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- Mpstruc XML interface updated: We have introduced URLs that provide direct access to XML representations of mpstruc data without having to visit the mpstruc web page. These URLs allow users' software tools to access the data directly. See the new expandable XML Representations section of the mpstruc page.
- XML data representations now available: 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.
- Queries directly to the mpstruc database now possible: There are other ways of viewing the data in the mpstruc database besides the hierarchical view presented on the main mpstruc web page. From the link here, on this page, you can make a variety of queries on the database.
Latest new protein entered: 15 May 2013 at 21:33 PDT.
Last database update: 15 May 2013 at 21:33 PDT
- ECF transporter complex: Lactobacillus brevis, 3.53 Å
- Folate ECF transporter complex: Lactobacillus brevis, 3.00 Å
- Smoothened (SMO) receptor with bound antagonist, LY2940680: Homo sapiens, 2.45 Å
- 5-HT2B serotonin receptor with bound ergotamine: Homo sapiens, 2.70 Å
- 5-HT1B serotonin receptor with bound ergotamine: Homo sapiens, 2.70 Å
- PiPT high-affinity phosphate transporter: Piriformospora indica, 2.90 Å
Unique proteins
in database = 402; number of coördinate files in database = 1253.
(Counts do not include pre-publication structures)
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.
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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Checkbox is enabled when Fuzziness Threshold is set to 0. When this is checked, the Search Text value is treated as a regular expression to search with. A quick summary of regular expressions is available here, and a gentle introduction is available here. |
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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. |
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mpstruc database queries
Links to the Protein Data Bank Site
Links to the Structural Biology Knowledgebase Site
| Protein | 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, 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. |
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Ram Prostaglandin H2 synthase-1 (COX-1): Ovis aries, 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. |
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Ram Prostaglandin H2 synthase-1 (COX-1): Ovis aries, 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. |
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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. |
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Ram Prostaglandin H2 synthase-1 (COX-1): Ovis aries, 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. |
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Ram Prostaglandin H2 synthase-1 (COX-1): Ovis aries, 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. |
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Ram Prostaglandin H2 synthase-1 (COX-1): Ovis aries, 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. |
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Ram Prostaglandin H2 synthase-1 (COX-1): Ovis aries (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. |
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Cyclooxygenase-2: Mus Musculus, 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. |
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Fatty acid α-dioxygenase (α-DOX): Arabidopsis thaliana (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; doi:10.1021/bi400013k. |
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Squalene-Hopene Cyclases
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Squalene-hopene cyclase: Alicyclobacillus acidocaldarius, 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. |
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Oxidases
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Monoamine Oxidase B: Human mitochondrial outer membrane (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. |
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Monoamine Oxidase B with bound Isatin: Human mitochondrial outer membrane (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. |
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Monoamine Oxidase A: Rat mitochondrial outer membrane (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. |
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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. |
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Monoamine Oxidase A with bound Harmine: Human mitochondrial outer membrane (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. |
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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; doi:10.1073/pnas.1218386110. |
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Hydrolases
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Fatty acid amide hydrolase: Rattus norvegicus, 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. |
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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; doi:10.1073/pnas.1206072109. |
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LpxI phosphodiester hydrolase for lipid A biosynthesis: Caulobacter crescentus (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; doi:10.1038/nsmb.2393. |
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Oxidoreductases (Monotopic)
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Sulfide:quinone oxidoreductase in complex with decylubiquinone: Aquifex aeolicus, 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. |
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Electron Transfer Flavoprotein-ubiquinone oxidoreductase (ETF-QO) with bound UQ: Sus scrofa, 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. |
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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; 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; doi:10.1038/nature11541. |
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Glycosyltransferases
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Peptidoglycan Glycosyltransferase: Staphylococccus aureus, 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. |
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Peptidoglycan Glycosyltransferase penicillin-binding protein 1a (PBP1a): Aquifex aeolicus (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. |
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Peptidoglycan Glycosyltransferase penicillin-binding protein 1b (PBP1b): Escherichia coli, 2.16 Å
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. |
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Monofunctional glycosyltransferase WaaA, substrate free: Aquifex aeolicus (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; doi:10.1073/pnas.1119894109. |
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Monofunctional glycosyltransferase in complex with Lipid II analog: Staphylococcus aureus (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; doi:10.1073/pnas.1203900109. |
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Peptidases
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Signal Peptidase (SPase) in complex with a β-lactam inhibitor: Escherichia coli, 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. |
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Signal Peptidase (SPase), apoprotein: Escherichia coli, 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. |
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Signal Peptidase (SPase) in complex with a lipopeptide inhibitor: Escherichia coli, 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. |
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Signal Peptide Peptidase (SppA), native protein: Eschericia coli, 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. |
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Signal Peptide Peptidase (SppA): Bacillus subtilis (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; doi:10.1016/j.jmb.2012.03.020. |
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Meprin β sheddase (metalloproteinase), pro-form: Homo sapiens (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; doi:10.1073/pnas.1211076109. |
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Dehydrogenases
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Glycerol-3-phosphate dehydrogenase (GlpD, native): Escherichia coli, 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. |
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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, 1.70 Å
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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. |
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Dihydroorotate Dehydrogenase: Escherichia coli, 1.90 Å
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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. |
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Dihydroorotate Dehydrogenase in complex with atovaquone: Rattus rattus (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. |
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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. |
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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. |
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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. |
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ADP-Ribosylation Factors
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ADP-ribosylation factor (ARF1), myristoylated: Saccharomyces cerevisiae (expressed in E. coli), NMR Structure
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Liu et al. (2009)
Liu Y, Kahn RA, & Prestegard JH (2009). Structure and Membrane Interaction of Myristoylated ARF1.
Structure 17:79-87. |
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ADP-ribosylation factor (ARF1*GTP), myristoylated: Saccharomyces cerevisiae (expressed in E. coli), NMR Structure
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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. |
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Isomerases
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RPE65 visual cycle retinoid isomerase: Bos taurus, 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. |
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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. |
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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, 1.8 Å
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Weiss & Schulz (1992)
Weiss MS & Schulz GE (1992). Structure of porin refined at 1.8 Å resolution.
J. Mol. Biol. 227:493-509. |
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Porin: Rhodopeudomonas blastica, 1.96 Å
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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; 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; doi:10.1002/pro.5560030108. |
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Schmid et al. (1998)
Schmid B, Maveyraud L, Krömer M, & Schulz GE (1998). Porin mutants with new channel properties.
Protein Sci 7:1603-1611; doi:10.1002/pro.5560070714. |
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Porin: Rhodopseudomonas blastica (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; doi:10.1093/protein/15.10.799. |
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OmpK36 osmoporin: Klebsiella pneumoniae, 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. |
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|
Omp32 anion-selective porin: Comamonas acidovorans, 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. |
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Omp32 anion-selective porin: Delftia acidovorans, 1.5 Å
With bound malate, 1.45 Å: 2FGQ |
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. |
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OmpF Porin: Escherichia coli, 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. |
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OmpF Porin from colicin-resistant E. coli: Escherichia coli, 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. |
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|
OmpF Porin: Escherichia coli, 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; 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; doi:10.1074/jbc.271.34.20669 . |
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OmpF Porin, D74A mutant: Escherichia coli (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; 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; doi:10.1021/bi010046k. |
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|
OmpF Porin: Escherichia coli, 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. |
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|
OmpF porin with a synthetic dibenzo-18-crown-6: Escherichia coli, 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; doi:10.1002/anie.200900457. |
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|
OmpF Porin in complex with colicin peptide OBS1: Escherichia coli, 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. |
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|
OmpF Porin: Escherichia coli, 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; doi:10.1016/j.jmb.2009.11.042. |
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|
OmpF Porin in presence of foscholine-12: Escherichia coli, 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; doi:10.1002/pro.369. |
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|
OmpF Porin: Salmonella typhi (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; doi:10.1016/j.jsb.2012.04.005. |
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|
OmpC Osmoporin: Escherichia coli, 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. |
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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; doi:10.1371/journal.pone.0025825. |
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|
OmpG *monomeric* porin: Escherichia coli, 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. |
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|
OmpG *monomeric* porin in open state: Escherichia coli, 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. |
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|
OmpG *monomeric* porin: Escherichia coli, 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. |
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|
PhoE: Escherichia coli, 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. |
||
|
LamB Maltoporin: Salmonella typhimurium, 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. |
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|
LamB Maltoporin: Escherichia coli, 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. |
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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. |
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|
LamB Maltoporin in complex with sucrose: Escherichia coli, 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. |
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|
ScrY sucrose-specific porin: Salmonella typhimurium, 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. |
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|
MspA mycobacterial porin: Mycobacterium smegmatis, 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. |
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|
OprP phosphate-specific transporter: Pseudomonas aeruginosa, 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. |
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|
OprB carbohydrate-specific transporter at high pH: Pseudomonas putida (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; doi:10.1074/jbc.M112.408518. |
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|
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. |
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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 (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. |
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|
OccD1 (OprD) basic amino acid uptake channel: Pseudomonas aeruginosa (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; doi:10.1371/journal.pbio.1001242. |
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|
OccD2 (OpdC) basic amino acid uptake channel: Pseudomonas aeruginosa (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; doi:10.1371/journal.pbio.1001242. |
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|
OccD3 (OpdP) basic amino acid uptake channel: Pseudomonas aeruginosa (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; doi:10.1371/journal.pbio.1001242. |
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|
OccK1 (OpdK) benzoate channel: Pseudomonas aeruginosa (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. |
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|
OccK1 (OpdK) benzoate channel: Pseudomonas aeruginosa (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; doi:10.1371/journal.pbio.1001242. |
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|
OccK2 (OpdF) glucuronate channel: Pseudomonas aeruginosa (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; doi:10.1371/journal.pbio.1001242. |
||
|
OccK3 (OpdO) aromatic hydrocarbon channel: Pseudomonas aeruginosa (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; doi:10.1371/journal.pbio.1001242. |
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|
OccK4 (OpdL) aromatic hydrocarbon channel: Pseudomonas aeruginosa (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; doi:10.1371/journal.pbio.1001242. |
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|
OccK5 (OpdH) aromatic hydrocarbon channel: Pseudomonas aeruginosa (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; doi:10.1371/journal.pbio.1001242. |
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|
OccK6 (OpdQ) aromatic hydrocarbon channel: Pseudomonas aeruginosa (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; doi:10.1371/journal.pbio.1001242. |
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|
BenF-like Porin (putative) benzoate channel: Pseudomonas fluorescens, 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. |
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Beta-Barrel Membrane Proteins: Monomeric/Dimeric
|
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TolC outer membrane protein: Escherichia coli, 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. |
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TolC outer membrane protein, ligand blocked: Escherichia coli, 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. |
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|
TolC outer membrane protein (Y362F, R367E), partially open state: Escherichia coli, 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. |
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|
VceC outer membrane protein: Vibrio cholerae, 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. |
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OprM drug discharge outer membrane protein: Pseudomonas aeruginosa, 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. |
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|
OprM drug discharge outer membrane protein: Pseudomonas aeruginosa (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. |
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|
CusC heavy metal discharge outer membrane protein: Escherichia coli, 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; doi:10.1371/journal.pone.0015610. |
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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. |
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BtuB with bound colicin E3 R-domain: Escherichia coli, 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. |
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|
apo BtuB by in meso crystallization: Escherichia coli, 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. |
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BtuB in complex with TonB: Escherichia coli, 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. |
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|
BtuB with bound colicin E2 R-domain: Escherichia coli, 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. |
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|
apo BtuB V10R1 spin-labeled: Escherichia coli, 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; 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, 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. |
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|
OmpA: Escherichia coli, 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. |
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|
OmpA: Escherichia coli, 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. |
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|
OmpA: Escherichia coli, 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. |
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OmpA with four shortened loops: Escherichia coli, 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. |
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|
OmpA: Klebsiella pneumoniae (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; doi:10.1016/j.jmb.2008.10.021. |
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OmpT outer membrane protease: Escherichia coli, 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. |
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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. |
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|
OmpW outer membrane protein: Escherichia coli, 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. |
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OprG outer membrane protein: Pseudomonas aeruginosa (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; doi:10.1371/journal.pone.0015016. |
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OprH, outer membrane protein H: Pseudomonas aeruginosa (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; doi:10.1074/jbc.M111.280933. |
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OmpX: Escherichia coli, 1.9 Å
Structure at 2.1 Å, 1QJ9 |
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. |
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OmpX: Escherichia coli, 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. |
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OmpX: Escherichia coli, 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. |
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OmpX in optimized nanodiscs: Escherichia coli, 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; doi:10.1021/ja310901f. |
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Ail adhesion protein: Yersinia pestis (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; doi:10.1016/j.str.2011.08.010. |
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TtoA Outer Membrane Protein (OMP): Thermus thermophilus HB27, 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. |
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OmpLA (PldA) outer membrane phospholipase A monomer: Escherichia coli, 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. |
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OmpLA (PldA) outer membrane phospholipase A monomer with Ca++: Escherichia coli, 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. |
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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. |
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OpcA adhesin protein: Neisseria meningitidis, 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. |
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OpcA adhesin protein: Neisseria meningitidis (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; doi:10.1002/prot.21841. |
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NspA surface protein: Neisseria meningitidis, 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. |
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NanC Porin, model for KdgM porin family: Escherichia coli, 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. |
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PagL LPS 3-O-deacylase: Pseudomonas aeruginosa, 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; doi:10.1073/pnas.0509392103. |
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LpxR lipid A deacylase: Salmonella typhimurium (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; doi:10.1073/pnas.0813064106 . |
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PagP outer membrane palimitoyl transferease: Escherichia coli, 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. |
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PagP outer membrane palimitoyl transferease: Escherichia coli, 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. |
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PagP outer membrane palimitoyl transferease crystallized from SDS/Co-solvent: Escherichia coli, 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. |
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FadL long-chain fatty acid transporter: Escherichia coli, 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. |
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FadL long-chain fatty acid transporter A77E/S100R mutant: Escherichia coli, 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. |
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FadL long-chain fatty acid transporter D348R mutant: Escherichia coli, 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; doi:10.1073/pnas.1018532108. |
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FadL homologue long-chain fatty acid transporter: Pseudomonas aeruginosa (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. |
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FauA alcaligin outer membrane transporter: Bordetella pertusssis (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. |
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TodX hydrocarbon transporter: Pseudomonas putida, 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. |
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TbuX hydrocarbon transporter: Ralstonia pickettii, 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. |
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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. |
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FhuA, Ferrichrome-iron receptor without ligand: Escherichia coli, 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. |
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FhuA: Escherichia coli, 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. |
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FhuA-AW140-LPS: Escherichia coli, 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. |
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FhuA in complex with albomycin: Escherichia coli, 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. |
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FhuA in complex with lipopolysaccharide and rifamycin CGP4832: Escherichia coli, 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. |
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FhuA in complex withTonB: Escherichia coli, 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. |
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FepA, Ferric enterobactin receptor: Escherichia coli, 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. |
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FecA, siderophore transporter: Escherichia coli, 2.0 Å
Structure at 2.5 Å: 1KMP |
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. |
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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. |
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FecA, siderophore transporter periplasmic signalling domain: Escherichia coli, 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. |
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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. |
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FptA, pyochelin outer membrane receptor: Pseudomonas aeruginosa, 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. |
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FpvA, Pyoverdine receptor: Pseudomonas aeruginosa, 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. |
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FpvA, Pyoverdine receptor (apo form): Pseudomonas aeruginosa, 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. |
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FpvA, Full-length structure bound to iron-pyoverdine: Pseudomonas aeruginosa, 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. |
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AlgE alginate export protein: Pseudomonas aeruginosa (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; doi:10.1073/pnas.1104984108. |
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P pilus usher translocation domain, PapC130-640: Escherichia coli, 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. |
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P pilus FimD usher bound to FimC:FimH substrate: Escherichia coli, 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; doi:10.1038/nature10109. |
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P pilus FimD usher in complex with FimC:FimF:FimG:FimH: Escherichia coli, 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; doi:10.1038/nature12007. |
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Transferrin binding protein A (TbpA) in complex with human transferrin: Neisseria meningitidis serogroup b (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; doi:10.1038/nature10823. |
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Outer Membrane Autotransporters
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NalP autotransporter translocator domain: Neisseria meningitidis (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. |
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Hia1022-1098 trimeric autotransporter: Haemophilus influenzae (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. |
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EspP autotransporter, post-cleavage state: Escherichia coli, 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. |
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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; doi:10.1016/j.jmb.2011.10.049. |
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EspP autotransporter passenger domain: Escherichia coli, 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; doi:10.1016/j.jmb.2011.09.028. |
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Hbp (hemoglobin protease) self-cleaving autotransporter with truncated passenger: Escherichia coli, 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; doi:10.1016/j.jmb.2010.06.068. |
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Hbp (hemoglobin protease) full-length passenger domain: Escherichia coli, 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; doi:10.1074/jbc.M412885200. |
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EstA Autotransporter, full length: Pseudomonas aeruginosa (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. |
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IcsA autotransporter (autochaperone region only): Shigella flexneri (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 ; doi:10.1128/JB.00790-10. |
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Intimin outer membrane β-domain: Escherichia coli, 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; doi:10.1016/j.str.2012.04.011. |
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Intimin C-terminal passenger domain in complex with receptor: Escherichia coli, 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; 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. |
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Invasin outer membrane β-domain: Yersinia pseudotuberculosis (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; doi:10.1016/j.str.2012.04.011. |
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Invasin C-terminal passenger domain: Yersinia pseudotuberculosis (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. |
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YadA trimeric adhesin autotransporter: Yersinia enterocolitica subsp. enterocolitica 8081 (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. |
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Omp85-TpsB Outer Membrane Transporter Superfamily
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FhaC Filamentous Hemagglutinin Transporter: Bordetella pertussis (expressed in E. coli), 3.15 Å
The first outer membrane protein from the Omp85–two-partner secretion B (TpsB) superfamily |
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. |
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FhaC Filamentous Hemagglutinin Transporter, R450A mutant: Bordetella pertussis (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; doi:10.1111/j.1742-4658.2010.07881.x. |
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TeOmp85-N POTRA domains: Thermosynechococcus elongatus (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. |
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anaOmp85-N POTRA domains (hexagonal crystals): Anabaena sp. PCC7120 (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. |
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BamA21-351 POTRA domains (periplasmic fragment, P212121): Escherichia coli, 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. |
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BamA21-410 POTRA domains (periplasmic fragment): Escherichia coli, 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. |
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BamA21-174 POTRA domains 1 and 2: Escherichia coli, 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. |
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BamA264-424 POTRA domains 4 and 5: Escherichia coli, 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. |
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BamA266-420 POTRA domains 4 and 5: Escherichia coli, 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; doi:10.1107/S1744309111014254. |
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BamB component of the Bam β-barrel assembly machine: Escherichia coli, 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. |
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BamB component of the Bam β-barrel assembly machine: Escherichia coli, 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. |
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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. |
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BamB component of the Bam β-barrel assembly machine: Escherichia coli, 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; doi:10.1074/jbc.M111.238931. |
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BamB component of the Bam β-barrel assembly machine: Escherichia coli, 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; doi:10.1107/S0907444912023141. |
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BamC component of the Bam β-barrel assembly machine: Escherichia coli, 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; doi:10.1074/jbc.M111.238931. |
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BamC component of the Bam β-barrel assembly machine: Escherichia coli, 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; 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, 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; 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, 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; doi:10.1107/S174430911103363X. |
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BamD component of the Bam β-barrel assembly machine: Rhodothermus marinus (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; doi:10.1016/j.jmb.2011.03.035. |
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BamD component of the Bam β-barrel assembly machine: Escherichia coli, 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; doi:10.1074/jbc.M111.238931. |
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BamD component of the Bam β-barrel assembly machine: Escherichia coli, 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; doi:10.1107/S0907444911051031. |
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BamE component of the Bam β-barrel assembly machine: Escherichia coli, 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. |
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BamE component of the Bam β-barrel assembly machine: Escherichia coli, 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; doi:10.1074/jbc.M111.238931. |
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BamCD complex of the Bam β-barrel assembly machine: Escherichia coli, 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; doi:10.1074/jbc.M111.298166. |
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Beta-Barrel Membrane Proteins: Mitochondrial Outer Membrane
|
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VDAC-1 voltage dependent anion channel: Human (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. |
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VDAC-1 voltage dependent anion channel: Human (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. |
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|
VDAC-1 voltage dependent anion channel: Murine (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. |
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Adventitious Membrane Proteins: Beta-sheet Pore-forming Toxins
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α-hemolysin: Staphylococcus aureus, 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. |
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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; doi:10.1073/pnas.0914229107 . |
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γ-hemolysin composed of LukF and Hlg2: Staphylococcus aureus (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; doi:10.1073/pnas.1110402108. |
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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. |
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Perfringolysin O (PFO) protomer: Clostridium perfringens (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. |
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|
Anthrax Protective Antigen (PA) and Lethal Factor (LF) Prechannel Complex: Bacillus anthraciss (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. |
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Lymphocyte preforin monomer: Mus musculus (expressed in S. frugiperda), 2.75 Å
The multimeric pore structure has been visualized by cyo-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. |
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|
Cytolysin pore-forming toxin: Vibrio cholerae (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; doi:10.1073/pnas.1017442108. |
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|
Cytolysin pore-forming toxin protomer: Vibrio cholerae (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; doi:10.1016/j.jmb.2005.05.045. |
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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, 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. |
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FraC eukaryotic pore-forming toxin from sea anemone: Actinia fragacea, 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. |
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Dermicidin hexameric anti-microbial peptide channel: Homo sapiens (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; doi:10.1073/pnas.1214739110. |
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Outer Membrane Proteins
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Wza translocon for capsular polysaccharides: Escherichia coli, 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. |
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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. |
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Type IV outer membrane secretion complex: Escherichia coli, 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. |
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Bacterial and Algal Rhodopsins
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Bacteriorhodopsin (BR): Halobacterium salinarium, 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. |
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Bacteriorhodopsin (BR): Halobacterium salinarium, 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. |
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Bacteriorhodopsin (BR): Halobacterium salinarium, 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. |
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Bacteriorhodopsin (BR): Halobacterium salinarium, 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. |
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|
Bacteriorhodopsin (BR): Halobacterium salinarium, 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. |
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|
Bacteriorhodopsin (BR), K intermediate: Halobacterium salinarium, 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. |
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Bacteriorhodopsin (BR), K intermediate (illuminated): Halobacterium salinarium, 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. |
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Bacteriorhodopsin (BR): Halobacterium salinarium, 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. |
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Bacteriorhodopsin (BR): Halobacterium salinarium, 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. |
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Bacteriorhodopsin (BR), D96N in bR state: Halobacterium salinarium, 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. |
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Bacteriorhodopsin in ground state: Halobacterium salinarium, 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; doi:10.1016/j.jmb.2011.04.038. |
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Bacteriorhodopsin phototaxis signalling mutant (A215T): Halobacterium sp. nrc-1 (expressed in Halobacterium salinarum), 3.01 Å
This mutant allows 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; doi:10.1016/j.jmb.2011.11.025. |
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Bacteriorhodopsin (BR); D96/F171C/F219L mutant: Halobacterium salinarium, 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; doi:10.1016/j.str.2012.12.018. |
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Halorhodopsin (HR): Halobacterium salinarium, 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. |
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Halorhodopsin (HR): Natronomonas pharaonis, 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. |
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Sensory Rhodopsin I (SRI): Anabaena (Nostoc) sp. PCC7120, 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. |
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Sensory Rhodopsin II (SRII): Natronomonas pharaonis, 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. |
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Sensory Rhodopsin II (SRII): Natronomonas pharaonis (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. |
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Sensory Rhodopsin II (SRII) with transducer: Natronomonas pharaonis (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. |
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|
Sensory Rhodopsin II (SRII): Natronomonas pharaonis (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. |
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|
Sensory Rhodopsin II (SRII) in active state: Natronomonas pharaonis (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; doi:10.1016/j.jmb.2011.07.022. |
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Archaerhodopsin-1 (aR-1): Halorubrum sp. aus-1, 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. |
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Archaerhodopsin-2 (aR-2): Haloroubrum sp. aus-2, 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. |
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|
Archaerhodopsin-2 (aR-2): Haloroubrum sp. aus-2, 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. |
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Xanthorhodopsin: Salinibacter ruber, 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. |
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Proteorhodopsin (green-light absorbing) : Uncultured marine gamma proteobacterium ebac31a08 (expressed in E. coli-based cell-free expression system), NMR Structure
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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; doi:10.1002/anie.201105648. |
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Acetabularia Rhodopsin II (ARII): Acetabularia acetabulum (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; doi:10.1016/j.jmb.2011.06.028. |
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Channelrhodopsin (ChR) chimera between ChR1 & ChR2: Chlamydomonas reinhardtii (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; doi:10.1038/nature10870. |
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G Protein-Coupled Receptors (GPCRs)
GPCR Network Home Page |
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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. |
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Rhodopsin: Bovine Rod Outer Segment, 2.6 Å
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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. |
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Rhodopsin: Bovine Rod Outer Segment, 2.65 Å
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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. |
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Rhodopsin: Bovine Rod Outer Segment, 2.2 Å
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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. |
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Rhodopsin: Bovine Rod Outer Segment (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. |
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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. |
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Rhodopsin in ligand-free state (opsin): Bovine Rod Outer Segment, 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. |
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Rhodopsin in Meta II state: Bovine Rod Outer Segment, 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. |
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Rhodopsin, Ops*-GαCT peptide complex: Bovine Rod Outer Segment, 3.2 Å
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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. |
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Rhodopsin in constitutively active meta-II state: Bos taurus (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; doi:10.1073/pnas.1114089108. |
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Rhodopsin, Squid: Todarodes pacificus, 2.50 Å
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Murakami & Kouyama (2008)
Murakami M & Kouyama T (2008). Crystal structure of squid rhodopsin.
Nature 453:363-367. |
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Rhodopsin, Squid: Todarodes pacificus, 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. |
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Rhodopsin, Squid; 9-cis isorhodopsin (Iso): Todarodes pacificus, 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; doi:10.1016/j.jmb.2011.08.044. |
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β1 adrenergic receptor (engineered): Meleagris gallopavo (turkey) (expressed in Trichoplusia ni), 2.7 Å
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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. |
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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. |
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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; doi:10.1073/pnas.1100185108. |
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β1 adrenergic receptor (engineered) with bound carvedilol: Meleagris gallopavo (turkey) (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; doi:10.1016/j.str.2012.03.014. |
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β1 adrenergic receptor oligomer, basal state: Meleagris gallopavo (expressed in Trichoplusia ni), 3.50 Å
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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; doi:10.1038/nsmb.2504. |
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β2 adrenergic receptor: Homo sapiens (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. |
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Methylated β2 adrenergic receptor: Homo sapiens (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. |
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β2 adrenergic receptor (engineered): Homo sapiens (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. |
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β2 adrenergic receptor (engineered): Homo sapiens (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. |
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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; doi:10.1021/ja105108q. |
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β2 adrenergic receptor (engineered) in nanobody-stabilized active state: Homo sapiens (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. |
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β2 adrenergic receptor (engineered) with irreversibly-bound agonist: Homo sapiens (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. |
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β2 adrenergic receptor-Gs protein complex: Homo sapiens (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; doi:10.1038/nature10361. |
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A2A adenosine receptor: Homo sapiens (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. |
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A2A adenosine receptor with bound agonist (UK-432097): Homo sapiens (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; doi:10.1126/science.1202793. |
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A2A adenosine receptor (engineered) with bound adenosine: Homo sapiens (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; 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; doi:10.1016/j.str.2011.06.014. |
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A2A adenosine receptor in complex inverse-agonist antibody: Homo sapiens (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; doi:10.1038/nature10750. |
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A2A adenosine receptor in complex with ZM241385: Homo sapiens (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; doi:10.1126/science.1219218. |
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CXCR1 chemokine receptor in phospholipid bilayers: Homo sapiens (expressed in E. coli), NMR Structure
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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; doi:10.1038/nature11580. |
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CXCR4 chemokine receptor complexed with IT1t antagonist: Homo sapiens (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. |
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Dopamine D3 receptor complexed with D2/D3-selective antagonist: Homo sapiens (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. |
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Histamine H1 receptor, complexed with doxepin: Homo sapiens (expressed in Pichia pastoris), 3.10 Å
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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; doi:10.1038/nature10236. |
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Sphingosine 1-phosphate receptor: Homo sapiens (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; doi:10.1126/science.1215904. |
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M2 human muscarinic acetylcholine receptor bound to an antagonist: Homo sapiens (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; doi:10.1038/nature10753. |
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M3 muscarinic acetylcholine receptor: Rattus norvegicus (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; doi:10.1038/nature10867. |
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κ-opioid receptor in complex with JDTic: Homo sapiens (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; doi:10.1038/nature10939. |
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μ-opioid receptor bound to a morphinan antagonist: Mus musculus (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; doi:10.1038/nature10954. |
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δ-opioid receptor in complex with naltrindol: Mus musculus (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; doi:10.1038/nature11111. |
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Nociceptin/orphanin FQ (N/OFQ) receptor with bound peptide: Homo sapiens (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; doi:10.1038/nature11085. |
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NTS1 neurotensin receptor in complex with neurotensin: Rattus norvegicus (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; doi:10.1038/nature11558. |
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Protease-activated receptor 1 (PAR1) bound with antagonist vorapaxar: Homo sapiens (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; 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; doi:10.1016/j.bbamem.2013.02.005. |
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5-HT1B serotonin receptor with bound ergotamine: Homo sapiens (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; doi:10.1126/science.1232807. |
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5-HT2B serotonin receptor with bound ergotamine: Homo sapiens (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; doi:10.1126/science.1232808. |
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Smoothened (SMO) receptor with bound antagonist, LY2940680: Homo sapiens (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; doi:10.1038/nature12167. |
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Autonomously Folding "Membrane Proteins" (Sec-independent)
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Mistic membrane-integrating protein: Bacillus subtilis, 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. |
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Virus Coat Proteins
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M13 Major Coat Protein in Dodecylphosphocholine micelles: Enterobacteria phage m13 (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; doi:10.1006/jmbi.1998.1860. |
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Pf1 Major Coat Protein: Pseudomonas phage Pf1, 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; doi:10.1016/j.jmb.2004.06.038. |
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Pf1 Major Coat Protein in lipid bilayers: Pseudomonas phage Pf1, 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; doi:10.1016/j.bpj.2010.06.009. |
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fd bacteriophage pVIII coat protein in lipid bilayers: Enterobacteria phage fd, 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; doi:10.1110/ps.0211503. |
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|
fd bacteriophage pVIII coat protein in SDS micelles: Enterobacteria phage fd, 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; doi:10.1006/jmbi.1997.1114. |
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Glycoproteins
|
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|
Glycophorin A transmembrane-domain dimer: Homo sapiens (expressed in E. coli), NMR Structure
|
MacKenzie et al. (1997)
MacKenzie KR, Prestegard JH, & Engelman DM (1997). A transmembrane helix dimer: structure and implications.
Science 276:131-133. |
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Epidermal Growth Factor Receptors
ErbB family of receptor tyrosine kinases |
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|
ErbB2 transmembrane segment dimer: Homo sapiens (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; doi:10.1074/jbcM709202200. |
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ErbB1/ErbB2 transmembrane segment heterodimer: Homo sapiens (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; doi:10.1016/j.jmb.2010.05.016. |
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ErbB3 transmembrane segment dimer: Homo sapiens (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; doi:10.1016/j.bbamem.2011.04.017. |
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ErbB4 transmembrane segment dimer: Homo sapiens (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; doi:10.1016/j.bbamem.2012.05.001. |
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Erythropoietin-Producing Hepatocellular Receptors
Eph family of receptor tyrosine kinases |
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EphA1 transmembrane segment dimer, pH 6.3: Homo sapiens (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; doi:10.1074/jbc.M803089200. |
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|
EphA2 transmembrane segment dimer: Homo sapiens (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; doi:10.1016/j.bpj.2009.11.008. |
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Integrin Adhesion Receptors
|
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Human Integrin αIIbβ3 transmembrane-cytoplasmic heterodimer: Homo sapiens (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. |
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Histidine Kinase Receptors
|
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ArcB (1-115) Aerobic Respiration Control sensor membrane domain: Escherichia coli (cell-free expression), 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. |
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QseC (1-185) Sensor protein membrane domain: Escherichia coli (cell-free expression), 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. |
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KdpD (397-502) Sensor protein membrane domain: Escherichia coli (cell-free expression), 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. |
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Immune Receptors
|
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Transmembrane ζ-ζ dimer of the TCR-CD3 complex: Homo sapiens (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. |
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|
DAP12 dimeric signaling domain in complex with activating receptor NKG2C: Homo sapiens (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. |
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SNARE Protein Family
|
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|
Syntaxin 1A/SNAP-25/Synaptobrevin-2 Complex with transmembrane regions: Rattus norvegicus (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. |
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|
Synaptobrevin, lipid-bound : Rattus norvegicus (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; doi:10.1073/pnas.0908317106. |
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Channels: Potassium and Sodium Ion-Selective
Ion Channel Research Aids |
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KcsA Potassium channel, H+ gated: Streptomyces lividans (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. |
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|
KcsA Potassium channel, H+ gated. Complexed with Fab.: Streptomyces lividans (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. |
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|
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; doi:10.1371/journal.pbio.0050121. |
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Full-length KcsA Potassium channel, H+ gated: Streptomyces lividans (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. |
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Full-length KcsA Potassium channel, H+ gated: Streptomyces lividans (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; doi:10.1073/pnas.1105112108. |
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KcsA Potassium channel in the presence of 150 mM Li+ and 3 mM K+: Streptomyces lividans (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. |
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|
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. |
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|
KcsA Potassium channel E71H-F103A inactivated-state mutant (closed state): Streptomyces lividans (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. |
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|
KcsA Potassium channel E71I modal-gating mutant: Streptomyces lividans (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. |
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|
KcsA Y82C with bound Cadmium : Streptomyces lividans (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; doi:10.1016/j.str.2012.03.027. |
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Two-Pore Domain Potassium Channel K2P1.1 (TWIK-1): Homo sapiens (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; doi:10.1126/science.121327. |
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Two-Pore Domain Potassium Channel K2P4.1 (TRAAK): Homo sapiens (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; doi:10.1126/science.1213808. |
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Two-Pore Domain Potassium Channel K2P4.1 (TRAAK): Homo sapiens (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; doi:10.1073/pnas.1218950110. |
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KvAP Voltage-gated potassium Channel in complex with Fab: Aeropyrum pernix (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.
Nature 423:33-41. Crystal structures. 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. Nature 423:42-48. Voltage sensor mechanism. |
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KvAP Voltage-gated potassium Channel in complex with Fv fragments: Aeropyrum pernix (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. |
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KvAP Voltage-Sensing Domain in phospholipid micelles: Aeropyrum pernix (expressed in E. coli), NMR Structure
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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. |
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Kv1.2 Voltage-gated potassium Channel: Rattus norvegicus (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. 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. |
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Kv1.2 Voltage-gated potassium Channel (full length): Rattus norvegicus (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. |
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Kv1.2/Kv2.1 Voltage-gated potassium channel chimera: Rattus norvegicus (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. |
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|
Kv1.2/Kv2.1 Voltage-gated potassium channel chimera: Rattus norvegicus (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. |
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|
KvLm voltaged-gated potassium channel: C-terminal pore module: Listeria monocytogenes (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; doi:10.1074/jbc.M112.415091. |
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MthK Potassium channel, Ca++ gated: Methanothermobacter thermautotrophicus (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.
Nature 417:515-22. Crystal structure and mechanism. 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. Nature 417:523-6. Open pore conformation. |
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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. |
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MthK Potassium channel, Ca++ gated: Methanothermobacter thermautotrophicus (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; doi:10.1073/pnas.1107229108. |
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MthK Potassium channel gating ring with bound Ba2+: Methanothermobacter thermautotrophicus (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; doi:10.1016/j.str.2012.09.014. |
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MthK Potassium channel pore (S68H,V77C mutant): Methanothermobacter thermautotrophicus (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; doi:10.1038/nsmb.2473. |
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Human BK (SLO1) Channel Ca2+-activation apparatus: Homo sapiens (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. |
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Human BK (SLO1) Channel Ca2+-activation apparatus: Homo sapiens (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. |
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BK (SLO1) Channel Ca2+ gating ring from zebra fish in the open state: Danio rerio (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; doi:10.1038/nature10670. |
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SLO3 K+ Channel pH-sensitive Gating Ring: Homo sapiens (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; doi:10.1073/pnas.1215078109. |
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GsuK multi-ligand gated K+ channel, L97D mutant: Geobacter sulfurreducens (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; doi:10.7554/eLife.00184. |
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Kir2.2 Inward-Rectifier Potassium Channel (Complete): Gallus gallus (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. |
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Kir2.2 Inward-Rectifier Potassium Channel in complex with PIP2: Gallus gallus (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; doi:10.1038/nature10370. |
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GIRK1 (Kir3.1) cytoplasmic domain: Mus musculus (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. |
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Kir3.1-Prokaryotic Ki | |||
