA, Liu ZJ, Wang MW, & Stevens RC (2017). Human GLP-1 receptor transmembrane domain structure in complex with allosteric modulators.
Nature 546 :312-315. PubMed Id: 28514449. doi:10.1038/nature22378. |
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Activated glucagon (GLP-1) receptor in complex with a G protein: Oryctolagus cuniculus E Eukaryota (expressed in Trichoplusia ni), 4.1 Å
cryo-EM structure |
Zhang et al. (2017).
Zhang Y, Sun B, Feng D, Hu H, Chu M, Qu Q, Tarrasch JT, Li S, Sun Kobilka T, Kobilka BK, & Skiniotis G (2017). Cryo-EM structure of the activated GLP-1 receptor in complex with a G protein.
Nature 546 :248-253. PubMed Id: 28538729. doi:10.1038/nature22394. |
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Class B GPCR: Calcitonin receptor-heterotrimeric Gs protein complex: Homo sapiens E Eukaryota (expressed in Trichoplusia ni), 4.1 Å
Phase-plate cryo-EM structure. |
Liang et al. (2017).
Liang YL, Khoshouei M, Radjainia M, Zhang Y, Glukhova A, Tarrasch J, Thal DM, Furness SGB, Christopoulos G, Coudrat T, Danev R, Baumeister W, Miller LJ, Christopoulos A, Kobilka BK, Wootten D, Skiniotis G, & Sexton PM (2017). Phase-plate cryo-EM structure of a class B GPCR-G-protein complex.
Nature 546 7656:118-123. PubMed Id: 28437792. doi:10.1038/nature22327. |
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GABAB receptor ectodomain GBR1-GBR2 heterodimer, apo form: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.35 Å
with bound antagonist 2-hydroxysaclofen, 2.22 Å: 4MQF with bound antagonist CGP54626, 2.15 Å: 4MR7 with bound antagonist CGP35348, 2.15 Å: 4MR8 with bound antagonist SCH50911, 2.35 Å:4MR9 with bound antagonist phaclofen, 2.86 Å: 4MRM with bound antagonist CGP46381, 2.25 Å: 4MS1 with bound endogenous agonist GABA, 2.50 Å: 4MS3 with bound agonist baclofen, 1.90 Å: 4MS4 |
Geng et al. (2013).
Geng Y, Bush M, Mosyak L, Wang F, & Fan QR (2013). Structural mechanism of ligand activation in human GABAB receptor.
Nature 504 :254-259. PubMed Id: 24305054. doi:10.1038/nature12725. |
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Class C GPCR Metabotropic Glutamate Receptor 1 (mGlu1) with bound allosteric modulator: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.80 Å
Engineered Protein: E. coli apocytochrome b562 RIL (BRIL) fused at N-terminal at I581. C-terminus truncated at residue V860. |
Wu et al. (2014).
Wu H, Wang C, Gregory KJ, Han GW, Cho HP, Xia Y, Niswender CM, Katritch V, Meiler J, Cherezov V, Conn PJ, & Stevens RC (2014). Structure of a class C GPCR metabotropic glutamate receptor 1 bound to an allosteric modulator.
Science 344 :58-64. PubMed Id: 24603153. doi:10.1126/science.1249489. |
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Class C GPCR Metabotropic Glutamate Receptor 5 (mGlu5) with bound negative allosteric modulator: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.60 Å
Engineered protein. T4 lysozyme inserted between TM helices V and VI; thermostabilized by five collective mutations in TM3 and TM5. |
Doré et al. (2014).
Doré AS, Okrasa K, Patel JC, Serrano-Vega M, Bennett K, Cooke RM, Errey JC, Jazayeri A, Khan S, Tehan B, Weir M, Wiggin GR, & Marshall FH (2014). Structure of class C GPCR metabotropic glutamate receptor 5 transmembrane domain.
Nature 511 :557-562. PubMed Id: 25042998. doi:10.1038/nature13396. |
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Class C GPCR Metabotropic Glutamate Receptor 5 (mGlu5) with bound compound 14: Homo sapiens E Eukaryota (expressed in S. frugiperda), 3.10 Å
with bound compound 25 (HTL14242), 2.60 Å: 5CGD Engineered protein. T4 lysozyme inserted between TM helices V and VI; thermostabilized by six collective mutations in TM3 and TM5. |
Christopher et al. (2015).
Christopher JA, Aves SJ, Bennett KA, Doré AS, Errey JC, Jazayeri A, Marshall FH, Okrasa K, Serrano-Vega MJ, Tehan BG, Wiggin GR, & Congreve M (2015). Fragment and Structure-Based Drug Discovery for a Class C GPCR: Discovery of the mGlu5 Negative Allosteric Modulator HTL14242 (3-Chloro-5-[6-(5-fluoropyridin-2-yl)pyrimidin-4-yl]benzonitrile).
J Med Chem 58 :6653-6664. PubMed Id: 26225459. doi:10.1021/acs.jmedchem.5b00892. |
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GPR40 free fatty-acid receptor 1 (FFAR1) bound to TAK-875: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.33 Å
Engineered protein: Four point mutations to improve thermostability and T4 lysozyme inserted between TM helices V and VI (intracellular loop 3). |
Srivastava et al. (2014).
Srivastava A, Yano J, Hirozane Y, Kefala G, Gruswitz F, Snell G, Lane W, Ivetac A, Aertgeerts K, Nguyen J, Jennings A, & Okada K (2014). High-resolution structure of the human GPR40 receptor bound to allosteric agonist TAK-875.
Nature 513 7516:124-127. PubMed Id: 25043059. doi:10.1038/nature13494. |
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Chrencik et al. (2015).
Chrencik JE, Roth CB, Terakado M, Kurata H, Omi R, Kihara Y, Warshaviak D, Nakade S, Asmar-Rovira G, Mileni M, Mizuno H, Griffith MT, Rodgers C, Han GW, Velasquez J, Chun J, Stevens RC, & Hanson MA (2015). Crystal Structure of Antagonist Bound Human Lysophosphatidic Acid Receptor 1.
Cell 161 :1633-1643. PubMed Id: 26091040. doi:10.1016/j.cell.2015.06.002. |
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Angiotensin type I receptor: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.9 Å
Structure determined using serial femtosecond crystallography (XFEL) Engineered protein: apocytochrome b562 RIL (BRIL) fused at amino terminal. |
Zhang et al. (2015).
Zhang H, Unal H, Gati C, Han GW, Liu W, Zatsepin NA, James D, Wang D, Nelson G, Weierstall U, Sawaya MR, Xu Q, Messerschmidt M, Williams GJ, Boutet S, Yefanov OM, White TA, Wang C, Ishchenko A, Tirupula KC, Desnoyer R, Coe J, Conrad CE, Fromme P, Stevens RC, Katritch V, Karnik SS, & Cherezov V (2015). Structure of the Angiotensin receptor revealed by serial femtosecond crystallography.
Cell 161 :833-844. PubMed Id: 25913193. doi:10.1016/j.cell.2015.04.011. |
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Angiotensin type I receptor with bound olmesartan: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.8 Å
Engineered protein: apocytochrome b562 RIL (BRIL) fused at amino terminal. |
Zhang et al. (2015).
Zhang H, Unal H, Desnoyer R, Han GW, Patel N, Katritch V, Karnik SS, Cherezov V, & Stevens RC (2015). Structural Basis for Ligand Recognition and Functional Selectivity at Angiotensin Receptor.
J Biol Chem 290 :29127-29139. PubMed Id: 26420482. doi:10.1074/jbc.M115.689000. |
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Angiotensin type II receptor in complex with compound 1 (monoclinic xtals): Homo Sapiens E Eukaryota (expressed in S. frugiperda), 2.8 Å
in complex with compound 1 (orthorhombic xtals), 2.8 Å: 5UNG in complex with compound 2, 2.9 Å: 5UNH Engineered protein. N-term residues 1-34 truncated; C-terminal residues 336-363 truncated. b562RIL fused to N-term. |
Zhang et al. (2017).
Zhang H, Han GW, Batyuk A, Ishchenko A, White KL, Patel N, Sadybekov A, Zamlynny B, Rudd MT, Hollenstein K, Tolstikova A, White TA, Hunter MS, Weierstall U, Liu W, Babaoglu K, Moore EL, Katz RD, Shipman JM, Garcia-Calvo M, Sharma S, Sheth P, Soisson SM, Stevens RC, Katritch V, & Cherezov V (2017). Structural basis for selectivity and diversity in angiotensin II receptors.
Nature 544 :327-332. PubMed Id: 28379944. doi:10.1038/nature22035. |
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Smoothened (SMO) receptor in complex with cholesterol (apo-SMOΔC): Homo sapiens E Eukaryota (expressed in HEK-293S-GnTI-), 3.2 Å
Engineered protein: N- and C-termini truncated; apocytochrome b562 RIL (BRIL) replaces intracellular loop 3. with bound vismodegib (vismo-SMOΔC), 3.3 Å: 5L7I |
Byrne et al. (2016).
Byrne EF, Sircar R, Miller PS, Hedger G, Luchetti G, Nachtergaele S, Tully MD, Mydock-McGrane L, Covey DF, Rambo RP, Sansom MS, Newstead S, Rohatgi R, & Siebold,C. (2016). Structural basis of Smoothened regulation by its extracellular domains.
Nature 535 :517-522. PubMed Id: 27437577. |
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Sec and Translocase Proteins
Membrane Proteins Involved with Protein Secretion and Insertion formerly listed as "Channels: Protein-Conducting" |
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SecYEβ translocon: Methanococcus jannaschii A Archaea, 3.5 Å
Coördinates of native complex: 1RHZ. Coördinates of double-mutant complex (K422R,V423T) 1RH5 (3.2 Å resolution). |
van den Berg et al. (2004).
van den Berg B, Clemons WM, Collinson I, Hartmann E, Harrison SC, & Rapoport TA (2004). X-ray structure of a protein-conducting channel.
Nature 427 :36-44. PubMed Id: 14661030. |
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SecYEβ translocon with full-plug (TM2a) deletion: Methanococcus jannaschii A Archaea, 3.6 Å
Coördinates of mutant with half-plug deletion 2YXQ (3.5 Å resolution). |
Li et al. (2007).
Li W, Schulman S, Boyd D, Erlandson K, Beckwith J & Rapoport TA (2007). The plug domain of the SecY protein stabilizes the closed state of the translocon channel and maintains a membrane seal.
Mol Cell 26 :1409-38. PubMed Id: 17531810. |
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SecYEβ "primed" translocon: Pyrococcus furiosus A Archaea (expressed in E. coli), 3.1 Å
|
Egea and Stroud (2010).
Egea PF & Stroud RM (2010). Lateral opening of a translocon upon entry of protein suggests the mechanism of insertion into membranes.
Proc Natl Acad Sci USA 107 :17182-17187. PubMed Id: 20855604. |
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SecYEG translocon in complex with SecA: Thermotoga maritima B Bacteria (expressed in E. coli), 4.5 Å
|
Zimmer et al. (2008).
Zimmer J, Nam Y, & Rapoport TA (2008). Structure of a complex of the ATPase SecA and the protein-translocation channel.
Nature 455 :936-943. PubMed Id: 18923516. |
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SecYE translocon in complex with B. subtilis SecA: Geobacillus thermodenitrificans B Bacteria (expressed in E. coli), 3.7 Å
An OmpA signal sequence is covalently inserted into SecA residue after residue 741. The insert carries a Cys residue that cross-links with a Cys residue in the so-called plug domain of SecY. |
Li et al. (2016).
Li L, Park E, Ling J, Ingram J, Ploegh H, & Rapoport TA (2016). Crystal structure of a substrate-engaged SecY protein-translocation channel.
Nature 531 :395-399. PubMed Id: 26950603. doi:10.1038/nature17163. |
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SecYE translocon in complex with a Fab fragment: Thermus thermophilus B Bacteria (expressed in E. coli), 3.20 Å
SecYE alone 2ZQP (6.0 Å resolution). |
Tsukazaki et al. (2008).
Tsukazaki T, Mori H, Fukai S, Ishitani R, Mori T, Dohmae N, Perederina A, Sugita Y, Vassylyev DG, Ito K, & Nureki O (2008). Conformational transition of Sec machinery inferred from bacterial SecYE structures.
Nature 455 :988-991. PubMed Id: 18923527. |
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SecYEG translocon, I222 space group: Thermus thermophilus B Bacteria (expressed in E. coli), 2.72 Å
C2221 space group, 3.64 Å: 5CH4 |
Tanaka et al. (2015).
Tanaka Y, Sugano Y, Takemoto M, Mori T, Furukawa A, Kusakizako T, Kumazaki K, Kashima A, Ishitani R, Sugita Y, Nureki O, & Tsukazaki T (2015). Crystal Structures of SecYEG in Lipidic Cubic Phase Elucidate a Precise Resting and a Peptide-Bound State.
Cell Rep 13 :1561-1568. PubMed Id: 26586438. doi:10.1016/j.celrep.2015.10.025. |
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YidC27-266 insertase: Bacillus halodurans B Bacteria (expressed in E. coli), 2.40 Å
YidC27-267, 3.20 Å: 3WO7 |
Kumazaki et al. (2014).
Kumazaki K, Chiba S, Takemoto M, Furukawa A, Nishiyama K, Sugano Y, Mori T, Dohmae N, Hirata K, Nakada-Nakura Y, Maturana AD, Tanaka Y, Mori H, Sugita Y, Arisaka F, Ito K, Ishitani R, Tsukazaki T, & Nureki O (2014). Structural basis of Sec-independent membrane protein insertion by YidC.
Nature 509 :516-520. PubMed Id: 24739968. doi:10.1038/nature13167. |
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YidC insertase, full length: Escherichia coli B Bacteria, 3.20 Å
|
Kumazaki et al. (2014).
Kumazaki K, Kishimoto T, Furukawa A, Mori H, Tanaka Y, Dohmae N, Ishitani R, Tsukazaki T, & Nureki O (2014). Crystal structure of Escherichia coli YidC, a membrane protein chaperone and insertase.
Sci Rep 4 :7299. PubMed Id: 25466392. doi:10.1038/srep07299. |
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DUF106 YidC-like protein: Methanocaldococcus jannaschi A Archaea (expressed in E. coli), 3.50 Å
This structure establishes the universality of the YidC/Oxa1/Alb3 family in the three domains of life |
Borowska et al. (2015).
Borowska MT, Dominik PK, Anghel SA, Kossiakoff AA, & Keenan RJ (2015). A YidC-like Protein in the Archaeal Plasma Membrane.
Structure 23 :1715-1724. PubMed Id: 26256539. doi:10.1016/j.str.2015.06.025. |
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SecDF protein-export enhancer: Thermus thermophilus B Bacteria (expressed in E. coli), 3.30 Å
SecDF associates with SecYEG to enhance protein export using the transmembrane proton motive force (PMF). It is a member of the resistance nodulation and cell division (RND) superfamily. A related member of the RND superfamily is the AcrB multi-drug efflux transporter. P1 periplasmic domain, 2.6 Å: 3AQO P4 periplasmic domain, NMR structure: 2RRN |
Tsukazaki et al. (2011).
Tsukazaki T, Mori H, Echizen Y, Ishitani R, Fukai S, Tanaka T, Perederina A, Vassylyev DG, Kohno T, Maturana AD, Ito K, & Nureki O (2011). Structure and function of a membrane component SecDF that enhances protein export.
Nature 474 :235-238. PubMed Id: 21562494. doi:10.1038/nature09980. |
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TatA twin-arginine translocase, model of oligomeric complex: Escherichia coli B Bacteria, NMR/Molecular Dynamics Model
TatA monomer, NMR Structure: 2LZR |
Rodriguez et al. (2013).
Rodriguez F, Rouse SL, Tait CE, Harmer J, De Riso A, Timmel CR, Sansom MS, Berks BC, & Schnell JR (2013). Structural model for the protein-translocating element of the twin-arginine transport system.
Proc Natl Acad Sci USA 110 :E1092-E1101. PubMed Id: 23471988. doi:10.1073/pnas.1219486110. |
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TatC twin-arginine translocase receptor: Aquifex aeolicus B Bacteria (expressed in E. coli), 3.50 Å
Crystallized using lauryl maltose neopentyl glycol (LMNG) |
Rollauer et al. (2012).
Rollauer SE, Tarry MJ, Graham JE, Jääskeläinen M, Jäger F, Johnson S, Krehenbrink M, Liu SM, Lukey MJ, Marcoux J, McDowell MA, Rodriguez F, Roversi P, Stansfeld PJ, Robinson CV, Sansom MS, Palmer T, Högbom M, Berks BC, & Lea SM (2012). Structure of the TatC core of the twin-arginine protein transport system.
Nature 492 :210-214. PubMed Id: 23201679. doi:10.1038/nature11683. |
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TatC twin-arginine translocase receptor: Aquifex aeolicus B Bacteria (expressed in E. coli), 4.00 Å
Crystallized using DHCP Structure using DDM for crystallization, 6.80 Å: 4HTT |
Ramasamy et al. (2013).
Ramasamy S, Abrol R, Suloway CJ, & Clemons WM Jr (2013). The Glove-like Structure of the Conserved Membrane Protein TatC Provides Insight into Signal Sequence Recognition in Twin-Arginine Translocation.
Structure 21 :777-788. PubMed Id: 23583035. doi:10.1016/j.str.2013.03.004. |
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Celluose Synthases
Membrane Imbedded Glycosyltransferases These use UDP-activated glucose to elongate nascent polysaccharides processively across membranes. |
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BcsA-BcsB cellulose synthase/cellulose translocation intermediate.: Rhodobacter sphaeroides B Bacteria (expressed in E. coli), 3.25 Å
Shows a translocating glucan |
Morgan et al. (2013).
Morgan JL, Strumillo J, & Zimmer J (2013). Crystallographic snapshot of cellulose synthesis and membrane translocation.
Nature 493 :181-186. PubMed Id: 23222542. doi:10.1038/nature11744. |
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PNPT Superfamily
PNPT: polyprenylphosphate N-acetyl hexosamine 1-phosphate transferase Proteins in this superfamily are responsible for the synthesis of cell envelope polymers |
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MraY phospho-MurNAc-pentapeptide translocase: Aquifex aeolicus B Bacteria (expressed in E. coli), 3.30 Å
|
Chung et al. (2013).
Chung BC, Zhao J, Gillespie RA, Kwon DY, Guan Z, Hong J, Zhou P, & Lee SY (2013). Crystal Structure of MraY, an Essential Membrane Enzyme for Bacterial Cell Wall Synthesis.
Science 341 :1012-1016. PubMed Id: 23990562. doi:10.1126/science.1236501. |
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MraY translocase in complex with Muraymycin D2: Aquifex aeolicus B Bacteria (expressed in E. coli), 2.95 Å
|
Chung et al. (2016).
Chung BC, Mashalidis EH, Tanino T, Kim M, Matsuda A, Hong J, Ichikawa S, & Lee SY (2016). Structural insights into inhibition of lipid I production in bacterial cell wall synthesis.
Nature 533 :557-560. PubMed Id: 27088606. doi:10.1038/nature17636. |
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Oligosaccharyltransferases (OST)
Catalyses Asparagine-linked (N-linked) Glycosylation |
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PglB OST in complex with acceptor peptide: Campylobacter lari B Bacteria (expressed in E. coli), 3.40 Å
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Lizak et al. (2011).
Lizak C, Gerber S, Numao S, Aebi M, & Locher KP (2011). X-ray structure of a bacterial oligosaccharyltransferase.
Nature 474 :350-355. PubMed Id: 21677752. doi:10.1038/nature10151. |
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AglB OST with bound zinc & sulfate (C2 space group): Archaeoglobus fulgidus A Archaea (expressed in E. coli), 2.50 Å
P43212 space group, 3.41 Å: 3WAK |
Matsumoto et al. (2013).
Matsumoto S, Shimada A, Nyirenda J, Igura M, Kawano Y, & Kohda D (2013). Crystal structures of an archaeal oligosaccharyltransferase provide insights into the catalytic cycle of N-linked protein glycosylation.
Proc Natl Acad Sci USA 110 :17868-17873. PubMed Id: 24127570. doi:10.1073/pnas.1309777110 . |
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Glycosyltransfereases
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GtrB polyisoprenyl-glycosyltransferase (PI-GT): Synechocystis sp. PCC6803 B Bacteria (expressed in E. coli), 3.19 Å
F215A mutant, 3.0 Å: 5EKE |
Ardiccioni et al. (2016).
Ardiccioni C, Clarke OB, Tomasek D, Issa HA, von Alpen DC, Pond HL, Banerjee S, Rajashankar KR, Liu Q, Guan Z, Li C, Kloss B, Bruni R, Kloppmann E, Rost B, Manzini MC, Shapiro L, & Mancia F (2016). Structure of the polyisoprenyl-phosphate glycosyltransferase GtrB and insights into the mechanism of catalysis.
Nat Commun 7 :10175. PubMed Id: 26729507. doi:10.1038/ncomms10175. |
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ArnT glycosyltransferase, apo form: Cupriavidus metallidurans B Bacteria (expressed in E. coli), 2.7 Å
This is a lipid-to-lipid glycosyltransferase. with bound lipid carrier undecaprenyl phosphate, 3.2 Å: 5F15 |
Petrou et al. (2016).
Petrou VI, Herrera CM, Schultz KM, Clarke OB, Vendome J, Tomasek D, Banerjee S, Rajashankar KR, Belcher Dufrisne M, Kloss B, Kloppmann E, Rost B, Klug CS, Trent MS, Shapiro L, & Mancia F (2016). Structures of aminoarabinose transferase ArnT suggest a molecular basis for lipid A glycosylation.
Science 351 :608-612. PubMed Id: 26912703. doi:10.1126/science.aad1172. |
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Diacylglyceryl Transferases
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Phosphatidylglycerol:prolipoprotein diacylglyceryl transferase (Lgt) in complex with phosphatidylglycerol: Escherichia coli B Bacteria, 1.9 Å
in complex with palmitic acid inhibitor, 1.6 Å: 5AZB |
Mao et al. (2016).
Mao G, Zhao Y, Kang X, Li Z, Zhang Y, Wang X, Sun F, Sankaran K, & Zhang XC (2016). Crystal structure of E. coli lipoprotein diacylglyceryl transferase.
Nat Commun 7 . PubMed Id: 26729647. doi:10.1038/ncomms10198. |
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Phosphoethanolamine (PEA) Transferases
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Lipid A phosphoethanolamine transferase: Neisseria meningitidis B Bacteria (expressed in E. coli), 2.75 Å
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Anandan et al. (2017).
Anandan A, Evans GL, Condic-Jurkic K, O'Mara ML, John CM, Phillips NJ, Jarvis GA, Wills SS, Stubbs KA, Moraes I, Kahler CM, & Vrielink A (2017). Structure of a lipid A phosphoethanolamine transferase suggests how conformational changes govern substrate binding.
Proc Natl Acad Sci USA 114 :2218-2223. PubMed Id: 28193899. doi:10.1073/pnas.1612927114. |
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Methyltransferases
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Isoprenylcysteine carboxyl methyltransferase (ICMT): Methanosarcina acetivorans A Archaea (expressed in E. coli), 3.40 Å
Catalyzes the final step of CAAX processing. The protein has 5 TM helices. |
Yang et al. (2011).
Yang J, Kulkarni K, Manolaridis I, Zhang Z, Dodd RB, Mas-Droux C, & Barford D (2011). Mechanism of Isoprenylcysteine Carboxyl Methylation from the Crystal Structure of the Integral Membrane Methyltransferase ICMT
Mol Cell 44 :997-1004. PubMed Id: 22195972. doi:10.1016/j.molcel.2011.10.020. |
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Phosphotransferases
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DgkA diacylglycerol kinase (DAGK): Escherichia coli B Bacteria, NMR structure (DPC micelles)
Domain-swapped homotrimer |
van Horn et al.. (2009).
van Horn WD, Kim HJ, Ellis CD, Hadziselimovic A, Sulistijo ES, Karra MD, Tian C, Sönnichsen FD, & Sanders CR (2009). Solution nuclear magnetic resonance structure of membrane-integral diacylglycerol kinase.
Science 324 :1726-1729. PubMed Id: 19556511. |
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Li et al. (2013).
Li D, Lyons JA, Pye VE, Vogeley L, Aragão D, Kenyon CP, Shah ST, Doherty C, Aherne M, & Caffrey M (2013). Crystal structure of the integral membrane diacylglycerol kinase.
Nature 497 :521-524. PubMed Id: 23676677. |
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DgkA diacylglycerol kinase (DAGK) Δ4 mutant with bound monoacylglycerol (9.9 MAG) and ACP: Escherichia coli B Bacteria, 2.70 Å
ACP = non-hydrolysable ATP analogue: adenylylmethylenediphosphonate Δ4 mutant with 9.9MAG, 3.15 Å: 4UXW Δ7 mutant with 7.9 MAG, 2.18 Å: 4UXZ Δ7 mutant with 7.9 MAG (by free-electron laser), 2.18 Å: 4UYO |
Li et al. (2015).
Li D, Stansfeld PJ, Sansom MS, Keogh A, Vogeley L, Howe N, Lyons JA, Aragao D, Fromme P, Fromme R, Basu S, Grotjohann I, Kupitz C, Rendek K, Weierstall U, Zatsepin NA, Cherezov V, Liu W, Bandaru S, English NJ, Gati C, Barty A, Yefanov O, Chapman HN, Diederichs K, Messerschmidt M, Boutet S, Williams GJ, Marvin Seibert M, & Caffrey M (2015). Ternary structure reveals mechanism of a membrane diacylglycerol kinase.
Nat Commun 6 :10140. PubMed Id: 26673816. doi:10.1038/ncomms10140. |
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Phosphatidic Acid Phosphatases
Membrane-integrated type II phosphatidic acid phosphatases (PAP2) |
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PgpB phosphatidylglycerophosphate phosphatase B: Escherichia coli B Bacteria, 3.20 Å
|
Fan et al. (2014).
Fan J, Jiang D, Zhao Y, Liu J, & Zhang XC (2014). Crystal structure of lipid phosphatase Escherichia coli phosphatidylglycerophosphate phosphatase B.
Proc Natl Acad Sci USA 111 :7636-7640. PubMed Id: 24821770. |
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UbiA Prenyltransferases
These enzymes are involved in the biosynthesis of a wide range molecules, including respiratory lipoquinones and archael lipids |
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Huang et al. (2014).
Huang H, Levin EJ, Liu S, Bai Y, Lockless SW, & Zhou M (2014). Structure of a Membrane-Embedded Prenyltransferase Homologous to UBIAD1.
PLoS Biol 12 7:e1001911. PubMed Id: 25051182. doi:10.1371/journal.pbio.1001911. |
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Phosphoenolpyruvate-Dependent Phosphotransferases (PTSs)
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ChbC EIIC phosphorylation-coupled saccharide transporter: Bacillus cereus B Bacteria (expressed in E. coli), 3.30 Å
The protein is a homodimer in an inward-facing occluded conformation. Each protomer contains a diacetylchitobiose. |
Cao et al. (2011).
Cao Y, Jin X, Levin EJ, Huang H, Zong Y, Quick M, Weng J, Pan Y, Love J, Punta M, Rost B, Hendrickson WA, Javitch JA, Rajashankar KR, & Zhou M (2011). Crystal structure of a phosphorylation-coupled saccharide transporter
Nature 473 :50-54. PubMed Id: 21471968. doi:10.1038/nature09939. |
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UlaA bacterial vitamin C transporter, C2 space group: Escherichia coli B Bacteria, 1.65 Å
P21 form, 2.36 Å: 4RP8 |
Luo et al. (2015).
Luo P, Yu X, Wang W, Fan S, Li X, & Wang J (2015). Crystal structure of a phosphorylation-coupled vitamin C transporter.
Nat Struct Mol Biol 22 3:238-241. PubMed Id: 25686089. doi:10.1038/nsmb.2975. |
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MalT EIIC phosphorylation-coupled maltose transporter: Bacillus cereus B Bacteria (expressed in E. coli), 2.55 Å
The protein is in an outward-facing conformation |
McCoy et al. (2016).
McCoy JG, Ren Z, Stanevich V, Lee J, Mitra S, Levin EJ, Poget S, Quick M, Im W, & Zhou M (2016). The Structure of a Sugar Transporter of the Glucose EIIC Superfamily Provides Insight into the Elevator Mechanism of Membrane Transport.
Structure 24 6:956-964. PubMed Id: 27161976. doi:10.1016/j.str.2016.04.003. |
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Intramembrane Proteases
( NSMB News & Views on three GlpG Structures) |
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GlpG rhomboid-family intramembrane protease: Escherichia coli B Bacteria, 2.1 Å
P32 space group. One molecule in asymmetric unit. |
Wang et al. (2006).
Wang Y, Zhang Y, & Ha Y (2006). Crystal structure of a rhomboid family intramembrane protease.
Nature 444 :179-183. PubMed Id: 17051161. |
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GlpG rhomboid-family intramembrane protease: Escherichia coli B Bacteria, 1.90 Å
W136A mutant, 1.70 Å: 3B44 |
Wang et al. (2007).
Wang Y, Maegawa S, Akiyama Y, & Ha Y (2007). The role of L1 loop in the mechanism of rhomboid intramembrane protease GlpG.
J Mol Biol 374 :1104-1113. PubMed Id: 17976648. |
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GlpG rhomboid-family intramembrane protease: Escherichia coli B Bacteria, 2.5 Å
Shows GlpG in a more open conformation. |
Wang & Ha (2007).
Wang Y & Ha Y (2007). Open-cap conformation of intramembrane protease GlpG.
Proc Natl Acad Sci USA 104 :2098-2102. PubMed Id: 17277078. |
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GlpG rhomboid-family intramembrane protease: Escherichia coli B Bacteria, 2.6 Å
P31 space group. Two anti-parallel molecules in asymmetric unit. |
Wu et al. (2006).
Wu Z, Yan N, Feng L, Oberstein A, Yan H, Baker RP, Gu L, Jeffrey PD, Urban S & Shi Y (2006). Structural analysis of a rhomboid family intramembrane protease reveals a gating mechanism for substrate entry.
Nature Struc. Molec. Biol. 13 :1084-1091. PubMed Id: 17099694. |
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GlpG rhomboid-family intramembrane protease: Escherichia coli B Bacteria, 2.3 Å
P21 space group. Two anti-parallel molecules in asymmetric unit. |
Ben-Shem et al. (2007).
Ben-Shem A, Fass D, & Bibi E (2007). Structural basis for intramembrane proteolysis by rhomboid serine proteases.
Proc Natl Acad Sci USA 104 :426-466. PubMed Id: 17190827. |
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GlpG rhomboid-family intramembrane protease: Escherichia coli B Bacteria, 1.65 Å
Acyl GlpG: GlpG with covalently bound isocoumarin inhibitor, 2.09 Å: 2XOW |
Vinothkumar et al. (2010).
Vinothkumar KR, Strisovsky K, Andreeva A, Christova Y, Verhelst S, & Freeman M (2010). The structural basis for catalysis and substrate specificity of a rhomboid protease.
EMBO J 29 :3797-3809. PubMed Id: 20890268. |
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GlpG rhomboid-family intramembrane protease with lipids: Escherichia coli B Bacteria, 1.70 Å
S201T active-site mutant in orthorhombic crystal form. S201T active-site mutant in trigonal crystal form, 1.85 Å: 2XTU |
Vinothkumar (2011).
Vinothkumar KR (2011). Structure of Rhomboid Protease in a Lipid Environment.
J Mol Biol 407 :232-247. PubMed Id: 21256137. |
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GlpG rhomboid-family intramembrane protease with a mechanism-based inhibitor: Escherichia coli B Bacteria, 2.30 Å
The inhibitor is diisopropyl fluorophosphonate, which mimics the oxyanion-containing tetrahedral intermediate of the hydrolytic reaction. |
Xue & Ha (2012).
Xue Y & Ha Y (2012). Catalytic Mechanism of Rhomboid Protease GlpG Probed by 3,4-Dichloroisocoumarin and Diisopropyl Fluorophosphonate.
J Biol Chem 287 :3099-3107. PubMed Id: 22130671. doi:10.1074/jbc.M111.310482. |
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GlpG rhomboid-family intramembrane protease in complex with phosphonofluoridate inhibitor: Escherichia coli B Bacteria, 2.60 Å
The phosphonofluoridate inhibitor is covalently bound to the catalytic serine |
Xue et al. (2012).
Xue Y, Chowdhury S, Liu X, Akiyama Y, Ellman J, & Ha Y (2012). Conformational Change in Rhomboid Protease GlpG Induced by Inhibitor Binding to Its S' Subsites.
Biochemistry 51 :3723-3731. PubMed Id: 22515733. doi:10.1021/bi300368b. |
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GlpG N-terminal cytoplasmic domain: Pseudomonas aeruginosa B Bacteria (expressed in E. coli), NMR Structure
|
Del Rio et al. (2007).
Del Rio A, Dutta K, Chavez J, Ubarretxena-Belandia I, & Ghose R (2007). Solution structure and dynamics of the N-terminal cytosolic domain of rhomboid intramembrane protease from Pseudomonas aeruginosa: insights into a functional role in intramembrane proteolysis.
J Mol Biol 365 :109-122. PubMed Id: 17059825. doi:10.1016/j.jmb.2006.09.047. |
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GlpG N-terminal cytoplasmic domain: Escherichia coli B Bacteria, NMR Structure
|
Sherratt et al. (2009).
Sherratt AR, Braganza MV, Nguyen E, Ducat T, & Goto NK (2009). Insights into the effect of detergents on the full-length rhomboid protease from Pseudomonas aeruginosa and its cytosolic domain.
BBA Biomembranes 1788 :2444-2453. PubMed Id: 19761755. doi:10.1016/j.bbamem.2009.09.003. |
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GlpG N-terminal cytoplasmic domain: Escherichia coli B Bacteria, 1.35 Å
Domain-swapped dimer. |
Lazareno-Saez et al. (2013).
Lazareno-Saez C, Arutyunova E, Coquelle N, & Lemieux MJ (2013). Domain Swapping in the Cytoplasmic Domain of the Escherichia coli Rhomboid Protease.
J Mol Biol 425 :1127-1142. PubMed Id: 23353827. doi:10.1016/j.jmb.2013.01.019. |
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Zoll et al. (2014).
Zoll S, Stanchev S, Began J, Skerle J, Lepšík M, Peclinovská L, Majer P, & Strisovsky K (2014). Substrate binding and specificity of rhomboid intramembrane protease revealed by substrate-peptide complex structures.
EMBO J 33 :2408-2421. PubMed Id: 25216680. doi:10.15252/embj.201489367. |
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GlpG rhomboid-family intramembrane protease in complex with Ac-VRMA-CHO: Escherichia coli B Bacteria, 2.3 Å
Y205F mutant crystalized from bicelles, 2.5 Å: 5F5D Y205F mutant in complex with Ac-RMA-CHO (from bicelles), 2.3 Å: 5F5G Y205F mutant in complex with Ac-VRMA-CHO (from bicelles), 2.4 Å: 5F5J Y205F mutant in complex with Ac-RKVRMA-CHO (from bicelles), 2.4 Å:5F5K |
Cho et al. (2016).
Cho S, Dickey SW, & Urban S (2016). Crystal Structures and Inhibition Kinetics Reveal a Two-Stage Catalytic Mechanism with Drug Design Implications for Rhomboid Proteolysis.
Mol Cell 61 3:329-340. PubMed Id: 26805573. doi:10.1016/j.molcel.2015.12.022. |
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GlpG rhomboid-family intramembrane protease: Haemophilus influenzae B Bacteria (expressed in E. coli), 2.2 Å
Shows three bound lipid molecules. Monoclinic C2 space group. |
Lemieux et al. (2007).
Lemieux MJ, Fischer SJ, Cherney MM, Bateman KS, & James MNG (2007). The crystal structure of the rhomboid peptidase from Haemophilus influenzae provides insight into intramembrane proteolysis.
Proc Natl Acad Sci USA 104 :750-754. PubMed Id: 17210913. |
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GlpG rhomboid-family intramembrane protease: Haemophilus influenzae B Bacteria (expressed in E. coli), 2.84 Å
Reveals disorder in loops 4 and 5 and helix 5. |
Brooks et al. (2011).
Brooks CL, Lazareno-Saez C, Lamoureux JS, Mak MW, & Lemieux MJ (2011). Insights into Substrate Gating inH. influenzaeRhomboid.
J Mol Biol 407 :687-697. PubMed Id: 21295583. |
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|
Site-2 Protease (S2P). Intramembrane Metalloprotease: Methanocaldococcus jannaschii A Archaea, 3.3 Å
Structure is of the transmembrane core only. |
Feng et al. (2007).
Feng L, Yan H, Wu Z, Yan N, Wang Z, Jeffrey PD, & Shi Y (2007). Structure of a site-2 protease family intramembrane metalloprotease.
Science 318 :1608-1612. PubMed Id: 18063795. |
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Signal Peptide Peptidase (SppA), native protein: Escherichia coli B Bacteria, 2.55 Å
SeMet protein, 2.76 Å: 3BEZ. Long thought to be a transmembrane protein, the structure reveals a peripheral homotetramer that likely is buried in the membrane interface. Each monomer has a putative N-terminal transmembrane helix for anchoring to the membrane. This anchor was removed for crystallization. Listed under TRANSMEMBRANE PROTEINS: ALPHA-HELICAL : Intramembrane Proteases, MONOTOPIC MEMBRANE PROTEINS : Peptidases. |
Kim et al. (2008).
Kim AC, Oliver DC, & Paetzel M (2008). Crystal structure of a bacterial signal Peptide peptidase.
J Mol Biol 376 :352-366. PubMed Id: 18164727. |
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Signal Peptide Peptidase (SppA): Bacillus subtilis B Bacteria (expressed in E. coli), 2.37 Å
Each monomer of the homooctamer has a putative N-terminal transmembrane helix for anchoring to the membrane. This anchor was removed for crystallization. Listed under TRANSMEMBRANE PROTEINS: ALPHA-HELICAL : Intramembrane Proteases, MONOTOPIC MEMBRANE PROTEINS : Peptidases. |
Nam et al. (2012).
Nam SE, Kim AC, & Paetzel M (2012). Crystal Structure of Bacillus subtilis Signal Peptide Peptidase A.
J Mol Biol 419 :347-358. PubMed Id: 22472423. doi:10.1016/j.jmb.2012.03.020. |
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Signal Peptide Peptidase (SppA) K199A mutant showing C-terminal peptide bound in eight active sites: Bacillus subtilis B Bacteria (expressed in E. coli), 2.39 Å
Each monomer of the homooctamer has a putative N-terminal transmembrane helix for anchoring to the membrane. This anchor was removed for crystallization. Listed under TRANSMEMBRANE PROTEINS: ALPHA-HELICAL : Intramembrane Proteases, MONOTOPIC MEMBRANE PROTEINS : Peptidases. |
Nam & Paetzel (2013).
Nam SE, & Paetzel M (2013). Structure of Signal Peptide Peptidase A with C-Termini Bound in the Active Sites: Insights into Specificity, Self-Processing, and Regulation.
Biochemistry 52 :8811-8822. PubMed Id: 24228759. |
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Li et al. (2013).
Li X, Dang S, Yan C, Gong X, Wang J, & Shi Y (2013). Structure of a presenilin family intramembrane aspartate protease.
Nature 493 :56-61. PubMed Id: 23254940. doi:10.1038/nature11801. |
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FlaK preflagellin aspartyl protease: Methanococcus maripaludis A Archaea (expressed in E. coli), 3.60 Å
This is a GXGD protease related to presenilln. |
Hu et al. (2011).
Hu J, Xue Y, Lee S, & Ha Y (2011). The crystal structure of GXGD membrane protease FlaK
Nature 475 :528-531. PubMed Id: 21765428. doi:10.1038/nature10218. |
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CAAX protease Ste24p: Saccharomyces mikatae E Eukaryota (expressed in S. cerevisiae), 3.10 Å
|
Pryor et al. (2013).
Pryor EE Jr, Horanyi PS, Clark KM, Fedoriw N, Connelly SM, Koszelak-Rosenblum M, Zhu G, Malkowski MG, Wiener MC, & Dumont ME (2013). Structure of the integral membrane protein CAAX protease Ste24p.
Science 339 :1600-1604. PubMed Id: 23539602. doi:10.1126/science.1232048. |
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CAAX protease ZMPSTE24: Homo sapiens E Eukaryota (expressed in S. frugiperda), 3.40 Å
E336A mutant in complex with C-terminus tetrapeptide from prelamin A, 3.80 Å: 2YPT |
Quigley et al. (2013).
Quigley A, Dong YY, Pike AC, Dong L, Shrestha L, Berridge G, Stansfeld PJ, Sansom MS, Edwards AM, Bountra C, von Delft F, Bullock AN, Burgess-Brown NA, & Carpenter EP (2013). The structural basis of ZMPSTE24-dependent laminopathies.
Science 339 :1604-1607. PubMed Id: 23539603. doi:doi:10.1126/science.1231513. |
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CAAX protease Rce1: Methanococcus maripaludis A Archaea (expressed in E. coli), 2.50 Å
|
Manolaridis et al. (2013).
Manolaridis I, Kulkarni K, Dodd RB, Ogasawara S, Zhang Z, Bineva G, O'Reilly N, Hanrahan SJ, Thompson AJ, Cronin N, Iwata S, & Barford D (2013). Mechanism of farnesylated CAAX protein processing by the intramembrane protease Rce1.
Nature 504 :301-305. PubMed Id: 24291792. doi:10.1038/nature12754. |
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γ-secretase: Homo sapiens E Eukaryota (expressed in HEK-293S cells), 4.32 Å
|
Sun et al. (2015).
Sun L, Zhao L, Yang G, Yan C, Zhou R, Zhou X, Xie T, Zhao Y, Wu S, Li X, & Shi Y (2015). Structural basis of human γ-secretase assembly.
Proc Natl Acad Sci USA 112 :6003-6008. PubMed Id: 25918421. doi:10.1073/pnas.1506242112. |
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γ-secretase: Homo sapiens E Eukaryota (expressed in HEK293F cells), 3.4 Å
single-particle Cryo-EM structure |
Bai et al. (2015).
Bai XC, Yan C, Yang G, Lu P, Ma D, Sun L, Zhou R, Scheres SH, & Shi Y (2015). An atomic structure of human γ-secretase.
Nature 525 :212-217. PubMed Id: 26280335. doi:10.1038/nature14892. |
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γ-secretase nicastrin extracellular domain: Homo sapiens E Eukaryota (expressed in HEK293F cells), 5.4 Å
Single-particle cryo-EM structure. 4.5 Å and 5.4 Å EM maps of the full protein including TM domains are available in the EMDB with accession codes EMD-2677 and EMD-2678, respectively. |
Lu et al. (2014).
Lu P, Bai XC, Ma D, Xie T, Yan C, Sun L, Yang G, Zhao Y, Zhou R, Scheres SH, & Shi Y (2014). Three-dimensional structure of human γ-secretase.
Nature 512 :166-170. PubMed Id: 25043039. doi:10.1038/nature13567. |
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γ-secretase nicastrin-a transmembrane domain in SDS:: Homo sapiens E Eukaryota (expressed in E. coli), NMR structure
in dodecylphosphocholine micelles, 2NR7 |
Li et al. (2016).
Li Y, Liew LS, Li Q, & Kang C (2016). Structure of the transmembrane domain of human nicastrin-a component of γ-secretase.
Sci Rep 6 :19522. PubMed Id: 26776682. doi:10.1038/srep19522. |
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γ-secretase nicastrin extracellular domain: Dictyostelium purpureum E Eukaryota (expressed in S. frugiperda), 1.95 Å
|
Xie et al. (2014).
Xie T, Yan C, Zhou R, Zhao Y, Sun L, Yang G, Lu P, Ma D, & Shi Y (2014). Crystal structure of the γ-secretase component nicastrin.
Proc Natl Acad Sci USA 111 37:13349-13354. PubMed Id: 25197054. doi:10.1073/pnas.1414837111. |
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|
Vogeley et al. (2016).
Vogeley L, El Arnaout T, Bailey J, Stansfeld PJ, Boland C, & Caffrey M (2016). Structural basis of lipoprotein signal peptidase II action and inhibition by the antibiotic globomycin.
Science 351 :876-880. PubMed Id: 26912896. doi:10.1126/science.aad3747. |
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Membrane-Bound Metalloproteases
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apo-FtsH ATP-dependent metalloprotease: Thermotoga maritima B Bacteria (expressed in E. coli), 2.60 Å
This is a homo-hexameric AAA+ protease. Each monomer is anchored to the cytoplasmic membrane by two transmembrane segments, which are missing in the structure. The protease can degrade both soluble and membrane proteins. |
Bieniossek et al. (2009).
Bieniossek C, Niederhauser B, & Baumann UM (2009). The crystal structure of apo-FtsH reveals domain movements necessary for substrate unfolding and translocation.
Proc Natl Acad Sci USA 106 :21579-21584. PubMed Id: 19955424. |
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apo-FtsH ATP-dependent metalloprotease: Aquifex aeolicus B Bacteria (expressed in E. coli), 2.96 Å
truncated protein, 3.25 Å: 4Z8X This is a homo-hexameric AAA+ protease. Each monomer is anchored to the cytoplasmic membrane by two transmembrane segments, which are missing in the structure. The protease can degrade both soluble and membrane proteins. |
Vostrukhina et al. (2015).
Vostrukhina M, Popov A, Brunstein E, Lanz MA, Baumgartner R, Bieniossek C, Schacherl M, & Baumann U (2015). The structure of Aquifex aeolicus FtsH in the ADP-bound state reveals a C2-symmetric hexamer.
Acta Crystallogr D Biol Crystallogr 71 :1307-1318. PubMed Id: 26057670. doi:10.1107/S1399004715005945. |
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H+/Cl-Exchange Transporters
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H+/Cl- Exchange Transporter: Salmonella typhimurium B Bacteria (expressed in E. coli), 3.0 Å
Formerly ClC Chloride Channel. Escherichia coli protein, 3.5 Å: 1KPK |
Dutzler et al. (2002).
Dutzler R, Campbell EB, Cadene M, Chait BT, & MacKinnon R (2002). X-ray structure of a ClC chloride channel at 3.0 Å reveals the molecular basis of anion selectivity.
Nature 415 :287-294. PubMed Id: 11796999. |
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Dutzler et al. (2003).
Dutzler R, Campbell EB, & MacKinnon R (2003). Gating the selectivity filter in ClC chloride channels.
Science 300 :108-112. PubMed Id: 12649487. |
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|
Lobet & Dutzler (2006).
Lobet S & Dutzler R (2006). Ion-binding properties of the ClC chloride selectivity filter.
EMBO J 25 :24-33. PubMed Id: 16341087. |
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Monomeric H+/Cl- Exchange Transporter: Escherichia coli B Bacteria, 3.10 Å
ClC transporter was engineered to place tryptophan residues (I201W; I422W) at the momomer-monomer interface to prevent dimerization. |
Robertson et al. (2010).
Robertson JL, Kolmakova-Partensky L, & Miller C (2010). Design, function and structure of a monomeric ClC transporter.
Nature 468 :844-847. PubMed Id: 21048711. |
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H+/Cl- Exchange Transporter in Glutamate: Escherichia coli B Bacteria, 3.02 Å
E148A mutant |
Feng et al. (2012).
Feng L, Campbell EB, & Mackinnon R (2012). Molecular mechanism of proton transport in CLC Cl-/H+ exchange transporters.
Proc Natl Acad Sci USA 109 :11699-11704. PubMed Id: 22753511. doi:10.1073/pnas.1205764109. |
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H+/Cl- Exchange Transporter (truncated): Escherichia coli B Bacteria, 2.50 Å
Truncation: Residues 2-16 at N-terminal and 461-464 at C-terminal. E202Y mutant, 3.20 Å: 4FTP |
Lim et al. (2012).
Lim HH, Shane T, & Miller C (2012). Intracellular proton access in a Cl-/H+ antiporter.
PLoS Biol 10 :e1001441. PubMed Id: 23239938. doi:10.1371/journal.pbio.1001441. |
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H+/Cl- Exchange Transporter, Cysless A399C-A432C mutant: Escherichia coli B Bacteria, 3.52 Å
Fab complex. |
Basilio et al. (2014).
Basilio D, Noack K, Picollo A, & Accardi A (2014). Conformational changes required for H+/Cl- exchange mediated by a CLC transporter.
Nat Struct Mol Biol 21 :456-463. PubMed Id: 24747941. doi:10.1038/nsmb.2814. |
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H+/Cl- Eukaryotic Exchange Transporter: Cyanidioschyzon merolae E Eukaryota (expressed in Trichoplusia ni), 3.50 Å
|
Feng et al. (2010).
Feng L, Campbell EB, Hsiung Y, & MacKinnon R (2010). Structure of a eukaryotic CLC transporter defines an intermediate state in the transport cycle.
Science 330 :635-641. PubMed Id: 20929736. |
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H+/Cl- Eukaryotic Exchange Transporter: Synechocystis sp. pcc 6803 B Bacteria (expressed in E. coli), 3.20 Å
In the presence of Br-, 3.60 Å: 3Q17 |
Jayaram et al. (2011).
Jayaram H, Robertson JL, Wu F, Williams C, & Miller C (2011). Structure of a Slow CLC Cl?/H+Antiporter from a Cyanobacterium.
Biochemistry 50 :788-794. PubMed Id: 21174448. |
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CorA Superfamily Ion Transporters
Channels and transporters for divalent cation homeostasis. These have a membrane domain in series with a cytoplasmic domain that together form a continuous channel. |
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CorA Mg2+ Transporter: Thermotoga maritima B Bacteria (expressed in E. coli), 3.9 Å
Cytoplasmic domain alone, 1.85 Å: 2BBH |
Lunin et al. (2006).
Lunin VV, Dobrovetsky E, Khutoreskaya G, Zhang R, Joachimiak A, Doyle DA, Bochkarev A, Maguire ME, Edwards AM, & Koth CM (2006). Crystal structure of the CorA Mg2+transporter.
Nature 440 :833-837. PubMed Id: 16598263. |
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CorA Mg2+ Transporter: Thermotoga maritima B Bacteria (expressed in E. coli), 2.9 Å
|
Eshaghi et al. (2006).
Eshaghi S, Niegowski D, Kohl A, Martinez Molina D, Lesley SA, & Nordlund P (2006). Crystal structure of a divalent metal ion transporter CorA at 2.9 angstrom resolution.
Science 313 :354-357. PubMed Id: 16857941. |
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CorA Mg2+ Transporter: Thermotoga maritima B Bacteria (expressed in E. coli), 3.7 Å
|
Payandeh & Pai (2006).
Payandeh J & Pai EF (2006). A structural basis for Mg2+ homeostasis and the CorA translocation cycle
EMBO J 25 :3762-3773. PubMed Id: 16902408. doi:10.1038/sj.emboj.7601269. |
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CorA Mg2+ Transporter, coiled-coil mutant in the absence of Mg2+: Thermotoga maritima B Bacteria (expressed in E. coli), 3.80 Å
Coiled-coil mutant in the presence of Mg2+, 3.92 Å: 4EED |
Pfoh et al. (2012).
Pfoh R, Li A, Chakrabarti N, Payandeh J, Pomès R, & Pai EF (2012). Structural asymmetry in the magnesium channel CorA points to sequential allosteric regulation.
Proc Natl Acad Sci USA 109 :18809-18814. PubMed Id: 23112165. doi:10.1073/pnas.1209018109. |
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Matthies et al. (2016).
Matthies D, Dalmas O, Borgnia MJ, Dominik PK, Merk A, Rao P, Reddy BG, Islam S, Bartesaghi A, Perozo E, & Subramaniam S (2016). Cryo-EM Structures of the Magnesium Channel CorA Reveal Symmetry Break upon Gating.
Cell 164 :747-756. PubMed Id: 26871634. doi:10.1016/j.cell.2015.12.055. |
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CorA Mg2+ Transporter: Methanocaldococcus jannaschii A Archaea (expressed in E. coli), 3.20 Å
Soluble domain, 2.50 Å: 4EGW |
Guskov et al. (2012).
Guskov A, Nordin N, Reynaud A, Engman H, Lundbäck AK, Jong AJ, Cornvik T, Phua T, & Eshaghi S (2012). Structural insights into the mechanisms of Mg2+ uptake, transport, and gating by CorA.
Proc Natl Acad Sci USA 109 :18459-18464. PubMed Id: 23091000. doi:10.1073/pnas.1210076109 . |
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ZntB Zn+2 transporter cytoplasmic domain: Vibrio parahaemolyticus B Bacteria (expressed in E. coli), 1.90 Å
|
Tan et al. (2009).
Tan K, Sather A, Robertson JL, Moy S, Roux B, & Joachimiak A (2009). Structure and electrostatic property of cytoplasmic domain of ZntB transporter
Protein Sci 18 :2043-2052. PubMed Id: 19653298. doi:10.1002/pro.215. |
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ZntB Zn+2 transporter cytoplasmic domain, P21 space group: Salmonella enterica B Bacteria (expressed in E. coli), 2.30 Å
C2 space group, 3.13 Å: 3NWI |
Wan et al. (2011).
Wan Q, Ahmad MF, Fairman J, Gorzelle B, de la Fuente M, Dealwis C, & Maguire ME (2011). X-Ray crystallography and isothermal titration calorimetry studies of the Salmonella zinc transporter ZntB
Structure 19 :700-710. PubMed Id: 21565704. doi:10.1016/j.str.2011.02.011. |
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Bacterial Mercury Detoxification Proteins
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MerF Hg(II) transporter: Morganella morganii B Bacteria (expressed in E. coli), NMR structure
Structure of truncated protein (AAs 13-72) determined in aligned bicelles. |
De Angelis et al. (2006).
De Angelis AA, Howell SC, Nevzorov AA, & Opella SJ (2006). Structure determination of a membrane protein with two trans-membrane helices in aligned phospholipid bicelles by solid-state NMR spectroscopy.
J AM Chem Soc 128 :12256-12267. PubMed Id: 16967977. |
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MerF Hg(II) transporter: Morganella morganii B Bacteria (expressed in E. coli), NMR structure
Structure of truncated protein (AAs 13-72) determined in SDS micelles. |
Howell et al. (2005).
Howell SC, Mesleh MF, & Opella SJ (2005). NMR structure determination of a membrane protein with two transmembrane helices in micelles: MerF of the bacterial mercury detoxification system.
Biochemistry 44 :5196-5206. PubMed Id: 15794657. |
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MerF Hg(II) transporter: Morganella morganii B Bacteria (expressed in E. coli), NMR Structure
Structure of truncated protein (AAs 13-70) determined in proteoliposomes. |
Das et al. (2012).
Das BB, Nothnagel HJ, Lu GJ, Son WS, Tian Y, Marassi FM, & Opella SJ (2012). Structure determination of a membrane protein in proteoliposomes.
J Amer Chem Soc 134 :2047-2056. PubMed Id: 22217388. doi:10.1021/ja209464f. |
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Rhodaneses
Thiosulfate-Cyanide sulfurtransfereases |
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Eichmann et al. (2014).
Eichmann C, Tzitzilonis C, Bordignon E, Maslennikov I, Choe S, & Riek R (2014). Solution NMR Structure and Functional Analysis of the Integral Membrane Protein YgaP from Escherichia coli.
J Biol Chem 289 :23482-23503. PubMed Id: 24958726. doi:10.1074/jbc.M114.571935. See also: Ling et al. (2016). Ling S, Wang W, Yu L, Peng J, Cai X, Xiong Y, Hayati Z, Zhang L, Zhang Z, Song L, & Tian C (2016). Structure of an E. coli integral membrane sulfurtransferase and its structural transition upon SCN- binding defined by EPR-based hybrid method.
Sci Rep 6 . PubMed Id: 26817826. doi:10.1038/srep20025. |
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Drug/Metabolite Transporter (DMT) Superfamily
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YddG aromatic amino acid exporter: Starkeya novella B Bacteria (expressed in E. coli), 2.4 Å
|
Tsuchiya et al. (2016).
Tsuchiya H, Doki S, Takemoto M, Ikuta T, Higuchi T, Fukui K, Usuda Y, Tabuchi E, Nagatoishi S, Tsumoto K, Nishizawa T, Ito K, Dohmae N, Ishitani R, & Nureki O (2016). Structural basis for amino acid export by DMT superfamily transporter YddG.
Nature 534 :417-420. PubMed Id: 27281193. doi:10.1038/nature17991. |
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Multi-Drug Efflux Transporters
Members of the multidrug/oligosaccharidyl-lipid/polysaccharide (MOP) transporter superfamily |
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AcrB bacterial multi-drug efflux transporter: Escherichia coli B Bacteria, 3.5 Å
AcrB is a member of the resistance nodulation and cell division (RND) superfamily, as is SecDF. |
Murakami et al. (2002).
Murakami S, Nakashima R, Yamashita E, & Yamaguchi A (2002). Crystal structure of bacterial multidrug efflux transporter AcrB.
Nature 419 :587-593. PubMed Id: 12374972. |
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AcrA fusion protein: Escherichia coli B Bacteria, 2.70 Å
This is a soluble periplasmic protein. It bridges the AcrB multi-drug efflux transporter to the TolC outer membrane protein 1EK9 |
Mikolosko et al. (2006).
Mikolosko J, Bobyk K, Zgurskaya HI, & Ghosh P (2006). Conformational flexibility in the multidrug efflux system protein AcrA.
Structure 14 :577-587. PubMed Id: 16531241. |
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Yu et al. (2003).
Yu EW, McDermott G, Zgurskaya HI, Nikaido H, & Koshland Jr, DE (2003). Structural basis of multiple drug-binding capacity of the AcrB multidrug efflux pump.
Science 300 :976-980. PubMed Id: 12738864. |
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Yu et al. (2005).
Yu EW, Aires JR, McDermott G, & Nikaido H (2005). A periplasmic drug-binding site of the AcrB multidrug efflux pump: a crystallographic and site-directed mutagenesis study.
J Bacteriol 187 :6804-6815. PubMed Id: 16166543. |
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Su et al. (2006).
Su CC, Li M, Gu R, Takatsuka Y, McDermott G, Nikaido H, & Yu EW (2006). Conformation of the AcrB multidrug efflux pump in mutants of the putative proton relay pathway.
J Bacteriol 188 :7290-7296. PubMed Id: 17015668. |
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AcrB bacterial multi-drug efflux transporter: Escherichia coli B Bacteria, 2.9 Å
Two crystal forms. C2: 2GIF. P1: 2HRT, 3.0 Å. Together, the two forms suggest a pump mechanism. |
Seeger et al. (2006).
Seeger MA, Schiefner A, Eicher T, Verrey F, Diederichs K, & Pos KM (2006). Structural asymmetry of ArcB trimer suggests a peristaltic pump mechanism.
Science 313 :1295-1298. PubMed Id: 16946072. |
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Murakami et al. (2006).
Murakami S, Nakashima R, Yamashita E, Matsumoto T, & Yamaguchi A (2006). Crystal structures of a bacterial multidrug transporter reveal a functionally rotating mechanism.
Nature 443 :173-179. PubMed Id: 16915237. |
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AcrB in complex with DARPin: Escherichia coli B Bacteria, 2.54 Å
|
Sennhauser et al. (2007).
Sennhauser G, Amstutz P, Briand C, Storchenegger O, & Grütter MG (2007). Drug export pathway of multidrug exporter AcrB revealed by DARPin inhibitors.
PLoS Biol. 5 1. PubMed Id: 17194213. doi:10.1371/journal.pbio.0050007. |
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AcrB bacterial multi-drug efflux transporter with YajC subunit: Escherichia coli B Bacteria, 3.5 Å
|
Törnroth-Horsefield et al. (2007).
Törnroth-Horsefield S, Gourdon P, Horsefield R, Brive L, Yamamoto N, Mori H, Snijder A, & Neutze R (2007). Crystal Structure of AcrB in Complex with a Single Transmembrane Subunit Reveals Another Twist.
Structure 15 :1663-1673. PubMed Id: 18073115. |
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AcrB bacterial multi-drug efflux transporter in complex with bile acid: Escherichia coli B Bacteria, 3.85 Å
|
Drew et al. (2008).
Drew D, Klepsch MM, Newstead S, Flaig R, De Gier JW, Iwata S, & Beis K (2008). The structure of the efflux pump AcrB in complex with bile acid.
Mol Membr Biol 25 :677-682. PubMed Id: 19023693. |
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AcrB bacterial multi-drug efflux transporter with bound rifampicin: Escherichia coli B Bacteria, 3.35 Å
This and the additional structures below reveal two discrete multisite binding pockets. Unliganded AcrB, 3.35 Å: 3AOA With bound erythromycin, 3.34 Aring;: 3AOC With bound rifampicin & minocyline, 3.30 Å: 3AOD |
Nakashima et al. (2011).
Nakashima R, Sakurai K, Yamasaki S, Nishino K, & Yamaguchi A (2011). Structures of the multidrug exporter AcrB reveal a proximal multisite drug-binding pocket.
Nature 480 :565-569. PubMed Id: 22121023. doi:10.1038/nature10641. |
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Eicher et al. (2012).
Eicher T, Cha HJ, Seeger MA, Brandstätter L, El-Delik J, Bohnert JA, Kern WV, Verrey F, Grütter MG, Diederichs K, & Pos KM (2012). Transport of drugs by the multidrug transporter AcrB involves an access and a deep binding pocket that are separated by a switch-loop.
Proc Natl Acad Sci USA 109 :5687-5692. PubMed Id: 22451937. doi:10.1073/pnas.1114944109. |
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AcrB bacterial multi-drug efflux transporter with bound ABI-PP inhibitor: Escherichia coli B Bacteria, 3.05 Å
|
Nakashima et al. (2013).
Nakashima R, Sakurai K, Yamasaki S, Hayashi K, Nagata C, Hoshino K, Onodera Y, Nishino K, & Yamaguchi A (2013). Structural basis for the inhibition of bacterial multidrug exporters.
Nature 500 :102-106. PubMed Id: 23812586. doi:10.1038/nature12300. |
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AcrB-AcrZ bacterial multi-drug efflux transporter complex: Escherichia coli B Bacteria, 3.30 Å
AcrB-AcrZ-DARPin complex, 3.70 Å: 4CDI |
Du et al. (2014).
Du D, Wang Z, James NR, Voss JE, Klimont E, Ohene-Agyei T, Venter H, Chiu W, & Luisi BF (2014). Structure of the AcrAB-TolC multidrug efflux pump.
Nature 509 :512-515. PubMed Id: 24747401. doi:10.1038/nature13205. |
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Eicher et al. (2014).
Eicher T, Seeger MA, Anselmi C, Zhou W, Brandstätter L, Verrey F, Diederichs K, Faraldo-Gómez JD, & Pos KM (2014). Coupling of remote alternating-access transport mechanisms for protons and substrates in the multidrug efflux pump AcrB.
Elife 3 :e03145. PubMed Id: 25248080. doi:10.7554/eLife.03145. |
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AcrB bacterial multi-drug efflux transporter in complex with fusidic acid: Escherichia coli B Bacteria, 2.5 Å
|
Oswald et al. (2016).
Oswald C, Tam HK, & Pos KM (2016). Transport of lipophilic carboxylates is mediated by transmembrane helix 2 in multidrug transporter AcrB.
Nat Commun 7 :13819. PubMed Id: 27982032. doi:10.1038/ncomms13819. |
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Wang et al. (2017).
Wang Z, Fan G, Hryc CF, Blaza JN, Serysheva II, Schmid MF, Chiu W, Luisi BF, & Du D (2017). An allosteric transport mechanism for the AcrAB-TolC multidrug efflux pump.
Elife 6 :e24905. PubMed Id: 28355133. doi:10.7554/eLife.24905. |
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MexB bacterial multi-drug efflux transporter: Pseudomonas aeruginosa B Bacteria (expressed in E. coli), 3.0 Å
|
Sennhauser et al. (2009).
Sennhauser G, Bukowska MA, Briand C, Grütter MG (2009). Crystal Structure of the Multidrug Exporter MexB from Pseudomonas aeruginosa.
J Mol Biol 389 :134-145. PubMed Id: 19361527. |
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Higgins et al. (2004).
Higgins MK, Bokma E, Koronakis E, Hughes C, & Koronakis V (2004). Structure of the periplasmic component of a bacterial drug efflux pump.
Proc Natl Acad Sci USA 101 :9994-9999. PubMed Id: 15226509. doi:10.1073/pnas.0400375101. |
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Akama et al. (2004).
Akama H, Matsuura T, Kashiwagi S, Yoneyama H, Narita S, Tsukihara T, Nakagawa A, & Nakae T (2004). Crystal structure of the membrane fusion protein, MexA, of the multidrug transporter in Pseudomonas aeruginosa.
J Biol Chem 279 :25939-25942. PubMed Id: 15117957. doi:10.1074/jbc.C400164200. |
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MexB bacterial multi-drug efflux transporter with bound ABI-PP inhibitor: Pseudomonas aeruginosa B Bacteria (expressed in E. coli), 3.15 Å
Drug-free MexB, 2.71 Å: 3W9I |
Nakashima et al. (2013).
Nakashima R, Sakurai K, Yamasaki S, Hayashi K, Nagata C, Hoshino K, Onodera Y, Nishino K, & Yamaguchi A (2013). Structural basis for the inhibition of bacterial multidrug exporters.
Nature 500 :102-106. PubMed Id: 23812586. doi:10.1038/nature12300. |
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ZneA Zn(II)/proton antiporter: Cupriavidus metallidurans B Bacteria (expressed in E. coli), 3.00 Å
Crystal form I. ZneA is a member of the resistance nodulation and cell division (RND) superfamily. Crystal form II, 3.71 Å: 4K0E |
Pak et al. (2013).
Pak JE, Ekendé EN, Kifle EG, O'Connell JD 3rd, De Angelis F, Tessema MB, Derfoufi KM, Robles-Colmenares Y, Robbins RA, Goormaghtigh E, Vandenbussche G, & Stroud RM (2013). Structures of intermediate transport states of ZneA, a Zn(II)/proton antiporter.
Proc Natl Acad Sci USA 110 :18484-18489. PubMed Id: 24173033. doi:10.1073/pnas.1318705110. |
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CusA metal-ion efflux pump: Escherichia coli B Bacteria, 3.52 Å
Pumps out Ag+ and Cu+ ions. |
Long et al. (2010).
Long F, Su CC, Zimmermann MT, Boyken SE, Rajashankar KR, Jernigan RL, & Yu EW (2010). Crystal structures of the CusA efflux pump suggest methionine-mediated metal transport.
Nature 467 :484-488. PubMed Id: 20865003. |
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CusBA heavy-metal efflux complex: Escherichia coli B Bacteria, 2.90 Å
CusA is the efflux transporter located in the inner membrane. CusB, located in the periplasmic space, is a so-called membrane fusion protein that bridges CusA to CusC to form the tripartite efflux complex CusCBA. |
Su et al. (2011).
Su CC, Long F, Zimmermann MT, Rajashankar KR, Jernigan RL, & Yu EW (2011). Crystal structure of the CusBA heavy-metal efflux complex of Escherichia coli.
Nature 470 :558-562. PubMed Id: 21350490. doi:10.1038/nature09743. |
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Su et al. (2009).
Su CC, Yang F, Long F, Reyon D, Routh MD, Kuo DW, Mokhtari AK, Van Ornam JD, Rabe KL, Hoy JA, Lee YJ, Rajashankar KR, & Yu EW (2009). Crystal structure of the membrane fusion protein CusB from Escherichia coli.
J Mol Biol 393 :342-355. PubMed Id: 19695261. doi:10.1016/j.jmb.2009.08.029. |
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Chen et al. (2007).
Chen YJ, Pornillos O, Lieu S, Ma C, Chen AP, & Chang G (2007). X-ray structure of EmrE supports dual topology model.
Proc Natl Acad Sci USA 104 :18999-19004. PubMed Id: 18024586. |
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NorM Multidrug and Toxin Compound Extrusion (MATE) transporter (apo form): Vibrio cholerae B Bacteria (expressed in E. coli), 3.65 Å
With bound Rb+, 4.20 Å: 3MKU |
He et al. (2010).
He X, Szewczyk P, Karyakin A, Evin M, Hong WX, Zhang Q, & Chang G (2010). Structure of a cation-bound multidrug and toxic compound extrusion transporter.
Nature 467 :991-994. PubMed Id: 20861838. |
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Lu et al. (2013).
Lu M, Symersky J, Radchenko M, Koide A, Guo Y, Nie R, & Koide S (2013). Structures of a Na+-coupled, substrate-bound MATE multidrug transporter.
Proc Natl Acad Sci USA 110 :2099-2104. PubMed Id: 23341609. doi:10.1073/pnas.1219901110. |
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NorM Multidrug and Toxin Compound Extrusion (MATE) transporter in complex with verapamil: Neisseria gonorrhoeae B Bacteria (expressed in E. coli), 3.00 Å
|
Radchenko et al. (2015).
Radchenko M, Symersky J, Nie R, & Lu M (2015). Structural basis for the blockade of MATE multidrug efflux pumps.
Nat Commun 6 :7995. PubMed Id: 26246409. doi:10.1038/ncomms8995. |
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Multidrug and Toxin Compound Extrusion (MATE) transporter; outward-open apo form, straight conformation: Pyrococcus furiosus A Archaea (expressed in E. coli), 2.40 Å
outward-open apo form, bent conformation, 2.50 Å: 3VVO in complex with Br-NRF, 2.91 Å: 3VVP in complex with MaL6, 2.40 Å: 3VVQ in complex with MaD5, 3.00 Å: 3VVR in complex with MaD3S, 2.60 Å: 3VVS |
Tanaka et al. (2013).
Tanaka Y, Hipolito CJ, Maturana AD, Ito K, Kuroda T, Higuchi T, Katoh T, Kato HE, Hattori M, Kumazaki K, Tsukazaki T, Ishitani R, Suga H, & Nureki O (2013). Structural basis for the drug extrusion mechanism by a MATE multidrug transporter.
Nature 496 :247-251. PubMed Id: 23535598. doi:10.1038/nature12014. |
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DinF-BH Multidrug and Toxin Compound Extrusion (MATE) transporter: Bacillus halodurans B Bacteria (expressed in E. coli), 3.20 Å
In complex with R6G, 3.70 Å: 4LZ9 |
Lu et al. (2013).
Lu M, Radchenko M, Symersky J, Nie R, & Guo Y (2013). Structural insights into H+-coupled multidrug extrusion by a MATE transporter.
Nat. Struct. Mol. Biol. 20 :1310-1317. PubMed Id: 24141706. doi:10.1038/nsmb.2687. |
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DinF-BH Multidrug and Toxin Compound Extrusion (MATE) transporter, D40N mutant: Bacillus halodurans B Bacteria (expressed in E. coli), 3.00 Å
with bound verapmil, 3.00 Å: 5C6O |
Radchenko et al. (2015).
Radchenko M, Symersky J, Nie R, & Lu M (2015). Structural basis for the blockade of MATE multidrug efflux pumps.
Nat Commun 6 :7995. PubMed Id: 26246409. doi:10.1038/ncomms8995. |
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MurJ MOP flippase: Thermosipho africanus B Bacteria (expressed in E. coli), 2.0 Å
This protein flips the lipid-linked PG precursor lipid II across the cytoplasmic membrane. It is a member of the MATE transporter family |
Kuk et al. (2017).
Kuk AC, Mashalidis EH, & Lee SY (2017). Crystal structure of the MOP flippase MurJ in an inward-facing conformation.
Nat. Struct. Mol. Biol. 24 :171-176. PubMed Id: 28024149. doi:10.1038/nsmb.3346. |
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MtrD Inner Membrane Multidrug Efflux Pump: Neisseria gonorrhoeae B Bacteria (expressed in E. coli), 3.54 Å
|
Bolla et al. (2014).
Bolla JR, Su CC, Do SV, Radhakrishnan A, Kumar N, Long F, Chou TH, Delmar JA, Lei HT, Rajashankar KR, Shafer WM, & Yu EW (2014). Crystal structure of the Neisseria gonorrhoeae MtrD inner membrane multidrug efflux pump.
PLoS ONE 9 6:e97903. PubMed Id: 24901477. doi:10.1371/journal.pone.0097903. |
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HpnN hopanoid transporter (crystal form I): Burkholderia multivorans B Bacteria (expressed in E. coli), 3.44 Å
crystal form II, 3.76 Å: 5KHS |
Kumar et al. (2017).
Kumar N, Su CC, Chou TH, Radhakrishnan A, Delmar JA, Rajashankar KR, & Yu EW (2017). Crystal structures of the Burkholderia multivorans hopanoid transporter HpnN.
Proc Natl Acad Sci USA 114 :6557-6562. PubMed Id: 28584102. doi:10.1073/pnas.1619660114. |
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AbgT Family of Transporters
Involved in bacterial folate synthesis through catabolite transport Proteins in this family may also function as drug efflux pumps |
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YdaH transporter: Alcanivorax borkumensis B Bacteria (expressed in E. coli), 2.96 Å
The first structure determined for a member of the AbgT family. |
Bolla et al. (2015).
Bolla JR, Su CC, Delmar JA, Radhakrishnan A, Kumar N, Chou TH, Long F, Rajashankar KR, & Yu EW (2015). Crystal structure of the Alcanivorax borkumensis YdaH transporter reveals an unusual topology.
Nat Commun 6 :6874. PubMed Id: 25892120. doi:10.1038/ncomms7874. |
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Membrane-Associated Proteins in Eicosanoid and Glutathione Metabolism (MAPEG)
|
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Microsomal Glutathione Transferase 1: Rattus norvegicus E Eukaryota, 3.2 Å
Electron Diffraction |
Holm et al. (2006).
Holm PJ, Bhakat P, Jegerschold C, Gyobu N, Mitsuoka K, Fujiyoshi Y, Morgenstern R, & Hebert H. (2006). Structural Basis for Detoxification and Oxidative Stress Protection in Membranes.
J Mol Biol 360 :934-945. PubMed Id: 16806268. |
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Microsomal Prostaglandin E Synthase 1: Homo sapiens E Eukaryota (expressed in E. coli), 3.5 Å
Electron Diffraction. In complex with glutathione. |
Jegerschöld et al. (2008).
Jegerschöld C, Pawelzik SC, Purhonen P, Bhakat P, Gheorghe KR, Gyobu N, Mitsuoka K, Morgenstern R, Jakobsson PJ, & Hebert H (2008). Structural basis for induced formation of the inflammatory mediator prostaglandin E2.
Proc Natl Acad Sci USA 105 :11110-11115. PubMed Id: 18682561. |
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Microsomal Prostaglandin E Synthase 1: Homo sapiens E Eukaryota (expressed in S. frugiperda), 1.16 Å
With GSH analog, 1.95 Å: 4AL1 |
Sjögren et al. (2013).
Sjögren T, Nord J, Ek M, Johansson P, Liu G, & Geschwindner S (2013). Crystal structure of microsomal prostaglandin E2 synthase provides insight into diversity in the MAPEG superfamily.
Proc Natl Acad Sci USA 110 :3806-3811. PubMed Id: 23431194. doi:10.1073/pnas.1218504110. |
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5-Lipoxygenase-Activating Protein (FLAP) with Bound MK-591 Inhibitor: Homo sapiens E Eukaryota (expressed in E. coli), 4.0 Å
FLAP with iodinated MK-591 analog: 2Q7R. |
Ferguson et al. (2007).
Ferguson AD, McKeever BM, Xu S, Wisniewski D, Miller DK, Yamin TT, Spencer RH, Chu L, Ujjainwalla F, Cunningham BR, Evans JF, & Becker JW (2007). Crystal structure of inhibitor-bound human 5-lipoxygenase-activating protein.
Science 317 :510-512. PubMed Id: 17600184. |
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Leukotriene LTC4 Synthase in complex with glutathione: Homo sapiens E Eukaryota (expressed in Shizosaccharomyces pombe), 3.3 Å
|
Ago et al. (2007).
Ago H, Kanaoka Y, Irikura D, Lam BK, Shimamura T, Austen KF, & Miyano M (2007). Crystal structure of a human membrane protein involved in cysteinyl leukotriene biosynthesis.
Nature 448 :609-612. PubMed Id: 17632548. |
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Leukotriene LTC4 Synthase in complex with glutathione: Homo sapiens E Eukaryota (expressed in Pichia pastoris), 2.15 Å
apo form: 2UUI, 2.00 Å. |
Molina et al. (2007).
Molina DM, Wetterholm A, Kohl A, McCarthy AA, Niegowski D, Ohlson E, Hammarberg T, Eshaghi S, Haeggstrom JZ, & Nordlund P (2007). Structural basis for synthesis of inflammatory mediators by human leukotriene C4synthase.
Nature 448 :613-616. PubMed Id: 17632546. |
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Niegowski et al. (2014).
Niegowski D, Kleinschmidt T, Olsson U, Ahmad S, Rinaldo-Matthis A, & Haeggström JZ (2014). Crystal Structures of Leukotriene C4 Synthase in Complex with Product Analogs: IMPLICATIONS FOR THE ENZYME MECHANISM.
J Biol Chem 289 :5199-5207. PubMed Id: 24366866. doi:10.1074/jbc.M113.534628. |
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SWEET and semiSWEET Transporters, and Their Relatives
SWEETs are monsaccharide and disaccharide transporters. Bacterial homologues are semiSWEETS. |
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semiSWEET transporter in occluded state: Leptospira biflexa B Bacteria (expressed in E. coli), 2.39 Å
|
Xu et al. (2014).
Xu Y, Tao Y, Cheung LS, Fan C, Chen LQ, Xu S, Perry K, Frommer WB, & Feng L (2014). Structures of bacterial homologues of SWEET transporters in two distinct conformations.
Nature 515 7527:448-452. PubMed Id: 25186729. doi:10.1038/nature13670. |
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semiSWEET transporter in outward-open state: Leptospira biflexa B Bacteria (expressed in E. coli), 2.8 Å
|
Latorraca et al. (2017).
Latorraca NR, Fastman NM, Venkatakrishnan AJ, Frommer WB, Dror RO, & Feng L (2017). Mechanism of Substrate Translocation in an Alternating Access Transporter.
Cell 169 :96-107.e12. PubMed Id: 28340354. doi:10.1016/j.cell.2017.03.010. |
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semiSWEET transporter in outward-open conformation: Vibrio sp. n418 B Bacteria (expressed in E. coli), 1.70 Å
|
Xu et al. (2014).
Xu Y, Tao Y, Cheung LS, Fan C, Chen LQ, Xu S, Perry K, Frommer WB, & Feng L (2014). Structures of bacterial homologues of SWEET transporters in two distinct conformations.
Nature 515 7527:448-452. PubMed Id: 25186729. doi:10.1038/nature13670. |
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semiSWEET transporter in occluded state: Thermodesulfovibrio yellowstonii B Bacteria (expressed in E. coli), 2.40 Å
|
Wang et al. (2014).
Wang J, Yan C, Li Y, Hirata K, Yamamoto M, Yan N, & Hu Q (2014). Crystal structure of a bacterial homologue of SWEET transporters.
Cell Res 24 12:1486-1489. PubMed Id: 25378180. doi:10.1038/cr.2014.144. |
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semiSWEET transporter in inward-open conformation (crystal I): Escherichia coli B Bacteria, 2.00 Å
outward-open state (crystal II), 3.00 Å: 4X5N (crystal I:P212121. Crystal II: C2) |
Lee et al. (2015).
Lee Y, Nishizawa T, Yamashita K, Ishitani R, & Nureki O (2015). Structural basis for the facilitative diffusion mechanism by SemiSWEET transporter.
Nat Commun 6 :6112. PubMed Id: 25598322. doi:10.1038/ncomms7112. |
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SWEET transporter in a homotrimeric complex: Oryza sativa E Eukaryota (expressed in Komagataella pastoris), 3.10 Å
lower resolution structure, 3.7 Å: 5CTH |
Tao et al. (2015).
Tao Y, Cheung LS, Li S, Eom JS, Chen LQ, Xu Y, Perry K, Frommer WB, & Feng L (2015). Structure of a eukaryotic SWEET transporter in a homotrimeric complex.
Nature 527 :259-263. PubMed Id: 26479032. doi:10.1038/nature15391. |
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PnuC vitamin B3 transporter: Neisseria mucosa B Bacteria (expressed in E. coli), 2.80 Å
|
Jaehme et al. (2014).
Jaehme M, Guskov A, & Slotboom DJ (2014). Crystal structure of the vitamin B3 transporter PnuC, a full-length SWEET homolog.
Nat Struct Mol Biol 21 11:1013-1015. PubMed Id: 25291599. doi:10.1038/nsmb.2909. |
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Major Facilitator Superfamily (MFS) Transporters
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LacY Lactose Permease Transporter (C154G mutant): Escherichia coli B Bacteria, 3.6 Å
1PV7 is with bound high-affinity lactose homolog, TDG. See 1PV6 for structure without TDG (3.5 Å). |
Abramson et al. (2003).
Abramson J, Smirnova I, Kasho V, Verner G, Kaback HR, & Iwata S (2003). Structure and mechanism of the lactose permease of Escherichia coli.
Science 301 :610-615. PubMed Id: 12893935. |
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LacY Lactose Permease (C154G mutant) without substrate at 2 pH values: Escherichia coli B Bacteria, 2.95 Å
2CFQ structure determined at pH 6.5. 2CFP structure determined at pH 5.6 (3.30 Å). |
Mirza et al. (2006).
Mirza O, Guan L, Verner G, Iwata S & Kaback HR (2006). Structural evidence for induced fit and a mechanism for sugar/H+symport in LacY.
EMBO J 25 :1177-1183. PubMed Id: 16525509. |
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LacY Lactose Permease (wild-type) with TDG: Escherichia coli B Bacteria, 3.6 Å
|
Guan et al. (2007).
Guan L, Mirza O, Verner G, Iwata S, & Kaback HR (2007). Structural determination of wild-type lactose permease.
Proc Natl Acad Sci USA 104 :15294-15298. PubMed Id: 17881559. |
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LacY Lactose Permease with covalently bound MTS-gal: Escherichia coli B Bacteria, 3.4 Å
methanethiosulfonyl-galactopyranoside (MTS-gal) is a 'suicide' substrate. |
Chaptal et al. (2011).
Chaptal V, Kwon S, Sawaya MR, Guan L, Kaback HR, & Abramson J (2011). Crystal structure of lactose permease in complex with an affinity inactivator yields unique insight into sugar recognition.
Proc Natl Acad Sci USA 108 :9361-9366. PubMed Id: 21593407. doi:10.1073/pnas.1105687108. |
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LacY Lactose Permease Transporter (G46W/G262W mutant) with bound lactose analog: Escherichia coli B Bacteria, 3.50 Å
Occluded, partially open to periplasmic side |
Kumar et al. (2014).
Kumar H, Kasho V, Smirnova I, Finer-Moore JS, Kaback HR, & Stroud RM (2014). Structure of sugar-bound LacY.
Proc Natl Acad Sci USA 111 :1784-1788. PubMed Id: 24453216. doi:10.1073/pnas.1324141111. |
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LacY Lactose Permease Transporter (G46W, G262W mutant) with bound α-NPG: Escherichia coli B Bacteria, 3.31 Å
|
Kumar et al. (2015).
Kumar H, Finer-Moore JS, Kaback HR, & Stroud RM (2015). Structure of LacY with an ?-substituted galactoside: Connecting the binding site to the protonation site.
Proc Natl. Acad Sc. USA 112 :9004-9009. PubMed Id: 26157133. doi:10.1073/pnas.1509854112. |
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LacY Lactose Permease Transporter (G46W, G262W mutant) with bound nanobody: Escherichia coli B Bacteria, 3.3 Å
|
Jiang et al. (2016).
Jiang X, Smirnova I, Kasho V, Wu J, Hirata K, Ke M, Pardon E, Steyaert J, Yan N, & Kaback HR (2016). Crystal structure of a LacY-nanobody complex in a periplasmic-open conformation.
Proc Natl Acad Sci USA 113 :12420-12425. PubMed Id: 27791182. doi:10.1073/pnas.1615414113. |
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FucP Fucose Transporter in outward-facing conformation: Escherichia coli B Bacteria, 3.1 Å
N162A mutant, 3.2 Å: 3O7P |
Dang et al. (2010).
Dang S, Sun L, Huang Y, Lu F, Liu Y, Gong H, Wang J, & Yan N (2010). Structure of a fucose transporter in an outward-open conformation.
Nature 467 :734-738. PubMed Id: 20877283. |
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MelB Na+/melibiose symporter: Salmonella typhimurium B Bacteria (expressed in E. coli), 3.35 Å
MelB catalyzes electrogenic symport of galactosides with Na+, Li+, or H+ |
Ethayathulla et al. (2014).
Ethayathulla AS, Yousef MS, Amin A, Leblanc G, Kaback HR, & Guan L (2014). Structure-based mechanism for Na+/melibiose symport by MelB.
Nat Commun 5 :3009. PubMed Id: 24389923. doi:10.1038/ncomms4009. |
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|
Sun et al. (2012).
Sun L, Zeng X, Yan C, Sun X, Gong X, Rao Y, & Yan N (2012). Crystal structure of a bacterial homologue of glucose transporters GLUT1-4.
Nature 490 :361-366. PubMed Id: 23075985. doi:10.1038/nature11524. |
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XylE proton:xylose symporter in partially occluded inward-open state: Escherichia coli B Bacteria, 3.80 Å
inward-open state, 4.20 Å: 4JA4 |
Quistgaard et al. (2013).
Quistgaard EM, Löw C, Moberg P, Trésaugues L, & Nordlund P (2013). Structural basis for substrate transport in the GLUT-homology family of monosaccharide transporters.
Nature Struc Mol Biol 20 :766-768. PubMed Id: 23624861. doi:10.1038/nsmb.2569. |
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XylE proton:xylose symporter, inward-facing open conformation: Escherichia coli B Bacteria, 3.51 Å
|
Wisedchaisri et al. (2014).
Wisedchaisri G, Park MS, Iadanza MG, Zheng H, & Gonen T (2014). Proton-coupled sugar transport in the prototypical major facilitator superfamily protein XylE.
Nat Comms 5 :4521. PubMed Id: 25088546. doi:10.1038/ncomms5521. |
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GlcP Glucose/H+ symporter: Staphylococcus epidermidis B Bacteria (expressed in E. coli), 3.20 Å
|
Iancu et al. (2013).
Iancu CV, Zamoon J, Woo SB, Aleshin A, & Choe JY (2013). Crystal structure of a glucose/H+ symporter and its mechanism of action.
Proc Natl Acad Sci USA 110 :17862-17867. PubMed Id: 24127585. doi:10.1073/pnas.1311485110. |
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GlpT Glycerol-3-Phosphate Transporter: Escherichia coli B Bacteria, 3.3 Å
|
Huang et al. (2003).
Huang Y, Lemieux MJ, Song J, Auer M, & Wang D-N (2003). Structure and mechanism of the glycerol-3-phosphate transporter from Eschericia coli.
Science 301 :616-620. PubMed Id: 12893936. |
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EmrD Multidrug Transporter: Escherichia coli B Bacteria, 3.5 Å
|
Yin et al. (2006).
Yin Y, He X, Szewczyk P, Nguyen T, & Chang G. (2006). Structure of the multidrug transporter EmrD from Escherichia coli.
Science 312 :741-744. PubMed Id: 16675700. |
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PepTSo Oligopeptide-proton symporter (POT family): Shewanella oneidensis B Bacteria (expressed in E. coli), 3.6 Å
The conformation appears to be that of an occluded state. |
Newstead et al. (2011).
Newstead S, Drew D, Cameron AD, Postis VL, Xia X, Fowler PW, Ingram JC, Carpenter EP, Sansom MS, McPherson MJ, Baldwin SA, & Iwata S (2011). Crystal structure of a prokaryotic homologue of the mammalian oligopeptide-proton symporters, PepT1 and PepT2.
EMBO J 30 :417-426. PubMed Id: 21131908. |
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Guettou et al. (2014).
Guettou F, Quistgaard EM, Raba M, Moberg P, Löw C, & Nordlund P (2014). Selectivity mechanism of a bacterial homolog of the human drug-peptide transporters PepT1 and PepT2.
Nat Struct Mol Biol 21 8:728-731. PubMed Id: 25064511. doi:10.1038/nsmb.2860. |
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PepTSo Oligopeptide-proton symporter (POT family), inward-open conformation: Shewanella oneidensi B Bacteria (expressed in E. coli), 3.00 Å
|
Fowler et al. (2015).
Fowler PW, Orwick-Rydmark M, Radestock S, Solcan N, Dijkman PM, Lyons JA, Kwok J, Caffrey M, Watts A, Forrest LR, & Newstead S (2015). Gating topology of the proton-coupled oligopeptide symporters.
Structure 23 2:290-301. PubMed Id: 25651061. doi:10.1016/j.str.2014.12.012. |
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PepTSt Oligopeptide-proton symporter (POT family): Streptococcus thermophilus B Bacteria (expressed in E. coli), 3.30 Å
Conformation appears to be that of an inward-facing state. |
Solcan et al. (2012).
Solcan N, Kwok J, Fowler PW, Cameron AD, Drew D, Iwata S, & Newstead S (2012). Alternating access mechanism in the POT family of oligopeptide transporters.
EMBO J 31 :3411-3421. PubMed Id: 22659829. doi:10.1038/emboj.2012.157. |
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PepTSt Oligopeptide-proton symporter (POT family) at 100 K: Streptococcus thermophilus B Bacteria (expressed in E. coli), 2.30 Å
data collected at 293 K, 2.80 Å: 4XNI Data collected by serial x-ray crystallography. |
Huang et al. (2015).
Huang CY, Olieric V, Ma P, Panepucci E, Diederichs K, Wang M, & Caffrey M (2015). In meso in situ serial X-ray crystallography of soluble and membrane proteins.
Acta Crystallogr D Biol Crystallogr 71 :1238-1256. PubMed Id: 26057665. doi:10.1107/S1399004715005210. |
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Proton-dependent oligopeptide transporter (POT): Geobacillus kaustophilus B Bacteria (expressed in E. coli), 1.90 Å
In complex with sulfate, 2.00 Å: 4IKW E310Q mutant, 2.30 Å: 4IKX E310Q mutant in complex with sulfate, 2.10 Å: 4IKY E310Q mutant in complex with dipeptide analog alafosfalin, 2.40 Å: 4IKZ |
Doki et al. (2013).
Doki S, Kato HE, Solcan N, Iwaki M, Koyama M, Hattori M, Iwase N, Tsukazaki T, Sugita Y, Kandori H, Newstead S, Ishitani R, & Nureki O (2013). Structural basis for dynamic mechanism of proton-coupled symport by the peptide transporter POT.
Proc Natl Acad Sci USA 110 28:11343-11348. PubMed Id: 23798427. doi:10.1073/pnas.1301079110. |
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YbgH peptide transporter (POT family), inward facing conformation: Escherichia coli B Bacteria, 3.40 Å
|
Zhao et al. (2014).
Zhao Y, Mao G, Liu M, Zhang L, Wang X, & Zhang XC (2014). Crystal Structure of the E. coli Peptide Transporter YbgH.
Structure 22 :1152-1160. PubMed Id: 25066136. doi:10.1016/j.str.2014.06.008. |
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PepT dipeptide transporter (POT family): Yersinia enterocolitica B Bacteria (expressed in E. coli), 3.02 Å
|
Boggavarapu et al. (2015).
Boggavarapu R, Jeckelmann JM, Harder D, Ucurum Z, & Fotiadis D (2015). Role of electrostatic interactions for ligand recognition and specificity of peptide transporters.
BMC Biol 13 1. PubMed Id: 26246134. doi:10.1186/s12915-015-0167-8. |
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PiPT high-affinity phosphate transporter: Piriformospora indica E Eukaryota (expressed in S. cerevisiae), 2.90 Å
|
Pedersen et al. (2013).
Pedersen BP, Kumar H, Waight AB, Risenmay AJ, Roe-Zurz Z, Chau BH, Schlessinger A, Bonomi M, Harries W, Sali A, Johri AK, & Stroud RM (2013). Crystal structure of a eukaryotic phosphate transporter.
Nature 496 :533-536. PubMed Id: 23542591. doi:10.1038/nature12042. |
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|
NarU nitrate transporter: Escherichia coli B Bacteria, 3.01 Å
First structure of a member of the nitrate/nitrite porter family (NNP) Selenomethionine derivative, 3.11 Å: 4IU8 |
Yan et al. (2013).
Yan H, Huang W, Yan C, Gong X, Jiang S, Zhao Y, Wang J, & Shi Y (2013). Structure and mechanism of a nitrate transporter.
Cell Rep 3 :716-723. PubMed Id: 23523348. doi:10.1016/j.celrep.2013.03.007. |
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NarK nitrate/nitrite exchanger: Escherichia coli B Bacteria, 2.60 Å
A member of the nitrate/nitrite porter family (NNP) with bound nitrite, 2.80 Å: 4JRE |
Zheng et al. (2013).
Zheng H, Wisedchaisri G, & Gonen T (2013). Crystal structure of a nitrate/nitrite exchanger.
Nature 497 :647-651. PubMed Id: 23665960. doi:10.1038/nature12139. |
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Fukuda et al. (2015).
Fukuda M, Takeda H, Kato HE, Doki S, Ito K, Maturana AD, Ishitani R, & Nureki O (2015). Structural basis for dynamic mechanism of nitrate/nitrite antiport by NarK.
Nat Commun 6 :7097. PubMed Id: 25959928. doi:10.1038/ncomms8097. |
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NRT1.1 nitrate transporter, apo form: Arabidopsis thaliana E Eukaryota (expressed in S. cerevisiae), 3.70 Å
Member of the NPF (NRT1/PTR) family. 5A2N supersedes 4CL4. in complex with nitrate, 3.71 Å: 5A2O 5A2O supersedes 4CL5. |
Parker et al. (2014).
Parker JL, & Newstead S (2014). Molecular basis of nitrate uptake by the plant nitrate transporter NRT1.1.
Nature 507 :68-72. PubMed Id: 24572366. doi:10.1038/nature13116. |
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NRT1.1 nitrate transporter, homodimer in inward-facing conformation: Arabidopsis thaliana E Eukaryota (expressed in S. frugiperda), 3.25 Å
|
Sun et al. (2014).
Sun J, Bankston JR, Payandeh J, Hinds TR, Zagotta WN, & Zheng N (2014). Crystal structure of the plant dual-affinity nitrate transporter NRT1.1.
Nature 507 :73-77. PubMed Id: 24572362. doi:10.1038/nature13074. |
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YajR drug efflux transporter: Escherichia coli B Bacteria, 3.15 Å
Belongs to the 12-TM drug-resistance H+-driven antiporter (DHA12) subfamily. |
Jiang et al. (2013).
Jiang D, Zhao Y, Wang X, Fan J, Heng J, Liu X, Feng W, Kang X, Huang B, Liu J, & Zhang XC (2013). Structure of the YajR transporter suggests a transport mechanism based on the conserved motif A.
Proc Natl Acad Sci USA 110 :14664-14669. PubMed Id: 23950222. doi:10.1073/pnas.1308127110. |
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|
Heng et al. (2015).
Heng J, Zhao Y, Liu M, Liu Y, Fan J, Wang X, Zhao Y, & Zhang XC (2015). Substrate-bound structure of the E. coli multidrug resistance transporter MdfA.
Cell Res 25 9:1060-1073. PubMed Id: 26238402. doi:10.1038/cr.2015.94. |
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GLUT1 glucose transporter (N45T/E329Q mutant): Homo sapiens E Eukaryota (expressed in Trichoplusia ni), 3.17 Å
GLUT1 is a uniporter that catalyzes movement of glucose down its concentration gradient |
Deng et al. (2014).
Deng D, Xu C, Sun P, Wu J, Yan C, Hu M, & Yan N (2014). Crystal structure of the human glucose transporter GLUT1.
Nature 510 :121-125. PubMed Id: 24847886. doi:10.1038/nature13306. |
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|
Kapoor et al. (2016).
Kapoor K, Finer-Moore JS, Pedersen BP, Caboni L, Waight A, Hillig RC, Bringmann P, Heisler I, Müller T, Siebeneicher H, & Stroud RM (2016). Mechanism of inhibition of human glucose transporter GLUT1 is conserved between cytochalasin B and phenylalanine amides.
Proc Natl Acad Sci USA 113 :4711-4716. PubMed Id: 27078104. doi:10.1073/pnas.1603735113. |
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GLUT3 glucose transporter (N45T mutant) with bound D-glucose, outward-occluded conformation: Homo sapiens E Eukaryota (expressed in S. frugiperda), 1.50 Å
with exofacial inhibitor maltose in outward-occluded conformation, 2.4 Å: 4ZWB with exofacial inhibitor maltose in outward-open conformation, 2.6 Å: 4ZWC |
Deng et al. (2015).
Deng D, Sun P, Yan C, Ke M, Jiang X, Xiong L, Ren W, Hirata K, Yamamoto M, Fan S, & Yan N (2015). Molecular basis of ligand recognition and transport by glucose transporters.
Nature 526 :391-396. PubMed Id: 26176916. doi:10.1038/nature14655. |
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Taniguchi et al. (2015).
Taniguchi R, Kato HE, Font J, Deshpande CN, Wada M, Ito K, Ishitani R, Jormakka M, & Nureki O (2015). Outward- and inward-facing structures of a putative bacterial transition-metal transporter with homology to ferroportin.
Nat Commun 6 :8545. PubMed Id: 26461048. doi:10.1038/ncomms9545. |
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GLUT5 fructose transporter, open-inward conformation: Bos taurus E Eukaryota, 3.20 Å
|
Nomura et al. (2015).
Nomura N, Verdon G, Kang HJ, Shimamura T, Nomura Y, Sonoda Y, Hussien SA, Qureshi AA, Coincon M, Sato Y, Abe H, Nakada-Nakura Y, Hino T, Arakawa T, Kusano-Arai O, Iwanari H, Murata T, Kobayashi T, Hamakubo T, Kasahara M, Iwata S, & Drew D (2015). Structure and mechanism of the mammalian fructose transporter GLUT5.
Nature 526 :397-401. PubMed Id: 26416735. doi:10.1038/nature14909. |
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GLUT5 fructose transporter, open-outward conformation: Rattus norvegicus E Eukaryota, 3.27 Å
|
Nomura et al. (2015).
Nomura N, Verdon G, Kang HJ, Shimamura T, Nomura Y, Sonoda Y, Hussien SA, Qureshi AA, Coincon M, Sato Y, Abe H, Nakada-Nakura Y, Hino T, Arakawa T, Kusano-Arai O, Iwanari H, Murata T, Kobayashi T, Hamakubo T, Kasahara M, Iwata S, & Drew D (2015). Structure and mechanism of the mammalian fructose transporter GLUT5.
Nature 526 :397-401. PubMed Id: 26416735. doi:10.1038/nature14909. |
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Solute Sodium Symporter (SSS) Family
|
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vSGLT Sodium Galactose Transporter: Vibrio parahaemolyticus B Bacteria (expressed in E. coli), 2.70 Å
Galactose-bound inward-occuluded conformation |
Faham et al. (2008).
Faham S, Watanabe A, Besserer GM, Cascio D, Specht A, Hirayama BA, Wright EM, & Abramson J (2008). The crystal structure of a sodium galactose transporter reveals mechanistic insights into Na+/sugar symport.
Science 321 :810-814. PubMed Id: 18599740. |
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vSGLT Sodium Galactose Transporter, K294A mutant: Vibrio parahaemolyticus B Bacteria (expressed in E. coli), 2.70 Å
inward-open conformation |
Watanabe et al. (2010).
Watanabe A, Choe S, Chaptal V, Rosenberg JM, Wright EM, Grabe M, & Abramson J (2010). The mechanism of sodium and substrate release from the binding pocket of vSGLT.
Nature 468 :988-991. PubMed Id: 21131949. |
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Solute Carrier (SLC) Transporter Superfamily
Active transporters that use Na+ or H+ electrochemical gradients |
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Concentrative nucleoside transporter (CNT) in complex with uridine: Vibrio cholerae B Bacteria (expressed in E. coli), 2.44 Å
Member of Solute Carrier Transporter Superfamily (SLC28) |
Johnson et al. (2012).
Johnson ZL, Cheong CG, & Lee SY (2012). Crystal structure of a concentrative nucleoside transporter from Vibrio cholerae at 2.4 Å
Nature 483 :489-493. PubMed Id: 22407322. doi:10.1038/nature10882. |
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Dicarboxylate/Sodium Symporter: Vibrio cholerae B Bacteria (expressed in E. coli), 3.20 Å
Member of Solute Carrier Transporter Superfamily (SLC13) |
Mancusso et al. (2012).
Mancusso R, Gregorio GG, Liu Q, & Wang DN (2012). Structure and mechanism of a bacterial sodium-dependent dicarboxylate transporter.
Nature 491 :622-626. PubMed Id: 23086149. doi:10.1038/nature11542. |
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DAT Dopamine transporter in complex with nortriptyline TCA (tricyclic antidepressant): Drosophila melanogaster E Eukaryota (expressed in HEK293 cells), 2.95 Å
Member of Solute Carrier Transporter Superfamily (SLC6) |
Penmatsa et al. (2013).
Penmatsa A, Wang KH, & Gouaux E (2013). X-ray structure of dopamine transporter elucidates antidepressant mechanism.
Nature 503 :85-90. PubMed Id: 24037379. doi:10.1038/nature12533. |
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DAT Dopamine transporter in complex with dopamine: Drosophila melanogaster E Eukaryota (expressed in HEK293 cells), 2.89 Å
in complex with: D-amphetamine, 2.80 Å: 4XP9 methamphetamine, 3.10 Å: 4XP6 3,4-dichlorophenethylamine, 2.95 Å: 4XPA cocaine, 2.80 Å: 4XP4 cocaine analogue-RTI55, 3.30 Å: 4XP5 D121G/S426M mutant with bound cocaine, 3.05 Å: 4XPB D121G/S426M mutant with bound RTI55, 3.27 Å: 4XPF D121G/S426M mutant with bound beta-CFT, 3.21 Å: 4XPG D121G/S426M mutant with bound 3,4-dichlorophenethylamine, 2.90 Å: 4XPH D121G/S426M mutant with EL2 deletion of 162-201 with bound 3,4-dichlorophen ethylamine, 3.36 Å: 4XPT |
Wang et al. (2015).
Wang KH, Penmatsa A, & Gouaux E (2015). Neurotransmitter and psychostimulant recognition by the dopamine transporter.
Nature 521 :322-327. PubMed Id: 25970245. doi:10.1038/nature14431. |
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DAT Dopamine transporter in complex with nisoxetine: Drosophila melanogaster E Eukaryota (expressed in HEK-293S cells), 2.98 Å
in complex with reboxetine, 3.0 Å: 4XNX |
Penmatsa et al. (2015).
Penmatsa A, Wang KH, & Gouaux E (2015). X-ray structures of Drosophila dopamine transporter in complex with nisoxetine and reboxetine.
Nat Struct Mol Biol 22 :506-508. PubMed Id: 25961798. doi:10.1038/nsmb.3029. |
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SLC11 (NRAMP) transition-metal ion transporter in complex with nanobodies: Staphylococcus capitis B Bacteria (expressed in E. coli), 3.10 Å
in complex with Mn2+, 3.40 Å: 4WGW |
Ehrnstorfer et al. (2014).
Ehrnstorfer IA, Geertsma ER, Pardon E, Steyaert J, & Dutzler R (2014). Crystal structure of a SLC11 (NRAMP) transporter reveals the basis for transition-metal ion transport.
Nat Struct Mol Biol 21 11:990-996. PubMed Id: 25326704. doi:10.1038/nsmb.2904. |
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NRAMP transition-metal ion transporter in inward facing apo form: Deinococcus radiodurans B Bacteria (expressed in E. coli), 3.94 Å
|
Bozzi et al. (2016).
Bozzi AT, Bane LB, Weihofen WA, Singharoy A, Guillen ER, Ploegh HL, Schulten K, & Gaudet R (2016). Crystal Structure and Conformational Change Mechanism of a Bacterial Nramp-Family Divalent Metal Transporter.
Structure 24 :2102-2114. PubMed Id: 27839948. doi:10.1016/j.str.2016.09.017. |
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SLC26 proton-coupled fumarate symporter in complex with nanobodies: Deinococcus geothermalis B Bacteria (expressed in E. coli), 3.20 Å
|
Geertsma et al. (2015).
Geertsma ER, Chang YN, Shaik FR, Neldner Y, Pardon E, Steyaert J, & Dutzler R (2015). Structure of a prokaryotic fumarate transporter reveals the architecture of the SLC26 family.
Nat Struct Mol Biol 22 :803-808. PubMed Id: 26367249. doi:10.1038/nsmb.3091. |
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Serotonin transporter (SERT) ts3 construct with bound paroxetine at central site: Homo sapiens E Eukaryota (expressed in S. frugiperda), 3.14 Å
Thermostabilized constructs: ts2: I291A, T439S. ts3:ts2+Y110A ts2 with bound paroxetine at central site, 4.53 Å: 5I6Z ts3 with bound s-citalopram at central site, 3.15 Å: 5I71 ts3 with s-citalopram at central and allosteric sites (soaked), 3.24 Å:5I73 ts3 with Br-citalopram at central site, 3.39 Å: 5I74 ts3 with s-citalopram at central site and Br-citalopram at allosteric site, 3.49 Å: 5I75 |
Coleman et al. (2016).
Coleman JA, Green EM, & Gouaux E (2016). X-ray structures and mechanism of the human serotonin transporter.
Nature 7599:334-339. PubMed Id: 27049939. doi:10.1038/nature17629. |
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CitS Citrate symporter: Salmonella enterica B Bacteria (expressed in E. coli), 2.5 Å
The CitS dimer reveals three different conformations of the active protomer |
Wöhlert et al. (2015).
Wöhlert D, Grötzinger MJ, Kühlbrandt W, & Yildiz Ö (2015). Mechanism of Na+-dependent citrate transport from the structure of an asymmetrical CitS dimer.
Elife 4 :e09375. PubMed Id: 26636752. doi:10.7554/eLife.09375. |
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EAAT1 excitatory amino acid transporter 1 in complex with L-Asp and the allosteric inhibitor UCPH101: Homo sapiens E Eukaryota (expressed in HEK293F cells), 3.25 Å
Member of the solute carrier 1 (SLC1) family of transporters. Engineered protein; thermostabilized. complex with the competitive inhibitor TFB-TBOA and the allosteric inhibitor UCPH101, 3.71 Å: 5MJU cryst-II mutant in complex with L-Asp and the allosteric inhibitor UCPH101, 3.1 Å: 5LM4 cryst-II mutant in complex with L-Asp, 3.32 Å: 5LLU |
Canul-Tec et al. (2017).
Canul-Tec JC, Assal R, Cirri E, Legrand P, Brier S, Chamot-Rooke J, & Reyes N (2017). Structure and allosteric inhibition of excitatory amino acid transporter 1.
Nature 544 :446-451. PubMed Id: 28424515. doi:10.1038/nature22064. |
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Translocator Protein (18 kDA) TSPO
Principally an outer mitochondrial membrane protein that binds to cholesterol and drug ligands, but occurs in diverse organisms Previously referred to as a peripheral-type benzodiazepine receptor (PBR). In mitochondria, it is part of large multimeric complex located in the outer mitochondrial membrane, and is closely associated with VDAC. |
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Mitochondrial translocator protein (TSPO) in complex with PK11195: Mus musculus E Eukaryota (expressed in E. coli), NMR Structure
|
Jaremko et al. (2014).
Jaremko L, Jaremko M, Giller K, Becker S, & Zweckstetter M (2014). Structure of the mitochondrial translocator protein in complex with a diagnostic ligand.
Science 343 :1363-1366. PubMed Id: 24653034. doi:10.1126/science.1248725. |
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Guo et al. (2015).
Guo Y, Kalathur RC, Liu Q, Kloss B, Bruni R, Ginter C, Kloppmann E, Rost B, & Hendrickson WA (2015). Protein structure. Structure and activity of tryptophan-rich TSPO proteins.
Science 347 6221:551-555. PubMed Id: 25635100. doi:10.1126/science.aaa1534. |
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Li et al. (2015).
Li F, Liu J, Zheng Y, Garavito RM, & Ferguson-Miller S (2015). Protein structure. Crystal structures of translocator protein (TSPO) and mutant mimic of a human polymorphism.
Science 347 6221:555-558. PubMed Id: 25635101. doi:10.1126/science.1260590. |
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Ca2+:Cation Antiporter (CaCA) Family
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Sodium/Calcium Exchanger (NCX), Lipidic Cubic Phase Crystallization: Methanocaldococcus jannaschii A Archaea (expressed in E. coli), 1.90 Å
Structure determined using conventional crystallization, 3.50 Å: 3V5S |
Liao et al. (2012).
Liao J, Li H, Zeng W, Sauer DB, Belmares R, & Jiang Y (2012). Structural insight into the ion-exchange mechanism of the sodium/calcium exchanger.
Science 335 :686-690. PubMed Id: 22323814. doi:10.1126/science.1215759. |
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Vcx1 Ca2+/H+ (CaX) antiporter: Saccharomyces cerevisiae E Eukaryota, 2.30 Å
|
Waight et al. (2013).
Waight AB, Pedersen BP, Schlessinger A, Bonomi M, Chau BH, Roe-Zurz Z, Risenmay AJ, Sali A, & Stroud RM (2013). Structural basis for alternating access of a eukaryotic calcium/proton exchanger.
Nature 499 :107-110. PubMed Id: 23685453. doi:10.1038/nature12233. |
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Ca2+/H+ (CaX) antiporter: Archaeoglobus fulgidus A Archaea (expressed in E. coli), 2.30 Å
|
Nishizawa et al. (2013).
Nishizawa T, Kita S, Maturana AD, Furuya N, Hirata K, Kasuya G, Ogasawara S, Dohmae N, Iwamoto T, Ishitani R, & Nureki O (2013). Structural Basis for the Counter-Transport Mechanism of a H+/Ca2+ Exchanger.
Science 341 :168-172. PubMed Id: 23704374. |
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YfkE Ca2+/H+ (CaX) antiporter: Bacillus subtilis B Bacteria (expressed in E. coli), 3.05 Å
Selenium substituted structure, 3.00 Å: 4KJR |
Wu et al. (2013).
Wu M, Tong S, Waltersperger S, Diederichs K, Wang M, & Zheng L (2013). Crystal structure of Ca2+/H+ antiporter protein YfkE reveals the mechanisms of Ca2+ efflux and its pH regulation.
Proc. Natl. Acad. Sci. U.S.A. 110 28:11367-11372. PubMed Id: 23798403. doi:10.1073/pnas.1302515110. |
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Nucleobase-Cation-Symport-1 (NCS1) Family
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Mhp1 Benzyl-hydantoin transporter (without substrate); outward-facing conformation: Microbacterium liquefaciens B Bacteria (expressed in E. coli), 2.85 Å
With hydantion substrate; closed conformation, 4.0 Å: 2JLO. |
Weyand et al. (2008).
Weyand S, Shimamura T, Yajima S, Suzuki S, Mirza O, Krusong K, Carpenter EP, Rutherford NG, Hadden JM, O'Reilly J, Ma P, Saidijam M, Patching SG, Hope RJ, Norbertczak HT, Roach PC, Iwata S, Henderson PJ, & Cameron AD (2008). Structure and Molecular Mechanism of a Nucleobase-Cation-Symport-1 Family Transporter.
Science 322 :709-713. PubMed Id: 18927357. |
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Mhp1 Benzyl-hydantoin transporter; inward-facing conformation: Microbacterium liquefaciens B Bacteria (expressed in E. coli), 3.8 Å
|
Shimamura et al. (2010).
Shimamura T, Weyand S, Beckstein O, Rutherford NG, Hadden JM, Sharples D, Sansom MS, Iwata S, Henderson PJ, & Cameron AD (2010). Molecular basis of alternating access membrane transport by the sodium-hydantoin transporter Mhp1.
Science 328 :470-473. PubMed Id: 20413494. |
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Nucleobase-Cation-Symport-2 (NCS2) Family
also known as nucleobase/ascorbate transporter (NAT) |
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UraA uracil/H+ symporter: Escherichia coli B Bacteria, 2.78 Å
First example of a NAT/NCS2 protein. It has 14 transmembrane segments divided into two inverted repeats. |
Lu et al. (2011).
Lu F, Li S, Jiang Y, Jiang J, Fan H, Lu G, Deng D, Dang S, Zhang X, Wang J, & Yan N (2011). Structure and mechanism of the uracil transporter UraA
Nature 472 :243-246. PubMed Id: 21423164. doi:10.1038/nature09885. |
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UapA purine/H+ symporter in complex with Xanthine: Aspergillus nidulans E Eukaryota (expressed in S. cerevisiae), 3.7 Å
The protein has 14 TM segments. Dimerization may be important in transport. |
Alguel et al. (2016).
Alguel Y, Amillis S, Leung J, Lambrinidis G, Capaldi S, Scull NJ, Craven G, Iwata S, Armstrong A, Mikros E, Diallinas G, Cameron AD, & Byrne B (2016). Structure of eukaryotic purine/H+ symporter UapA suggests a role for homodimerization in transport activity.
Nat Commun 7 :11336. PubMed Id: 27088252. doi:10.1038/ncomms11336. |
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Solute Carrier Family 4 (anion exchanger)
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Erythrocyte Band 3 anion exchanger: Homo sapiens E Eukaryota, 3.5 Å
|
Arakawa et al. (2015).
Arakawa T, Kobayashi-Yurugi T, Alguel Y, Iwanari H, Hatae H, Iwata M, Abe Y, Hino T, Ikeda-Suno C, Kuma H, Kang D, Murata T, Hamakubo T, Cameron AD, Kobayashi T, Hamasaki N, & Iwata S (2015). Crystal structure of the anion exchanger domain of human erythrocyte band 3.
Science 350 :680-684. PubMed Id: 26542571. doi:10.1126/science.aaa4335. |
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Band 3 cytoplasmic domain: Homo sapiens E Eukaryota (expressed in E. coli), 2.60 Å
|
Zhang et al. (2000).
Zhang D, Kiyatkin A, Bolin JT, & Low PS (2000). Crystallographic structure and functional interpretation of the cytoplasmic domain of erythrocyte membrane band 3.
Blood 96 :2925-2933. PubMed Id: 11049968. |
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Betaine/Choline/Carnitine Transporter (BCCT) Family
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BetP glycine betaine transporter: Corynebacterium glutamicum B Bacteria (expressed in E. coli), 3.35 Å
A Na+-coupled symporter in an intermediate state. Formerly PDB 2W8A. |
Ressl et al. (2009).
Ressl S, Terwisscha van Scheltinga AC, Vonrhein C, Ott V, & Ziegler C (2009). Molecular basis of transport and regulation in the Na+/betaine symporter BetP.
Nature 458 :47-52. PubMed Id: 19262666. |
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BetP glycine betaine transporter in outward-facing conformation: Corynebacterium glutamicum B Bacteria (expressed in E. coli), 3.25 Å
BetP with asymmetric protomers, 3.10 Å: 4AIN |
Perez et al. (2012).
Perez C, Koshy C, Yildiz O, & Ziegler C (2012). Alternating-access mechanism in conformationally asymmetric trimers of the betaine transporter BetP.
Nature 490 :126-130. PubMed Id: 22940865. doi:10.1038/nature11403. |
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BetP glycine betaine transporter with bound lipids: Corynebacterium glutamicum B Bacteria (expressed in E. coli), 2.70 Å
|
Koshy et al. (2013).
Koshy C, Schweikhard ES, Gärtner RM, Perez C, Yildiz O, & Ziegler C (2013). Structural evidence for functional lipid interactions in the betaine transporter BetP.
EMBO J 32 :3096-3105. PubMed Id: 24141878. doi:10.1038/emboj.2013.226. |
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CaiT carnitine transporter: Escherichia coli B Bacteria, 3.15 Å
This is a precursor/product antiporter that catalyzes the exchange of L-carnitine wtih γ-butyrobetaine. The protein is a homotrimer with each monomer containing 12 transmembrane helices. |
Tang et al. (2010).
Tang L, Bai L, Wang WH, & Jiang T (2010). Crystal structure of the carnitine transporter and insights into the antiport mechanism.
Nat Struct Mol Biol 17 :492-496. PubMed Id: 20357772. |
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CaiT carnitine transporter: Escherichia coli B Bacteria, 3.50 Å
Fully-open inward-facing conformation. |
Schulze et al. (2010).
Schulze S, Köster S, Geldmacher U, Terwisscha van Scheltinga AC, & Kühlbrandt W. (2010). Structural basis of Na+-independent and cooperative substrate/product antiport in CaiT.
Nature 467 :233-236. PubMed Id: 20829798. |
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CaiT carnitine transporter: Proteus mirabilis B Bacteria, 2.3 Å
Fully-open inward-facing conformation. |
Schulze et al. (2010).
Schulze S, Köster S, Geldmacher U, Terwisscha van Scheltinga AC, & Kühlbrandt W. (2010). Structural basis of Na+-independent and cooperative substrate/product antiport in CaiT.
Nature 467 :233-236. PubMed Id: 20829798. |
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CaiT carnitine transporter, R262E mutant with bound γ-butyrobetaine: Proteus mirabilis B Bacteria (expressed in E. coli), 3.29 Å
|
Kalayil et al. (2013).
Kalayil S, Schulze S, & Kühlbrandt W (2013). Arginine oscillation explains Na+ independence in the substrate/product antiporter CaiT.
Proc Natl Acad Sci USA 110 43:17296-17301. PubMed Id: 24101465. doi:10.1073/pnas.1309071110. |
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Amino Acid/Polyamine/Organocation (APC) Superfamily
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AdiC Arginine:Agmatine Antiporter: Escherichia coli B Bacteria, 3.61 Å
3LRB is a re-refinement of the original 3H5B structure, which contained a register shift of 3-4 amino acids relative to 3NCY and 3GIA (below). |
Gao et al. (2009).
Gao X, Lu F, Zhou L, Dang S, Sun L, Li X, Wang J, & Shi Y. (2009). Structure and mechanism of an amino acid antiporter.
Science 324 :1565-1568. PubMed Id: 19478139. |
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AdiC Arginine:Agmatine Antiporter (N22A, L123W mutant) with bound Arginine: Escherichia coli B Bacteria, 3.0 Å
Outward-facing occluded state |
Gao et al. (2010).
Gao X, Zhou L, Jiao X, Lu F, Yan C, Zeng X, Wang J, & Shi Y (2010). Mechanism of substrate recognition and transport by an amino acid antiporter.
Nature 463 :828-832. PubMed Id: 20090677. |
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AdiC Arginine:Agmatine Antiporter (N101A mutant) with bound Arginine: Escherichia coli B Bacteria, 3.0 Å
Reveals AdiC in the open-to-out conformation. |
Kowalczyk et al. (2011).
Kowalczyk L, Ratera M, Paladino A, Bartoccioni P, Errasti-Murugarren E, Valencia E, Portella G, Bial S, Zorzano A, Fita I, Orozco M, Carpena X, Vázquez-Ibar JL, & Palacín M (2011). Molecular basis of substrate-induced permeation by an amino acid antiporter.
Proc Natl Acad Sci USA 108 :3935-3940. PubMed Id: 21368142. |
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AdiC Arginine:Agmatine Antiporter in complex with agmatine: Escherichia coli B Bacteria, 2.59 Å
apo protein, 2.21 Å: 5J4I |
Ilgü et al. (2016).
Ilgü H, Jeckelmann JM, Gapsys V, Ucurum Z, de Groot BL, & Fotiadis D (2016). Insights into the molecular basis for substrate binding and specificity of the wild-type L-arginine/agmatine antiporter AdiC.
Proc. Natl. Acad. Sci. U.S.A. 113 37:10358-10363. PubMed Id: 27582465. doi:10.1073/pnas.1605442113. |
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AdiC Arginine:Agmatine Antiporter (with Fab fragment): Salmonella enterica B Bacteria (expressed in E. coli), 3.2 Å
PDB ID was originally 3HQK, which has been superseded by 3NCY. |
Fang et al. (2009).
Fang Y, Jayaram H, Shane T, Kolmakova-Partensky L, Wu F, Williams C, Xiong Y, & Miller C (2009). Structure of a prokaryotic virtual proton pump at 3.2 Å resolution.
Nature 460 :1040-1043. PubMed Id: 19578361. |
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|
Shaffer et al. (2009).
Shaffer PL, Goehring A, Shankaranarayanan A, & Gouaux E (2009). Structure and Mechanism of a Na+-independent amino acid transporter.
Science 325 :1010-1014. PubMed Id: 19608859. |
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Ma et al. (2012).
Ma D, Lu P, Yan C, Fan C, Yin P, Wang J, & Shi Y (2012). Structure and mechanism of a glutamate-GABA antiporter.
Nature 483 :632-636. PubMed Id: 22407317. doi:10.1038/nature10917. |
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Amino Acid Secondary Transporters
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LeuTAa Leucine transporter: Aquifex aeolicus B Bacteria (expressed in E. coli), 1.65 Å
|
Yamashita et al. (2005).
Yamashita A, Singh SK, Kawate T, Jin Y, & Gouaux E (2005). Crystal structure of a bacterial homologue of Na+/Cl--dependent neurotransmitter transporters.
Nature 437 :215-223. PubMed Id: 16041361. |
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|
Singh et al. (2007).
Singh SK, Yamashita A, & Gouaux E (2007). Antidepressant binding site in a bacterial homologue of neurotransmitter transporters.
Nature 448 :952-956. PubMed Id: 17687333. |
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LeuT Leucine transporter with bound Na+ and tryptophan: Aquifex aeolicus B Bacteria (expressed in E. coli), 2.00 Å
Shows the transporter in an open-to-out conformation. w. bound glycine, 2.15 Å: 3F4J w. bound alanine, 1.90 Å: 3F48 w. bound leucine (30mM), 1.80 Å: 3F3E w. bound methionine, 1.90 Å: 3F3D w. bound selenomethionine, 1.95 Å: 3F4I w. bound 4-fluorophenylalanine, 2.10 Å: 3F3C |
Singh et al. (2009).
Singh SK, Piscitelli CL, Yamashita A, & Gouaux E (2009). A competitive inhibitor traps LeuT in an open-to-out conformation.
Science 322 :1655-1661. PubMed Id: 19074341. |
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LeuT Leucine Transporter with Bound Desipramine: Aquifex aeolicus B Bacteria (expressed in E. coli), 2.9 Å
|
Zhou et al. (2007).
Zhou Z, Zhen J, Karpowich NK, Goetz RM, Law CJ, Reith ME, & Wang DN (2007). LeuT-desipramine structure reveals how antidepressants block neurotransmitter reuptake.
Science 317 :1390-1393. PubMed Id: 17690258. |
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Wild-type LeuT transporter with bound octylglucopyranoside (OG): Aquifex aeolicus B Bacteria (expressed in E. coli), 2.0 Å
E290S mutant with bound OG, 2.8 Å: 3GJC |
Quick et al. (2009).
Quick M, Winther AM, Shi L, Nissen P, Weinstein H, & Javitch JA (2009). Binding of an octylglucoside detergent molecule in the second substrate (S2) site of LeuT establishes an inhibitor-bound conformation.
Proc. Natl. Acad. Sci. USA 106 :5563-5568. PubMed Id: 19307590. |
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Mutant LeuT transporter with Nitroxide Spin Label (F177R1): Aquifex aeolicus B Bacteria (expressed in E. coli), 2.25 Å
I204R1 mutant, 2.25 Å: 3MPQ |
Kroncke et al. (2010).
Kroncke BM, Horanyi PS, Columbus L. (2010). Structural Origins of Nitroxide Side Chain Dynamics on Membrane Protein α-Helical Sites.
Biochemistry 49 :10045-10060. PubMed Id: 20964375. |
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Piscitelli & Gouaux (2012).
Piscitelli CL & Gouaux E (2012). Insights into transport mechanism from LeuT engineered to transport tryptophan.
EMBO J 31 :228-235. PubMed Id: 21952050. doi:10.1038/emboj.2011.353. |
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Crystal Structure of LeuT in the outward-open conformation in complex with Fab: Aquifex aeolicus B Bacteria (expressed in E. coli), 3.10 Å
(LeuTK(Y108F)-2B12 Complex) LeuT in the inward-open conformation in complex with Fab, 3.22 Å: 3TT3 (LeuTK(TSY)-6A10 complex) LeuT mutant T355V, S354A, K288A in complex with alanine and sodium, 2.99 Å: 3TU0 (LeuTK(TS) complex with Ala) |
Krishnamurthy & Gouaux (2012).
Krishnamurthy H & Gouaux E (2012). X-ray structures of LeuT in substrate-free outward-open and apo inward-open states.
Nature 481 :469-474. PubMed Id: 22230955. doi:10.1038/nature10737. |
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LeuT Leucine Transporter Crystallized from Bicelles: Aquifex aeolicus B Bacteria (expressed in E. coli), 2.50 Å
3USG is designated as LeuT-Leu (C2 bicelle) LeuT-Leu (P2 bicelle), 3.11 Å: 3USI LeuT-Leu (P21 form A bicelle), 3.50 Å: 3USJ LeuT-Leu (P21 form B bicelle), 4.50 Å: 3USK LeuT-SeMet (C2 bicelle), 2.71 Å: 3USL LeuT-SeMet (C2 bicelle, collected at 1.2 Å), 3.01 Å: 3USM LeuT-SeMet (P21212 bicelle), 4.50 Å: 3USO LeuT-β-SeHG (C2 β-SeHG), 2.10 Å: 3USP |
Wang et al. (2012).
Wang H, Elferich J, & Gouaux E (2012). Structures of LeuT in bicelles define conformation and substrate binding in a membrane-like context.
Nature Struc Mol Biol 19 :212-219. PubMed Id: 22245965. doi:10.1038/nsmb.2215. |
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Malinauskaite et al. (2016).
Malinauskaite L, Said S, Sahin C, Grouleff J, Shahsavar A, Bjerregaard H, Noer P, Severinsen K, Boesen T, Schiφtt B, Sinning S, & Nissen P (2016). A conserved leucine occupies the empty substrate site of LeuT in the Na+-free return state.
Nat Commun 7 :11673. PubMed Id: 27221344. doi:10.1038/ncomms11673. |
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LeuBAT Δ13 mutant with bound paroxetine: Aquifex aeolicus B Bacteria (expressed in E. coli), 2.89 Å
LeuBAT is an engineered LeuT harboring the human biogenic amine transporter (BAT) binding motif. Δ13 mutant with bound sertraline, 3.20 Å: 4MM5 Δ13 mutant with bound duloxetine, 3.10 Å: 4MM6 Δ13 mutant with bound desvenlafaxine, 2.85 Å: 4MM7 Δ13 mutant with bound fluoxetine, 3.31 Å: 4MM8 Δ13 mutant with bound fluvoxamine, 2.90 Å: 4MM9 Δ13 mutant with bound clomipramine, 3.30 Å: 4MMA Δ6 mutant with bound sertraline, 2.25 Å: 4MMB Δ6 mutant with bound desvenlafaxine, 2.30 Å: 4MMC Δ6 mutant with bound duloxetine, 2.30 Å: 4MMD Δ6 mutant with bound mazindol, 2.50 Å: 4MME Δ5 mutant with bound mazindol, 2.70 Å: 4MMF |
Wang et al. (2013).
Wang H, Goehring A, Wang KH, Penmatsa A, Ressler R, & Gouaux E (2013). Structural basis for action by diverse antidepressants on biogenic amine transporters.
Nature 503 :141-145. PubMed Id: 24121440. doi:10.1038/nature12648. |
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Glutamate Transporter Homologue (GltPh): Pyrococcus horikoshii A Archaea (expressed in E. coli), 3.50 Å
Outward-facing state |
Yernool et al. (2004).
Yernool D, Boudker O, Jin Y, & Gouaux E (2004). Structure of a glutamate transporter homologue from Pyrococcus horikoshii.
Nature 431 :811-818. PubMed Id: 15483603. |
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Glutamate Transporter Homologue (GltPh): Pyrococcus horikoshii A Archaea (expressed in E. coli), 3.51 Å
Inward-facing state |
Reyes et al. (2009).
Reyes N, Ginter C, & Boudker O (2009). Transport mechanism of a bacterial homologue of glutamate transporters.
Nature 462 :880-885. PubMed Id: 19924125. |
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Glutamate Transporter Homologue (GltPh), cross-linked V216C-M385C mutant: Pyrococcus horikoshii A Archaea (expressed in E. coli), 3.80 Å
Two protomers are inward facing and a third is outward facing. V198C, A380C mutant, 4.66 Å: 3V8G |
Verdon & Boudker (2012).
Verdon G & Boudker O (2012). Crystal structure of an asymmetric trimer of a bacterial glutamate transporter homolog.
Nature Struc Mol Biol 19 :355-357. PubMed Id: 22343718. doi:10.1038/nsmb.2233. |
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Glutamate Transporter Homologue (GltPh), inward-facing apo form: Pyrococcus horikoshii A Archaea (expressed in E. coli), 3.25 Å
Tl+-bound, inward-facing apo conformation, 3.75 Å: 4P1A alkali-free, inward-facing, 3.50 Å: 4P3J Tl+-bound inward-facing, bound conformation, 4.08 Å: 4P6H R397A mutant, outward-facing, 4.00 Å: 4OYE R397A mutant, outward-facing, Na+-bound, 3.39 Å: 4OYF R397A mutant, outward-facing, Na+/Asp-bound, 3.50 Å: 4OYG |
Verdon et al. (2014).
Verdon G, Oh S, Serio RN, & Boudker O (2014). Coupled ion binding and structural transitions along the transport cycle of glutamate transporters.
eLife 3 :e02283. PubMed Id: 24842876. doi:10.7554/eLife.02283. |
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Glutamate Transporter Homologue (GltPh), R276S/M395R mutant, inward facing: Pyrococcus horikoshii A Archaea (expressed in E. coli), 4.21 Å
|
Akyuz et al. (2015).
Akyuz N, Georgieva ER, Zhou Z, Stolzenberg S, Cuendet MA, Khelashvili G, Altman RB, Terry DS, Freed JH, Weinstein H, Boudker O, & Blanchard SC (2015). Transport domain unlocking sets the uptake rate of an aspartate transporter.
Nature 518 7537:68-73. PubMed Id: 25652997. doi:10.1038/nature14158. |
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Boudker et al. (2007).
Boudker O, Ryan RM, Yernool D, Shimamoto K, & Gouaux E (2007). Coupling substrate and ion binding to extracellular gate of a sodium-dependent aspartate transporter.
Nature 445 :387-393. PubMed Id: 17230192. |
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Aspartate Transporter, substrate-free: Thermococcus kodakarensis A Archaea (expressed in E. coli), 3.00 Å
|
Jensen et al. (2013).
Jensen S, Guskov A, Rempel S, Hänelt I, & Slotboom DJ (2013). Crystal structure of a substrate-free aspartate transporter.
Nat Struct Mol Biol 20 :1224-1226. PubMed Id: 24013209. doi:10.1038/nsmb.2663. |
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Aspartate Transporter, apo form: Thermococcus kodakarensis B Bacteria (expressed in E. coli), 2.7 Å
with bound aspartate and Na+, 2.8 Å: 5E9S |
Guskov et al. (2016).
Guskov A, Jensen S, Faustino I, Marrink SJ, & Slotboom DJ (2016). Coupled binding mechanism of three sodium ions and aspartate in the glutamate transporter homologue GltTk.
Nat Commun 7 :13420. PubMed Id: 27830699. doi:10.1038/ncomms13420. |
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MhsT multi-hydrophobic amino acid transporter, occluded inward-facing state: Bacillus halodurans B Bacteria (expressed in Lactococcus lactis), 2.10 Å
lipidic cubic phase form, 2.60 Å: 4US4 |
Malinauskaite et al. (2014).
Malinauskaite L, Quick M, Reinhard L, Lyons JA, Yano H, Javitch JA, & Nissen P (2014). A mechanism for intracellular release of Na(+) by neurotransmitter/sodium symporters.
Nat Struct Mol Biol 21 11:1006-1012. PubMed Id: 25282149. doi:10.1038/nsmb.2894. |
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Cation Diffusion Facilitator (CDF) Family
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YiiP Zinc Transporter: Escherichia coli B Bacteria, 3.8 Å
9-18, 2005) |
Lu & Fu (2007).
Lu M & Fu D (2007). Structure of the zinc transporter YiiP.
Science 317 :1746-1748. PubMed Id: 17717154. |
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YiiP Zinc Transporter: Escherichia coli B Bacteria, 2.9 Å
9-18, 2005) |
Lu et al. (2009).
Lu M, Chai J, & Fu D (2009). Structural basis for autoregulation of the zinc transporter YiiP.
Nat Struct Mol Biol 16 :1063-1067. PubMed Id: 19749753. |
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Antiporters
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NhaA Na+/H+ antiporter: Escherichia coli B Bacteria, 3.45 Å
|
Hunte et al. (2005).
Hunte C, Screpanti E, Venturi M, Rimon A, Padan E, & Michel H (2005). Structure of a Na(+)/H(+) antiporter and insights into mechanism of action and regulation by pH.
Nature 435 :1197-1202. PubMed Id: 15988517. |
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NhaA Na+/H+ antiporter: Escherichia coli B Bacteria, by electron crystallography
Difference maps show structural changes with changes in pH. |
Appel et al. (2009).
Appel M, Hizlan D, Vinothkumar KR, Ziegler C, Kühlbrandt W (2009). Conformations of NhaA, the Na/H exchanger from Escherichia coli, in the pH-activated and ion-translocating states.
J Mol Biol 386 :351-365. PubMed Id: 19135453. |
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NhaA Na+/H+ antiporter in dimeric state (inward-facing): Escherichia coli B Bacteria, 3.70 Å
triple mutant (A109T, Q277G, L296M), 3.50 Å: 4ATV |
Lee et al. (2014).
Lee C, Yashiro S, Dotson DL, Uzdavinys P, Iwata S, Sansom MS, von Ballmoos C, Beckstein O, Drew D, & Cameron AD (2014). Crystal structure of the sodium-proton antiporter NhaA dimer and new mechanistic insights.
J Gen Physiol 144 6:529-544. PubMed Id: 25422503. doi:10.1085/jgp.201411219. |
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NapA Na+/H+ antiporter: Thermus thermophilus B Bacteria (expressed in E. coli), 2.98 Å
|
Lee et al. (2013).
Lee C, Kang HJ, von Ballmoos C, Newstead S, Uzdavinys P, Dotson DL, Iwata S, Beckstein O, Cameron AD, & Drew D (2013). A two-domain elevator mechanism for sodium/proton antiport.
Nature 501 :573-577. PubMed Id: 23995679. doi:10.1038/nature12484. |
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NapA Na+/H+ antiporter, outward facing: Thermus thermophilus B Bacteria (expressed in E. coli), 2.3 Å
inward facing, 3.7 Å: 5BZ2 |
Coincon et al. (2016).
Coincon M, Uzdavinys P, Nji E, Dotson DL, Winkelmann I, Abdul-Hussein S, Cameron AD, Beckstein O, & Drew D (2016). Crystal structures reveal the molecular basis of ion translocation in sodium/proton antiporters.
Nat Struct Mol Biol 23 :248-255. PubMed Id: 26828964. doi:10.1038/nsmb.3164. |
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Wöhlert et al. (2014).
Wöhlert D, Kühlbrandt W, & Yildiz Ö (2014). Structure and substrate ion binding in the sodium/proton antiporter PaNhaP.
Elife 3 :e03579. PubMed Id: 25426802. doi:10.7554/eLife.03579. |
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NhaP1 Na+/H+ antiporter, pH 8: Methanocaldococcus jannaschii A Archaea (expressed in E. coli), 3.50 Å
EM 2D crystal reconstruction structure, pH 4. In-plane resolution 6 Å: 4D0A |
Paulino et al. (2014).
Paulino C, Wöhlert D, Kapotova E, Yildiz Ö, & Kühlbrandt W (2014). Structure and transport mechanism of the sodium/proton antiporter MjNhaP1.
Elife 3 :e03583. PubMed Id: 25426803. doi:10.7554/eLife.03583. |
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Mitochondrial ADP/ATP Carrier: Bos taurus heart mitochondria E Eukaryota, 2.2 Å
Monomeric, in complex with carboxyatractyloside inhibitor. |
Pebay-Peyroula et al. (2003).
Pebay-Peyroula E, Dahout-Gonzalez C, Kahn R, Trezeguet V, Lauquin GJ, & Brandolin G (2003). Structure of mitochondrial ADP/ATP carrier in complex with carboxyatractyloside.
Nature 426 :39-44. PubMed Id: 14603310. |
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Mitochondrial ADP/ATP Carrier: Bos taurus heart mitochondria E Eukaryota, 2.8 Å
Biological dimer with endogenous cardiolipins. |
Nury et al. (2005).
Nury H, Dahout-Gonzalez C, Trézéguet V, Lauquin G, Brandolin G, & Pebay-Peyroula E (2005). Structural basis for lipid-mediated interactions between mitochondrial ADP/ATP carrier monomers.
FEBS Lett 579 :13561-13556. PubMed Id: 16226253. |
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UCP2 mitochondrial uncoupling protein 2: Mus musculus E Eukaryota (expressed in E. coli), NMR structure
Solved by a combination of NMR residual dipolar couplings, paramagnetic relaxation enhancement, and molecular fragment replacement. |
Berardi et al. (2011).
Berardi MJ, Shih WM, Harrison SC, & Chou JJ (2011). Mitochondrial uncoupling protein 2 structure determined by NMR molecular fragment searching
Nature 476 :109-113. PubMed Id: 21785437. doi:10.1038/nature10257. |
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Mitochondrial ADP/ATP Carrier; isoform 2 inhibited by carboxyatractyloside (C2221 crystal form): Saccharomyces cerevisiae E Eukaryota, 2.49 Å
isoform 2 inhibited by carboxyatractyloside (P212121 crystal form), 3.20 Å: 4C9H isoform 3 inhibited by carboxyatractyloside (P21 crystal form), 3.20 Å: 4C9Q isoform 3 inhibited by carboxyatractyloside (P212121 crystal form), 3.40 Å: 4C9J |
Ruprecht et al. (2014).
Ruprecht JJ, Hellawell AM, Harding M, Crichton PG, McCoy AJ, & Kunji ER (2014). Structures of yeast mitochondrial ADP/ATP carriers support a domain-based alternating-access transport mechanism.
Proc. Natl. Acad. Sci. U.S.A. 111 :E426-E434. PubMed Id: 24474793. doi:10.1073/pnas.1320692111. |
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Apical Sodium-Dependent Bile Acid Transporters (ASBT)
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Hu et al. (2011).
Hu NJ, Iwata S, Cameron AD, & Drew D (2011). Crystal structure of a bacterial homologue of the bile acid sodium symporter ASBT.
Nature 478 :408-411. PubMed Id: 21976025. doi:10.1038/nature10450. |
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Bacterial homologue of ASBT (ASBTYf), inward-open conformation: Yersinia frederiksenii B Bacteria (expressed in E. coli), 1.95 Å
E254A mutant, probable outward-open conformation, 2.50 Å: 4N7X |
Zhou et al. (2014).
Zhou X, Levin EJ, Pan Y, McCoy JG, Sharma R, Kloss B, Bruni R, Quick M, & Zhou M (2014). Structural basis of the alternating-access mechanism in a bile acid transporter.
Nature 505 :569-573. PubMed Id: 24317697. doi:10.1038/nature12811. |
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Energy-Coupling Factor (ECF) Transporters
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RibU, S Component of the Riboflavin Transporter: Staphylococcus aureus B Bacteria (expressed in E. coli), 3.6 Å
|
Zhang et al. (2010).
Zhang P, Wang J, & Shi Y (2010). Structure and mechanism of the S component of a bacterial ECF transporter.
Nature 468 :717-720. PubMed Id: 20972419. |
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ThiT, S component of the Thiamin Transporter: Lactococcus lactis B Bacteria, 2.00 Å
|
Erkens et al. (2011).
Erkens GB, Berntsson RP, Fulyani F, Majsnerowska M, Vujčić-Žagar A, Ter Beek J, Poolman B, & Slotboom DJ (2011). The structural basis of modularity in ECF-type ABC transporters.
Nat Struct Mol Biol 18 :755-760. PubMed Id: 21706007. doi:10.1038/nsmb.2073. |
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BioY, S component of the Biotin Transporter: Lactococcus lactis B Bacteria, 2.09 Å
|
Berntsson et al. (2012).
Berntsson RP, ter Beek J, Majsnerowska M, Duurkens RH, Puri P, Poolman B, & Slotboom DJ (2012). Structural divergence of paralogous S components from ECF-type ABC transporters.
Proc Natl Acad Sci USA 109 :13990-13995. PubMed Id: 22891302. doi:10.1073/pnas.1203219109. |
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Folate ECF transporter complex: Lactobacillus brevis B Bacteria (expressed in E. coli), 3.00 Å
Structure of the intact transporter consisting of FolT, EcfT, EcfA, and EcfA'. |
Xu et al. (2013).
Xu K, Zhang M, Zhao Q, Yu F, Guo H, Wang C, He F, Ding J, & Zhang P (2013). Crystal structure of a folate energy-coupling factor transporter from Lactobacillus brevis.
Nature 497 :268-271. PubMed Id: 23584589. doi:10.1038/nature12046. |
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ECF transporter complex: Lactobacillus brevis B Bacteria (expressed in E. coli), 3.53 Å
Thought to be specific for hydroxymethylpyrimidine (HMP). |
Wang et al. (2013).
Wang T, Fu G, Pan X, Wu J, Gong X, Wang J, & Shi Y (2013). Structure of a bacterial energy-coupling factor transporter.
Nature 497 :272-276. PubMed Id: 23584587. |
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Swier et al. (2016).
Swier LJ, Guskov A, & Slotboom DJ (2016). Structural insight in the toppling mechanism of an energy-coupling factor transporter.
Nat Commun 7 :11072. PubMed Id: 27026363. doi:10.1038/ncomms11072. |
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ECF-PanT energy-coupling factor pantothenate transporter: Lactobacillus brevis B Bacteria, 3.23 Å
|
Zhang et al. (2014).
Zhang M, Bao Z, Zhao Q, Guo H, Xu K, Wang C, & Zhang P (2014). Structure of a pantothenate transporter and implications for ECF module sharing and energy coupling of group II ECF transporters.
Proc Natl Acad Sci USA 111 52:18560-18565. PubMed Id: 25512487. doi:10.1073/pnas.1412246112. |
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ATP Binding Cassette (ABC) Transporters
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BtuCD Vitamin B12 Transporter: Escherichia coli B Bacteria, 3.2 Å
|
Locher et al. (2002).
Locher KP, Lee AT, & Rees DC (2002). The E. coli BtuCD structure: A framework for ABC transporter architecture and mechanism.
Science 296 :1091-1098. PubMed Id: 12004122. |
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BtuCD-F Complex; BtuCD B12 Transporter + BtuF binding protein: Escherichia coli B Bacteria, 2.6 Å
|
Hvorup et al. (2007).
Hvorup RN, Goetz BA, Niederer M, Hollenstein K, Perozo E, & Locher KP (2007). Asymmetry in the structure of the ABC transporter-binding protein complex BtuCD-BtuF.
Science 317 :1387-1390. PubMed Id: 17673622. |
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BtuCD-F Vitamin B12 Transporter with bound AMP-PNP: Escherichia coli B Bacteria, 3.47 Å
Has engineered disulphide cross-linking. Structure suggests a peristaltic transport mechanism. |
Korkhov et al. (2012).
Korkhov VM, Mireku SA, & Locher KP (2012). Structure of AMP-PNP-bound vitamin B12 transporter BtuCD-F.
Nature 490 :367-372. PubMed Id: 23000901. doi:10.1038/nature11442. |
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Sav1866 Multidrug Transporter: Staphylococcus aureus B Bacteria, 3.0 Å
|
Dawson and Locher (2006).
Dawson RJP & Locher KP (2006). Structure of a bacterial multidrug ABC transporter.
Nature 443 :180-185. PubMed Id: 16943773. |
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Hollenstein et al. (2007).
Hollenstein K, Frei DC, & Locher KP (2007). Structure of an ABC transporter in complex with its binding protein.
Nature 446 :213-216. PubMed Id: 17322901. |
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ModBC Molybdate ABC Transporter in a trans-inhibited state: Methanosarcina acetivorans A Archaea, 3.0 Å
|
Gerber et al. (2008).
Gerber S, Comellas-Bigler M, Goetz BA, & Locher KP (2008). Structural basis of trans-inhibition in a molybdate/tungstate ABC transporter.
Science 321 :246-250. PubMed Id: 18511655. |
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HI1470/1 Putative Metal-Chelate-type ABC Transporter: Haemophilus influenzae B Bacteria, 2.4 Å
First structure showing an inward-facing conformation of an ABC transporter |
Pinkett et al. (2007).
Pinkett HW, Lee AT, Lum P, Locher KP & Rees DC (2007). An inward-facing conformation of a putative metal-chelate-type ABC transporter.
Science 315 :373-377. PubMed Id: 17158291. |
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MsbA Lipid "flippase" with bound AMPPNP: Salmonella typhimurium B Bacteria (expressed in E. coli), 3.7 Å
MsbA with bound AMPPNP used for initial model: 3B5Y, 4.5 Å ADP + Vanadate-bound conformation: 3B5Z, 4.2 Å Open apo-conformation (E. coli): 3B5W, 5.3 Å Closed apo-conformation (Vibrio cholerae expressed in E. coli): 3B5X, 5.5 Å |
Ward et al. (2007).
Ward A, Reyes CL, Yu J, Roth CB, & Chang G (2007). Flexibility in the ABC transporter MsbA: Alternating access with a twist.
Proc Natl Acad Sci U S A 104 :19005-19010. PubMed Id: 18024585. |
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Aller et al. (2009).
Aller SG, Yu J, Ward A, Weng Y, Chittaboina S, Zhuo R, Harrell PM, Trinh YT, Zhang Q, Urbatsch IL, & Chang G. (2009). Structure of P-glycoprotein reveals a molecular basis for poly-specific drug binding.
Science 323 :1718-1722. PubMed Id: 19325113. |
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Li et al. (2014).
Li J, Jaimes KF, & Aller SG (2014). Refined structures of mouse P-glycoprotein.
Protein Sci. 23 :34-46. PubMed Id: 24155053. doi:10.1002/pro.2387. |
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Szewczyk et al. (2015).
Szewczyk P, Tao H, McGrath AP, Villaluz M, Rees SD, Lee SC, Doshi R, Urbatsch IL, Zhang Q, & Chang G (2015). Snapshots of ligand entry, malleable binding and induced helical movement in P-glycoprotein.
Acta Crystallogr D Biol Crystallogr 71 :732-741. PubMed Id: 25760620. doi:10.1107/S1399004715000978. |
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P-Glycoprotein: Caenorhabditis elegans E Eukaryota (expressed in Pichia pastoris), 3.40 Å
|
Jin et al. (2012).
Jin MS, Oldham ML, Zhang Q, & Chen J (2012). Crystal structure of the multidrug transporter P-glycoprotein from Caenorhabditis elegans.
Nature 490 :566-569. PubMed Id: 23000902. doi:10.1038/nature11448. |
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Kodan et al. (2014).
Kodan A, Yamaguchi T, Nakatsu T, Sakiyama K, Hipolito CJ, Fujioka A, Hirokane R, Ikeguchi K, Watanabe B, Hiratake J, Kimura Y, Suga H, Ueda K, & Kato H (2014). Structural basis for gating mechanisms of a eukaryotic P-glycoprotein homolog.
Proc Natl Acad Sci USA 111 :4049-4054. PubMed Id: 24591620. doi:10.1073/pnas.1321562111. |
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MalFGK2-MBP Maltose uptake transporter complex: Escherichia coli B Bacteria, 2.8 Å
Complex includes maltose-binding protein (MBP), maltose, and ATP |
Oldham et al. (2007).
Oldham ML, Khare D, Quiocho FA, Davidson AL, & Chen J (2007). Crystal structure of a catalytic intermediate of the maltose transporter.
Nature 450 :515-521. PubMed Id: 18033289. |
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MalFGK2 uptake transporter: Escherichia coli B Bacteria, 4.5 Å
Helix TM1 deleted. Shows transporter in the inward conformation in the resting state. |
Khare et al. (2009).
Khare D, Oldham ML, Orelle C, Davidson AL, & Chen J (2009). Alternating access in maltose transporter mediated by rigid-body rotations.
Mol Cell 27 :528-536. PubMed Id: 19250913. |
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MalFGK2-MBP Maltose uptake transporter complex: Escherichia coli B Bacteria, 3.10 Å
The structure shows the transporter in the pretranslocation (pre-T) state using a mutant maltose binding protein MBPG69C/S337C that stabilizes the closed substrate-bound conformation. Complex with MBPG69C/S337C and AMP-PNP, 2.9 Å: 3PUZ Complex with wt. MBP and AMP-PNP, 3.1 Å: 3PUY |
Oldham & Chen (2011).
Oldham ML & Chen J (2011). Crystal structure of the maltose transporter in a pretranslocation intermediate State
Science 332 :1202-1205. PubMed Id: 21566157. doi:10.1126/science.1200767. |
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Oldham & Chen (2011).
Oldham ML & Chen J (2011). Snapshots of the maltose transporter during ATP hydrolysis.
Proc Natl Acad Sci USA 108 :15152-15156. PubMed Id: 21825153. doi:10.1073/pnas.1108858108. |
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MalFGK2 in complex with glucose-specific enzyme IIA: Escherichia coli B Bacteria, 3.91 Å
The structure provides a structural framework for understanding carbon catabolite represion. |
Chen et al. (2013).
Chen S, Oldham ML, Davidson AL, & Chen J (2013). Carbon catabolite repression of the maltose transporter revealed by X-ray crystallography.
Nature 499 7458:364-368. PubMed Id: 23770568. doi:10.1038/nature12232. |
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MalFGK2-MBP Maltose uptake transporter complex; pre-translocation conformation bound to maltoheptaose : Escherichia coli B Bacteria, 2.90 Å
Outward-facing conformation bound to maltohexaose, 2.38 Å: 4KI0 |
Oldham et al. (2013).
Oldham ML, Chen S, & Chen J (2013). Structural basis for substrate specificity in the Escherichia coli maltose transport system.
Proc Natl Acad Sci USA 110 :18132-18137. PubMed Id: 24145421. doi:10.1073/pnas.1311407110. |
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MetNI Methionine uptake transporter complex: Escherichia coli B Bacteria, 3.7 Å
MetN-C2 domain 3DHX, 2.1 Å |
Kadaba et al. (2008).
Kadaba NS, Kaiser JT, Johnson E, Lee A, & Rees DC (2008). The high-affinity E. coli methionine ABC transporter: structure and allosteric regulation.
Science 321 :250-253. PubMed Id: 18621668. |
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FbpC ferric iron-uptake transporter nucleotide-binding domain: Neisseria gonorrhoeae B Bacteria, 1.9 Å
A domain-swapped neucleotide-binding domain dimer |
Newstead et al. (2009).
Newstead S, Fowler PW, Bilton P, Carpenter EP, Sadler PJ, Campopiano DJ, Sansom MS, & Iwata S (2009). Insights into how nucleotide-binding domains power ABC transport.
Structure 17 :1213-1222. PubMed Id: 19748342. |
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Heterodimeric ABC exporter TM287-TM288: Thermotoga maritima B Bacteria (expressed in E. coli), 2.90 Å
Protein is in the inward-facing conformation. |
Hohl et al. (2012).
Hohl M, Briand C, Grütter MG, & Seeger MA (2012). Crystal structure of a heterodimeric ABC transporter in its inward-facing conformation.
Nature Struc Mol Biol 19 :395-402. PubMed Id: 22447242. doi:10.1038/nsmb.2267. |
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Hohl et al. (2014).
Hohl M, Hürlimann LM, Böhm S, Schöppe J, Grütter MG, Bordignon E, & Seeger MA (2014). Structural basis for allosteric cross-talk between the asymmetric nucleotide binding sites of a heterodimeric ABC exporter.
Proc Natl Acad Sci USA 111 :11025-11030. PubMed Id: 25030449. doi:10.1073/pnas.1400485111. |
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Bukowska et al. (2015).
Bukowska MA, Hohl M, Geertsma ER, Hürlimann LM, Grütter MG, & Seeger MA (2015). A Transporter Motor Taken Apart: Flexibility in the Nucleotide Binding Domains of a Heterodimeric ABC Exporter.
Biochemistry 54 :3086-3099. PubMed Id: 25947941. doi:10.1021/acs.biochem.5b00188. |
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HmuUV heme transporter: Yersinia pestis B Bacteria (expressed in E. coli), 3.00 Å
|
Woo et al. (2012).
Woo JS, Zeltina A, Goetz BA, & Locher KP (2012). X-ray structure of the Yersinia pestis heme transporter HmuUV
Nature Struc Mol Biol 19 :1310-1314. PubMed Id: 23142986. doi:10.1038/nsmb.2417. |
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ABCB10 Mitochondrial ABC transporter with bound AMPPC: Homo sapiens E Eukaryota (expressed in S. frugiperda), 2.85 Å
Supersedes 2YL4. This is the first human ABC transporter and also the first mitochondrial ABC transporter. The protein conformation is open-inward (residues 152-738). Rod form B, 2.90 Å: 4AYX Plate form, 3.30 Å: 4AYW Nucleotide-free rod form, 2.85 Å: 3ZDQ |
Shintre et al. (2013).
Shintre CA, Pike AC, Li Q, Kim JI, Barr AJ, Goubin S, Shrestha L, Yang J, Berridge G, Ross J, Stansfeld PJ, Sansom MS, Edwards AM, Bountra C, Marsden BD, von Delft F, Bullock AN, Gileadi O, Burgess-Brown NA, & Carpenter EP (2013). Structures of ABCB10, a human ATP-binding cassette transporter in apo- and nucleotide-bound states.
Proc Natl Acad Sci USA 110 :9710–9715. PubMed Id: 23716676. doi:10.1073/pnas.1217042110. |
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Lee et al. (2014).
Lee JY, Yang JG, Zhitnitsky D, Lewinson O, & Rees DC (2014). Structural basis for heavy metal detoxification by an Atm1-type ABC exporter.
Science 343 :1133-1136. PubMed Id: 24604198. doi:10.1126/science.1246489. |
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Atm1 mitochondrial ABC transporter, apo form: Saccharomyces cerevisiae E Eukaryota (expressed in E. coli), 3.06 Å
in complex with GSH, 3.38 Å: 4MYH |
Srinivasan et al. (2014).
Srinivasan V, Pierik AJ, & Lill R (2014). Crystal structures of nucleotide-free and glutathione-bound mitochondrial ABC transporter Atm1.
Science 343 :1137-1140. PubMed Id: 24604199. doi:10.1126/science.1246729. |
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McjD antimicrobial peptide transporter: Escherichia coli B Bacteria, 2.70 Å
Structure shows transporter in a novel outward occluded state |
Choudhury et al. (2014).
Choudhury HG, Tong Z, Mathavan I, Li Y, Iwata S, Zirah S, Rebuffat S, van Veen HW, & Beis K (2014). Structure of an antibacterial peptide ATP-binding cassette transporter in a novel outward occluded state.
Proc Natl Acad Sci USA 111 :9145-9150. PubMed Id: 24920594. doi:10.1073/pnas.1320506111. |
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Yu et al. (2015).
Yu J, Ge J, Heuveling J, Schneider E, & Yang M (2015). Structural basis for substrate specificity of an amino acid ABC transporter.
Proc Natl Acad Sci USA 112 :5243-5248. PubMed Id: 25848002. doi:10.1073/pnas.1415037112. |
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Peptidase-containing ABC transporter (PCAT): Ruminiclostridium thermocellum B Bacteria (expressed in E. coli), 3.61 Å
E648Q mutant with bound ATPγS, 5.51 Å: 4S0F |
Lin et al. (2015).
Lin DY, Huang S, & Chen J (2015). Crystal structures of a polypeptide processing and secretion transporter.
Nature 523 :425-430. PubMed Id: 26201595. doi:10.1038/nature14623. |
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Alginate transporter AlgM1M2SS with bound periplasmic protein AlgQ2: Sphingomonas sp. B Bacteria (expressed in E. coli), 3.20 Å
AlgQ2-free structure, 4.50 Å: 4TQV |
Maruyama et al. (2015).
Maruyama Y, Itoh T, Kaneko A, Nishitani Y, Mikami B, Hashimoto W, & Murata K (2015). Structure of a Bacterial ABC Transporter Involved in the Import of an Acidic Polysaccharide Alginate.
Structure 23 9:1643-1654. PubMed Id: 26235029. doi:10.1016/j.str.2015.06.021. |
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Perez et al. (2015).
Perez C, Gerber S, Boilevin J, Bucher M, Darbre T, Aebi M, Reymond JL, & Locher KP (2015). Structure and mechanism of an active lipid-linked oligosaccharide flippase.
Nature 524 :433-438. PubMed Id: 26266984. doi:10.1038/nature14953. |
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ABCG5/ABCG8 sterol transporter: Homo sapiens E Eukaryota (expressed in Komagataella pastoris), 3.93 Å
|
Lee et al. (2016).
Lee JY, Kinch LN, Borek DM, Wang J, Wang J, Urbatsch IL, Xie XS, Grishin NV, Cohen JC, Otwinowski Z, Hobbs HH, & Rosenbaum DM (2016). Crystal structure of the human sterol transporter ABCG5/ABCG8.
Nature 533 :561-564. PubMed Id: 27144356. doi:10.1038/nature17666. |
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ABCA1 lipid exporter: Homo sapiens E Eukaryota (expressed in S. frugiperda), 4.1 Å
cryo-EM structure |
Qian et al. (2017).
Qian H, Zhao X, Cao P, Lei J, Yan N, & Gong X (2017). Structure of the Human Lipid Exporter ABCA1.
Cell 169 7:1228-1239.e10. PubMed Id: 28602350. doi:10.1016/j.cell.2017.05.020. |
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BhuU/BhuV haem importer, inward facing: Burkholderia cenocepacia B Bacteria (expressed in E. coli), 2.8 Å
in complex with periplasmic heme binding protein BhuT, 3.21 Å: 5B58 |
Naoe et al. (2016).
Naoe Y, Nakamura N, Doi A, Sawabe M, Nakamura H, Shiro Y, & Sugimoto H (2016). Crystal structure of bacterial haem importer complex in the inward-facing conformation.
Nat Commun 7 :13411. PubMed Id: 27830695. doi:10.1038/ncomms13411. |
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Cystic Fibrosis Transmembrane Conductance Regulator (CFTR): Danio rerio E Eukaryota (expressed in Sf9 cells), 3.73 Å
Cryo-EM structure |
Zhang & Chen (2016).
Zhang Z, & Chen J (2016). Atomic Structure of the Cystic Fibrosis Transmembrane Conductance Regulator.
Cell 167 :1586-1597.e9. PubMed Id: 27912062. doi:10.1016/j.cell.2016.11.014. |
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Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) in dephosphorylated, ATP-free state: Homo sapiens E Eukaryota (expressed in HEK293S cells), 3.87 Å
cryo-EM structure |
Liu et al. (2017).
Liu F, Zhang Z, Csanády L, Gadsby DC, & Chen J (2017). Molecular Structure of the Human CFTR Ion Channel.
Cell 169 1:85-95.e8. PubMed Id: 28340353. doi:10.1016/j.cell.2017.02.024. |
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Transporter associated with antigen processing (TAP) bound to ICP47: Homo sapiens E Eukaryota (expressed in Pichia pastoris), 4.0 Å
cryo-EM structure |
Oldham et al. (2016).
Oldham ML, Grigorieff N, & Chen J (2016). Structure of the transporter associated with antigen processing trapped by herpes simplex virus.
Elife 5 :e21829. PubMed Id: 27935481. doi:10.7554/eLife.21829. |
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TmrAB antigen transporter homolog: Thermus thermophilus B Bacteria (expressed in E. coli), 2.7 Å
|
Nöll et al. (2017).
Nöll A, Thomas C, Herbring V, Zollmann T, Barth K, Mehdipour AR, Tomasiak TM, Büchert S, Joseph B, Abele R, Oliéric V, Wang M, Diederichs K, Hummer G, Stroud RM, Pos KM, & Tampé R (2017). Crystal structure and mechanistic basis of a functional homolog of the antigen transporter TAP.
Proc Natl Aca. Sci USA 114 :E438-E447. PubMed Id: 28069938. doi:10.1073/pnas.1620009114. |
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PrtD Type-1 secretion system ABC transporter: Aquifex aeolicus B Bacteria (expressed in E. coli), 3.15 Å
|
Morgan et al. (2017).
Morgan JL, Acheson JF, & Zimmer J (2017). Structure of a Type-1 Secretion System ABC Transporter.
Structure 25 :522-529. PubMed Id: 28216041. doi:10.1016/j.str.2017.01.010. |
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MRP1 Multidrug resistance protein 1: Bos taurus E Eukaryota (expressed in S. frugiperda), 3.49 Å
cryo-EM structure with bound LTC4, 3.34 Å: 5UJA |
Johnson & Chen (2017).
Johnson ZL, & Chen J (2017). Structural Basis of Substrate Recognition by the Multidrug Resistance Protein MRP1.
Cell 168 :1075-1085. PubMed Id: 28238471. doi:10.1016/j.cell.2017.01.041. |
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Lipopolysaccharide transporter complex LptB2FG (nucleotide free): Pseudomonas aeruginosa B Bacteria (expressed in E. coli), 3.46 Å
|
Luo et al. (2017).
Luo Q, Yang X, Yu S, Shi H, Wang K, Xiao L, Zhu G, Sun C, Li T, Li D, Zhang X, Zhou M, & Huang Y (2017). Structural basis for lipopolysaccharide extraction by ABC transporter LptB2FG.
Nat Struct Mol Biol 24 :469-474. PubMed Id: 28394325. doi:10.1038/nsmb.3399. |
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Multidrug transporter ABCG2: Homo sapiens E Eukaryota (expressed in HEK293), 3.78 Å
cryo-EM structure part of the structure that could be built de novo, 3.78 Å: |
Taylor et al. (2017).
Taylor NMI, Manolaridis I, Jackson SM, Kowal J, Stahlberg H, & Locher KP (2017). Structure of the human multidrug transporter ABCG2.
Nature 546 :504-509. PubMed Id: 28554189. doi:10.1038/nature22345. |
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CDP-Alcohol Phosphotransferases
These enzymes facilitate the conjugation of polar headgroups to diacylglycerol lipid tails |
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Sciara et al. (2014).
Sciara G, Clarke OB, Tomasek D, Kloss B, Tabuso S, Byfield R, Cohn R, Banerjee S, Rajashankar KR, Slavkovic V, Graziano JH, Shapiro L, & Mancia F (2014). Structural basis for catalysis in a CDP-alcohol phosphotransferase.
Nat Commun 5 :4068. PubMed Id: 24923293. doi:10.1038/ncomms5068. |
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CDP-alcohol phosphotransferase domain (DIPPS) with fused nucleotidyltransferase domain: Archaeoglobus fulgidus B Bacteria (expressed in E. coli), 2.66 Å
|
Nogly et al. (2014).
Nogly P, Gushchin I, Remeeva A, Esteves AM, Borges N, Ma P, Ishchenko A, Grudinin S, Round E, Moraes I, Borshchevskiy V, Santos H, Gordeliy V, & Archer M (2014). X-ray structure of a CDP-alcohol phosphatidyltransferase membrane enzyme and insights into its catalytic mechanism.
Nat Commun 5 4169. PubMed Id: 24942835. doi:10.1038/ncomms5169. |
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Phosphatidylinositol-phosphate synthase with bound CDP-diacylglycerol: Renibacterium salmoninarum B Bacteria (expressed in E. coli), 3.6 Å
without bound CDP-diacylglycerol, 2.5 Å: 5D92 |
Clarke et al. (2015).
Clarke OB, Tomasek D, Jorge CD, Dufrisne MB, Kim M, Banerjee S, Rajashankar KR, Shapiro L, Hendrickson WA, Santos H, & Mancia F (2015). Structural basis for phosphatidylinositol-phosphate biosynthesis.
Nat Commun 6 :8505. PubMed Id: 26510127. doi:10.1038/ncomms9505. |
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Insulin-Induced Gene Products: Insig Proteins
These are components of the sterol regulatory element-binding protein (SREBP) pathway |
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Ren et al. (2015).
Ren R, Zhou X, He Y, Ke M, Wu J, Liu X, Yan C, Wu Y, Gong X, Lei X, Yan SF, Radhakrishnan A, & Yan N (2015). PROTEIN STRUCTURE: Crystal structure of a mycobacterial Insig homolog provides insight into how these sensors monitor sterol levels.
Science 349 6244:187-191. PubMed Id: 26160948. doi:10.1126/science.aab1091. |
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Sterol Reductases
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Δ14 Sterol reductase: Methylomicrobium alcaliphilum B Bacteria (expressed in E. coli), 2.74 Å
|
Li et al. (2015).
Li X, Roberti R, & Blobel G (2015). Structure of an integral membrane sterol reductase from Methylomicrobium alcaliphilum.
Nature 517 :104-107. PubMed Id: 25307054. doi:10.1038/nature13797. |
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Sterol-Sensing Domain (SSD) Proteins
These proteins are involved in cholesterol trafficking in the cholesterol-uptake pathway |
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Niemann-Pick C1 protein: Homo sapiens E Eukaryota (expressed in 293 GnTI- cells), 3.35 Å
|
Li et al. (2016).
Li X, Wang J, Coutavas E, Shi H, Hao Q, & Blobel G (2016). Structure of human Niemann-Pick C1 protein.
Proc Natl Acad Sci USA 113 :8212-8217. PubMed Id: 27307437. doi:10.1073/pnas.1607795113. |
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Fatty Acid Desaturases
These enzymes maintain the cellular balance of saturated and monounsaturated lipids |
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Stearoyl-coenzyme A desaturase (SCD1) in complex with substrate: Homo sapiens E Eukaryota (expressed in S. frugiperda), 3.25 Å
|
Wang et al. (2015).
Wang H, Klein MG, Zou H, Lane W, Snell G, Levin I, Li K, & Sang BC (2015). Crystal structure of human stearoyl-coenzyme A desaturase in complex with substrate.
Nat Struct Mol Biol 22 :581-585. PubMed Id: 26098317. doi:10.1038/nsmb.3049. |
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Stearoyl-coenzyme A desaturase (SCD1) in complex with substrate: Mus musculus E Eukaryota (expressed in Trichoplusia ni), 2.61 Å
|
Bai et al. (2015).
Bai Y, McCoy JG, Levin EJ, Sobrado P, Rajashankar KR, Fox BG, & Zhou M (2015). X-ray structure of a mammalian stearoyl-CoA desaturase.
Nature 252 :252-256. PubMed Id: 26098370. doi:10.1038/nature14549. |
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Superfamily of K+ Transporters (SKT proteins)
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TrkH potassium ion transporter: Vibrio parahaemolyticus B Bacteria (expressed in E. coli), 3.51 Å
Lacking a Na+/K+-ATPase, non-animal cells require two different systems for K+ uptake, one of which is the SKT family of proteins. |
Cao et al. (2011).
Cao Y, Jin X, Huang H, Derebe MG, Levin EJ, Kabaleeswaran V, Pan Y, Punta M, Love J, Weng J, Quick M, Ye S, Kloss B, Bruni R, Martinez-Hackert E, Hendrickson WA, Rost B, Javitch JA, Rajashankar KR, Jiang Y, & Zhou M (2011). Crystal structure of a potassium ion transporter, TrkH.
Nature 471 :336-340. PubMed Id: 21317882. |
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TrkH potassium ion transporter in complex with TrkA: Vibrio parahaemolyticus B Bacteria (expressed in E. coli), 3.80 Å
TrkA Gating ring bound to ATP-gamma-S, 3.05 Å: 4J9V |
Cao et al. (2013).
Cao Y, Pan Y, Huang H, Jin X, Levin EJ, Kloss B, & Zhou M (2013). Gating of the TrkH ion channel by its associated RCK protein TrkA.
Nature 496 :317-322. PubMed Id: 23598339. doi:10.1038/nature12056. |
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Vieira-Pires et al. (2013).
Vieira-Pires RS, Szollosi A, & Morais-Cabral JH (2013). The structure of the KtrAB potassium transporter.
Nature 496 :323-328. PubMed Id: 23598340. doi:10.1038/nature12055. |
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Potassium-importing KdpFABC membrane complex: Escherichia coli B Bacteria, 2.9 Å
The complex has a channel-like subunit (KdpA) and a pump-like P-type ATPase (KdpB). |
Huang et al. (2017).
Huang CS, Pedersen BP, & Stokes DL (2017). Crystal structure of the potassium-importing KdpFABC membrane complex.
Nature 546 :681-685. PubMed Id: 28636601. doi:10.1038/nature22970. |
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Membrane-Integral Pyrophosphatases (M-PPases)
Ion-Translocating Pyrophosphatases Link Pyrophosphate (PPi) Hydrolysis to Sodium or Proton Pumping V-ATPases and H+-PPases coexist on plant vacuolar membranes |
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H+-translocating M-PPase: Vigna radiata E Eukaryota (expressed in S. cerevisiae), 2.35 Å
Structure shows protein in complex with the non-hydrolysable substrate analog imidodiphosphate (IDP). The protein has 16 TM helices. |
Lin et al. (2012).
Lin SM, Tsai JY, Hsiao CD, Huang YT, Chiu CL, Liu MH, Tung JY, Liu TH, Pan RL, & Sun YJ (2012). Crystal structure of a membrane-embedded H+-translocating pyrophosphatase.
Nature 484 :399-403. PubMed Id: 22456709. doi:10.1038/nature10963. |
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H+-translocating M-PPase: Vigna radiata E Eukaryota (expressed in S. crevisiae), 3.5 Å
|
Li et al. (2016).
Li KM, Wilkinson C, Kellosalo J, Tsai JY, Kajander T, Jeuken LJ, Sun YJ, & Goldman A (2016). Membrane pyrophosphatases from Thermotoga maritima and Vigna radiata suggest a conserved coupling mechanism.
Nat Commun 7 :13596. PubMed Id: 27922000. doi:10.1038/ncomms13596. |
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Na+-translocating M-PPase with metal ions in active site: Thermotoga maritima B Bacteria (expressed in S. cerevisiae), 2.60 Å
In complex with phosphate and magnesium, 4.00 Å: 4AV6 |
Kellosalo et al. (2012).
Kellosalo J, Kajander T, Kogan K, Pokharel K, & Goldman A (2012). The structure and catalytic cycle of a sodium-pumping pyrophosphatase.
Science 337 :473-476. PubMed Id: 22837527. doi:10.1126/science.1222505. |
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Na+-translocating M-PPase in complex with imidodiphosphate and magnesium, and with bound sodium ion: Thermotoga maritima E Eukaryota (expressed in S. cerevisiae), 3.49 Å
in complex with tungstate and magnesium, 4.0 Å: 5LZR |
Li et al. (2016).
Li KM, Wilkinson C, Kellosalo J, Tsai JY, Kajander T, Jeuken LJ, Sun YJ, & Goldman A (2016). Membrane pyrophosphatases from Thermotoga maritima and Vigna radiata suggest a conserved coupling mechanism.
Nat Commun 7 :13596. PubMed Id: 27922000. doi:10.1038/ncomms13596. |
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Bacterial V-type ATPase
Also called A-type ATPase |
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Rotor of V-type Na+-ATPase: Enterococcus hirae B Bacteria, 2.1 Å
|
Murata et al. (2005).
Murata T, Yamato I, Kakinuma Y, Leslie AG, & Walker JE (2005). Structure of the rotor of the V-Type Na+-ATPase from Enterococcus hirae.
Science 308 :654-659. PubMed Id: 15802565. |
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V-ATPase central-axis DF complex: Enterococcus hirae B Bacteria (expressed in Cell-free synthesis), 2.00 Å
|
Saijo et al. (2011).
Saijo S, Arai S, Hossain KM, Yamato I, Suzuki K, Kakinuma Y, Ishizuka-Katsura Y, Ohsawa N, Terada T, Shirouzu M, Yokoyama S, Iwata S, & Murata T (2011). Crystal structure of the central axis DF complex of the prokaryotic V-ATPase.
Proc Natl Acad Sci USA 108 :19955-19960. PubMed Id: 22114184. doi:10.1073/pnas.1108810108. |
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Arai et al. (2013).
Arai S, Saijo S, Suzuki K, Mizutani K, Kakinuma Y, Ishizuka-Katsura Y, Ohsawa N, Terada T, Shirouzu M, Yokoyama S, Iwata S, Yamato I, & Murata T (2013). Rotation mechanism of Enterococcus hirae V1-ATPase based on asymmetric crystal structures.
Nature 493 :703-707. PubMed Id: 23334411. doi:10.1038/nature11778. |
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Suzuki et al. (2016).
Suzuki K, Mizutani K, Maruyama S, Shimono K, Imai FL, Muneyuki E, Kakinuma Y, Ishizuka-Katsura Y, Shirouzu M, Yokoyama S, Yamato I, & Murata T (2016). Crystal structures of the ATP-binding and ADP-release dwells of the V1 rotary motor.
Nat Commun 7 :13235. PubMed Id: 27807367. doi:10.1038/ncomms13235. |
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V1-ATPase atomic model derived from Cryo-EM reconstructions.: Thermus thermophilus B Bacteria, 9.7 Å
|
Lau & Rubinstein (2012).
Lau WC & Rubinstein JL (2012). Subnanometre-resolution structure of the intact Thermus thermophilus H+-driven ATP synthase.
Nature 481 :214-218. PubMed Id: 22178924. doi:10.1038/nature10699. |
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V1-ATPase Complex (V-ATPase soluble domain) with bound nucleotide: Thermus thermophilus B Bacteria, 4.51 Å
Without nucleotide, 4.80 Å: 3A5D |
Numoto et al. (2009).
Numoto N, Hasegawa Y, Takeda K, & Miki K (2009). Inter-subunit interaction and quaternary rearrangement defined by the central stalk of prokaryotic V1-ATPase.
EMBO Rep 10 :1228-1234. PubMed Id: 19779483. |
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A3B3 complex of V1-ATPase: Thermus thermophilus B Bacteria (expressed in E. coli), 2.8 Å
|
Maher et al. (2009).
Maher MJ, Akimoto S, Iwata M, Nagata K, Hori Y, Yoshida M, Yokoyama S, Iwata S, & Yokoyama K (2009). Crystal structure of A3B3complex of V-ATPase from Thermus thermophilus.
EMBO J 28 :3771-3779. PubMed Id: 19893485. |
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Peripheral stalk of H+-dependent V-ATP Synthase: Thermus thermophilus B Bacteria (expressed in E. coli), 3.10 Å
So-called PS1 structure. |
Lee et al. (2010).
Lee LK, Stewart AG, Donohoe M, Bernal RA, & Stock D (2010). The structure of the peripheral stalk of Thermus thermophilus H+-ATPase/synthase.
Nat Struct Mol Biol 17 :373-378. PubMed Id: 20173764. |
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Peripheral stalk of H+-dependent V-ATP Synthase: Thermus thermophilus B Bacteria (expressed in E. coli), 2.25 Å
So-called PS2 structure. |
Stewart et al. (2012).
Stewart AG, Lee LK, Donohoe M, Chaston JJ, & Stock D (2012). The dynamic stator stalk of rotary ATPases.
Nature Commun 3 :687. PubMed Id: 22353718. doi:10.1038/ncomms1693. |
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A3B3DF complex of V1-ATPase: Thermus thermophilus B Bacteria, 3.90 Å
|
Nagamatsu et al. (2013).
Nagamatsu Y, Takeda K, Kuranaga T, Numoto N, & Miki K (2013). Origin of Asymmetry at the Intersubunit Interfaces of V1-ATPase from Thermus thermophilus.
J Mol Biol 425 15:2699-2708. PubMed Id: 23639357. doi:10.1016/j.jmb.2013.04.022. |
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Peripheral stalk of H+-dependent V-ATP Synthase: Pyrococcus horikoshii A Archaea (expressed in E. coli), 3.65 Å
|
Balakrishna et al. (2012).
Balakrishna AM, Hunke C, & Grüber G (2012). The structure of subunit E of the Pyrococcus horikoshii OT3 A-ATP synthase gives insight into the elasticity of the peripheral stalk.
J Mol Biol 420 :155-183. PubMed Id: 22516614. doi:10.1016/j.jmb.2012.04.012. |
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Vacuolar ATPase (V-ATPase)
Eukaryotic V-ATPases |
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Heterotrimeric EGChead Peripheral Stalk Complex: Saccharomyces cerevisiae E Eukaryota, 2.90 Å
Second conformation, 2.82 Å: 4EFA |
Oot et al. (2012).
Oot RA, Huang LS, Berry EA, & Wilkens S (2012). Crystal Structure of the Yeast Vacuolar ATPase Heterotrimeric EGC(head) Peripheral Stalk Complex.
Structure 20 :1881-1892. PubMed Id: 23000382. doi:10.1016/j.str.2012.08.020. |
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Subunits DF complex: Saccharomyces cerevisiae E Eukaryota (expressed in E. coli), 3.18 Å
|
Balakrishna et al. (2015).
Balakrishna AM, Basak S, Manimekalai MS, & Grüber G (2015). Crystal structure of subunits D and F in complex gives insight into energy transmission of the eukaryotic V-ATPase from Saccharomyces cerevisiae.
J Biol Chem 290 :3183-3196. PubMed Id: 25505269. doi:10.1074/jbc.M114.622688. |
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Zhao et al. (2015).
Zhao J, Benlekbir S, & Rubinstein JL (2015). Electron cryomicroscopy observation of rotational states in a eukaryotic V-ATPase.
Nature 521 :241-245. PubMed Id: 25971514. doi:10.1038/nature14365. |
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Complete V1-ATPase in auto-inhibited state by cryo-EM: Saccharomyces cerevisiae E Eukaryota, 6.2 Å
7 Å structure, 5BW9 |
Oot et al. (2016).
Oot RA, Kane PM, Berry EA, & Wilkens S (2016). Crystal structure of yeast V1-ATPase in the auto-inhibited state.
EMBO J 35 :1694-1706. PubMed Id: 27295975. doi:10.15252/embj.201593447. |
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membrane-embedded VO motor of V-ATPase: Saccharomyces cerevisiae E Eukaryota, 3.9 Å
cryo-EM structure |
Mazhab-Jafari et al. (2016).
Mazhab-Jafari MT, Rohou A, Schmidt C, Bueler SA, Benlekbir S, Robinson CV, & Rubinstein JL (2016). Atomic model for the membrane-embedded VO motor of a eukaryotic V-ATPase.
Nature 539 :118-122. PubMed Id: 27776355. doi:10.1038/nature19828. |
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F-type ATPase
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F1-ATPase from bovine heart mitochondria: Bos taurus E Eukaryota, 2.8 Å
|
Abrahams et al. (1994).
Abrahams JP, Leslie AG, Lutter R, & Walker JE (1994). Structure at 2.8 Å resolution of F1-ATPase from bovine heart mitochondria.
Nature 370 :621-628. PubMed Id: 8065448. |
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F1-ATPase complexed with antibiotic inhibitor aurovertin B: Bos taurus E Eukaryota, 3.10 Å
|
van Raaij et al. (1996).
van Raaij MJ, Abrahams JP, Leslie AG, & Walker JE (1996). The structure of bovine F1-ATPase complexed with the antibiotic inhibitor aurovertin B.
Proc Natl Acad Sci USA 93 :6913-6917. PubMed Id: 8692918. |
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F1-ATPase complexed with peptide antibiotic efrapeptin: Bos taurus E Eukaryota, 3.10 Å
|
Abrahams et al. (1996).
Abrahams JP, Buchanan SK, Van Raaij MJ, Fearnley IM, Leslie AG, & Walker JE (1996). The structure of bovine F1-ATPase complexed with the peptide antibiotic efrapeptin.
Proc Natl Acad Sci USA 93 :9420-9424. PubMed Id: 8790345. |
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F1-ATPase complexed with azide: Bos taurus E Eukaryota, 1.95 Å
|
Bowler et al. (2006).
Bowler MW, Montgomery MG, Leslie AG, & Walker JE (2006). How azide inhibits ATP hydrolysis by the F-ATPases.
Proc Natl Acad Sci USA 103 :8646-8649. PubMed Id: 16728506. |
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F1-ATPase, Ground State Structure: Bos taurus E Eukaryota, 1.90 Å
|
Bowler et al. (2007).
Bowler MW, Montgomery MG, Leslie AG, & Walker JE (2007). Ground state structure of F1-ATPase from bovine heart mitochondria at 1.9 Å resolution.
J Biol Chem 282 :14238-14242. PubMed Id: 17350959. |
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ATP Synthase Extrinsic Region: Bos taurus E Eukaryota, 3.2 Å
|
Rees et al. (2009).
Rees DM, Leslie AG, Walker JE (2009). The structure of the membrane extrinsic region of bovine ATP synthase.
Proc Natl Acad Sci USA 106 :21597-21601. PubMed Id: 19995987. |
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F1-ATPase inhibited by AMP-PNP and ADP in the presence of thiophosphate: Bos taurus E Eukaryota, 3.10 Å
inhibited by three copies of the inhibitor protein IF1 crystallised in the presence of thiophosphate, 3.30 Å: 4Z1M |
Bason et al. (2015).
Bason JV, Montgomery MG, Leslie AG, & Walker JE (2015). How release of phosphate from mammalian F1-ATPase generates a rotary substep.
Proc Natl Acad Sci USA 112 :6009-6014. PubMed Id: 25918412. doi:10.1073/pnas.1506465112. |
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F1-c-ring (c8) complex: Bos taurus E Eukaryota, 3.50 Å
|
Watt et al. (2010).
Watt IN, Montgomery MG, Runswick MJ, Leslie AG, & Walker JE (2010). Bioenergetic cost of making an adenosine triphosphate molecule in animal mitochondria.
Proc Natl Acad Sci USA 107 :16823-16827. PubMed Id: 20847295. doi:10.1073/pnas.1011099107. |
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Subunit C of the F1FO ATP synthase: Escherichia coli B Bacteria, NMR Structure
|
Girvin et al. (1998).
Girvin ME, Rastogi VK, Abildgaard F, Markley JL, & Fillingame RH (1998). Solution structure of the transmembrane H+-transporting subunit c of the F1F0 ATP synthase.
Biochemistry 37 :8817-8824. PubMed Id: 9636021. doi:10.1021/bi980511m. |
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F1-ATPase in an autoinhibited conformation: Escherichia coli B Bacteria, 3.26 Å
|
Cingolani & Duncan (2011).
Cingolani G & Duncan TM (2011). Structure of the ATP synthase catalytic complex (F1) from Escherichia coli in an autoinhibited conformation.
Nat Struct Mol Biol 18 :701-707. PubMed Id: 21602818. doi:10.1038/nsmb.2058. |
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Sobti et al. (2016).
Sobti M, Smits C, Wong AS, Ishmukhametov R, Stock D, Sandin S, & Stewart AG (2016). Cryo-EM structures of the autoinhibited E. coli ATP synthase in three rotational states.
Elife 5 :e21598. PubMed Id: 28001127. doi:10.7554/eLife.21598. |
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Vinothkumar et al. (2016).
Vinothkumar KR, Montgomery MG, Liu S, & Walker JE (2016). Structure of the mitochondrial ATP synthase from Pichia angusta determined by electron cryo-microscopy.
Proc Natl Acad Sci USA 113 :12709-12714. PubMed Id: 27791192. doi:10.1073/pnas.1615902113. |
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Stock et al. (1999).
Stock S, Leslie AGW, & Walker JE (1999). Molecular architecture of rotary motor in ATP synthase.
Science 286 :1700-1705. PubMed Id: 10576729. |
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F1-ATPase: Saccharomyces cerevisiae E Eukaryota, 2.80 Å
|
Kabaleeswaran et al. (2006).
Kabaleeswaran V, Puri N, Walker JE, Leslie AG, & Mueller DM (2006). Novel features of the rotary catalytic mechanism revealed in the structure of yeast F1ATPase.
EMBO J 25 :5433-5442. PubMed Id: 17082766. |
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F1-ATPase inhibited by its regulatory protein IF1: Saccharomyces cerevisiae E Eukaryota, 2.50 Å
|
Robinson et al. (2013).
Robinson GC, Bason JV, Montgomery MG, Fearnley IM, Mueller DM, Leslie AG, & Walker JE (2013). The structure of F1-ATPase from Saccharomyces cerevisiae inhibited by its regulatory protein IF1.
Open Biol 3 :120164. PubMed Id: 23407639. doi:10.1098/rsob.120164. |
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Symersky et al. (2012).
Symersky J, Pagadala V, Osowski D, Krah A, Meier T, Faraldo-Gómez JD, & Mueller DM (2012). Structure of the c10 ring of the yeast mitochondrial ATP synthase in the open conformation.
Nature Struc Mol Biol 19 :485-491. PubMed Id: 22504883. doi:10.1038/nsmb.2284. |
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ATP Synthase c10 ring with bound oligomycin: Saccharomyces cerevisiae E Eukaryota, 1.90 Å
|
Symersky et al. (2012).
Symersky J, Osowski D, Walters DE, & Mueller DM (2012). Oligomycin frames a common drug-binding site in the ATP synthase.
Proc Natl Acad Sci USA 109 :13961-13965. PubMed Id: 22869738. doi:10.1073/pnas.1207912109. |
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F1-c-ring (c10) complex: Saccharomyces cerevisiae E Eukaryota, 3.43 Å
|
Dautant et al. (2010).
Dautant A, Velours J, & Giraud MF (2010). Crystal structure of the Mg·ADP-inhibited state of the yeast F1c10-ATP synthase.
J Biol Chem 285 :29502-29510. PubMed Id: 20610387. doi:10.1074/jbc.M110.124529. |
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Rotor (c11) of Na+-dependent F-ATP Synthase: Ilyobacter tartaricus B Bacteria, 2.4 Å
|
Meier et al. (2005).
Meier T, Polzer P, Diederichs K, Welte W, & Dimroth P (2005). Structure of the rotor ring of F-type Na-ATPase from Ilyobacter tartaricus.
Science 308 :659-662. PubMed Id: 15860619. |
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Rotor (c11) of Na+-dependent F-ATP Synthase with complete ion-coördination structure: Ilyobacter tartaricus B Bacteria, 2.35 Å
|
Meier et al. (2009).
Meier T, Krah A, Bond PJ, Pogoryelov D, Diederichs K, & Faraldo-Gómez JD (2009). Complete Ion-Coordination Structure in the Rotor Ring of Na+-Dependent F-ATP Synthases.
J Mol Biol 391 :498-507. PubMed Id: 19500592. |
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Rotor (c14) of H+-dependent F-ATP Synthase of spinach chloroplasts: Spinacia oleracea E Eukaryota, 3.80 Å
|
Vollmar et al. (2009).
Vollmar M, Schlieper D, Winn M, Büchner C, & Groth G (2009). Structure of the c14Rotor Ring of the Proton Translocating Chloroplast ATP Synthase.
J Biol Chem 284 :18228-18235. PubMed Id: 19423706. |
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Rotor (c14) of H+-dependent F-ATP Synthase of green pea chloroplasts: Pisum sativum E Eukaryota, 3.40 Å
|
Saroussi et al. (2012).
Saroussi S, Schushan M, Ben-Tal N, Junge W, & Nelson N (2012). Structure and flexibility of the C-ring in the electromotor of rotary F0F1-ATPase of pea chloroplasts.
PLoS ONE 7 . PubMed Id: 23049735. doi:10.1371/journal.pone.0043045. |
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Rotor (c15) of H+-dependent F-ATP Synthase of an alkaliphilic cyanobacterium: Spirulina platensis B Bacteria, 2.1 Å
|
Pogoryelov et al. (2009).
Pogoryelov D, Yildiz O, Faraldo-Gómez JD, & Meier T (2009). High-resolution structure of the rotor ring of a proton-dependent ATP synthase.
Nat Struct Mol Biol 16 :1068-1073. PubMed Id: 19783985. |
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Rotor (c13) of H+-dependent F-ATP Synthase: Bacillus pseudofirmus OF4 B Bacteria, 2.5 Å
|
Preiss et al. (2010).
Preiss L, Yildiz O, Hicks DB, Krulwich TA, & Meier T (2010). A New Type of Proton Coordination in an F1F0-ATP Synthase Rotor Ring.
PLoS Biol 8 :e1000443. PubMed Id: 20689804. doi:10.1371/journal.pbio.1000443. |
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Rotor (c12) of H+-dependent F-ATP Synthase mutant: Bacillus pseudofirmus OF4 B Bacteria, 4.10 Å
In this mutant, the GxGxGxG motif has been replaced by AxAxAxA. |
Preiss et al. (2013).
Preiss L, Klyszejko AL, Hicks DB, Liu J, Fackelmayer OJ, Yildiz Ö, Krulwich TA, & Meier T (2013). The c-ring stoichiometry of ATP synthase is adapted to cell physiological requirements of alkaliphilic Bacillus pseudofirmus OF4.
Proc Natl Acad Sci USA 110 19:7874-7879. PubMed Id: 23613590. doi:10.1073/pnas.1303333110. |
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F1Fo synthase (complete structure; dimeric): Yarrowia lipolytica E Eukaryota, 3.5 Å
|
Hahn et al. (2016).
Hahn A, Parey K, Bublitz M, Mills DJ, Zickermann V, Vonck J, Kühlbrandt W, & Meier T (2016). Structure of a Complete ATP Synthase Dimer Reveals the Molecular Basis of Inner Mitochondrial Membrane Morphology.
Mol Cell 63 3:445-456. PubMed Id: 27373333. doi:10.1016/j.molcel.2016.05.037. |
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F1-ATPase, wild-type: Caldalkalibacillus thermarum B Bacteria (expressed in E. coli), 3.0 Å
epsilon mutant, 2.6 Å: 5IK2 |
Ferguson et al. (2016).
Ferguson SA, Cook GM, Montgomery MG, Leslie AG, & Walker JE (2016). Regulation of the thermoalkaliphilic F1-ATPase from Caldalkalibacillus thermarum.
Proc Natl Acad Sci USA 113 :10860-10865. PubMed Id: 27621435. doi:10.1073/pnas.1612035113. |
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P-type ATPase
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Calcium ATPase; rabbit sarcoplasmic reticulum. E1 state with bound calcium: Oryctolagus cuniculus E Eukaryota, 2.4 Å
This structure supersedes 1EUL. These ATPases are referred to as SERCA pumps; SERCA: Sarco(Endo)plasmic Reticulum CAlcium |
Toyoshima et al. (2000).
Toyoshima C, Nakasako M, Nomura H, & Ogawa H (2000). Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 Å resolution.
Nature 405 :647-655. PubMed Id: 10864315. |
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Calcium ATPase; rabbit sarcoplasmic reticulum. E1 state with bound calcium, magnesium, and an ATP analog: Oryctolagus cuniculus E Eukaryota, 2.9 Å
|
Toyoshima & Mizutani (2004).
Toyoshima C & Mizutani T (2004). Crystal structure of the calcium pump with a bound ATP analogue.
Nature 430 :529-35. PubMed Id: 15229613. |
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Calcium ATPase; rabbit sarcoplasmic reticulum. E2 state without bound calcium: Oryctolagus cuniculus E Eukaryota, 3.1 Å
|
Toyoshima & Nomura (2002).
Toyoshima C & Nomura H (2002). Structural changes in the calcium pump accompanying the dissociation of calcium.
Nature 418 :605-611. PubMed Id: 12167852. |
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Calcium ATPase; rabbit sarcoplasmic reticulum. E2 state calcium-free with bound magnesium fluoride: Oryctolagus cuniculus E Eukaryota, 2.3 Å
E1 state with bound AlFx and ADP, 2.40 Å: 2ZDB (supersedes 1WPE, which was superseded by 2Z9R) |
Toyoshima et al. (2004).
Toyoshima C, Nomura H, & Tsuda T (2004). Lumenal gating mechanism revealed in calcium pump crystal structures with phosphate analogues.
Nature 432 :361-368. PubMed Id: 15448704. |
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Calcium ATPase; rabbit sarcoplamic reticulum. E1 state with bound calcium and AMPPC: Oryctolagus cuniculus E Eukaryota, 2.6 Å
E1 state with bound calcium and ADP:AlF4–, 2.9 Å: 1T5T |
Sørensen et al. (2004).
Sørensen TL, Jensen AM Møller JV, & Nissen P (2004). Phosphoryl transfer and calcium ion occlusion in the calcium pump.
Science 304 :1672-1675. PubMed Id: 15192230. |
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Calcium ATPase; rabbit sarcoplasmic reticulum. E2 state with bound AlF4– calcium-free: Oryctolagus cuniculus E Eukaryota, 3.0 Å
|
Olesen et al. (2004).
Olesen C, Sørensen TL, Nielsen RC, Møller JV, & Nissen P (2004). Dephosphorylation of the calcium pump coupled to counterion occlusion.
Science 306 :2251-2255. PubMed Id: 15618517. |
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Calcium ATPase; rabbit sarcoplasmic reticulum. Ca2+-free, with bound BHQ and thapsigargin: Oryctolagus cuniculus E Eukaryota, 3.0 Å
|
Obara et al. (2005).
Obara K, Miyashita N, Xu C, Toyoshima I, Sugita Y, Inesi G, & Toyoshima C (2005). Structural role of countertransport revealed in Ca2+pump crystal structure in the absence of Ca2+.
Proc Natl Acad Sci U S A 102 :14489-14496. PubMed Id: 16150713. |
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Calcium ATPase; rabbit sarcoplasmic reticulum. With bound synthesized derivative of thapsigargin: Oryctolagus cuniculus E Eukaryota, 3.30 Å
|
Søhoel et al. (2006).
Søhoel H, Jensen AM, Møller JV, Nissen P, Denmeade SR, Isaacs JT, Olsen CE, Christensen SB (2006). Natural products as starting materials for development of second-generation SERCA inhibitors targeted towards prostate cancer cells.
Bioorg Med Chem 14 :2810-2815. PubMed Id: 16150713. |
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Jensen et al. (2006).
Jensen AM, Sørensen TL, Olesen C, Møller JV, & Nissen P (2006). Modulatory and catalytic modes of ATP binding by the calcium pump.
EMBO J 25 :2305-2314. PubMed Id: 16710301. |
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Calcium ATPase; rabbit sarcoplamic reticulum. Calcium-free with bound AlF4– and cyclopiazonic acid (CPA): Oryctolagus cuniculus E Eukaryota, 2.65 Å
Calcium-free with bound CPA and ADP, 3.4 Å: 2OA0 |
Moncoq et al. (2007).
Moncoq K, Trieber CA, & Young HS (2007). The molecular basis for cyclopiazonic acid inhibition of the sarcoplasmic reticulum calcium pump.
J Biol Chem 282 :9748-9757. PubMed Id: 17259168. |
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Olesen et al. (2007).
Olesen C, Picard M, Winther A-M L, Gyrup C, Morth JP, Oxvig C, Møller JV & Nissen P (2007). The structural basis of calcium transport by the calcium pump.
Nature 450 :1036-1042. PubMed Id: 18075584. |
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Calcium ATPase; rabbit sarcoplamic reticulum. Ca2+-free E2 state with debutanoyl thapsigargin: Oryctolagus cuniculus E Eukaryota, 3.10 Å
Structural analysis of the Type I crystal structure reveals the location and thickness of the lipid bilayer |
Sonntag et al. (2011).
Sonntag Y, Musgaard M, Olesen C, Schiφtt B, Mφller JV, Nissen P, & Thφgersen L. (2011). Mutual adaptation of a membrane protein and its lipid bilayer during conformational changes.
Nat Commun 2 :304. PubMed Id: 21556058. doi:10.1038/ncomms1307. |
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Calcium ATPase; rabbit sarcoplasmic reticulum with bound sarcolipin: Oryctolagus cuniculus E Eukaryota, 3.10 Å
|
Winther et al. (2013).
Winther AM, Bublitz M, Karlsen JL, Møller JV, Hansen JB, Nissen P, & & Buch-Pedersen MJ (2013). The sarcolipin-bound calcium pump stabilizes calcium sites exposed to the cytoplasm.
Nature 495 :265-268. PubMed Id: 23455424. doi:10.1038/nature11900. |
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Toyoshima et al. (2013).
Toyoshima C, Iwasawa S, Ogawa H, Hirata A, Tsueda J, & Inesi G (2013). Crystal structures of the calcium pump and sarcolipin in the Mg2+-bound E1 state.
Nature 495 :260-264. PubMed Id: 23455422. doi:10.1038/nature11899. |
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Calcium ATPase; rabbit sarcoplasmic reticulum with bound phospholamban: Oryctolagus cuniculus E Eukaryota, 2.83 Å
|
Akin et al. (2013).
Akin BL, Hurley TD, Chen Z, & Jones LR (2013). The structural basis for phospholamban inhibition of the calcium pump in sarcoplasmic reticulum.
J Biol Chem 288 42:30181-30191. PubMed Id: 23996003. doi:10.1074/jbc.M113.501585. |
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Calcium ATPase; rabbit sarcoplasmic reticulum E309Q mutant in Ca2E1 state: Oryctolagus cuniculus E Eukaryota (expressed in S. cerevisiae), 3.50 Å
|
Clausen et al. (2013).
Clausen JD, Bublitz M, Arnou B, Montigny C, Jaxel C, Møller JV, Nissen P, Andersen JP, & le Maire M (2013). SERCA mutant E309Q binds two Ca(2+) ions but adopts a catalytically incompetent conformation.
EMBO J. 32 :3231-3243. PubMed Id: 24270570. doi:10.1038/emboj.2013.250. |
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Takahashi et al. (2007).
Takahashi M, Kondou Y, & Toyoshima C (2007). Interdomain communication in calcium pump as revealed in the crystal structures with transmembrane inhibitors.
Proc Natl Acad Sci USA 104 :5800-5805. PubMed Id: 17389383. |
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Calcium ATPase; structure determined by electron crystallography using ultrathin protein crystals: Oryctolagus cuniculus E Eukaryota, 3.40 Å
Electron crystallography of the ultrathin crystals permit determination of atomic models with charges. |
Yonekura et al. (2015).
Yonekura K, Kato K, Ogasawara M, Tomita M, & Toyoshima C (2015). Electron crystallography of ultrathin 3D protein crystals: Atomic model with charges.
Proc Natl Acad Sci USA 112 11:3368-3373. PubMed Id: 25730881. doi:10.1073/pnas.1500724112. |
||
|
Calcium ATPase; rabbit sarcoplasmic reticulum. E1 state with bound calcium and AMPPC by free-electron laser: Oryctolagus cuniculus E Eukaryota, 2.80 Å
Structure determined using an x-ray free-electron laser. |
Bublitz et al. (2015).
Bublitz M, Nass K, Drachmann ND, Markvardsen AJ, Gutmann MJ, Barends TR, Mattle D, Shoeman RL, Doak RB, Boutet S, Messerschmidt M, Seibert MM, Williams GJ, Foucar L, Reinhard L, Sitsel O, Gregersen JL, Clausen JD, Boesen T, Gotfryd K, Wang KT, Olesen C, Møller JV, Nissen P, & Schlichting I (2015). Structural studies of P-type ATPase-ligand complexes using an X-ray free-electron laser.
IUCrJ 2 :409-420. PubMed Id: 26175901. doi:10.1107/S2052252515008969. |
||
|
Clausen et al. (2016).
Clausen JD, Bublitz M, Arnou B, Olesen C, Andersen JP, Møller JV, & Nissen P (2016). Crystal Structure of the Vanadate-Inhibited Ca2+-ATPase.
Structure 24 :617-623. PubMed Id: 27050689. doi:10.1016/j.str.2016.02.018. |
|||
|
Norimatsu et al. (2017).
Norimatsu Y, Hasegawa K, Shimizu N, & Toyoshima C (2017). Protein-phospholipid interplay revealed with crystals of a calcium pump.
Nature 545 7653:193-198. PubMed Id: 28467821. doi:10.1038/nature22357. |
|||
|
Na,K-ATPase; pig kidney : Sus scrofa E Eukaryota, 3.5 Å
|
Morth et al. (2007).
Morth JP, Pedersen BP, Kohl A,Toustrup-Jensen MS, Sørensen TL-M D, Petersen J, Petersen JP, Vilsen B, & Nissen P (2007). Crystal structure of the sodium-potassim pump.
Nature 450 :1043-1049. PubMed Id: 18075585. |
||
|
Na,K-ATPase, phosphorylated form in complex with ouabain: Sus scrofa E Eukaryota, 4.60 Å
|
Yatime et al. (2011).
Yatime L, Laursen M, Morth JP, Esmann M, Nissen P, & Fedosova NU (2011). Structural insights into the high affinity binding of cardiotonic steroids to the Na+,K+-ATPase.
J Struct Biol 174 :296-306. PubMed Id: 21182963. doi:10.1016/j.jsb.2010.12.004. |
||
|
Na,K-ATPase-ouabain complex with Mg2+ in cation binding site: Sus scrofa E Eukaryota, 3.40 Å
|
Laursen et al. (2013).
Laursen M, Yatime L, Nissen P, & Fedosova NU (2013). Crystal structure of the high-affinity Na+,K+-ATPase-ouabain complex with Mg+2 bound in the cation binding site.
Proc Natl Acad Sci USA 110 :10958-10963. PubMed Id: 23776223. doi:10.1073/pnas.1222308110. |
||
|
Na,K-ATPase; pig kidney in the Na+-bound state: Sus scrofa E Eukaryota, 4.30 Å
|
Nyblom et al. (2013).
Nyblom M, Poulsen H, Gourdon P, Reinhard L, Andersson M, Lindahl E, Fedosova N, & Nissen P (2013). Crystal Structure of Na+, K+-ATPase in the Na+-Bound State.
Science 342 :123-127. PubMed Id: 24051246. |
||
|
Na,K-ATPase with bound Na+ preceding the E1P state: Sus scrofa E Eukaryota, 2.80 Å
With oligomycin, 2.80 Å: 3WGV |
Kanai et al. (2013).
Kanai R, Ogawa H, Vilsen B, Cornelius F, & Toyoshima C (2013). Crystal structure of a Na+-bound Na+,K+-ATPase preceding the E1P state.
Nature 502 :201-206. PubMed Id: 24089211. doi:10.1038/nature12578. |
||
|
Na,K-ATPase, phosphorylated form in complex with bufalin: Sus scrofa E Eukaryota, 3.41 Å
in complex with digoxin, 4.00 Å: 4RET |
Laursen et al. (2015).
Laursen M, Gregersen JL, Yatime L, Nissen P, & Fedosova NU (2015). Structures and characterization of digoxin- and bufalin-bound Na+,K+-ATPase compared with the ouabain-bound complex.
Proc Natl Acad Sci USA 112 :1755-1760. PubMed Id: 25624492. doi:10.1073/pnas.1422997112. |
||
|
Na,K-ATPase; bovine kidney: Bos taurus E Eukaryota, 3.9 Å
|
Gregersen et al. (2016).
Gregersen JL, Mattle D, Fedosova NU, Nissen P, & Reinhard L (2016). Isolation, crystallization, and crystal structure determination of bovine kidney Na+,K+-ATPase.
Acta Crystallogr F Struct Biol Commun 72 :282-287. PubMed Id: 27050261. doi:10.1107/S2053230X1600279X. |
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|
Na,K-ATPase; shark: Squalus acanthias E Eukaryota, 2.4 Å
Includes α and β subunits plus FXYD regulatory protein. Reveals coordination of K+ in the transmembrane binding site. |
Shinoda et al. (2009).
Shinoda T, Ogawa H, Cornelius F, & Toyoshima C (2009). Crystal structure of the sodium-potassium pump at 2.4 Å resolution.
Nature 459 :446-450. PubMed Id: 19458722. |
||
|
Na,K-ATPase with bound ouabain and K+: Squalus acanthias E Eukaryota, 2.80 Å
|
Ogawa et al. (2009).
Ogawa H, Shinoda T, Cornelius F, & Toyoshima C (2009). Crystal structure of the sodium-potassium pump (Na+,K+-ATPase) with bound potassium and ouabain.
Proc Natl Acad Sci USA 106 :13742-13747. PubMed Id: 19666591. doi:10.1073/pnas.0907054106. |
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|
Na,K-ATPase, E2.MgF42-, Tl+ substitution at 0.75 min: Squalus acanthias E Eukaryota, 2.60 Å
Tl+ substitution at various times: 1.5 min, 2.70 Å: 5AVR 3.5 min, 2.90 Å: 5AVS 5.0 min, 2.90 Å: 5AVT 7.0 min, 2.55 Å: 5AVU 8.5 min, 2.90 Å: 5AVV 16.5 min, 2.60 Å: 5AVW 20.0 min, 3.30 Å: 5AVX 20.0 min, 3.45 Å: 5AVY 55.0 min, 3.20 Å: 5AVZ 85.0 min, 3.35 Å: 5AW1 85.0 min, 3.20 Å 5AW2 100.0 min, 3.35 Å: 5AW3 Rb+ substitution at various times: 1.5 min, 2.80 Å: 5AW4 2.2 min, 2.90 Å: 5AW5 5.5 min, 2.80 Å: 5AW6 11.3 min, 2.90 Å: 5AW7 Rb+ crystal, 2.80 Å: 5AW8 native 2K+ crystal, 2.80 Å: 5AW9 |
Ogawa et al. (2015).
Ogawa H, Cornelius F, Hirata A, & Toyoshima C (2015). Sequential substitution of K+ bound to Na+,K+-ATPase visualized by X-ray crystallography.
Nat Commun 6 :8004. PubMed Id: 26258479. doi:10.1038/ncomms9004. |
||
|
Na,K-ATPase Regulatory Protein FXYD1: Homo sapiens E Eukaryota (expressed in E. coli), NMR Structure
|
Teriete et al. (2007).
Teriete P, Franzin CM, Choi J, & Marassi FM (2007). Structure of the Na,K-ATPase regulatory protein FXYD1 in micelles.
Biochemistry 46 :6774-6783. PubMed Id: 17511473. |
||
|
Oxenoid and Chou (2005).
Oxenoid K & Chou JJ (2005). The structure of phospholamban pentamer reveals a channel-like architecture in membranes.
Proc Natl Acad Sci USA 102 :10870-10875. PubMed Id: 16043693. |
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|
Phospholamban homopentamer in T state: Homo sapiens E Eukaryota (expressed in E. coli), NMR Structure
|
Verardi et al. (2011).
Verardi R, Shi L, Traaseth NJ, Walsh N, & Veglia G (2011). Structural topology of phospholamban pentamer in lipid bilayers by a hybrid solution and solid-state NMR method.
Proc Natl Acad Sci USA 108 :9101-9106. PubMed Id: 21576492. doi:10.1073/pnas.1016535108. |
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|
Phospholamban homopentamer in phosphorylated state: Oryctolagus cuniculus E Eukaryota (expressed in E. coli), NMR Structure
|
Vostrikov et al. (2013).
Vostrikov VV, Mote KR, Verardi R, & Veglia G (2013). Structural dynamics and topology of phosphorylated phospholamban homopentamer reveal its role in the regulation of calcium transport.
Structure 21 :2119-2130. PubMed Id: 24207128. doi:10.1016/j.str.2013.09.008. |
||
|
Plasma Membrane H+-ATPase: Arabidopsis thaliana E Eukaryota, 3.6 Å
|
Pedersen et al. (2007).
Pedersen BP, Buch-Pedersen MJ, Morth JP, Palmgren MG, Lauquin GJ, & Nissen P (2007). Crystal structure of the plasma membrane proton pump.
Nature 450 :1111-1114. PubMed Id: 18075595. |
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|
Copper-transporting ATPase type PIB: Legionella pneumophila B Bacteria (expressed in E. coli), 3.20 Å
The structure suggests a three-stage copper transport pathway |
Gourdon et al. (2011).
Gourdon P, Liu XY, Skjφrringe T, Morth JP, Mφller LB, Pedersen BP, & Nissen P (2011). Crystal structure of a copper-transporting PIB-type ATPase.
Nature 475 :59-64. PubMed Id: 21716286. doi:10.1038/nature10191. |
||
|
Copper-transporting ATPase type PIB (E2P state): Legionella pneumophila B Bacteria (expressed in E. coli), 2.75 Å
|
Andersson et al. (2014).
Andersson M, Mattle D, Sitsel O, Klymchuk T, Nielsen AM, Møller LB, White SH, Nissen P, & Gourdon P (2014). Copper-transporting P-type ATPases use a unique ion-release pathway.
Nat Struct Mol Biol 21 :43-48. PubMed Id: 24317491. doi:10.1038/nsmb.2721. |
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|
Hydrolases
|
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|
Estrone Sulfatase: Homo sapiens placenta E Eukaryota, 2.6 Å
|
Hernandez-Guzman et al. (2003).
Hernandez-Guzman FG, Higashiyama T, Pangborn W, Osawa Y, & Ghosh D (2003). Structure of human estrone sulfatase suggests functional roles of membrane association.
J Biol Chem 278 :22989-22997. PubMed Id: 12657638. |
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|
Oxygenases
|
|||
|
Particulate methane monooxgenase (pMMO): Methylococcus capsulatus B Bacteria, 2.8 Å
|
Lieberman & Rosenzweig (2005).
Lieberman RL & Rosenzweig AC (2005). Crystal structure of a membrane-bound metalloenzyme that catalyses the biological oxidation of methane.
Nature 434 :177-181. PubMed Id: 15674245. |
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|
Particulate methane monooxgenase (pMMO): Methylosinus trichosporium OB3b B Bacteria, 3.90 Å
|
Hakemian et al. (2008).
Hakemian AS, Kondapalli KC, Telser J, Hoffman BM, Stemmler TL, & Rosenzweig AC (2008). The metal centers of particulate methane monooxygenase from Methylosinus trichosporium OB3b.
Biochemistry 47 :6793-6801. PubMed Id: 18540635. |
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|
Transhydrogenases
|
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|
Nicotinamide nucleotide transhydrogenase (TH) proton channel domain: Thermus thermophilus B Bacteria (expressed in E. coli), 2.77 Å
holo-TH, 6.92 Å: 4O9U |
Leung et al. (2015).
Leung JH, Schurig-Briccio LA, Yamaguchi M, Moeller A, Speir JA, Gennis RB, & Stout CD (2015). Division of labor in transhydrogenase by alternating proton translocation and hydride transfer.
Science 347 6218:178-181. PubMed Id: 25574024. doi:10.1126/science.1260451. |
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|
Mo/Wbis-MGD Oxidoreductases
|
|||
|
Jormakka et al. (2008).
Jormakka M, Yokoyama K, Yano T, Tamakoshi M, Akimoto S, Shimamura T, Curmi P, & Iwata S (2008). Molecular mechanism of energy conservation in polysulfide respiration.
Nat Struct Mol Biol 15 :730-737. PubMed Id: 18536726. |
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|
Oxidoreductases
|
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|
Sulfide:quinone oxidoreductase in complex with decylubiquinone: Aquifex aeolicus B Bacteria, 2.0 Å
"as-purified" protein, 2.30 Å: 3HYV in complex with aurachin C, 2.9 Å: 3HYX This monotopic membrane protein is thought to be buried about 12 Å in the bilayer interface. Listed under TRANSMEMBRANE PROTEINS: ALPHA-HELICAL : Oxidoreductases, MONOTOPIC MEMBRANE PROTEINS : Oxidoreductases (Monotopic). |
Marcia et al. (2009).
Marcia M, Ermler U, Peng G, & Michel H (2009). The structure of Aquifex aeolicus sulfide:quinone oxidoreductase, a basis to understand sulfide detoxification and respiration.
Proc Natl Acad Sci USA 106 :9625-9630. PubMed Id: 19487671. |
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|
Electron Transfer Flavoprotein-ubiquinone oxidoreductase (ETF-QO) with bound UQ: Sus scrofa E Eukaryota, 2.5 Å
UQ-free structure, 2.6 Å: 2GMJ. Because this is a mitochondrial respiratory chain protein, it is listed under TRANSMEMBRANE PROTEINS: ALPHA-HELICAL : Oxidoreductases and MONOTOPIC MEMBRANE PROTEINS : Oxidoreductases (Monotopic). |
Zhang et al. (2006).
Zhang J, Frerman FE, & Kim J-JP (2006). Structure of electron transfer flavoprotein-ubiquinone oxidoreductase and electron transfer to the mitochondrial ubiquinone pool.
Proc Natl Acad Sci U S A 103 :16212-16217. PubMed Id: 17050691. |
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|
Glycerol-3-phosphate dehydrogenase (GlpD, native): Escherichia coli B Bacteria, 1.75 Å
SeMet-GlpD, 1.95 Å: 2R4J GlpD-2-PGA, 2.3 Å: 2R45 GlpD-PEP, 2.1 Å: 2R46 GlpD-DHAP, 2.1 Å: 2R4E Listed under MONOTOPIC MEMBRANE PROTEINS : Dehydrogenases, TRANSMEMBRANE PROTEINS: ALPHA-HELICAL : Oxidoreductases. |
Yeh et al. (2008).
Yeh JI, Chinte U, & Du S (2008). Structure of glycerol-3-phosphate dehydrogenase, an essential monotopic membrane enzyme involved in respiration and metabolism.
Proc. Natl. Acad. Sci. USA 105 :3280-3285. PubMed Id: 18296637. |
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|
NarGHI Nitrate Reductase A: Escherichia coli B Bacteria, 1.9 Å
|
Bertero et al. (2003).
Bertero MG, Rothery RA, Palak M, Hou C, Lim D, Blasco F, Weiner JH, & Strynadka NC (2003). Insights into the respiratory electron transfer pathway from the structure of nitrate reductase A.
Nature Structural Biol 10 :681-687. PubMed Id: 12910261. |
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NarGHI Nitrate Reductase A catalytic domain NarG with FS0 cluster: Escherichia coli B Bacteria, 2.2 Å
|
Rothery et al. (2004).
Rothery RA, Bertero MG, Cammack R, Palak M, Blasco F, Strynadka NC, & Weiner JH (2004). The catalytic subunit of Escherichia coli nitrate reductase A contains a novel [4Fe-4S] cluster with a high-spin ground state.
Biochemistry 43 :5324-5333. PubMed Id: 15122898. |
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|
Bertero et al. (2005).
Bertero MG, Rothery RA, Boroumand N, Palak M, Blasco F, Ginet N, Weiner JH, Strynadka NC (2005). Structural and biochemical characterization of a quinol binding site of Escherichia coli nitrate reductase A.
J Biol Chem 280 :14836-14843. PubMed Id: 15615728. |
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|
NrfH Cytochrome C Quinol Dehydrogenase: Desulfovibrio vulgaris B Bacteria, 2.3 Å
In complex with NrfA cytochrome c nitrite reductase. |
Rodrigues et al. (2006).
Rodrigues ML, Oliveira TF, Pereira AC & Archer M (2006). X-ray structure of the membrane-bound cytochrome c quinol dehydrogenase NrfH reveals novel haem coordination.
EMBO J 25 :5951-5960. PubMed Id: 17139260. |
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DsbB-DsbA Periplasmic Oxidase Complex: Escherichia coli B Bacteria, 3.7 Å
DsbB is a four-helix bundle membrane protein that works with the periplasmic DsbA oxidase to introduce disulfide bonds into periplasmic proteins. |
Inaba et al. (2006).
Inaba K, Murakami S, Suzuki M, Nakagawa A, Yamashita E, Okada K, & Ito K (2006). Crystal structure of the DsbA-DsbB complex reveals a mechanism of disulfide bond generation.
Cell 127 :789-801. PubMed Id: 17110337. |
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|
DsbB-Fab complex: Escherichia coli B Bacteria, 3.4 Å
Shows the principal Cys104-Cys130 disulfide Updated DsbB-DsbA complex: 3.7 Å 2ZUP |
Inaba et al. (2009).
Inaba K, Murakami S, Nakagawa A, Iida H, Kinjo M, Ito K, & Suzuki M (2009). Dynamic nature of disulphide bond formation catalysts revealed by crystal structures of DsbB.
EMBO J 28 :779-791. PubMed Id: 19214188. |
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|
wtDsbB-DsbA(Cys133A)-Q8 Complex: Escherichia coli B Bacteria, 3.7 Å
|
Malojcic et al. (2008).
Malojcic G, Owen RL, Grimshaw JP, & Glockshuber R (2008). Preparation and structure of the charge-transfer intermediate of the transmembrane redox catalyst DsbB.
FEBS Lett 582 :3301-3307. PubMed Id: 18775700. |
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|
Zhou et al. (2008).
Zhou Y, Cierpicki T, Jimenez RH, Lukasik SM, Ellena JF, Cafiso DS, Kadokura H, Beckwith J, & Bushweller JH (2008). NMR solution structure of the integral membrane enzyme DsbB: functional insights into DsbB-catalyzed disulfide bond formation.
Mol Cell 31 :896-908. PubMed Id: 18922471. |
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|
DsbB in POPE lipid bilayer: Escherichia coli B Bacteria, 1.35 Å
Cys41Ser mutant. Solid-state NMR used to refine the X-ray structure 2ZUQ |
Tang et al. (2013).
Tang M, Nesbitt AE, Sperling LJ, Berthold DA, Schwieters CD, Gennis RB, & Rienstra CM (2013). Structure of the Disulfide Bond Generating Membrane Protein DsbB in the Lipid Bilayer.
J Mol Biol 425 :1670-1682. PubMed Id: 23416557. doi:10.1016/j.jmb.2013.02.009. |
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CcdA electron transporter: Archaeoglobus fulgidus A Archaea (expressed in E. coli), NMR structure
|
Williamson et al. (2015).
Williamson JA, Cho SH, Ye J, Collet JF, Beckwith JR, & Chou JJ (2015). Structure and multistate function of the transmembrane electron transporter CcdA.
Nat Struct Mol Biol 22 :809-814. PubMed Id: 26389738. doi:10.1038/nsmb.3099. |
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Vitamin K epoxide reductase: Synechococcus sp. B Bacteria (expressed in E. coli), 3.60 Å
|
Li et al. (2010).
Li W, Schulman S, Dutton RJ, Boyd D, Beckwith J, Rapoport TA (2010). Structure of a bacterial homologue of vitamin K epoxide reductase.
Nature 463 :507-512. PubMed Id: 20110994. |
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|
Liu et al. (2014).
Liu S, Cheng W, Fowle Grider R, Shen G, & Li W (2014). Structures of an intramembrane vitamin K epoxide reductase homolog reveal control mechanisms for electron transfer.
Nat Commun 5 :3110. PubMed Id: 24477003. doi:10.1038/ncomms4110. |
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|
O2-tolerant Hydrogenase-1 in complex with cytochrome b: Escherichia coli B Bacteria, 3.30 Å
Structure includes transmembrane helices. |
Volbeda et al. (2013).
Volbeda A, Darnault C, Parkin A, Sargent F, Armstrong FA, & Fontecilla-Camps JC (2013). Crystal Structure of the O2-Tolerant Membrane-Bound Hydrogenase 1 from Escherichia coli in Complex with Its Cognate Cytochrome b.
Structure 21 :184-190. PubMed Id: 23260654. doi:10.1016/j.str.2012.11.010. |
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|
Volbeda et al. (2012).
Volbeda A, Amara P, Darnault C, Mouesca JM, Parkin A, Roessler MM, Armstrong FA, & Fontecilla-Camps JC (2012). X-ray crystallographic and computational studies of the O2-tolerant [NiFe]-hydrogenase 1 from Escherichia coli.
Proc Natl Acad Sci USA 109 :5305-5310. PubMed Id: 22431599. doi:10.1073/pnas.1119806109. |
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Mitochondrial rhodoquinol-fumarate reductase: Ascaris suum E Eukaryota, 2.81 Å
with flutolanil inhibitor and fumarate substrate, 2.91 Å: 3VRB |
Shimizu et al. (2012).
Shimizu H, Osanai A, Sakamoto K, Inaoka DK, Shiba T, Harada S, & Kita K (2012). Crystal structure of mitochondrial quinol-fumarate reductase from the parasitic nematode Ascaris suum.
J Biochem 151 :589-592. PubMed Id: 22577165. doi:10.1093/jb/mvs051. |
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|
Lu et al. (2014).
Lu P, Ma D, Yan C, Gong X, Du M, & Shi Y (2014). Structure and mechanism of a eukaryotic transmembrane ascorbate-dependent oxidoreductase.
Proc Natl Acad Sci USA 111 :1813-1818. PubMed Id: 24449903. doi:10.1073/pnas.1323931111. |
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|
Steuber et al. (2014).
Steuber J, Vohl G, Casutt MS, Vorburger T, Diederichs K, & Fritz G (2014). Structure of the V. cholerae Na+-pumping NADH:quinone oxidoreductase.
Nature 516 7529:62-67. PubMed Id: 25471880. doi:10.1038/nature14003. |
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Electron Transport Chain Complexes: Complex I
|
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|
Complex I membrane domain: Escherichia coli B Bacteria, 3.90 Å
|
Efremov et al. (2010).
Efremov RG, Baradaran R, & Sazanov LA (2010). High-resolution The architecture of respiratory complex I.
Nature 465 :441-445. PubMed Id: 20505720. |
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|
Complex I membrane domain: Escherichia coli B Bacteria, 3.00 Å
|
Efremov & Sazanov (2011).
Efremov RG & Sazanov LA (2011). Structure of the membrane domain of respiratory complex I.
Nature 476 :414-420. PubMed Id: 21831629. doi:10.1038/nature10330. |
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|
Complex I complete: Thermus thermophilus B Bacteria, 4.50 Å
|
Efremov et al. (2010).
Efremov RG, Baradaran R, & Sazanov LA (2010). High-resolution The architecture of respiratory complex I.
Nature 465 :441-445. PubMed Id: 20505720. |
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|
Baradaran et al. (2013).
Baradaran R, Berrisford JM, Minhas GS, & Sazanov LA (2013). Crystal structure of the entire respiratory complex I.
Nature 494 :443-448. PubMed Id: 23417064. doi:10.1038/nature11871. |
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|
Complex I soluble domain, oxidized (4 mol/ASU): Thermus thermophilus B Bacteria, 3.30 Å
|
Sazanov & Hinchliffe (2006).
Sazanov LA & Hinchliffe P (2006). Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus
Science 311 :1430-1436. PubMed Id: 16469879. doi:10.1126/science.1123809. |
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|
Berrisford & Sazanov (2009).
Berrisford JM & Sazanov LA (2009). Structural basis for the mechanism of respiratory complex I
J Biol Chem 284 :29773-29783. PubMed Id: 19635800. doi:10.1074/jbc.M109.032144. |
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Respiratory Complex I, single-particle cryo-EM structure: Bos taurus E Eukaryota, 4.95 Å
EM map of deposited in EM Data Bank under accession number EMD-2676 |
Vinothkumar et al. (2014).
Vinothkumar KR, Zhu J, & Hirst J (2014). Architecture of mammalian respiratory complex I.
Nature 515 7525:80-84. PubMed Id: 25209663. doi:10.1038/nature13686. |
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|
Zhu et al. (2016).
Zhu J, Vinothkumar KR, & Hirst J (2016). Structure of mammalian respiratory complex I.
Nature 536 :354-358. PubMed Id: 27509854. doi:10.1038/nature19095. |
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|
Respiratory Complex I, single-particle cryo-EM structure: Ovis aries E Eukaryota, 3.9 Å
|
Fiedorczuk et al. (2016).
Fiedorczuk K, Letts JA, Degliesposti G, Kaszuba K, Skehel M, & Sazanov LA (2016). Atomic structure of the entire mammalian mitochondrial complex I.
Nature 538 :406-410. PubMed Id: 27595392. doi:10.1038/nature19794. |
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|
Mitochondrial Complex I: Yarrowia lipolytica E Eukaryota, 3.8 Å
Anisotropic crystals. Structure was refined at 3.9 Å x 3.9 Å x 3.6 Å. |
Zickermann et al. (2015).
Zickermann V, Wirth C, Nasiri H, Siegmund K, Schwalbe H, Hunte C, & Brandt U (2015). Structural biology. Mechanistic insight from the crystal structure of mitochondrial complex I.
Science 347 6217:44-49. PubMed Id: 25554780. doi:10.1126/science.1259859. |
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Electron Transport Chain Complexes: Complex II
|
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|
Fumarate Reductase Complex: Escherichia coli B Bacteria, 3.3 Å
This structure has been replaced by 1L0V, below. |
Iverson et al. (1999).
Iverson TM, Luna-Chavez C, Cecchini G, & Rees DC (1999). Structure of the Escherichia coli fumerate reductase respiratory complex.
Science 284 :1961-1966. PubMed Id: 10373108. |
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|
Iverson et al. (2002).
Iverson TM, Luna-Chavez C, Croal LR, Cecchini G, & Rees DC (2002). Crystallographic studies of the Escherichia coli quinol-fumarate reductase with inhibitors bound to the quinol-binding site.
J Biol Chem 277 :16124-16130. PubMed Id: 11850430. |
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Fumarate Reductase Complex: Wolinella succinogenes B Bacteria, 1.78 Å
This structure supersedes 1QLA at 2.2 Å published by Lancaster et al.. 2BS2 has small unit cell. 1QLB, 2.2 Å, has a larger unit cell. |
Madej et al. (2006).
Madej MG, Nasiri HR, Hilgendorff NS, Schwalbe H, & Lancaster CR (2006). Evidence for transmembrane proton transfer in a dihaem-containing membrane protein complex.
EMBO J 25 :4963-4970. PubMed Id: 17024183. doi:10.1038/sj.emboj.7601361. See also: Lancaster et al. (1999). Lancaster CRD, Kröger A, Auer M, & Michel H (1999). Structure of fumarate reductase from Wolinella succinogenes at 2.2 Å resolution.
Nature 402 :377-385. PubMed Id: 10586875. |
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|
Formate dehydrogenase-N: Escherichia coli B Bacteria, 1.6 Å (native structure)
HQNO complex, 2.8 Å: 1KQG |
Jormakka et al. (2002).
Jormakka M, Tornroth S, Byrne B, & Iwata S (2002). Molecular basis of proton motive force generation: structure of formate dehydrogenase-N.
Science 295 :1863-1868. PubMed Id: 11884747. |
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|
Succinate:quinone oxidoreductase (SQR, Complex II): Escherichia coli B Bacteria, 2.6 Å
DNP-17 Complex, 2.9 Å: 1NEN |
Yankovskaya et al. (2003).
Yankovskaya V, Horsefield R, Törnroth S, Luna-Chavez C, Miyoshi H, Léger C, Byrne B, Cecchini G, & Iwata S (2003). Architecture of succinate dehydrogenase and reactive oxygen species generation.
Science 299 :700-704. PubMed Id: 12560550. |
||
|
Succinate:quinone oxidoreductase (SQR, Complex II) with Atpenin A5: Escherichia coli B Bacteria, 3.10 Å
|
Horsefield et al. (2006).
Horsefield R, Yankovskaya V, Sexton G, Whittingham W, Shiomi K, Omura S, Byrne B, Cecchini G, & Iwata S (2006). Structural and computational analysis of the quinone-binding site of complex II (succinate-ubiquinone oxidoreductase): a mechanism of electron transfer and proton conduction during ubiquinone reduction.
J Biol Chem 281 :7309-7316. PubMed Id: 16407191. |
||
|
Ruprecht et al. (2009).
Ruprecht J, Yankovskaya V, Maklashina E, Iwata S, & Cecchini G (2009). Structure of Escherichia coli succinate:quinone oxidoreductase with an occupied and empty quinone-binding site.
J Biol Chem 284 :29836-29846. PubMed Id: 19710024. doi:10.1074/jbc.M109.010058. |
|||
|
Succinate:quinone oxidoreductase (SQR, Complex II), H207T SdhB mutant: Escherichia coli B Bacteria, 2.70 Å
|
Ruprecht et al. (2011).
Ruprecht J, Iwata S, Rothery RA, Weiner JH, Maklashina E, & Cecchini G (2011). Perturbation of the quinone-binding site of complex II alters the electronic properties of the proximal [3Fe-4S] iron-sulfur cluster
J Biol Chem 286 :12756-12765. PubMed Id: 21310949. doi:10.1074/jbc.M110.209874. |
||
|
Succinate:ubiquinone oxidoreductase (SQR, Complex II; pig heart): Sus scrofa E Eukaryota, 2.4 Å
with inhibitors, 3.5 Å: 1ZP0 |
Sun et al. (2005).
Sun F, Huo X, Zhai Y, Wang A, Xu J, Su D, Bartlam M, & Rao Z (2005). Crystal structure of mitochondrial respiratory membrane protein complex II.
Cell 121 :1043-1057. PubMed Id: 15989954. |
||
|
Huang et al. (2006).
Huang LS, Sun G, Cobessi D, Wang AC, Shen JT, Tung EY, Anderson VE, & Berry EA (2006). 3-nitropropionic acid is a suicide inhibitor of mitochondrial respiration that, upon oxidation by complex II, forms a covalent adduct with a catalytic base arginine in the active site of the enzyme.
J Biol Chem 281 :5965-5972. PubMed Id: 16371358. |
|||
|
Succinate:ubiquinone oxidoreductase (SQR, Complex II; chicken heart) with TEO at the active site: Gallus gallus E Eukaryota, 1.74 Å
with bound malonate at the active site, 2.40 Å: 2H89 |
Huang et al. (2006).
Huang LS, Shen JT, Wang AC, & Berry EA (2006). Crystallographic studies of the binding of ligands to the dicarboxylate site of Complex II, and the identity of the ligand in the "oxaloacetate-inhibited" state.
Biochim Biophys Acta 1757 :1073-1083. PubMed Id: 16935256. |
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|
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Information about Cytochrome bc1 |
|||
|
Cytochrome bc1: Bos taurus E Eukaryota, 2.7 Å
Bovine heart mitochondria, 5 subunits |
Xia et al. (1997).
Xia D, Yu C-A, Kim H, Xia J-Z, Kachurin AM, Zhang L, Yu L, & Deisenhofer, J (1997). Crystal structure of the cytochrome bc1complex from bovine heart mitochondria.
Science 277 :60-66. PubMed Id: 9204897. |
||
|
Cytochrome bc1: Bos taurus E Eukaryota, 3.0 Å
Bovine Heart Mitochondria, 11 subunits. |
Iwata et al. (1998).
Iwata S, Lee JW, Okada K, Lee JK, Iwata M, Rasmussen B, Link TA, Ramaswamy S, & Jap BK (1998). Complete structure of the 11-subunit bovine mitochondrial cytochrome bc1complex.
Science 281 :64-71. PubMed Id: 9651245. |
||
|
Cytochrome bc1: Bos taurus E Eukaryota, 2.26 Å
Bovine Heart Mitochondria, with jg144 inhibitor |
Esser et al. (2006).
Esser L, Gong X, Yang S, Yu L, Yu CA, & Xia D (2006). Surface-modulated motion switch: capture and release of iron-sulfur protein in the cytochrome bc1complex.
Proc Natl Acad Sci U S A 103 :13045-13050. PubMed Id: 16924113. |
||
|
Gao et al. (2003).
Gao X, Wen X, Esser L, Quinn B, Yu L, Yu CA, & Xia D. (2003). Structural basis for the quinone reduction in the bc1complex: a comparative analysis of crystal structures of mitochondrial cytochrome bc1with bound substrate and inhibitors at the Qisite.
Biochemistry 42 :9067-9080. PubMed Id: 12885240. |
|||
|
Esser et al. (2004).
Esser L, Quinn B, Li YF, Zhang M, Elberry M, Yu L, Yu CA, & Xia D (2004). Crystallographic studies of quinol oxidation site inhibitors: a modified classification of inhibitors for the cytochrome bc1> complex.
J Mol Biol 341 :281-302. PubMed Id: 15312779. |
|||
|
Huang et al. (2005).
Huang LS, Cobessi D, Tung EY, & Berry EA (2005). Binding of the respiratory chain inhibitor antimycin to the mitochondrial bc1complex: a new crystal structure reveals an altered intramolecular hydrogen-bonding pattern.
J Mol Biol 351 :573-597. PubMed Id: 16024040. |
|||
|
Zhang et al. (1998).
Zhang ZL, Huang LS, Shulmeister VM, Chi Y-I, Kim K K, Hung L-W, Crofts AR, Berry EA, & Kim S-H (1998). Electron transfer by domain movement in cytochrome bc1.
Nature 392 :677-684. PubMed Id: 9565029. |
|||
|
Cytochrome bc1: Saccharomyces cerevisiae E Eukaryota, 2.3 Å
yeast, 9 subunits. |
Hunte et al. (2000).
Hunte C, Koepe J, Lange C, Rossmanith T, & Michel H (2000). Structure at 2.3 Å resolution of cytochrome bc1complex from the yeast Saccharomyces cerevisiae co-crystallized with an antibody Fv fragment.
Structure 8 :669-684. PubMed Id: 10873857. |
||
|
Cytochrome bc1: Saccharomyces cerevisiae E Eukaryota, 2.3 Å
With phospholipids. |
Lange et al. (2001).
Lange C, Nett JH, Trumpower BL, & Hunte C (2001). Specific roles of protein-phospholipid interactions in the yeast cytochrome bc1complex structure.
EMBO J 20 :6591-6600. PubMed Id: 11726495. |
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|
Cytochrome bc1: Saccharomyces cerevisiae E Eukaryota, 2.5 Å
With HHDBT inhibitor. |
Palsdottir et al. (2003).
Palsdottir H, Lojero CG, Trumpower BL, & Hunte C (2003). Structure of the yeast cytochrome bc1complex with a hydroxyquinone anion Qosite inhibitor bound.
J Biol Chem 278 :31303-31311. PubMed Id: 12782631. |
||
|
Cytochrome bc1: Saccharomyces cerevisiae E Eukaryota, 2.3 Å
With bound stigmatellin. |
Lancaster et al. (2007).
Lancaster CR, Hunte C, Kelley J 3rd, Trumpower BL, Ditchfield R (2007). A comparison of stigmatellin conformations, free and bound to the photosynthetic reaction center and the cytochrome bc1complex.
J Mol Biol 368 :197-208. PubMed Id: 17337272. |
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|
Cytochrome bc1: Saccharomyces cerevisiae E Eukaryota, 1.9 Å
With bound isoform-1 cytochrome c. With bound isoform-2 cytochrome c, 2.50 Å: 3CXH |
Solmaz & Hunte (2008).
Solmaz SR & Hunte C (2008). Structure of complex III with bound cytochrome c in reduced state and definition of a minimal core interface for electron transfer.
J Biol Chem 283 :17452-17459. PubMed Id: 18390544. |
||
|
Cytochrome bc1: Rhodobacter sphaeroides B Bacteria, 3.20 Å
|
Esser et al. (2006).
Esser L, Gong X, Yang S, Yu L, Yu CA, & Xia D (2006). Surface-modulated motion switch: capture and release of iron-sulfur protein in the cytochrome bc1complex.
Proc Natl Acad Sci U S A 103 :13045-13050. PubMed Id: 16924113. |
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|
Cytochrome bc1: Rhodobacter capsulatus B Bacteria, 3.50 Å
|
Berry et al. (2004).
Berry EA, Huang LS, Saechao LK, Pon NG, Valkova-Valchanova M, & Daldal F (2004). X-Ray Structure of Rhodobacter Capsulatus Cytochrome bc (1): Comparison with its Mitochondrial and Chloroplast Counterparts.
Photosynth Res 81 :251-275. PubMed Id: 16034531. |
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|
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis
|
|||
|
Cytochrome b6f complex: Mastigocladus laminosus B Bacteria, 3.0 Å
(Original PDB file 1UM3 replaced by 1VF5) |
Kurisu et al. (2003).
Kurisu G, Zhang H, Smith JL, & Cramer WA (2003). Structure of the cytochrome b6f complex of oxygenic photosynthesis: tuning the cavity.
Science 302 :1009-1014. PubMed Id: 14526088. |
||
|
Cytochrome b6f complex: Mastigocladus laminosus B Bacteria, 3.80 Å
In complex with quinone analogue inhibitor DBMIB. |
Yan et al. (2006).
Yan J, Kurisu G, & Cramer WA (2006). Intraprotein transfer of the quinone analogue inhibitor 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone in the cytochrome b6f complex.
Proc Natl Acad Sci U S A 103 :69-74. PubMed Id: 16371475. |
||
|
Yamashita et al. (2007).
Yamashita E, Zhang H, & Cramer WA (2007). Structure of the cytochrome b6f complex: quinone analogue inhibitors as ligands of heme cn.
J Mol Biol 370 :39-52. PubMed Id: 17498743. |
|||
|
Cytochrome b6f complex with bound TDS:: Mastigocladus laminosus B Bacteria, 3.07 Å
with bound inhibitor NQNO, 3.25 Å: 4H0L |
Hasan et al. (2013).
Hasan SS, Yamashita E, Baniulis D, & Cramer WA (2013). Quinone-dependent proton transfer pathways in the photosynthetic cytochrome b6f complex.
Proc Natl Acad Sci USA 110 :4297-4302. PubMed Id: 23440205. doi:10.1073/pnas.1222248110. |
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|
Cytochrome b6f complex: Chlamydomonas reinhardtii E Eukaryota, 3.1 Å
|
Stroebel et al. (2003).
Stroebel D, Choquet Y, Popot JL, & Picot D (2003). An atypical haem in the cytochrome b(6)f complex.
Nature 426 :413-418. PubMed Id: 14647374. |
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|
Cytochrome b6f complex: Nostoc sp. PCC 7120 B Bacteria, 3.0 Å
|
Baniulis et al. (2010).
Baniulis D, Yamashita E, Whitelegge JP, Zatsman AI, Hendrich MP, Hasan SS, Ryan CM, & Cramer WA (2010). Structure-function, stability, and chemical modification of the cyanobacterial cytochrome b6f complex from Nostoc sp. PCC 7120.
J Biol Chem 284 :9861-9869. PubMed Id: 19189962. |
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|
Cytochrome b6f complex: Nostoc sp. PCC 7120 B Bacteria, 2.70 Å
|
Hasan et al. (2013).
Hasan SS, Yamashita E, Baniulis D, & Cramer WA (2013). Quinone-dependent proton transfer pathways in the photosynthetic cytochrome b6f complex.
Proc Natl Acad Sci USA 110 :4297-4302. PubMed Id: 23440205. doi:10.1073/pnas.1222248110. |
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|
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
( Information about cytochrome c oxidases) |
|||
|
Cytochrome C Oxidase, aa3: Bos taurus (bovine) heart mitochndria E Eukaryota, 2.8 Å
|
|
Tsukihara et al. (1996).
Tsukihara T, Aoyama H, Yamashita E, Tomizaki T, Yamaguchi H, Shinzawa-Itoh K, Nakashima R, & Yoshikawa S (1996). The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 Å.
Science 272 :1136-1144. PubMed Id: 8638158. |
|
|
Fully Oxidized Cytochrome C Oxidase, aa3: Bos taurus (bovine) heart mitochndria E Eukaryota, 1.80 Å
Fully reduced form, 1.90 Å: 1V55 |
Tsukihara et al. (2003).
Tsukihara T, Shimokata K, Katayama Y, Shimada H, Muramoto K, Aoyama H, Mochizuki M, Shinzawa-Itoh K, Yamashita E, Yao M, Ishimura Y, Yoshikawa S (2003). The low-spin heme of cytochrome c oxidase as the driving element of the proton-pumping process.
Proc Natl Acad Sci USA 100 :15304-15309. PubMed Id: 14673090. |
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|
Cytochrome C Oxidase, aa3 with bound cyanide: Bos taurus E Eukaryota, 2.00 Å
|
Yano et al. (2015).
Yano N, Muramoto K, Mochizuki M, Shinzawa-Itoh K, Yamashita E, Yoshikawa S, & Tsukihara T (2015). X-ray structure of cyanide-bound bovine heart cytochrome c oxidase in the fully oxidized state at 2.0 Å resolution.
Acta Crystallogr F Struct Biol Commun 71 :726-730. PubMed Id: 26057802. doi:10.1107/S2053230X15007025. |
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Cytochrome C Oxidase, aa3: Paracoccus denitrificans B Bacteria, 2.70 Å
|
Iwata et al. (1995).
Iwata S, Ostermeier C, Ludwig B, & Michel H (1995). Structure at 2.8 Å resolution of cytochrome c oxidase from Paracoccus denitrificans.
Nature 376 :660-669. PubMed Id: 7651515. See also: Ostermeier et al. (1997). Ostermeier C, Harrenga A, Ermler U, & Michel H (1997). Structure at 2.7 Å resolution of the Paracoccus denitrificans two-subunit cytochrome c oxidase complexed with an antibody FV fragment.
Proc Natl Acad Sci USA 94 :10547-10553. PubMed Id: 9380672. |
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|
Cytochrome C Oxidase, aa3, Fully Oxidized: Paracoccus denitrificans B Bacteria, 3.00 Å
|
Harrenga & Michel H (1999).
Harrenga A & Michel H (1999). The cytochrome c oxidase from Paracoccus denitrificans does not change the metal center ligation upon reduction.
J Biol Chem 274 :33296-33299. PubMed Id: 10559205. |
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|
Cytochrome C Oxidase, aa3, N131D variant: Paracoccus denitrificans B Bacteria, 2.32 Å
|
Dürr et al. (2008).
Dürr KL, Koepke J, Hellwig P, Müller H, Angerer H, Peng G, Olkhova E, Richter OM, Ludwig B, Michel H (2008). A D-pathway mutation decouples the Paracoccus denitrificans cytochrome c oxidase by altering the side-chain orientation of a distant conserved glutamate.
J Mol Biol 384 :865-877. PubMed Id: 18930738. |
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|
Cytochrome C Oxidase, aa3: Paracoccus denitrificans B Bacteria, 2.25 Å
|
Koepke et al. (2009).
Koepke J, Olkhova E, Angerer H, Müller H, Peng G, Michel H (2009). High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase: new insights into the active site and the proton transfer pathways.
Biochim Biophys Acta 1787 :635-645. PubMed Id: 19374884. |
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|
Cytochrome Oxidase, cbb3: Pseudomonas stutzeri B Bacteria, 3.2 Å
|
Buschmann et al. (2010).
Buschmann S, Warkentin E, Xie H, Langer JD, Ermler U, Michel H. (2010). The structure of cbb3cytochrome oxidase provides insights into proton pumping.
Science 329 :327-330. PubMed Id: 20576851. |
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|
Cytochrome ba3: Thermus thermophilus B Bacteria, 2.40 Å
|
Soulimane et al. (2000).
Soulimane T, Buse G, Bourenkov GP, Bartunik HD, Huber R, & Than ME (2000). Structure and mechanism of the aberrant ba3-cytochrome c oxidase from Thermus thermophilus.
EMBO J 19 :1766-1776. PubMed Id: 10775261. See also: Soulimane et al. (2000). Soulimane T, Than ME, Dewor M, Huber R, & Buse G (2000). Primary structure of a novel subunit in ba3-cytochrome oxidase from Thermus thermophilus.
Protein Sci 9 :2068-2073. PubMed Id: 11152118. doi:10.1110/ps.9.11.2068. |
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Cytochrome ba3 with bound xenon: Thermus thermophilus B Bacteria, 3.37 Å
|
Luna et al. (2008).
Luna VM, Chen Y, Fee JA, & Stout CD (2008). Crystallographic studies of Xe and Kr binding within the large internal Cavity of Cytochrome ba3from Thermus thermophilus: Structural Analysis and Role of Oxygen Transport Channels in the Heme-Cu Oxidases.
Biochemistry 47 :4657-4665. PubMed Id: 18376849. |
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|
Cytochrome C Oxidase, caa3: Thermus thermophilus B Bacteria, 2.36 Å
Crystallized in meso |
Lyons et al. (2012).
Lyons JA, Aragão D, Slattery O, Pisliakov AV, Soulimane T, & Caffrey M (2012). Structural insights into electron transfer in caa3-type cytochrome oxidase.
Nature 487 :514-518. PubMed Id: 22763450. doi:10.1038/nature11182. |
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|
Cytochrome C Oxidase wild-type: Rhodobacter sphaeroides B Bacteria, 2.30 Å
EQ(I-286) mutant, 3.00 Å: 1M57 |
Svensson-Ek et al. (2002).
Svensson-Ek M, Abramson J, Larsson G, Törnroth S, Brzezinski P, & Iwata S (2002). The X-ray crystal structures of wild-type and EQ(I-286) mutant cytochrome c oxidases from Rhodobacter sphaeroides.
J Mol Biol 321 :329-339. PubMed Id: 12144789. |
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|
Cytochrome C Oxidase, two-subunit catalytic core: Rhodobacter sphaeroides B Bacteria, 2.0 Å
|
Qin et al. (2006).
Qin G, Hiser C, Mulichak A, Garavito RM, & Ferguson-Miller S (2006). Identification of conserved lipid/detergent-binding sites in a high-resolution structure of the membrane protein cytochrome c oxidase.
Proc. Natl. Acad. Sci. USA 103 :16117-16122. PubMed Id: 17050688. |
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|
Ubiquinol Oxidase, cytochrome bo3: Escherichia coli B Bacteria, 3.5 Å
|
Abramson et al. (2000).
Abramson J, Riistama S, Larsson G, Jasaitis A, Svensson-Ek M, Laakkonen L, Puustinen A, Iwata S, & Wikstrom M (2000). The structure of the ubiquinol oxidase from Escherichia coli and its ubiquinone binding site.
Nat Struct Biol 7 :910-917. PubMed Id: 11017202. |
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|
Cytochrome bd-type oxidase (anisotropy corrected): Geobacillus thermodenitrificans B Bacteria, 3.05 Å
anisotropic structure, 3.8 Å: 5IR6 |
Safarian et al. (2016).
Safarian S, Rajendran C, Müller H, Preu J, Langer JD, Ovchinnikov S, Hirose T, Kusumoto T, Sakamoto J, & Michel H (2016). Structure of a bd oxidase indicates similar mechanisms for membrane-integrated oxygen reductases.
Science 352 :583-586. PubMed Id: 27126043. doi:10.1126/science.aaf2477. |
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|
Electron Transport Chain Super Complexes (Respirasome)
|
|||
|
Letts et al. (2016).
Letts JA, Fiedorczuk K, & Sazanov LA (2016). The architecture of respiratory supercomplexes.
Nature 537 :644-648. PubMed Id: 27654913. doi:10.1038/nature19774. |
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|
Electron Transport Chain (ETC) Super Complex comprised of ETC complexes I, III, and IV: Sus scrofa E Eukaryota, 5.4 Å
cryo-EM structure |
Gu et al. (2016).
Gu J, Wu M, Guo R, Yan K, Lei J, Gao N, & Yang M (2016). The architecture of the mammalian respirasome.
Nature 537 :639-643. PubMed Id: 27654917. doi:10.1038/nature19359. |
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|
Electron Transport Chain (ETC) Super Complex I1III2IV1: Sus scrofa E Eukaryota, 4.0 Å
Cryo-EM structure |
Wu et al. (2016).
Wu M, Gu J, Guo R, Huang Y, & Yang M (2016). Structure of Mammalian Respiratory Supercomplex I1III2IV1.
Cell 167 :1598-1609.e10. PubMed Id: 27912063. doi:10.1016/j.cell.2016.11.012. |
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|
Nitric Oxide Reductases
|
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|
Nitric Oxide Reductase: Pseudomonas aeruginosa B Bacteria, 2.70 Å
Crystallized with cNOR antibody (Fab) |
Hino et al. (2010).
Hino T, Matsumoto Y, Nagano S, Sugimoto H, Fukumori Y, Murata T, Iwata S, & Shiro Y (2010). Structural basis of biological N2O generation by bacterial nitric oxide reductase.
Science 330 :1666-1670. PubMed Id: 21109633. |
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|
Nitric Oxide Reductase qNOR wild-type: Geobacillus stearothermophilus B Bacteria (expressed in E. coli), 2.5 Å
HQNO complex, 2.7 Å: 3AYG |
Matsumoto et al. (2012).
Matsumoto Y, Tosha T, Pisliakov AV, Hino T, Sugimoto H, Nagano S, Sugita Y, & Shiro Y (2012). Crystal structure of quinol-dependent nitric oxide reductase from Geobacillus stearothermophilus.
Nat Struct Mol Biol 19 :238-245. PubMed Id: 22266822. doi:10.1038/nsmb.2213. |
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|
Nitric Oxide Reductase BC complex: Roseobacter denitrificans B Bacteria, 2.85 Å
|
Crow et al. (2016).
Crow A, Matsuda Y, Arata H, & Oubrie A (2016). Structure of the Membrane-intrinsic Nitric Oxide Reductase from Roseobacter denitrificans.
Biochemistry 55 23:3198-3203. PubMed Id: 27185533. doi:10.1021/acs.biochem.6b00332. |
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|
Photosystems
|
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|
Photosystem I: Thermosynechococcus elongatus B Bacteria, 4.0 Å
|
Schubert et al. (1997).
Schubert W-D, Klukas O, Krauß N, Saenger W, Fromme P, & Witt HT (1997). Photosystem I of Synechococcus elongatus at 4 Å resolution: Comprehensive structure analysis.
J Mol Biol 272 :741-769. PubMed Id: 9368655. |
||
|
Photosystem I: Thermosynechococcus elongatus B Bacteria, 2.5 Å
|
Jordan et al. (2001).
Jordan P, Fromme P, Witt HT, Klukas O, Saenger W, & Krauss N (2001). Three-dimensional structure of cyanobacterial photosystem I at 2.5 Å resolution.
Nature 411 :909-917. PubMed Id: 11418848. |
||
|
Photosystem I (plant): Pisum sativum E Eukaryota, 4.44 Å
|
Ben-Shem et al. (2003).
Ben-Shem A, Frolow F, & Nelson N (2003). Crystal structure of plant photosystem I.
Nature 426 :630-635. PubMed Id: 14668855. |
||
|
Photosystem I (plant): Pisum sativum E Eukaryota, 3.40 Å
|
Amunts et al. (2007).
Amunts A, Drory O, & Nelson N (2007). The structure of a plant photosystem I supercomplex at 3.4 Å resolution.
Nature 447 :58-63. PubMed Id: 17476261. |
||
|
Photosystem I (Plant): Pisum sativum E Eukaryota, 3.30 Å
|
Amunts et al. (2010).
Amunts A, Toporik H, Borovikova A, & Nelson N (2010). Structure determination and improved model of plant photosystem I.
J Biol Chem 285 :3478-3486. PubMed Id: 19923216. doi:10.1074/jbc.M109.072645. |
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|
Photosystem I (plant): Pisum sativum E Eukaryota, 2.80 Å
|
Qin et al. (2015).
Qin X, Suga M, Kuang T, & Shen JR (2015). Photosynthesis. Structural basis for energy transfer pathways in the plant PSI-LHCI supercomplex.
Science 348 :989-995. PubMed Id: 26023133. doi:10.1126/science.aab0214. |
||
|
Photosystem II: Thermosynechococcus elongatus B Bacteria, 3.8 Å
|
Zouni et al. (2001).
Zouni A, Horst-Tobias W, Kern J, Fromme P, Krauss N, Saenger W, & Orth P (2001). Crystal structure of photosystem II from Synechococcus elongatus at 3.8 Å resolution.
Nature 409 :739-743. PubMed Id: 11217865. |
||
|
Photosystem II: Thermosynechococcus elongatus B Bacteria, 3.5 Å
Resolution sufficient to reveal oxygen-evolving center. |
|
Ferreira et al. (2004).
Ferreira KN, Iverson TM, Maghlaoui K, Barber J, & Iwata S (2004). Architecture of the photosynthetic oxygen-evolving center.
Science 303 :1831-1838. PubMed Id: 14764885. |
|
|
Photosystem II: Thermosynechococcus elongatus B Bacteria, 3.0 Å
Shows locations of 77 cofactors per monomer and provides info on Mn4Ca cluster. |
Loll et al. (2005).
Loll B, Kern J, Saenger W, Zouni A, & Biesiadka J (2005). Towards complete cofactor arrangement in the 3.0 A resolution structure of photosystem II.
Nature 438 :1040-1044. PubMed Id: 16355230. |
||
|
Photosystem II: Thermosynechococcus elongatus B Bacteria, 2.9 Å
Includes all 20 protein subunits and all 35 chlorophyll a molecules. Part 2 of coördinate file: 3BZ2 |
Guskov et al. (2009).
Guskov A, Kern J, Gabdulkhakov A, Broser M, Zouni A, & Saenger W (2009). Cyanobacterial photosystem II at 2.9-Å resolution and the role of quinones, lipids, channels and chloride.
Nat Struct Mol Biol 16 :334-342. PubMed Id: 19219048. |
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|
Photosystem II in S1 state by femtosecond x-ray laser: Thermosynechococcus elongatus B Bacteria, 5.00 Å
In S state after two flashes (S3), 5.50 Å: 4Q54 |
Kupitz et al. (2014).
Kupitz C, Basu S, Grotjohann I, Fromme R, Zatsepin NA, Rendek KN, Hunter MS, Shoeman RL, White TA, Wang D, James D, Yang JH, Cobb DE, Reeder B, Sierra RG, Liu H, Barty A, Aquila AL, Deponte D, Kirian RA, Bari S, Bergkamp JJ, Beyerlein KR, Bogan MJ, Caleman C, et al. & Fromme P (2014). Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser.
Nature 513 7517:261-265. PubMed Id: 25043005. doi:10.1038/nature13453. |
||
|
Photosystem II imaged using imperfect crystals (Bragg peaks only): Thermosynechococcus elongatus B Bacteria, 4.5 Å
pseudo-crystal refinement, 3.5 Å: 5E79 |
Ayyer et al. (2016).
Ayyer K, Yefanov OM, Oberthür D, Roy-Chowdhury S, Galli L, Mariani V, Basu S, Coe J, Conrad CE, Fromme R, Schaffer A, Dörner K, James D, Kupitz C, Metz M, Nelson G, Xavier PL, Beyerlein KR, Schmidt M, Sarrou I, Spence JC, Weierstall U, White TA, Yang JH, Zhao Y, Liang M, Aquila A, Hunter MS, Robinson JS, Koglin JE, Boutet S, Fromme P, Barty A, & Chapman HN (2016). Macromolecular diffractive imaging using imperfect crystals.
Nature 530 :202-206. PubMed Id: 26863980. doi:10.1038/nature16949. |
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|
Young et al. (2016).
Young ID, Ibrahim M, Chatterjee R, Gul S, Fuller FD, Koroidov S, Brewster AS, Tran R, Alonso-Mori R, Kroll T, Michels-Clark T, Laksmono H, Sierra RG, Stan CA, Hussein R, Zhang M, Douthit L, Kubin M, de Lichtenberg C, Vo Pham L, Nilsson H, Cheah MH, Shevela D, Saracini C, Bean MA, Seuffert I, Sokaras D, Weng TC, Pastor E, Weninger C, Fransson T, Lassalle L, Bräuer P, Aller P, Docker PT, Andi B, Orville AM, Glownia JM, Nelson S, Sikorski M, Zhu D, Hunter MS, Lane TJ, Aquila A, Koglin JE, Robinson J, Liang M, Boutet S, Lyubimov AY, Uervirojnangkoorn M, Moriarty NW, Liebschner D, Afonine PV, Waterman DG, Evans G, Wernet P, Dobbek H, Weis WI, Brunger AT, Zwart PH, Adams PD, Zouni A, Messinger J, Bergmann U, Sauter NK, Kern J, Yachandra VK, & Yano J (2016). Structure of photosystem II and substrate binding at room temperature.
Nature 540 :453-457. PubMed Id: 27871088. doi:10.1038/nature20161. |
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|
Photosystem II: Thermosynechococcus vulcanus B Bacteria, 3.7 Å
|
Kamiya & Shen (2003).
Kamiya N & Shen JR (2003). Crystal structure of oxygen-evolving photosystem II from Thermosynechococcus vulcanus at 3.7-Å resolution.
Proc Natl Acad Sci USA 100 :98-103. PubMed Id: 12518057. |
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Photosystem II, Br-substituted: Thermosynechococcus vulcanus B Bacteria, 3.7 Å
Br-substitution reveals location of chlorides. I-substituted, 4.0 Å: 3A0H |
Kawakami et al. (2009).
Kawakami K, Umena Y, Kamiya N, & Shen JR (2009). Location of chloride and its possible functions in oxygen-evolving photosystem II revealed by X-ray crystallography.
Proc Natl Acad Sci USA 106 :8567-8572. PubMed Id: 19433803. |
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|
Photosystem II: Thermosynechococcus vulcanus B Bacteria, 1.90 Å
Reveals the structure of the Mn4CaO5 cluster and all of their ligands. More than 1300 water molecules are observed in each monomer. |
Umena et al. (2011).
Umena Y, Kawakami K, Shen JR, & Kamiya N (2011). Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 Å;
Nature 473 :55-60. PubMed Id: 21499260. doi:10.1038/nature09913. |
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|
Photosystem II, Sr-substituted: Thermosynechococcus vulcanus B Bacteria, 2.10 Å
|
Koua et al. (2013).
Koua FH, Umena Y, Kawakami K, & Shen JR (2013). Structure of Sr-substituted photosystem II at 2.1 Å resolution and its implications in the mechanism of water oxidation.
Proc Natl Acad Sci USA 110 :3889-3894. PubMed Id: 23426624. doi:10.1073/pnas.1219922110. |
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|
Photosystem II by femtosecond X-ray pulses, data set 1: Thermosynechococcus vulcanus B Bacteria, 1.95 Å
Data set 2, 1.95 Å: 4UB8 |
Suga et al. (2015).
Suga M, Akita F, Hirata K, Ueno G, Murakami H, Nakajima Y, Shimizu T, Yamashita K, Yamamoto M, Ago H, & Shen J (2015). Native structure of photosystem II at 1.95 Å resolution viewed by femtosecond X-ray pulses.
Nature 517 :99-103. PubMed Id: 25470056. doi:10.1038/nature13991. |
||
|
Suga et al. (2017).
Suga M, Akita F, Sugahara M, Kubo M, Nakajima Y, Nakane T, Yamashita K, Umena Y, Nakabayashi M, Yamane T, Nakano T, Suzuki M, Masuda T, Inoue S, Kimura T, Nomura T, Yonekura S, Yu LJ, Sakamoto T, Motomura T, Chen JH, Kato Y, Noguchi T, Tono K, Joti Y, Kameshima T, Hatsui T, Nango E, Tanaka R, Naitow H, Matsuura Y, Yamashita A, Yamamoto M, Nureki O, Yabashi M, Ishikawa T, Iwata S, & Shen JR (2017). Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL.
Nature 543 :131-135. PubMed Id: 28219079. doi:10.1038/nature21400. |
|||
|
Photosystem II from a red alga: Cyanidium caldarium E Eukaryota, 2.77 Å
|
Ago et al. (2016).
Ago H, Adachi H, Umena Y, Tashiro T, Kawakami K, Kamiya N, Tian L, Han G, Kuang T, Liu Z, Wang F, Zou H, Enami I, Miyano M, & Shen JR (2016). Novel Features of Eukaryotic Photosystem II Revealed by Its Crystal Structure Analysis from a Red Alga.
J Biol Chem 291 :5676-5687. PubMed Id: 26757821. doi:10.1074/jbc.M115.711689. |
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Photosystem+Light-Harvesting Complex Supercomplex
|
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Photosystem II in complex with Light-Harvesting Complex II: Spinacia oleracea E Eukaryota, 3.2 Å
Cryo-EM structure |
Wei et al. (2016).
Wei X, Su X, Cao P, Liu X, Chang W, Li M, Zhang X, & Liu Z (2016). Structure of spinach photosystem II-LHCII supercomplex at 3.2?Å resolution.
Nature 534 :69-74. PubMed Id: 27251276. doi:10.1038/nature18020. |
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|
Photoprotection Proteins
These proteins limit photo-oxidative damage to plants |
|||
|
Fan et al. (2015).
Fan M, Li M, Liu Z, Cao P, Pan X, Zhang H, Zhao X, Zhang J, & Chang W (2015). Crystal structures of the PsbS protein essential for photoprotection in plants.
Nat Struct Mol Biol 22 :729-735. PubMed Id: 26258636. doi:10.1038/nsmb.3068. |
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Light-Harvesting Complexes
|
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Light Harvesting Complex: Rhodoblastus acidophilus B Bacteria, 2.50 Å
Former species name: Rhodopseudomonas acidophila |
Prince et al. (1997).
Prince SM, Papiz MZ, Freer AA, McDermott G, Hawthornthwaite-Lawless AM, Cogdell RJ, & Isaacs NW (1997). Apoprotein structure in the LH2 complex from Rhodopseudomonas acidophila strain 10050: modular assembly and protein pigment interactions.
J Mol Biol 268 :412-423. PubMed Id: 9159480. doi:10.1006/jmbi.1997.0966. See also: McDermott et al. (1995) McDermott G, Prince SM, Freer AA, Hawthornthwaite-Lawless AM, Papiz MZ, Cogdell RJ & Isaacs NW (1995). Crystal structure of an integral membrane light-harvesting complex from photosynthetic bacteria.
Nature 374 :517-521. doi:10.1038/374517a0. |
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Light-Harvesting Complex: Rhodoblastus acidophila B Bacteria, 2.0 Å
Former species name: Rhodopseudomonas acidophila |
Papiz et al. (2003).
Papiz MZ, Prince SM, Howard T, Cogdell RJ, & Isaacs NW (2003). The structure and thermal motion of the B800-850 LH2 complex from Rps.acidophila at 2.0A resolution and 100K: new structural features and functionally relevant motions.
J Mol Biol 278 :31303-31311. PubMed Id: 12595263. |
||
|
Light-Harvesting Complex: Rhodospirillum molischianum B Bacteria, 2.4 Å
|
Koepke et al. (1996).
Koepke J, Hu XC, Muenke C, Schulten K, & Michel H (1996). The crystal structure of the light-harvesting complex II (B800- 850) from Rhodospirillum molischianum.
Structure 4 :581-597. PubMed Id: 8736556. |
||
|
Light-Harvesting Complex LHC-II, Spinach Photosystem II: Spinacia oleracea E Eukaryota, 2.72 Å
|
Liu et al. (2004).
Liu Z, Yan H, Wang K, Kuang T, Zhang J, Gui L, An X, & Chang W (2004). Crystal structure of spinach major light-harvesting complex at 2.72 Å resolution.
Nature 428 :287-292. PubMed Id: 15029188. |
||
|
Light-Harvesting Complex CP29, Spinach Photosystem II: Spinacia oleracea E Eukaryota, 2.80 Å
|
Pan et al. (2011).
Pan X, Li M, Wan T, Wang L, Jia C, Hou Z, Zhao X, Zhang J, & Chang W (2011). Structural insights into energy regulation of light-harvesting complex CP29 from spinach.
Nat Struc Mol Biol 18 :309-315. PubMed Id: 21297637. |
||
|
Light-Harvesting Complex LHC-II, Pea Photosystem II: Pisum sativum E Eukaryota, 2.50 Å
|
Standfuss et al. (2005).
Standfuss J, Terwisscha van Scheltinga AC, Lamborghini M, Kühlbrandt W (2005). Mechanisms of photoprotection and nonphotochemical quenching in pea light-harvesting complex at 2.5 Å resolution.
EMBO J 24 :919-928. PubMed Id: 15719016. |
||
|
Photosynthetic Reaction Centers
|
|||
|
Photosynthetic Reaction Center: Blastochloris viridis B Bacteria, 2.3 Å
The first high-resolution crystallographic structure of a membrane protein Former species name: Rhodopseudomonas virdis |
Deisenhofer et al. (1985).
Deisenhofer J, Epp O, Miki K, Huber R, & Michel H (1985). Structure of the protein subunits in the photosynthetic reaction centre of Rhodospeudomonas viridis at 3 Å resolution.
Nature 318 :618-624. PubMed Id: 22439175. |
||
|
Photosynthetic Reaction Center: Blastochloris viridis B Bacteria, 1.86 Å
Lipidic sponge-phase structure. Reveals lipids on protein surface. Low x-ray dose structure, 1.95 Å: 2WJM |
Wöhri et al. (2009).
Wöhri AB, Wahlgren WY, Malmerberg E, Johansson LC, Neutze R, & Katona G (2009). Lipidic sponge phase crystal structure of a photosynthetic reaction center reveals lipids on the protein surface.
Biochemistry 48 :9831-9838. PubMed Id: 19743880. |
||
|
Photosynthetic Reaction Center: Blastochloris viridis B Bacteria, 3.50 Å
Structure determined by serial femtosecond crystallography |
Johansson et al. (2013).
Johansson LC, Arnlund D, Katona G, White TA, Barty A et al. (2013). Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography.
Nat Commun 4 :2911. PubMed Id: 24352554. doi:10.1038/ncomms3911. |
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|
Photosynthetic Reaction Center: Rhodobacter sphaeroides B Bacteria, 2.80 Å
|
Allen et al. (1987).
Allen JP, Feher G, Yeates TO, Komiya H, & Rees DC (1987). Structure of the reaction center from Rhodobacter sphaeroides R-26: the protein subunits.
Proc Natl Acad Sci USA 84 :6162-6166. PubMed Id: 2819866. See also: Allen et al. (1987). Allen JP, Feher G, Yeates TO, Komiya H, & Rees DC (1987). Structure of the reaction center from Rhodobacter sphaeroides R-26: the cofactors.
Proc Natl Acad Sci USA 84 :5730-5734. PubMed Id: 3303032. Yeates et al. (1988). Yeates TO, Komiya H, Chirino A, Rees DC, Allen JP, & Feher G (1988). Structure of the reaction center from Rhodobacter sphaeroides R-26 and 2.4.1: protein-cofactor (bacteriochlorophyll, bacteriopheophytin, and carotenoid) interactions.
Proc Natl Acad Sci USA 85 :7993-7997. PubMed Id: 3186702. |
||
|
Photosynthetic Reaction Center: Rhodobacter sphaeroides B Bacteria, 3.1 Å
|
Chang et al. (1991).
Chang CH, Elkabbani O, Tiede D, Norris J, & Schiffer M. (1991). Structure of the membrane-bound protein photosynthetic reaction center from Rhodobacter sphaeroides.
Biochemistry 30 :5352-5360. PubMed Id: 2036404. |
||
|
Photosynthetic Reaction Center: Rhodobacter sphaeroides B Bacteria, 3.00 Å
M202HL mutant, 3.00 Å: 1PST |
Chirino et al. (1994).
Chirino AJ, Lous EJ, Huber M, Allen JP, Schenck CC, Paddock ML, Feher G, & Rees DC (1994). Crystallographic analyses of site-directed mutants of the photosynthetic reaction center from Rhodobacter sphaeroides.
Biochemistry 33 :4584-4593. PubMed Id: 8161514. doi:10.1021/bi00181a020. |
||
|
Photosynthetic Reaction Center: Rhodobacter sphaeroides (dark state) B Bacteria, 2.2 Å
Illuminated state, 2.60 Å 1AIG |
Stowell et al. (1997).
Stowell MH, McPhillips TM, Rees DC, Soltis SM, Abresch E, & Feher G (1997). Light-induced structural changes in photosynthetic reaction center: implications for mechanism of electron-proton transfer.
Science 276 :812-816. PubMed Id: 9115209. |
||
|
Photosynthetic Reaction Center: Rhodobacter sphaeroides B Bacteria, 2.35 Å
Lipidic cubic phase crystallization. |
Katona et al. (2003).
Katona K, Andréasson U, Landau EM, Andr?asson L-K, & Neutze R (2003). Lipidic cubic phase crystal structure of the photosynthetic reaction centre from Rhodobacter sphaeroides at 2.35 Å.
J Mol Biol 331 :681-692. PubMed Id: 12899837. |
||
|
Photosynthetic Reaction Center: Rhodobacter sphaeroides B Bacteria, 1.87 Å
pH 8 neutral state. pH 8 charge-separated state, 2.07 Å: 2J8D |
Koepke et al. (2007).
Koepke J, Krammer EM, Klingen AR, Sebban P, Ullmann GM, & Fritzsch G. (2007). pH modulates the quinone position in the photosynthetic reaction center from Rhodobacter sphaeroides in the neutral and charge separated states.
J Mol Biol 371 :396-409. PubMed Id: 17570397. |
||
|
Photosynthetic Reaction Center, Zn-substituted: Rhodobacter sphaeroides B Bacteria, 2.85 Å
M(L214H) variant, 2.85 Å: 4N7L |
Saer et al. (2014).
Saer RG, Pan J, Hardjasa A, Lin S, Rosell F, Mauk AG, Woodbury NW, Murphy ME, & Beatty JT (2014). Structural and kinetic properties of Rhodobacter sphaeroides photosynthetic reaction centers containing exclusively Zn-coordinated bacteriochlorophyll as bacteriochlorin cofactors.
Biochim Biophys Acta 1837 :366-374. PubMed Id: 24316146. doi:10.1016/j.bbabio.2013.11.015. |
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|
Photosynthetic Reaction Center: Thermochromatium tepidum B Bacteria, 2.2 Å
|
Nogi et al. (2000).
Nogi T, Fathir I, Kobayashi M, Nozawa T, & Miki K (2000). Crystal structures of photosynthetic reaction center and high-potential iron-sulfur protein from Thermochromatium tepidum: thermostability and electron transfer.
Proc Natl Acad Sci USA 97 :6031-6036. PubMed Id: 11095707. |
||
|
Light-Harvesting+Reaction Center Complexes
|
|||
|
LH1-RC complex, P21 crystal form: Thermochromatium tepidum B Bacteria, 3.01 Å
Supersedes 3WMN. C2 crystal form. 3.01 Å: 3WMM |
Niwa et al. (2014).
Niwa S, Yu LJ, Takeda K, Hirano Y, Kawakami T, Wang-Otomo ZY, & Miki K (2014). Structure of the LH1-RC complex from Thermochromatium tepidum at 3.0 Å.
Nature 508 7495:228-232. PubMed Id: 24670637. doi:10.1038/nature13197. |
||
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mpstruc Taxonomic Domain data are derived from the UniProt Knowledgebase, which is based on the NCBI taxonomy database. These taxa can be searched for using 'Text Search of Table', above. The following icons are used in the table, as appropriate:
The table provides useful information about integral membrane proteins whose crystallographic, or sometimes NMR, structures have been determined to a resolution sufficient to identify TM helices of helix-bundle membrane proteins (typically 4 - 4.5 Å). It is based upon Reference is made to all of the protein types whose structures have been determined. We have attempted to make the database as inclusive as possible. If you find errors or omissions, please send a message to .
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This database emphasizes structures determined by diffraction methods, although some NMR structures are included. A comprehensive list of NMR-determined structures is available from Dror Warschawski.
Useful Membrane Protein Structure Resources
Progress of membrane protein structure determination. See also White (2009)
Structural Biology Knowledgebase Membrane Protein Hub
Research Collaboratory for Structural Bioinformatics (RCSB)
Bilayer Insertion of Membrane Proteins (Structural Bioinformatics and Computational Biochemistry Unit, Oxford)
Protein Data Bank of Transmembrane Proteins (Institute of Enzymology, Budapest)
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