from the Stephen White laboratory at UC Irvine
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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.
- Bulletin Board for Unpublished MP Structures Now Available: We have created a bulletin board service for unpublished MP structures released by the Protein Data Bank. If you wish to announce new structures that have not yet been published, send the released pdb id code(s), author list, tentative paper title, and a concise, pertinent description (if appropriate) to Stephen White or Craig Snider (please see the bulletin board page for email information).
Latest new protein entered: 13 May 2012 at 23:14 PDT.
Last database update: 13 May 2012 at 23:14 PDT
- GlpG rhomboid-family intramembrane protease in complex with phosphonofluoridate inhibitor: Escherichia coli, 2.60 Å
- ATP synthase (F1c10), pH 8.3: Saccharomyces cerevisiae, 2.00 Å
- Monofunctional glycosyltransferase in complex with Lipid II analog: Staphylococcus aureus , 2.30 Å
- NaK channel chimera with grafted C-terminal region of a NaV channel: Bacillus weihenstephanensis (NaK) and Sulfitobacter pontiacus (NaV), 3.20 Å
- Monofunctional glycosyltransferase WaaA, substrate free: Aquifex aeolicus, 2.00 Å
- SpoIIQ-SpoIIIAH Complex: Bacillus subtilis, 2.82 Å
Unique proteins
in database = 332; number of coördinate files in database = 1002.
(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.
New Pre-Publication Structures: (links to mpstruc bulletin board):
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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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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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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Monoamine 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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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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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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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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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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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 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.
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OmpK36 osmoporin: Klebsiella pneumoniae, 3.2 Å
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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
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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 Matrix 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 Matrix 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 Matrix 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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OmpC Osmoporin: Escherichia coli, 2.0 Å
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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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OmpG *monomeric* porin: Escherichia coli, 2.3 Å
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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)
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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: Escherihia coli, 3.0 Å
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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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LamB Maltoporin: Salmonella typhimurium, 2.4 Å
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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
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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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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.
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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; doi:e15610.
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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
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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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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, x-ray diffraction, 2.5 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, x-ray diffraction, 1.6 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 (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 (in 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)
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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/jmb.2008.10.021.
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OmpT outer membrane protease: Escherichia coli, 2.6 Å
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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; doi:e15016.
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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)
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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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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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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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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, x-ray, 1.9 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, x-ray, 1.4 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.
|
||
|
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.
|
||
|
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.
|
||
|
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.
|
||
|
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.
|
||
|
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.
|
||
|
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.
|
|||
|
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.
|
||
|
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.
|
|||
|
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.
|
||
|
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.
|
||
|
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.
|
||
|
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.
|
||
|
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.
|
||
|
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.
|
||
|
Outer Membrane Autotransporters
|
|||
|
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.
|
||
|
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.
|
||
|
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.
|
||
|
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.
|
|||
|
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.
|
||
|
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.
|
||
|
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.
|
||
|
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.
|
||
|
Omp85-TpsB Outer Membrane Transporter Superfamily
|
|||
|
FhaC Filamentous Hemagglutinin Transporter: Bordetella pertussis, 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.
|
||
|
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.
|
||
|
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.
|
||
|
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.
|
||
|
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.
|
||
|
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.
|
||
|
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.
|
||
|
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.
|
||
|
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.
|
||
|
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.
|
||
|
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.
|
||
|
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.
|
||
|
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.
|
||
|
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.
|
||
|
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.
|
||
|
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.
|
||
|
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
|
|||
|
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.
|
||
|
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.
|
||
|
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.
|
||
|
Adventitious Membrane Proteins: Beta-sheet Pore-forming Toxins
|
|||
|
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.
|
||
|
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.
|
||
|
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.
|
|||
|
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.
|
||
|
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.
|
||
|
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.
|
||
|
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.
|
||
|
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.
|
||
|
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
|
|||
|
Adventitious Membrane Proteins: Alpha-helical Pore-forming Toxins.
|
|||
|
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.
|
||
|
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.
|
||
|
Outer Membrane Proteins
|
|||
|
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.
|
||
|
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.
|
|||
|
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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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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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)
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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
|
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
|
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
|
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
|
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
|
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
|
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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β2 adrenergic receptor: Homo sapiens (expressed in Spodoptera 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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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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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
|
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: 3V3Y |
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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|
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 ; doi:10.1038/nature10939.
Epub ahead of print
|
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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 ; doi:10.1038/nature10954.
Epub ahead of print
|
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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 constitutive 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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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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|
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.
|
||
|
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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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
|
|||
|
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.
|
||
|
Immune Receptors
|
|||
|
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.
|
||
|
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.
|
||
|
Channels: Potassium and Sodium Ion-Selective
(more information) |
|||
|
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.
|
||
|
KcsA Potassium channel, H+ gated: 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.
|
||
|
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.
|
||
|
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.
|
||
|
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.
|
||
|
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.
|
|||
|
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.
|
||
|
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.
|
||
|
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.
|
||
|
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.
|
||
|
KvAP Voltage-Sensing Domain in phospholipid micelles: Aeropyrum pernix (expressed in E. coli), NMR Structure
|
Butterwick & MacKinnon (2010)
Butterwick JA & MacKinnon R (2010). Solution structure and phospholipid interactions of the isolated voltage-sensor domain from KvAP. J Mol Biol 403:591-606.
|
||
|
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. |
||
|
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.
|
||
|
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.
|
||
|
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.
|
||
|
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. |
||
|
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.
|
|||
|
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.
|
||
|
Human BK 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.
|
||
|
Human BK 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 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.
|
||
|
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 Kir Chimera: Mus musculus & Burkholderia xenovornas (expressed in Escherichia coli), 2.2 Å
|
Nishida et al (2007)
Nishida M, Cadene M, Chait, BT & MacKinnon R (2007). Crystal structure of a Kir3.1-prokaryotic Kir channel chimera. EMBO J 26:4005-4015.
|
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|
Kir3.1 cytoplasmic domain: Mus musculus (expressed in E. coli), 2.0 Å
|
Xu et al (2009)
Xu Y, Shin HG, Szép S, & Lu Z (2009). Physical determinants of strong voltage sensitivity of K+channel block. Nat Struct Mol Biol 16:1252-1258.
|
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|
Whorton & Mackinnon (2011)
Whorton MR & Mackinnon R (2011). Crystal Structure of the Mammalian GIRK2 K+ Channel and Gating Regulation by G Proteins, PIP2, and Sodium Cell 147:199-208; doi:10.1016/j.cell.2011.07.046.
|
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|
KirBac1.1 Inward-Rectifier Potassium channel (closed state): Burkholderia pseudomallei, 3.65 Å
For re-refined structure, see 2WLL |
Kuo et al (2003)
Kuo A, Gulbis JM, Antcliff JF, Rahman T, Lowe ED, Zimmer J, Cuthbertson J, Ashcroft FM, Ezaki T, & Doyle DA (2003). Crystal structure of the potassium channel KirBac1.1 in the closed state. Science 300:1922-1926.
|
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|
KirBac3.1 Inward-Rectifier Potassium channel (semi-latched): Magnetospirillum magnetotacticum (expressed in E. coli), 2.60 Å
(Re-refinement of 1XL4) Latched State, 2.80 Å: 2WLK (re-refinement of 1XL6) Semi-latched State, 3.09 Å: 2WLI Semi-latched State, 4.20 Å: 2WLO Semi-latched State, 3.61 Å: 2WLM Unlatched State, 3.44 Å: 2WLN Unlatched State, 3.28 Å: 2WLH Q170A mutant (stalled), 3.10 Å: 2X6A Q170A mutant (blocked with Ba++), 3.30 Å: 2X6B Q170A mutant (conductive), 2.70 Å: 2X6C |
Clarke et al. (2010)
Clarke OB, Caputo AT, Hill AP, Vandenberg JI, Smith BJ & Gulbis JM (2010). Domain reorientation and rotation of an intracellular assembly regulate conduction in Kir potassium channels. Cell 141:1018-1029.
|
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KirBac3.1 Open-State Channel (S129R mutant): Magnetospirillum magnetotacticum (expressed in E. coli), 3.05 Å
|
Bavro et al. (2012)
Bavro VN, De Zorzi R, Schmidt MR, Muniz JR, Zubcevic L, Sansom MS, Vénien-Bryan C, & Tucker SJ (2012). Structure of a KirBac potassium channel with an open bundle crossing indicates a mechanism of channel gating. Nature Struc Mol Biol 19:158-163; doi:10.1038/nsmb.2208.
|
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|
MlotiK1 cyclic nucleotide-regulated K+-channel: Mesorhizobium loti (expressed in E. coli), 3.1 Å
|
Clayton et al. (2008)
Clayton GM, Altieri S, Heginbotham L, Unger VM, & Morais-Cabral JH (2008). Structure of the transmembrane regions of a bacterial cyclic nucleotide-regulated channel. Proc Natl Acad Sci U S A 105:1511-1515.
|
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|
NaK channel (Na+complex): Bacillus cereus (expressed in E. coli), 2.4 Å
K+ complex, 2.8 Å: 2AHZ. |
Shi et al. (2006)
Shi N, Ye S, Alam A, Chen L, & Jiang Y (2006). Atomic structure of a Na+- and K+-conducting channel. Nature 440:570-574.
|
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|
Alam et al. (2007)
Alam A, Shi N, & Jiang Y (2007). Structural insight into Ca2+ specificity in tetrameric cation channels. Proc Natl Acad Sci USA 104:15334-15339.
|
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|
NaK channel in open state (NΔ19 mutant): Bacillus cereus (expressed in E. coli), 1.60 Å
|
Alam & Jiang (2009)
Alam A & Jiang Y (2009). High-resolution structure of the open NaK channel. Nat Struct Mol Biol 16:30-34.
|
||
|
CNG-mimicking NaK channel mutant; NaK-ETPP/K+ complex: Bacillus cereus (expressed in E. coli), 1.95 Å
CNG-mimicking mutant; NaK-NTPP/K+ complex, 1.58 Å: 3K06 CNG-mimicking mutant; NaK-ETPP/Na+ complex, 1.95 Å: 3K0G CNG-mimicking mutant; NaK-DTPP/Na+ complex, 1.58 Å: 3K04 CNG-mimicking mutant; NaK-NTPP/Na+ complex, 1.62 Å: 3K08 |
Derebe et al. (2011)
Derebe MG, Zeng W, Li Y, Alam A, & Jiang Y (2011). Structural studies of ion permeation and Ca2+blockage of a bacterial channel mimicking the cyclic nucleotide-gated channel pore. Proc Natl Acad Sci USA 108:592-597.
|
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|
Derebe et al. (2011)
Derebe MG, Sauer DB, Zeng W, Alam A, Shi N, & Jiang Y (2011). Tuning the ion selectivity of tetrameric cation channels by changing the number of ion binding sites. Proc Natl Acad Sci USA 108:598-602.
|
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|
Sauer et al. (2011)
Sauer DB, Zeng W, Raghunathan S, & Jiang Y (2011). Protein interactions central to stabilizing the K+ channel selectivity filter in a four-sited configuration for selective K+ permeation. Proc Natl Acad Sci USA 108:16634-16639; doi:10.1073/pnas.1111688108.
|
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|
NaK channel chimera with grafted C-terminal region of a NaV channel: Bacillus weihenstephanensis (NaK) and Sulfitobacter pontiacus (NaV) (expressed in E. coli), 3.20 Å
The NaVSulP C-terminal region grafted onto the C-terminus of NaK forms a four-helix bundle. |
Irie et al. (2012)
Irie K, Shimomura T, & Fujiyoshi Y (2012). The C-terminal helical bundle of the tetrameric prokaryotic sodium channel accelerates the inactivation rate. Nature Commun 3:793; doi:10.1038/ncomms1797.
|
||
|
Payandeh et al. (2011)
Payandeh J, Scheuer T, Zheng N, & Catterall WA (2011). The crystal structure of a voltage-gated sodium channel. Nature 475:353-358; doi:10.1038/nature10238.
|
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|
Channels: Other Ion Channels
|
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|
GluA2 Glutamate receptor (AMPA-subtype): Rattus norvegicus (expressed in sf9 cells), 3.60 Å
3KG2 is in complex with the competitive antagonist ZK 200775 GluA2 ligand-binding core complex with bound glutamate, 1.55 Å: 3KGC |
Sobolevsky et al. (2009)
Sobolevsky AI, Rosconi MP, & Gouaux E (2009). X-ray structure, symmetry and mechanism of an AMPA-subtype glutamate receptor. Nature 462:745-756.
|
||
|
M2 proton channel (AM2): Influenza A (synthesized), 2.05 Å
with amantadine inhibitor, 3.50 Å: 3C9J |
Stouffer et al. (2008)
Stouffer AL, Acharya R, Salom D, Levine AS, Di Costanzo L, Soto CS, Tereshko V, Nanda V, Stayrook S, & DeGrado WF. (2008). Structural basis for the function and inhibition of an influenza virus proton channel. Nature 451:596-599.
|
||
|
M2 proton channel (AM2): Influenza A (expressed in E. coli), NMR structure
with rimantadine inhibitor |
Schnell & Chou. (2008)
Schnell JR & Chou JJ (2008). Structure and mechanism of the M2 proton channel of influenza A virus. Nature 451:591-595.
|
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|
M2 proton channel (AM2) in a hydrated lipid bilayer: Influenza A (expressed in E. coli), NMR structure
|
Sharma et al. (2010)
Sharma M, Yi M, Dong H, Qin H, Peterson E, Busath DD, Zhou HX, & Cross TA (2010). Insight into the mechanism of the influenza A proton channel from a structure in a lipid bilayer. Science 330:509-512.
|
||
|
M2 proton channel (BM2): Influenza B (expressed in Escherichia coli), NMR Structure
Cytoplasmic domain, NMR Structure: 2KJ1 |
Wang et al. (2009)
Wang J, Pielak RM, McClintock MA, & Chou JJ (2009). Solution structure and functional analysis of the influenza B proton channel. Nat Struct Mol Biol 16:1267-1271.
|
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|
M2A-M2B chimeric proton channel (AM2-BM2): Influenza A/Influenza B (expressed in E. coli), NMR Structure
With rimantadine inhibitor, NMR structure: 2LJC |
Pielak et al. (2011)
Pielak RM, Oxenoid K, & Chou JJ (2011). Structural Investigation of Rimantadine Inhibition of the AM2-BM2 Chimera Channel of Influenza Viruses. Structure 19:1655-1663; doi:10.1016/j.str.2011.09.003.
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ASIC1 Acid-Sensing Ion Channel (ΔASIC1; N- and C-term deletions): Gallus gallus (expressed in SF9 cells), 1.9 Å
Construct does not exhibit proton-dependent gating |
Jasti et al. (2007)
Jasti J, Furukawa H, Gonzales EB, & Gouaux E (2007). Structure of acid-sensing ion channel 1 at 1.9 Å resolution and low pH. Nature 449:316-323.
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ASIC1 Acid-Sensing Ion Channel (ASIC1mfc; minimal functional channel): Gallus gallus (expressed in SF9 cells), 3.0 Å
Desensitized State |
Gonzales et al. (2009)
Gonzales EB, Kawate T, & Gouaux E (2009). Pore architecture and ion sites in acid-sensing ion channels and P2X receptors. Nature 460:599-604.
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MscL Mechanosensitive channel: Mycobacterium tuberculosis, 3.5 Å
|
Chang et al. (1998)
Chang G, Spencer RH, Lee AT, Barclay MT, & Rees DC (1998). Structure of the MscL homolog from Mycobacterium tuberculosis: A gated mechanosensitive ion channel. Science 282:2220-2226.
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MscL Mechanosensitive channel, Δ95-120: Staphylococcus aureus, 3.8 Å
Shows MscL in an expanded intermediate state. |
Liu et al. (2009)
Liu Z, Gandhi CS, & Rees DC (2009). Structure of a tetrameric MscL in an expanded intermediate state. Nature 461:120-124.
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MscS voltage-modulated mechanosensitive channel: Escherichia coli, 3.7 Å
|
Bass et al. (2002)
Bass RB, Strop P, Barclay M, & Rees DC (2002). Crystal Structure of Escherichia coli MscS, a Voltage-modulated and mechanosensitive channel. Science 298:1582-1587.
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MscS mechanosensitive channel in the open form: Escherichia coli, 3.45 Å
|
Wang et al. (2008)
Wang W, Black SS, Edwards MD, Miller S, Morrison EL, Bartlett W, Dong C, Naismith JH, & Booth IR (2008). The structure of an open form of an E. coli mechanosensitive channel at 3.45 Å resolution. Science 321:1179-1183.
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Hattori et al. (2007)
Hattori M, Tanaka Y, Fukai S, Ishitani R, & Nureki O (2007). Crystal structure of the MgtE Mg2+transporter. Nature 448:1072-1075.
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MgtE Mg2+ Transporter: Thermus thermophilus (expressed in E. coli), 2.9 Å
|
Hattori et al. (2009)
Hattori M, Iwase N, Furuya N, Tanaka Y, Tsukazaki T, Ishitani R, Maguire ME, Ito K, Maturana A, & Nureki O (2009). Mg(2+)-dependent gating of bacterial MgtE channel underlies Mg(2+) homeostasis. EMBO J 28:3602-3612.
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Chen et al. (2010)
Chen YH, Hu L, Punta M, Bruni R, Hillerich B, Kloss B, Rost B, Love J, Siegelbaum SA, & Hendrickson WA (2010). Homologue structure of the SLAC1 anion channel for closing stomata in leaves. Nature 467:1074-1080.
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ATP-gated P2X4 ion channel (apo protein): Danio rerio (zebra fish) (expressed in SF9 cells), 3.1 Å
Closed state. A construct, 3.5 Å: 3I5D |
Kawate et al. (2009)
Kawate T, Michel JC, Birdsong WT, & Gouaux E (2009). Crystal structure of the ATP-gated P2X4ion channel in the closed state. Nature 460:592-598.
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Cys-Loop Receptor Family
Cation-selective and Anion-selective Ligand-gated Channels Cation-selective include nicotinic acetylcholine and serotonin 5-HT3 receptors. Anion-selective include γ-aminobutyric, glycine, and invertebrate glutamate-gated chloride channels (GluCl) |
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Nicotinic Acetylcholine Receptor Pore (closed state): Torpedo marmorata, 4.0 Å
Electron Diffraction |
Miyazawa et al. (2003)
Miyazawa A, Fujiyoshi Y, & Unwin N (2003). Structure and gating mechanism of the acetylcholine receptor pore. Nature 423:949-955.
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Nicotinic Acetylcholine Receptor, refined structure: Torpedo marmorata, 4.0 Å
Electron Diffraction |
Unwin (2005)
Unwin N. (2005). Refined structure of the nicotinic acetylcholine receptor at 4 Å resolution. J Mol Biol 346:967-989.
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Prokaryotic pentameric ligand-gated ion channel (ELIC): Erwinia chrysanthemi (expressed in E. coli), 3.3 Å
First high-resolution x-ray structure of an AChR-like channel. |
Hilf & Dutzler (2008)
Hilf RJC & Dutzler R (2008). X-ray structure of a prokaryotic pentameric ligand-gated ion channel. Nature 452:375-379.
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Prokaryotic pentameric ligand-gated ion channel (ELIC) in complex with acetylcholine: Erwinia chrysanthemi (expressed in E. coli), 2.91 Å
Apo protein, 3.09 Å: 3RQU |
Pan et al. (2012)
Pan J, Chen Q, Willenbring D, Yoshida K, Tillman T, Kashlan OB, Cohen A, Kong XP, Xu Y, & Tang P (2012). Structure of the pentameric ligand-gated ion channel ELIC cocrystallized with its competitive antagonist acetylcholine. Nature Commun 3:714; doi:10.1038/ncomms1703.
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Prokaryotic pentameric ligand-gated ion channel (GLIC): Gloebacter violaceus (expressed in E. coli), 3.1 Å
Related to ELIC (above), this pentameric channel is apparently in an open state. E221A mutant, 3.50 Å: 3EI0 |
Hilf & Dutzler (2009)
Hilf RJC & Dutzler R (2009). Structure of a potentially open state of a proton-activated pentameric ligand-gated ion channel. Nature 457:115-118.
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Prokaryotic pentameric ligand-gated ion channel (GLIC): Gloebacter violaceus (expressed in E. coli), 2.9 Å
Related to ELIC (above), this pentameric channel is apparently in an open state. |
Bocquet et al. (2009)
Bocquet N, Nury H, Baaden M, Le Poupon C, Changeux JP, Delarue M, & Corringer PJ (2009). X-ray structure of a pentameric ligand-gated ion channel in an apparently open conformation. Nature 457:111-114.
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Prokaryotic "pentameric" ligand-gated ion channel (GLIC) with hexameric quaternary structure: Gloebacter violaceus (expressed in E. coli), 2.3 Å
|
Nury et al. (2010)
Nury H, Bocquet N, Le Poupon C, Raynal B, Haouz A, Corringer PJ, & Delarue M (2010). Crystal structure of the extracellular domain of a bacterial ligand-gated ion channel. J Mol Biol 395:1114-1127.
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Prokaryotic pentameric ligand-gated ion channel (GLIC), wildtype-TBSb complex: Gloebacter violaceus (expressed in E. coli), 3.70 Å
Wildtype-TEAs complex, 3.50 Å: 2XQ5 E221D-TEAs complex, 3.20 Å: 2XQ9 Wildtype-TMAs complex, 3.60 Å: 2XQ4 Wildtype-bromo-lidocaine complex, 3.50 Å: 2XQ3 Wildtype-Cd2+ complex, 3.40 Å: 2XQ7 Wildtype-Zn2+ complex, 3.60 Å: 2XQ8 Wildtype-Cs+ complex, 3.70 Å: 2XQ6 |
Hilf et al. (2010)
Hilf RJ, Bertozzi C, Zimmermann I, Reiter A, Trauner D, & Dutzler R (2010). Structure of a potentially open state of a proton-activated pentameric ligand-gated ion channel. Nat Struct Mol Biol 17:1330-1336.
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Prokaryotic pentameric ligand-gated ion channel (GLIC) in complex with propofol anesthetic: Gloebacter violaceus (expressed in E. coli), 3.30 Å
In complex with desflurane, 3.20 Å: 3P4W |
Nury et al. (2011)
Nury H, Van Renterghem C, Weng Y, Tran A, Baaden M, Dufresne V, Changeux JP, Sonner JM, Delarue M, & Corringer PJ (2011). X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channe. Nature 469:428-431.
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Hibbs & Gouaux (2011)
Hibbs RE & Gouaux E (2011). Principles of activation and permeation in an anion-selective Cys-loop receptor Nature 474:54-60; doi:10.1038/nature10139.
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Channels: Aquaporins and Glyceroporins
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AQP0 aquaporin water channel: Bovine lens, 2.24 Å
|
Harries et al. (2004)
Harries WE, Akhavan D, Miercke LJ, Khademi S, & Stroud RM (2004). The channel architecture of aquaporin 0 at a 2.2 Å resolution. Proc Natl Acad Sci U S A 101:14045-14050.
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AQP0 aquaporin water channel from sheep lens.: Ovis aries, 3.0 Å
AQP0 reconstituted with dimyristoylphosphatidylcholine and organized as a membrane junction. Electron Diffraction. Resolution: 3 Å in membrane plane, 3.5 Å normal to membrane plane. |
Gonen et al. (2004)
Gonen T, Sliz P, Kistler J, Cheng Y, & Walz T (2004). Aquaporin-0 membrane junctions reveal the structure of a closed water pore. Nature 429:193-197.
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AQP0 aquaporin sheep lens junction: Ovis aries, 1.90 Å
Electron Diffraction Non-junctional form, 2.4 Å: 2B6P |
Gonen et al. (2005)
Gonen T, Cheng Y, Sliz P, Hiroaki Y, Fujiyoshi Y, Harrison SC, & Walz T (2005). Lipid-protein interactions in double-layered two-dimensional AQP0 crystals. Nature 438:633-638.
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AQP0 aquaporin sheep lens junction: Ovis aries, 2.5 Å
Electron Diffraction. AQP0 reconstituted with E. coli polar lipids and organized as a membrane junction |
Hite et al. (2010)
Hite RK, Li Z, & Walz T. (2010). Principles of membrane protein interactions with annular lipids deduced from aquaporin-0 2D crystals. EMBO J 29:1652-1658.
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AQP1 red blood cell aquaporin water channel: Homo sapiens, 3.8 Å
Electron Diffraction. Resolution shown is in-plane. |
Murata et al. (2000)
Murata K, Mitsuoka K, Hirai T, Walz T, Agre P, Heymann J B, Engel A, & Fujiyoshi Y (2000). Structural determinants of water permeation through aquaporin-1. Nature 407:599-605.
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AQP1 red blood cell aquaporin water channel: Homo sapiens, 3.7 Å
Electron Diffraction. Protein in vitreous ice. |
Ren et al. (2001)
Ren G, Reddy VS, Cheng A, Melnyk P, & Mitra AK (2001). Visualization of a water-selective pore by electron crystallography in vitreous ice. Proc Natl Acad Sci USA 98:1398-1403.
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AQP1 aquaporin red blood cell water channel: Bos taurus, 2.20 Å
X-ray Diffraction |
Sui et al. (2001)
Sui H, Han BG, Lee JK, Walian P, & Jap BK (2001). Structural basis of water-specific transport through the AQP1 water channel. Nature 414:872-8.
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AQP4 aquaporin rat glial cell water channel: Rattus norvegicus (expressed in S. frugiperda), 3.2 Å
Electron Diffraction. |
Hiroaki et al. (2005)
Hiroaki Y, Tani K, Kamegawa A, Gyobu N, Nishikawa K, Suzuki H, Walz T, Sasaki S, Mitsuoka K, Kimura K, Mizoguchi A, & Fujiyoshi Y (2005). Implications of the Aquaporin-4 Structure on Array Formation and Cell Adhesion. J Mol Biol 355:628-639.
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AQP4 aquaporin rat glial cell water channel: Rattus norvegicus (expressed in S. frugiperda), 2.80 Å
Electron Diffraction. S180D mutant. Structure reveals five lipids associated with AQP4. |
Tani et al. (2009)
Tani K, Mitsuma T, Hiroaki Y, Kamegawa A, Nishikawa K, Tanimura Y, & Fujiyoshi Y (2009). Mechanism of aquaporin-4's fast and highly selective water conduction and proton exclusion. J Mol Biol 389:694-706.
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AQP4 aquaporin water channel: Human (expressed in Pichia pastoris), 1.8 Å
|
Ho et al. (2009)
Ho JD, Yeh R, Sandstrom A, Chorny I, Harries WE, Robbins RA, Miercke LJ, & Stroud RM (2009). Crystal structure of human aquaporin 4 at 1.8 A and its mechanism of conductance. Proc Natl Acad Sci USA 106:7437-74422.
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AQP5 aquaporin water channel (HsAQP5): human (expressed in Pichia pastoris), 2.0 Å
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Horsefield et al. (2008)
Horsefield R, Nordén K, Fellert M, Backmark A, Törnroth-Horsefield S, Terwisscha van Scheltinga AC, Kvassman J, Kjellbom P, Johanson U, & Neutze R. (2008). High-resolution x-ray structure of human aquaporin 5. Proc Natl Acad Sci USA 105:13327-13332.
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AqpM aquaporin water channel: Methanothermobacter marburgensis (expressed in E. coli), 1.68 Å
Initial structure, 2.3 Å: 2EVU |
Lee et al. (2005)
Lee JK, Kozono D, Remis J, Kitagawa Y, Agre P, & Stroud RM (2005). Structural basis for conductance by the archaeal aquaporin AqpM at 1.68 Å. Proc Natl Acad Sci USA 102:18932-18937.
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AqpZ aquaporin water channel: Escherichia coli, 2.5 Å
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Savage et al. (2003)
Savage DF, Egea PF, Robles-Colmenares Y, Iii JD, & Stroud RM (2003). Architecture and Selectivity in Aquaporins: 2.5 Å X-Ray Structure of Aquaporin Z. PLoS Biol 1:334-340.
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AqpZ aquaporin showing two conformations of Arg-189: Escherichia coli, 3.2 Å
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Jiang et al. (2006)
Jiang J, Daniels BV, & Fu D (2006). Crystal structure of AqpZ tetramer reveals two distinct R189 conformations associated with water permeation through the narrowest constriction of the water-conducting channel. J Biol Chem 281:454-460.
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Savage & Stroud (2007)
Savage DF & Stroud RM (2007). Structural basis of aquaporin inhibition by mercury. J Mol Biol 368:607-617.
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Savage et al. (2010)
Savage DF, O'Connell JD 3rd, Miercke LJ, Finer-Moore J, & Stroud RM (2010). Structural context shapes the aquaporin selectivity filter. Proc Natl Acad Sci USA 107:17164-17169.
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SoPIP2;1 plant aquaporin (closed conformation): Spinacia oleracea (expressed in Pichia pastoris), 2.1 Å
Open conformation, 3.9 Å: 2B5F |
Törnroth-Horsefield et al. (2006)
Törnroth-Horsefield S, Wang Y, Hedfalk K, Johanson U, Karlsson M, Tajkhorshid E, Neutze R, & Kjellbom P (2006). Structural mechanism of plant aquaporin gating. Nature 439:688-694.
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GlpF glycerol facilitator channel: Escherichia coli, 2.2 Å
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Fu et al. (2000)
Fu D, Libson A, Miercke LJW, Weitzman C, Nollert P, Krucinski J, & Stroud RM (2000). Structure of a glycerol-conducting channel and the basis for its selectivity. Science 290:481-486.
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Tajkhorshid et al. (2002)
Tajkhorshid E, Nollert P, Jensen MØ, Miercke LJ, O'Connell J, Stroud RM, & Schulten K (2002). Control of the selectivity of the aquaporin water channel family by global orientational tuning. Science 296:525-530.
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PfAQP aquaglyceroporin: Plasmodium falciparum, 2.05 Å
Transports water and glycerol equally well. |
Newby et al. (2008)
Newby ZE, O'Connell J 3rd, Robles-Colmenares Y, Khademi S, Miercke LJ, & Stroud RM (2008). Crystal structure of the aquaglyceroporin PfAQP from the malarial parasite Plasmodium falciparum. Nature Struc Mol Biol 15:619-625.
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Aqy1 yeast aquaporin (pH 3.5): Pischia pastoris, 1.15 Å
pH 8.0, 1.40 Å: 2W1P |
Fischer et al. (2009)
Fischer G, Kosinska-Eriksson U, Aponte-Santamaría C, Palmgren M, Geijer C, Hedfalk K, Hohmann S, de Groot BL, Neutze R, & Lindkvist-Petersson K. (2009). Crystal structure of a yeast aquaporin at 1.15 Å reveals a novel gating mechanism. PLoS Bio 76; doi:e1000130.
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Channels : Formate/Nitrite Transporter (FNT) Family
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FocA, pentameric aquaporin-like formate transporter: Escherichia coli, 2.20 Å
3KCU structure is for P212121 space group. P32 space group: 3KCV, 3.2 Å |
Wang et al. (2009)
Wang Y, Huang Y, Wang J, Cheng C, Huang W, Lu P, Xu YN, Wang P, Yan N, & Shi Y (2009). Structure of the formate transporter FocA reveals a pentameric aquaporin-like channel. Nature 462:467-472.
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FocA formate transporter without formate: Vibrio cholerae (expressed in E. coli), 2.10 Å
FocA with bound formate: 3KLZ, 2.50 Å |
Waight et al. (2010)
Waight AB, Love J, & Wang DN (2010). Structure and mechanism of a pentameric formate channel. Nat Struct Mol Biol 17:31-37.
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FocA formate transporter at pH 4.0: Salmonela typhimurium, 2.80 Å
Three different conformations are observed in the asymmetric unit: Open, Intermediate, & closed |
Lü et al. (2011)
Lü W, Du J, Wacker T, Gerbig-Smentek E, Andrade SL, & Einsle O (2011). pH-dependent gating in a FocA formate channel Science 332:352-354; doi:10.1126/science.1199098.
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Czyzewski & Wang (2012)
Czyzewski BK & Wang DN (2012). Identification and characterization of a bacterial hydrosulphide ion channel. Nature 483:494-497; doi:10.1038/nature10881.
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Channels: Urea Transporters
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Urea transporter: Desulfovibrio vulgaris (expressed in E. coli), 2.30 Å
Structure with bound dimethyl urea: 3K3G, 2.40 Å |
Levin et al. (2009)
Levin EJ, Quick M, & Zhou MG (2009). Crystal structure of a bacterial homologue of the kidney urea transporter. Nature 462:757-761.
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Channels: Amt/Rh proteins
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Khademi et al. (2004)
Khademi S, O'Connell J 3rd, Remis J, Robles-Colmenares Y, Miercke LJ, & Stroud RM (2004). Mechanism of ammonia transport by Amt/MEP/Rh: structure of AmtB at 1.35 Å. Science 305:1587-1594.
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AmtB ammonia channel (wild-type): Escherichia coli, 1.8 Å (P63 crystal form)
R3 crystal form: 1XQE, 2.1 Å resolution |
Zheng et al. (2004)
Zheng L, Kostrewa D, Berneche S, Winkler FK, & Li XD (2004). The mechanism of ammonia transport based on the crystal structure of AmtB of Escherichia coli. Proc Natl Acad Sci U S A 101:17090-17095.
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AmtB ammonia channel (wild-type): Escherichia coli, 2.1 Å
Wild-type in the presence of ammonium with imidazole: 2NOP, 2.0 Å H168E mutant in the presence of ammonium: 2NOW, 2.2 Å H168A mutant in the presence of ammonium with imidazole: 2NPC, 2.1 Å H168F mutant in the presence of ammonium with imidazole: 2NPD, 2.1 Å H318A mutant in the absence of ammonium: 2NPE, 2.1 Å H318F mutant in the presence of ammonium: 2NPG, 2.0 Å H318F mutant in the presence of ammonium with imidazole: 2NPJ, 2.0 Å H168A/H318A mutant in the presence of ammonium with imidazole: 2NPK, 2.0 Å |
Javelle et al. (2006)
Javelle A, Lupo D, Zheng L, Li XD, Winkler FK, & Merrick M (2006). An unusual twin-his arrangement in the pore of ammonia channels is essential for substrate conductance. J Biol Chem 281:39492-39498.
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AmtB ammonia channel in complex with GlnK: Escherichia coli, 2.5 Å
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Conroy et al. (2007)
Conroy MJ, Durand A, Lupo D, Li X-D, Bullough PA, Winkler FK, & Merrick M (2007). The crystal structure of the Escherichia coli AmtB-GlnK complex reveals how GlnK regulates the ammonia channel. Proc Natl Acad Sci USA 104:1213-1218.
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AmtB ammonia channel in complex with inhibitory GlnK: Escherichia coli, 1.96 Å
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Gruswitz et al. (2007)
Gruswitz F, O'Connell III J, & Stroud RM (2007). Inhibitory complex of the transmembrane ammonia channel, AmtB, and the cytosolic regulatory protein, GlnK, at 1.96 Å. Proc Natl Acad Sci USA 104:42-47.
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Andrade et al. (2005)
Andrade SL, Dickmanns A, Ficner R, & Einsle O (2005). Crystal structure of the archaeal ammonium transporter Amt-1 from Archaeoglobus fulgidus. Proc Natl Acad Sci U S A 102:14994-14999.
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Rh protein, possible ammonia or CO2 channel: Nitrosomonas europaea (expressed in Methylococcus capsulatus), 1.85 Å
CO2 pressurized protein, 1.85 Å: 3B9Z |
Li et al. (2007)
Li X, Jayachandran S, Nguyen HH, & Chan MK (2007). Structure of the Nitrosomonas europaea Rh protein. Proc Natl Acad Sci U S A 104:19279-19284.
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Rh protein, possible ammonia or CO2 channel: Nitrosomonas europaea (expressed in E. coli), 1.30 Å
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Lupo et al. (2007)
Lupo D, Li XD, Durand A, Tomizaki T, Cherif-Zahar B, Matassi G, Merrick M, & Winkler FK (2007). The 1.3-Å resolution structure of Nitrosomonas europaea Rh50 and mechanistic implications for NH3transport by Rhesus family proteins. Proc Natl Acad Sci U S A 104:19303-19308.
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Human Rh C glycoprotein ammonia transporter: Homo sapiens (expressed in HEK293s cells), 2.10 Å
|
Gruswitz et al. (2010)
Gruswitz F, Chaudhary S, Ho JD, Schlessinger A, Pezeshki B, Ho CM, Sali A, Westhoff CM, & Stroud RM (2010). Function of human Rh based on structure of RhCG at 2.1 Å. Proc Natl Acad Sci USA 107:9638-9643.
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Channels: Gap Junctions
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Connexin 26 (Cx26; GJB2) gap junction: Human (expressed in Sf9 cells), 3.5 Å
|
Maeda et al. (2009)
Maeda S, Nakagawa S, Suga M, Yamashita E, Oshima A, Fujiyoshi Y, & Tsukihara T (2009). Structure of the connexin 26 gap junction channel at 3.5 Å resolution. Nature 458:597-602.
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Channels: Intercellular
Channels found in sporulating bacteria that connect mother cell to forespore |
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SpoIIQ-SpoIIIAH Complex: Bacillus subtilis (expressed in E. coli), 2.26 Å
This is the protomer structure. Modeling studies suggest that the pore is formed from 12 protomers to form a channel with a diameter of 60 Å. |
Levdikov et al. (2012)
Levdikov VM, Blagova EV, McFeat A, Fogg MJ, Wilson KS, & Wilkinson AJ (2012). Structure of components of an intercellular channel complex in sporulating Bacillus subtilis. Proc Natl Acad Sci USA 109:5441-5445; doi:10.1073/pnas.1120087109.
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SpoIIQ-SpoIIIAH Complex: Bacillus subtilis (expressed in E. coli), 2.82 Å
The structure is of the protomer. Modeling studies suggest that the pore is formed from 15 or 18 protomers to form a channel with a diameter of 82 or 116 Å. |
Meisner et al. (2012)
Meisner J, Maehigashi T, André I, Dunham CM, & Moran CP Jr (2012). Structure of the basal components of a bacterial transporter. Proc Natl Acad Sci USA 109:5446-5451; doi:10.1073/pnas.1120113109.
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Sec Proteins
Membrane Proteins Involved with Protein Insertion and Secretion formerly listed as "Channels: Protein-Conducting" |
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SecYEβ protein-conducting channel: Methanococcus jannaschii, 3.5 Å
Coördinates of native complex: 1RHZ. Coördinates of double-mutant complex (K422R,V423T) 1RH5 (3.2 Å resolution). |
van den Berg et al. (2004)
van den Berg B, Clemons WM, Collinson I, Hartmann E, Harrison SC, & Rapoport TA (2004). X-ray structure of a protein-conducting channel. Nature 427:36-44.
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SecYEβ protein-conducting channel with full-plug (TM2a) deletion: Methanococcus jannaschii, 3.6 Å
Coördinates of mutant with half-plug deletion 2YXQ (3.5 Å resolution). |
Li et al. (2007)
Li W, Schulman S, Boyd D, Erlandson K, Beckwith J & Rapoport TA (2007). The plug domain of the SecY protein stabilizes the closed state of the translocon channel and maintains a membrane seal. Mol Cell 26:1409-38.
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SecYEβ "primed" protein-conducting channel: Pyrococcus furiosus (expressed in E. coli), 3.1 Å
|
Egea and Stroud (2010)
Egea PF & Stroud RM (2010). Lateral opening of a translocon upon entry of protein suggests the mechanism of insertion into membranes. Proc Natl Acad Sci USA 107:17182-17187.
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SecYEG protein-conducting channel in complex with SecA: Thermotoga maritima (expressed in E. coli), 4.5 Å
|
Zimmer et al. (2008)
Zimmer J, Nam Y, & Rapoport TA (2008). Structure of a complex of the ATPase SecA and the protein-translocation channel. Nature 455:936-943.
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SecYE protein-conducting channel in complex with a Fab fragment: Thermus thermophilus (expressed in E. coli), 3.20 Å
SecYE alone 2ZQP (6.0 Å resolution). |
Tsukazaki et al. (2008)
Tsukazaki T, Mori H, Fukai S, Ishitani R, Mori T, Dohmae N, Perederina A, Sugita Y, Vassylyev DG, Ito K, & Nureki O (2008). Conformational transition of Sec machinery inferred from bacterial SecYE structures. Nature 455:988-991.
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SecDF protein-export enhancer: Thermus thermophilus (expressed in E. coli), 3.30 Å
SecDF associates with SecYEG to enhance protein export using the transmembrane proton motive force (PMF). It is a member of the resistance nodulation and cell division (RND) superfamily. A related member of the RND superfamily is the AcrB multi-drug efflux transporter. P1 periplasmic domain, 2.6 Å: 3AQO P4 periplasmic domain, NMR structure: 2RRN |
Tsukazaki et al. (2011)
Tsukazaki T, Mori H, Echizen Y, Ishitani R, Fukai S, Tanaka T, Perederina A, Vassylyev DG, Kohno T, Maturana AD, Ito K, & Nureki O (2011). Structure and function of a membrane component SecDF that enhances protein export. Nature 474:235-238; doi:10.1038/nature09980.
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Oligosaccharyltransferases (OST)
Catalyses Asparagine-linked (N-linked) Glycosylation |
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PglB OST in complex with acceptor peptide: Campylobacter lari (expressed in E. coli), 3.40 Å
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Lizak et al. (2011)
Lizak C, Gerber S, Numao S, Aebi M, & Locher KP (2011). X-ray structure of a bacterial oligosaccharyltransferase. Nature 474:350-355; doi:10.1038/nature10151.
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Intramembrane Proteases
( NSMB News & Views on three GlpG Structures) |
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GlpG rhomboid-family intramembrane protease: Eschericia coli, 2.1 Å
P32 space group. One molecule in asymmetric unit. |
Wang et al. (2006)
Wang Y, Zhang Y, & Ha Y (2006). Crystal structure of a rhomboid family intramembrane protease. Nature 444:179-183.
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GlpG rhomboid-family intramembrane protease: Eschericia coli, 1.90 Å
W136A mutant, 1.70 Å: 3B44 |
Wang et al. (2007)
Wang Y, Maegawa S, Akiyama Y, & Ha Y (2007). The role of L1 loop in the mechanism of rhomboid intramembrane protease GlpG. J Mol Biol 374:1104-1113.
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GlpG rhomboid-family intramembrane protease: Eschericia coli, 2.5 Å
Shows GlpG in a more open conformation. |
Wang & Ha (2007)
Wang Y & Ha Y (2007). Open-cap conformation of intramembrane protease GlpG. Proc Natl Acad Sci USA 104:2098-2102.
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GlpG rhomboid-family intramembrane protease: Eschericia coli, 2.6 Å
P31 space group. Two anti-parallel molecules in asymmetric unit. |
Wu et al. (2006)
Wu Z, Yan N, Feng L, Oberstein A, Yan H, Baker RP, Gu L, Jeffrey PD, Urban S & Shi Y (2006). Structural analysis of a rhomboid family intramembrane protease reveals a gating mechanism for substrate entry. Nature Struc. Molec. Biol. 13:1084-1091.
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GlpG rhomboid-family intramembrane protease: Eschericia coli, 2.3 Å
P21 space group. Two anti-parallel molecules in asymmetric unit. |
Ben-Shem et al. (2007)
Ben-Shem A, Fass D, & Bibi E (2007). Structural basis for intramembrane proteolysis by rhomboid serine proteases. Proc Natl Acad Sci USA 104:426-466.
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GlpG rhomboid-family intramembrane protease: Eschericia coli, 1.65 Å
Acyl GlpG: GlpG with covalently bound isocoumarin inhibitor, 2.09 Å: 2XOW |
Vinothkumar et al. (2010)
Vinothkumar KR, Strisovsky K, Andreeva A, Christova Y, Verhelst S, & Freeman M (2010). The structural basis for catalysis and substrate specificity of a rhomboid protease. EMBO J 29:3797-3809.
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GlpG rhomboid-family intramembrane protease with lipids: Eschericia coli, 1.70 Å
S201T active-site mutant in orthorhombic crystal form. S201T active-site mutant in trigonal crystal form, 1.85 Å: 2XTU |
Vinothkumar (2011)
Vinothkumar KR (2011). Structure of Rhomboid Protease in a Lipid Environment. J Mol Biol 407:232-247.
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GlpG rhomboid-family intramembrane protease with a mechanism-based inhibitor: Escherichia coli, 2.30 Å
The inhibitor is diisopropyl fluorophosphonate, which mimics the oxyanion-containing tetrahedral intermediate of the hydrolytic reaction. |
Xue & Ha (2012)
Xue Y & Ha Y (2012). Catalytic Mechanism of Rhomboid Protease GlpG Probed by 3,4-Dichloroisocoumarin and Diisopropyl Fluorophosphonate. J Biol Chem 287:3099-3107; doi:10.1074/jbc.M111.310482.
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GlpG rhomboid-family intramembrane protease in complex with phosphonofluoridate inhibitor: Escherichia coli, 2.60 Å
The phosphonofluoridate inhibitor is covalently bound to the catalytic serine |
Xue et al. (2012)
Xue Y, Chowdhury S, Liu X, Akiyama Y, Ellman J, & Ha Y (2012). Conformational Change in Rhomboid Protease GlpG Induced by Inhibitor Binding to Its S' Subsites. Biochemistry 51:3723-3731; doi:10.1021/bi300368b.
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GlpG rhomboid-family intramembrane peptidase: Haemophilus influenzae (expressed in E. coli), 2.2 Å
Shows three bound lipid molecules. Monoclinic C2 space group. |
Lemieux et al. (2007)
Lemieux MJ, Fischer SJ, Cherney MM, Bateman KS, & James MNG (2007). The crystal structure of the rhomboid peptidase from Haemophilus influenzae provides insight into intramembrane proteolysis. Proc Natl Acad Sci USA 104:750-754.
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GlpG rhomboid-family intramembrane peptidase: Haemophilus influenzae (expressed in E. coli), 2.84 Å
Reveals disorder in loops 4 and 5 and helix 5. |
Brooks et al. (2011)
Brooks CL, Lazareno-Saez C, Lamoureux JS, Mak MW, & Lemieux MJ (2011). Insights into Substrate Gating inH. influenzaeRhomboid. J Mol Biol 407:687-697.
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Site-2 Protease (S2P). Intramembrane Metalloprotease: Methanocaldococcus jannaschii, 3.3 Å
Structure is of the transmembrane core only. |
Feng et al. (2007)
Feng L, Yan H, Wu Z, Yan N, Wang Z, Jeffrey PD, & Shi Y (2007). Structure of a site-2 protease family intramembrane metalloprotease. Science 318:1608-1612.
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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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FlaK preflagellin aspartyl protease: Methanococcus maripaludis (expressed in E. coli), 3.60 Å
This is a GXGD protease related to presenilln. |
Hu et al. (2011)
Hu J, Xue Y, Lee S, & Ha Y (2011). The crystal structure of GXGD membrane protease FlaK Nature 475:528-531; doi:10.1038/nature10218.
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Membrane-Bound Metalloproteases
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apo-FtsH ATP-dependent metalloprotease: Thermotoga maritima (expressed in E. coli), 2.60 Å
This is a homo-hexameric AAA+ protease. Each monomer is anchored to the cytoplasmic membrane by two transmembrane segments, which are missing in the structure. The protease can degrade both soluble and membrane proteins. |
Bieniossek et al. (2009)
Bieniossek C, Niederhauser B, & Baumann UM (2009). The crystal structure of apo-FtsH reveals domain movements necessary for substrate unfolding and translocation. Proc Natl Acad Sci USA 106:21579-21584.
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H+/Cl-Exchange Transporters
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H+/Cl- Exchange Transporter: Salmonella typhimurium (expressed in E. coli), 3.0 Å
Formerly ClC Chloride Channel. Eschericia coli protein, 3.5 Å: 1KPK |
Dutzler et al. (2002)
Dutzler R, Campbell EB, Cadene M, Chait BT, & MacKinnon R (2002). X-ray structure of a ClC chloride channel at 3.0 Å reveals the molecular basis of anion selectivity. Nature 415:287-294.
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Dutzler et al. (2003)
Dutzler R, Campbell EB, & MacKinnon R (2003). Gating the selectivity filter in ClC chloride channels. Science 300:108-112.
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Lobet & Dutzler (2006)
Lobet S & Dutzler R (2006). Ion-binding properties of the ClC chloride selectivity filter. EMBO J 25:24-33.
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Monomeric H+/Cl- Exchange Transporter: Escherichia coli, 3.10 Å
ClC transporter was engineered to place tryptophan residues (I201W; I422W) at the momomer-monomer interface to prevent dimerization. |
Robertson et al. (2010)
Robertson JL, Kolmakova-Partensky L, & Miller C (2010). Design, function and structure of a monomeric ClC transporter. Nature 468:844-847.
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H+/Cl- Eukaryotic Exchange Transporter: Cyanidioschyzon merolae (expressed in Trichoplusia ni), 3.50 Å
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Feng et al. (2010)
Feng L, Campbell EB, Hsiung Y, & MacKinnon R (2010). Structure of a eukaryotic CLC transporter defines an intermediate state in the transport cycle. Science 330:635-641.
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H+/Cl- Eukaryotic Exchange Transporter: Synechocystis sp. pcc 6803 (expressed in E. coli), 3.20 Å
In the presence of Br-, 3.60 Å: 3Q17 |
Jayaram et al. (2011)
Jayaram H, Robertson JL, Wu F, Williams C, & Miller C (2011). Structure of a Slow CLC Cl?/H+Antiporter from a Cyanobacterium. Biochemistry 50:788-794.
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CorA Superfamily Ion Transporters
Channels and transporters for divalent cation homeostasis. These have a membrane domain in series with a cytoplasmic domain that together form a continuous channel. |
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CorA Mg2+ Transporter: Thermotoga maritima (expressed in E. coli), 3.9 Å
Cytoplasmic domain alone, 1.85 Å: 2BBH |
Lunin et al. (2006)
Lunin VV, Dobrovetsky E, Khutoreskaya G, Zhang R, Joachimiak A, Doyle DA, Bochkarev A, Maguire ME, Edwards AM, & Koth CM (2006). Crystal structure of the CorA Mg2+transporter. Nature 440:833-837.
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CorA Mg2+ Transporter: Thermotoga maritima (expressed in E. coli), 2.9 Å
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Eshaghi et al. (2006)
Eshaghi S, Niegowski D, Kohl A, Martinez Molina D, Lesley SA, & Nordlund P (2006). Crystal structure of a divalent metal ion transporter CorA at 2.9 angstrom resolution. Science 313:354-357.
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CorA Mg2+ Transporter: Thermotoga maritima (expressed in E. coli), 3.7 Å
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Payandeh & Pai (2006)
Payandeh J & Pai EF (2006). A structural basis for Mg2+ homeostasis and the CorA translocation cycle EMBO J 25:3762-3773; doi:10.1038/sj.emboj.7601269.
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ZntB Zn+2 transporter cytoplasmic domain: Vibrio parahemolyticus (expressed in E. coli), 1.90 Å
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Tan et al. (2009)
Tan K, Sather A, Robertson JL, Moy S, Roux B, & Joachimiak A (2009). Structure and electrostatic property of cytoplasmic domain of ZntB transporter Protein Sci 18:2043-2052; doi:10.1002/pro.215.
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ZntB Zn+2 transporter cytoplasmic domain, P21 space group: Salmonella enterica (expressed in E. coli), 2.30 Å
C2 space group, 3.13 Å: 3NWI |
Wan et al. (2011)
Wan Q, Ahmad MF, Fairman J, Gorzelle B, de la Fuente M, Dealwis C, & Maguire ME (2011). X-Ray crystallography and isothermal titration calorimetry studies of the Salmonella zinc transporter ZntB Structure 19:700-710; doi:10.1016/j.str.2011.02.011.
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Bacterial Mercury Detoxification Proteins
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MerF Hg(II) transporter: Morganella morganii (expressed in E. coli), NMR structure
Structure of truncated protein (AAs 13-72) determined in aligned bicelles. |
De Angelis et al. (2006)
De Angelis AA, Howell SC, Nevzorov AA, & Opella SJ (2006). Structure determination of a membrane protein with two trans-membrane helices in aligned phospholipid bicelles by solid-state NMR spectroscopy. J AM Chem Soc 128:12256-12267.
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MerF Hg(II) transporter: Morganella morganii (expressed in E. coli), NMR structure
Structure of truncated protein (AAs 13-72) determined in SDS micelles. |
Howell et al. (2005)
Howell SC, Mesleh MF, & Opella SJ (2005). NMR structure determination of a membrane protein with two transmembrane helices in micelles: MerF of the bacterial mercury detoxification system. Biochemistry 44:5196-5206.
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MerF Hg(II) transporter: Morganella morganii (expressed in E. coli), NMR Structure
Structure of truncated protein (AAs 13-70) determined in proteoliposomes. |
Das et al. (2012)
Das BB, Nothnagel HJ, Lu GJ, Son WS, Tian Y, Marassi FM, & Opella SJ (2012). Structure determination of a membrane protein in proteoliposomes. J Amer Chem Soc 134:2047-2056; doi:10.1021/ja209464f.
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Multi-Drug Efflux Transporters
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AcrB bacterial multi-drug efflux transporter: Escherichia coli, 3.5 Å
AcrB is a member of the resistance nodulation and cell division (RND) superfamily, as is SecDF. |
Murakami et al. (2002)
Murakami S, Nakashima R, Yamashita E, & Yamaguchi A (2002). Crystal structure of bacterial multidrug efflux transporter AcrB. Nature 419:587-593.
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Yu et al. (2003)
Yu EW, McDermott G, Zgurskaya HI, Nikaido H, & Koshland Jr, DE (2003). Structural basis of multiple drug-binding capacity of the AcrB multidrug efflux pump. Science 300:976-980.
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Yu et al. (2005)
Yu EW, Aires JR, McDermott G, & Nikaido H (2005). A periplasmic drug-binding site of the AcrB multidrug efflux pump: a crystallographic and site-directed mutagenesis study. J Bacteriol 187:6804-6815.
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Su et al. (2006)
Su CC, Li M, Gu R, Takatsuka Y, McDermott G, Nikaido H, & Yu EW (2006). Conformation of the AcrB multidrug efflux pump in mutants of the putative proton relay pathway. J Bacteriol 188:7290-7296.
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AcrB bacterial multi-drug efflux transporter: Escherichia coli, 2.9 Å
Two crystal forms. C2: 2GIF. P1: 2HRT, 3.0 Å. Together, the two forms suggest a pump mechanism. |
Seeger et al. (2006)
Seeger MA, Schiefner A, Eicher T, Verrey F, Diederichs K, & Pos KM (2006). Structural asymmetry of ArcB trimer suggests a peristaltic pump mechanism. Science 313:1295-1298.
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Murakami et al. (2006)
Murakami S, Nakashima R, Yamashita E, Matsumoto T, & Yamaguchi A (2006). Crystal structures of a bacterial multidrug transporter reveal a functionally rotating mechanism. Nature 443:173-179.
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AcrB bacterial multi-drug efflux transporter with YajC subunit: Escherichia coli, 3.5 Å
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Törnroth-Horsefield et al. (2007)
Törnroth-Horsefield S, Gourdon P, Horsefield R, Brive L, Yamamoto N, Mori H, Snijder A, & Neutze R (2007). Crystal Structure of AcrB in Complex with a Single Transmembrane Subunit Reveals Another Twist. Structure 15:1663-1673.
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AcrB bacterial multi-drug efflux transporter in complex with bile acid: Escherichia coli, 3.85 Å
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Drew et al. (2008)
Drew D, Klepsch MM, Newstead S, Flaig R, De Gier JW, Iwata S, & Beis K (2008). The structure of the efflux pump AcrB in complex with bile acid. Mol Membr Biol 25:677-682.
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AcrB bacterial multi-drug efflux transporter with bound rifampicin: Escherichia coli, 3.35 Å
This and the additional structures below reveal two discrete multisite binding pockets. Unliganded AcrB, 3.35 Å: 3AOA With bound erythromycin, 3.34 Aring;: 3AOC With bound rifampicin & minocyline, 3.30 Å: 3AOD |
Nakashima et al. (2011)
Nakashima R, Sakurai K, Yamasaki S, Nishino K, & Yamaguchi A (2011). Structures of the multidrug exporter AcrB reveal a proximal multisite drug-binding pocket. Nature 480:565-569; doi:10.1038/nature10641.
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MexB bacterial multi-drug efflux transporter: Pseudomonas aeruginosa (expressed in E. coli), 3.0 Å
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Sennhauser et al. (2009)
Sennhauser G, Bukowska MA, Briand C, Grütter MG (2009). Crystal Structure of the Multidrug Exporter MexB from Pseudomonas aeruginosa. J Mol Biol 389:134-145.
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Higgins et al. (2004)
Higgins MK, Bokma E, Koronakis E, Hughes C, & Koronakis V (2004). Structure of the periplasmic component of a bacterial drug efflux pump. Proc Natl Acad Sci USA 101:9994-9999; doi:10.1073/pnas.0400375101.
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MexA membrane fusion protein: Pseudomonas aeruginosa, 2.40 Å
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Akama et al. (2004)
Akama H, Matsuura T, Kashiwagi S, Yoneyama H, Narita S, Tsukihara T, Nakagawa A, & Nakae T (2004). Crystal structure of the membrane fusion protein, MexA, of the multidrug transporter in Pseudomonas aeruginosa. J Biol Chem 279:25939-25942; doi:10.1074/jbc.C400164200.
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CusA metal-ion efflux pump: Escherichia coli, 3.52 Å
Pumps out Ag+ and Cu+ ions. |
Long et al. (2010)
Long F, Su CC, Zimmermann MT, Boyken SE, Rajashankar KR, Jernigan RL, & Yu EW (2010). Crystal structures of the CusA efflux pump suggest methionine-mediated metal transport. Nature 467:484-488.
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CusBA heavy-metal efflux complex: Escherichia coli, 2.90 Å
CusA is the efflux transporter located in the inner membrane. CusB, located in the periplasmic space, is a so-called membrane fusion protein that bridges CusA to CusC to form the tripartite efflux complex CusCBA. |
Su et al. (2011)
Su CC, Long F, Zimmermann MT, Rajashankar KR, Jernigan RL, & Yu EW (2011). Crystal structure of the CusBA heavy-metal efflux complex of Escherichia coli. Nature 470:558-562; doi:10.1038/nature09743.
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Su et al. (2009)
Su CC, Yang F, Long F, Reyon D, Routh MD, Kuo DW, Mokhtari AK, Van Ornam JD, Rabe KL, Hoy JA, Lee YJ, Rajashankar KR, & Yu EW (2009). Crystal structure of the membrane fusion protein CusB from Escherichia coli. J Mol Biol 393:342-355; doi:10.1016/j.jmb.2009.08.029.
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Chen et al. (2007)
Chen YJ, Pornillos O, Lieu S, Ma C, Chen AP, & Chang G (2007). X-ray structure of EmrE supports dual topology model. Proc Natl Acad Sci USA 104:18999-19004.
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NorM Multidrug and Toxin Compound Extrusion (MATE) transporter (apo form): Vibrio cholerae (expressed in E. coli), 3.65 Å
With bound Rb+, 4.20 Å: 3MKU |
He et al. (2010)
He X, Szewczyk P, Karyakin A, Evin M, Hong WX, Zhang Q, & Chang G (2010). Structure of a cation-bound multidrug and toxic compound extrusion transporter. Nature 467:991-994.
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Membrane-Associated Proteins in Eicosanoid and Glutathione Metabolism (MAPEG)
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Microsomal Glutathione Transferase 1: Rattus norvegicus, 3.2 Å
Electron Diffraction |
Holm et al. (2006)
Holm PJ, Bhakat P, Jegerschold C, Gyobu N, Mitsuoka K, Fujiyoshi Y, Morgenstern R, & Hebert H. (2006). Structural Basis for Detoxification and Oxidative Stress Protection in Membranes. J Mol Biol 360:934-945.
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Microsomal Prostaglandin E Synthase 1: Homo sapiens (expressed in E. coli), 3.5 Å
Electron Diffraction. In complex with glutathione. |
Jegerschöld et al. (2008)
Jegerschöld C, Pawelzik SC, Purhonen P, Bhakat P, Gheorghe KR, Gyobu N, Mitsuoka K, Morgenstern R, Jakobsson PJ, & Hebert H (2008). Structural basis for induced formation of the inflammatory mediator prostaglandin E2. Proc Natl Acad Sci USA 105:11110-11115.
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5-Lipoxygenase-Activating Protein (FLAP) with Bound MK-591 Inhibitor: Human (expressed in E. coli), 4.0 Å
FLAP with iodinated MK-591 analog: 2Q7R. |
Ferguson et al. (2007)
Ferguson AD, McKeever BM, Xu S, Wisniewski D, Miller DK, Yamin TT, Spencer RH, Chu L, Ujjainwalla F, Cunningham BR, Evans JF, & Becker JW (2007). Crystal structure of inhibitor-bound human 5-lipoxygenase-activating protein. Science 317:510-512.
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Leukotriene LTC4 Synthase in complex with glutathione: Human (expressed in Shizosaccharomyces pombe), 3.3 Å
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Ago et al. (2007)
Ago H, Kanaoka Y, Irikura D, Lam BK, Shimamura T, Austen KF, & Miyano M (2007). Crystal structure of a human membrane protein involved in cysteinyl leukotriene biosynthesis. Nature 448:609-612.
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Leukotriene LTC4 Synthase in complex with glutathione: Human (expressed in Pichia pastoris), 2.15 Å
apo form: 2UUI, 2.00 Å. |
Molina et al. (2007)
Molina DM, Wetterholm A, Kohl A, McCarthy AA, Niegowski D, Ohlson E, Hammarberg T, Eshaghi S, Haeggstrom JZ, & Nordlund P (2007). Structural basis for synthesis of inflammatory mediators by human leukotriene C4synthase. Nature 448:613-616.
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Major Facilitator Superfamily (MFS) Transporters
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LacY Lactose Permease Transporter (C154G mutant): Escherichia coli, 3.6 Å
1PV7 is with bound high-affinity lactose homolog, TDG. See 1PV6 for structure without TDG (3.5 Å). |
Abramson et al. (2003)
Abramson J, Smirnova I, Kasho V, Verner G, Kaback HR, & Iwata S (2003). Structure and mechanism of the lactose permease of Escherichia coli. Science 301:610-615.
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LacY Lactose Permease (C154G mutant) without substrate at 2 pH values: Escherichia coli, 2.95 Å
2CFQ structure determined at pH 6.5. 2CFP structure determined at pH 5.6 (3.30 Å). |
Mirza et al. (2006)
Mirza O, Guan L, Verner G, Iwata S & Kaback HR (2006). Structural evidence for induced fit and a mechanism for sugar/H+symport in LacY. EMBO J 25:1177-1183.
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LacY Lactose Permease (wild-type) with TDG: Escherichia coli, 3.6 Å
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Guan et al. (2007)
Guan L, Mirza O, Verner G, Iwata S, & Kaback HR (2007). Structural determination of wild-type lactose permease. Proc Natl Acad Sci USA 104:15294-15298.
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LacY Lactose Permease with covalently bound MTS-gal: Escherichia coli, 3.4 Å
methanethiosulfonyl-galactopyranoside (MTS-gal) is a 'suicide' substrate. |
Chaptal et al. (2011)
Chaptal V, Kwon S, Sawaya MR, Guan L, Kaback HR, & Abramson J (2011). Crystal structure of lactose permease in complex with an affinity inactivator yields unique insight into sugar recognition. Proc Natl Acad Sci USA 108:9361-9366; doi:10.1073/pnas.1105687108.
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FucP Fucose Transporter in outward-facing conformation: Escherichia coli, 3.1 Å
N162A mutant, 3.2 Å: 3O7P |
Dang et al. (2010)
Dang S, Sun L, Huang Y, Lu F, Liu Y, Gong H, Wang J, & Yan N (2010). Structure of a fucose transporter in an outward-open conformation. Nature 467:734-738.
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GlpT Glycerol-3-Phosphate Transporter: Escherichia coli, 3.3 Å
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Huang et al. (2003)
Huang Y, Lemieux MJ, Song J, Auer M, & Wang D-N (2003). Structure and mechanism of the glycerol-3-phosphate transporter from Eschericia coli. Science 301:616-620.
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EmrD Multidrug Transporter: Escherichia coli, 3.5 Å
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Yin et al. (2006)
Yin Y, He X, Szewczyk P, Nguyen T, & Chang G. (2006). Structure of the multidrug transporter EmrD from Escherichia coli. Science 312:741-744.
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PepTSo Oligopeptide-proton symporter: Shewanella oneidensis (expressed in E. coli), 3.6 Å
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Newstead et al. (2011)
Newstead S, Drew D, Cameron AD, Postis VL, Xia X, Fowler PW, Ingram JC, Carpenter EP, Sansom MS, McPherson MJ, Baldwin SA, & Iwata S (2011). Crystal structure of a prokaryotic homologue of the mammalian oligopeptide-proton symporters, PepT1 and PepT2. EMBO J 30:417-426.
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Solute Sodium Symporter (SSS) Family
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vSGLT Sodium Galactose Transporter: Vibrio parahaemolyticus (expressed in E. coli), 2.70 Å
Galactose-bound inward-occuluded conformation |
Faham et al. (2008)
Faham S, Watanabe A, Besserer GM, Cascio D, Specht A, Hirayama BA, Wright EM, & Abramson J (2008). The crystal structure of a sodium galactose transporter reveals mechanistic insights into Na+/sugar symport. Science 321:810-814.
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vSGLT Sodium Galactose Transporter, K294A mutant: Vibrio parahaemolyticus (expressed in E. coli), 2.70 Å
inward-open conformation |
Watanabe et al. (2010)
Watanabe A, Choe S, Chaptal V, Rosenberg JM, Wright EM, Grabe M, & Abramson J (2010). The mechanism of sodium and substrate release from the binding pocket of vSGLT. Nature 468:988-991.
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Sodium/Calcium Exchanger (NCX), Lipidic Cubic Phase Crystallization: Methanocaldococcus jannaschii (expressed in E. coli), 1.90 Å
Structure determined using conventional crystallization, 3.50 Å: 3V5S |
Liao et al. (2012)
Liao J, Li H, Zeng W, Sauer DB, Belmares R, & Jiang Y (2012). Structural insight into the ion-exchange mechanism of the sodium/calcium exchanger. Science 335:686-690; doi:10.1126/science.1215759.
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Concentrative Nucleoside Transporters (CNT)
Solute Carrier Transporter Superfamily (SLC28) Active transporters that use the Na+ electrochemical gradient |
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Concentrative nucleoside transporter in complex with uridine: Vibrio cholerae (expressed in E. coli), 2.44 Å
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Johnson et al. (2012)
Johnson ZL, Cheong CG, & Lee SY (2012). Crystal structure of a concentrative nucleoside transporter from Vibrio cholerae at 2.4 Å Nature 483:489-493; doi:10.1038/nature10882.
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Nucleobase-Cation-Symport-1 (NCS1) Family
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Mhp1 Benzyl-hydantoin transporter (without substrate); outward-facing conformation: Microbacterium liquefaciens (expressed in E. coli), 2.85 Å
With hydantion substrate; closed conformation, 4.0 Å: 2JLO. |
Weyand et al. (2008)
Weyand S, Shimamura T, Yajima S, Suzuki S, Mirza O, Krusong K, Carpenter EP, Rutherford NG, Hadden JM, O'Reilly J, Ma P, Saidijam M, Patching SG, Hope RJ, Norbertczak HT, Roach PC, Iwata S, Henderson PJ, & Cameron AD (2008). Structure and Molecular Mechanism of a Nucleobase-Cation-Symport-1 Family Transporter. Science 322:709-713.
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Mhp1 Benzyl-hydantoin transporter; inward-facing conformation: Microbacterium liquefaciens (expressed in E. coli), 3.8 Å
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Shimamura et al. (2010)
Shimamura T, Weyand S, Beckstein O, Rutherford NG, Hadden JM, Sharples D, Sansom MS, Iwata S, Henderson PJ, & Cameron AD (2010). Molecular basis of alternating access membrane transport by the sodium-hydantoin transporter Mhp1. Science 328:470-473.
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Nucleobase-Cation-Symport-2 (NCS2) Family
also known as nucleobase/ascorbate transporter (NAT) |
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UraA uracil/H+ symporter: Escherichia coli, 2.78 Å
First example of a NAT/NCS2 protein. It has 14 transmembrane segments divided into two inverted repeats. |
Lu et al. (2011)
Lu F, Li S, Jiang Y, Jiang J, Fan H, Lu G, Deng D, Dang S, Zhang X, Wang J, & Yan N (2011). Structure and mechanism of the uracil transporter UraA Nature 472:243-246; doi:10.1038/nature09885.
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Betaine/Choline/Carnitine Transporter (BCCT) Family
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BetP glycine betaine transporter: Corynebacterium glutamicum (expressed in E. coli), 3.35 Å
A Na+-coupled symporter in an intermediate state. Formerly PDB 2W8A. |
Ressl et al. (2009)
Ressl S, Terwisscha van Scheltinga AC, Vonrhein C, Ott V, & Ziegler C (2009). Molecular basis of transport and regulation in the Na+/betaine symporter BetP. Nature 458:47-52.
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CaiT carnitine transporter: Escherichia coli, 3.15 Å
This is a precursor/product antiporter that catalyzes the exchange of L-carnitine wtih γ-butyrobetaine. The protein is a homotrimer with each monomer containing 12 transmembrane helices. |
Tang et al. (2010)
Tang L, Bai L, Wang WH, & Jiang T (2010). Crystal structure of the carnitine transporter and insights into the antiport mechanism. Nat Struct Mol Biol 17:492-496.
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CaiT carnitine transporter: Escherichia coli, 3.50 Å
Fully-open inward-facing conformation. |
Schulze et al. (2010)
Schulze S, Köster S, Geldmacher U, Terwisscha van Scheltinga AC, & Kühlbrandt W. (2010). Structural basis of Na+-independent and cooperative substrate/product antiport in CaiT. Nature 467:233-236.
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CaiT carnitine transporter: Proteus mirabilis, 2.3 Å
Fully-open inward-facing conformation. |
Schulze et al. (2010)
Schulze S, Köster S, Geldmacher U, Terwisscha van Scheltinga AC, & Kühlbrandt W. (2010). Structural basis of Na+-independent and cooperative substrate/product antiport in CaiT. Nature 467:233-236.
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Amino Acid/Polyamine/Organocation (APC) Superfamily
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AdiC Arginine:Agmatine Antiporter: Escherichia coli, 3.61 Å
3LRB is a re-refinement of the original 3H5B structure, which contained a register shift of 3-4 amino acids relative to 3NCY and 3GIA (below). |
Gao et al. (2009)
Gao X, Lu F, Zhou L, Dang S, Sun L, Li X, Wang J, & Shi Y. (2009). Structure and mechanism of an amino acid antiporter. Science 324:1565-1568.
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AdiC Arginine:Agmatine Antiporter (N22A, L123W mutant) with bound Arginine: Escherichia coli, 3.0 Å
Outward-facing occluded state |
Gao et al. (2010)
Gao X, Zhou L, Jiao X, Lu F, Yan C, Zeng X, Wang J, & Shi Y (2010). Mechanism of substrate recognition and transport by an amino acid antiporter. Nature 463:828-832.
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AdiC Arginine:Agmatine Antiporter (N101A mutant) with bound Arginine: Escherichia coli, 3.0 Å
Reveals AdiC in the open-to-out conformation. |
Kowalczyk et al. (2011)
Kowalczyk L, Ratera M, Paladino A, Bartoccioni P, Errasti-Murugarren E, Valencia E, Portella G, Bial S, Zorzano A, Fita I, Orozco M, Carpena X, Vázquez-Ibar JL, & Palacín M (2011). Molecular basis of substrate-induced permeation by an amino acid antiporter. Proc Natl Acad Sci USA 108:3935-3940.
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AdiC Arginine:Agmatine Antiporter (with Fab fragment): Salmonella enterica (expressed in E. coli), 3.2 Å
PDB ID was originally 3HQK, which has been superseded by 3NCY. |
Fang et al. (2009)
Fang Y, Jayaram H, Shane T, Kolmakova-Partensky L, Wu F, Williams C, Xiong Y, & Miller C (2009). Structure of a prokaryotic virtual proton pump at 3.2 Å resolution. Nature 460:1040-1043.
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Shaffer et al. (2009)
Shaffer PL, Goehring A, Shankaranarayanan A, & Gouaux E (2009). Structure and Mechanism of a Na+-independent amino acid transporter. Science 325:1010-1014.
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GadC glutamate-GABA antiporter: Escherichia coli, 3.10 Å
Structure at 3.19 Å: 4DJI |
Ma et al. (2012)
Ma D, Lu P, Yan C, Fan C, Yin P, Wang J, & Shi Y (2012). Structure and mechanism of a glutamate-GABA antiporter. Nature 483:632-636; doi:10.1038/nature10917.
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Amino Acid Secondary Transporters
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LeuTAa Leucine transporter: Aquifex aeolicus (expressed in E. coli), 1.65 Å
|
Yamashita et al. (2005)
Yamashita A, Singh SK, Kawate T, Jin Y, & Gouaux E (2005). Crystal structure of a bacterial homologue of Na+/Cl--dependent neurotransmitter transporters. Nature 437:215-223.
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Singh et al. (2007)
Singh SK, Yamashita A, & Gouaux E (2007). Antidepressant binding site in a bacterial homologue of neurotransmitter transporters. Nature 448:952-956.
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LeuT Leucine transporter with bound Na+ and tryptophan: Aquifex aeolicus (expressed in E. coli), 2.00 Å
Shows the transporter in an open-to-out conformation. w. bound glycine, 2.15 Å: 3F4J w. bound alanine, 1.90 Å: 3F48 w. bound leucine (30mM), 1.80 Å: 3F3E w. bound methionine, 1.90 Å: 3F3D w. bound selenomethionine, 1.95 Å: 3F4I w. bound 4-fluorophenylalanine, 2.10 Å: 3F3C |
Singh et al. (2009)
Singh SK, Piscitelli CL, Yamashita A, & Gouaux E (2009). A competitive inhibitor traps LeuT in an open-to-out conformation. Science 322:1655-1661.
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LeuT Leucine Transporter with Bound Desipramine: Aquifex aeolicus (expressed in E. coli), 2.9 Å
|
Zhou et al. (2007)
Zhou Z, Zhen J, Karpowich NK, Goetz RM, Law CJ, Reith ME, & Wang DN (2007). LeuT-desipramine structure reveals how antidepressants block neurotransmitter reuptake. Science 317:1390-1393.
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Wild-type LeuT transporter with bound octylglucopyranoside (OG): Aquifex aeolicus (expressed in E. coli), 2.0 Å
E290S mutant with bound OG, 2.8 Å: 3GJC |
Quick et al. (2009)
Quick M, Winther AM, Shi L, Nissen P, Weinstein H, & Javitch JA (2009). Binding of an octylglucoside detergent molecule in the second substrate (S2) site of LeuT establishes an inhibitor-bound conformation. Proc. Natl. Acad. Sci. USA 106:5563-5568.
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Mutant LeuT transporter with Nitroxide Spin Label (F177R1): Aquifex aeolicus (expressed in E. coli), 2.25 Å
I204R1 mutant, 2.25 Å: 3MPQ |
Kroncke et al. (2010)
Kroncke BM, Horanyi PS, Columbus L. (2010). Structural Origins of Nitroxide Side Chain Dynamics on Membrane Protein α-Helical Sites. Biochemistry 49:10045-10060.
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Piscitelli & Gouaux (2012)
Piscitelli CL & Gouaux E (2012). Insights into transport mechanism from LeuT engineered to transport tryptophan. EMBO J 31:228-235; doi:10.1038/emboj.2011.353.
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Crystal Structure of LeuT in the outward-open conformation in complex with Fab: Aquifex aeolicus (expressed in E. coli), 3.10 Å
(LeuTK(Y108F)-2B12 Complex) LeuT in the inward-open conformation in complex with Fab, 3.22 Å: 3TT3 (LeuTK(TSY)-6A10 complex) LeuT mutant T355V, S354A, K288A in complex with alanine and sodium, 2.99 Å: 3TU0 (LeuTK(TS) complex with Ala) |
Krishnamurthy & Gouaux (2012)
Krishnamurthy H & Gouaux E (2012). X-ray structures of LeuT in substrate-free outward-open and apo inward-open states. Nature 481:469-474; doi:10.1038/nature10737.
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LeuT Leucine Transporter Crystallized from Bicelles: Aquifex aeolicus (expressed in E. coli), 2.50 Å
3USG is designated as LeuT-Leu (C2 bicelle) LeuT-Leu (P2 bicelle), 3.11 Å: 3USI LeuT-Leu (P21 form A bicelle), 3.50 Å: 3USJ LeuT-Leu (P21 form B bicelle), 4.50 Å: 3USK LeuT-SeMet (C2 bicelle), 2.71 Å: 3USL LeuT-SeMet (C2 bicelle, collected at 1.2 Å), 3.01 Å: 3USM LeuT-SeMet (P21212 bicelle), 4.50 Å: 3USO LeuT-β-SeHG (C2 β-SeHG), 2.10 Å: 3USP |
Wang et al. (2012)
Wang H, Elferich J, & Gouaux E (2012). Structures of LeuT in bicelles define conformation and substrate binding in a membrane-like context. Nature Struc Mol Biol 19:212-219; doi:10.1038/nsmb.2215.
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Glutamate Transporter Homologue (GltPh): Pyrococcus horikoshii (expressed in E. coli), 3.50 Å
Outward-facing state |
Yernool et al. (2004)
Yernool D, Boudker O, Jin Y, & Gouaux E (2004). Structure of a glutamate transporter homologue from Pyrococcus horikoshii. Nature 431:811-818.
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Glutamate Transporter Homologue (GltPh): Pyrococcus horikoshii (expressed in E. coli), 3.51 Å
Inward-facing state |
Reyes et al. (2009)
Reyes N, Ginter C, & Boudker O (2009). Transport mechanism of a bacterial homologue of glutamate transporters. Nature 462:880-885.
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Glutamate Transporter Homologue (GltPh), cross-linked V216C-M385C mutant: Pyrococcus horikoshii (expressed in E. coli), 3.80 Å
Two protomers are inward facing and a third is outward facing. V198C, A380C mutant, 4.66 Å: 3V8G |
Verdon & Boudker (2012)
Verdon G & Boudker O (2012). Crystal structure of an asymmetric trimer of a bacterial glutamate transporter homolog. Nature Struc Mol Biol 19:355-357; doi:10.1038/nsmb.2233.
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Boudker et al. (2007)
Boudker O, Ryan RM, Yernool D, Shimamoto K, & Gouaux E (2007). Coupling substrate and ion binding to extracellular gate of a sodium-dependent aspartate transporter. Nature 445:387-393.
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Cation Diffusion Facilitator (CDF) Family
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YiiP Zinc Transporter: Escherichia coli, 3.8 Å
9-18, 2005) |
Lu & Fu (2007)
Lu M & Fu D (2007). Structure of the zinc transporter YiiP. Science 317:1746-1748.
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YiiP Zinc Transporter: Escherichia coli, 2.9 Å
9-18, 2005) |
Lu et al. (2009)
Lu M, Chai J, & Fu D (2009). Structural basis for autoregulation of the zinc transporter YiiP. Nat Struct Mol Biol 16:1063-1067.
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Antiporters
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NhaA Na+/H+ antiporter: Escherichia coli, 3.45 Å
|
Hunte et al. (2005)
Hunte C, Screpanti E, Venturi M, Rimon A, Padan E, & Michel H (2005). Structure of a Na(+)/H(+) antiporter and insights into mechanism of action and regulation by pH. Nature 435:1197-1202.
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NhaA Na+/H+ antiporter: Escherichia coli, by electron crystallography
Difference maps show structural changes with changes in pH. |
Appel et al. (2009)
Appel M, Hizlan D, Vinothkumar KR, Ziegler C, Kühlbrandt W (2009). Conformations of NhaA, the Na/H exchanger from Escherichia coli, in the pH-activated and ion-translocating states. J Mol Biol 386:351-365.
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Mitochondrial ADP/ATP Carrier: Bovine heart mitochondria, 2.2 Å
Monomeric, in complex with carboxyatractyloside inhibitor. |
Pebay-Peyroula et al. (2003)
Pebay-Peyroula E, Dahout-Gonzalez C, Kahn R, Trezeguet V, Lauquin GJ, & Brandolin G (2003). Structure of mitochondrial ADP/ATP carrier in complex with carboxyatractyloside. Nature 426:39-44.
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Mitochondrial ADP/ATP Carrier: Bovine heart mitochondria, 2.8 Å
Biological dimer with endogenous cardiolipins. |
Nury et al. (2005)
Nury H, Dahout-Gonzalez C, Trézéguet V, Lauquin G, Brandolin G, & Pebay-Peyroula E (2005). Structural basis for lipid-mediated interactions between mitochondrial ADP/ATP carrier monomers. FEBS Lett 579:13561-13556.
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UCP2 mitochondrial uncoupling protein 2: Mus musculus (expressed in E. coli), NMR structure
Solved by a combination of NMR residual dipolar couplings, paramagnetic relaxation enhancement, and molecular fragment replacement. |
Berardi et al. (2011)
Berardi MJ, Shih WM, Harrison SC, & Chou JJ (2011). Mitochondrial uncoupling protein 2 structure determined by NMR molecular fragment searching Nature 476:109-113; doi:10.1038/nature10257.
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Apical Sodium-Dependent Bile Acid Transporters (ASBT)
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Hu et al. (2011)
Hu NJ, Iwata S, Cameron AD, & Drew D (2011). Crystal structure of a bacterial homologue of the bile acid sodium symporter ASBT. Nature 478:408-411; doi:10.1038/nature10450.
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Energy-Coupling Factor (ECF) Transporters
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RibU, S Component of the Riboflavin Transporter: Staphylococcus aureus (expressed in E. coli), 3.6 Å
|
Zhang et al. (2010)
Zhang P, Wang J, & Shi Y (2010). Structure and mechanism of the S component of a bacterial ECF transporter. Nature 468:717-720.
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ThiT, S component of the Thiamin Transporter: Lactococcus lactis, 2.00 Å
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Erkens et al. (2011)
Erkens GB, Berntsson RP, Fulyani F, Majsnerowska M, Vujčić-Žagar A, Ter Beek J, Poolman B, & Slotboom DJ (2011). The structural basis of modularity in ECF-type ABC transporters. Nat Struct Mol Biol 18:755-760; doi:10.1038/nsmb.2073.
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ATP Binding Cassette (ABC) Transporters
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BtuCD Vitamin B12 Transporter: Escherichia coli, 3.2 Å
|
Locher et al. (2002)
Locher KP, Lee AT, & Rees DC (2002). The E. coli BtuCD structure: A framework for ABC transporter architecture and mechanism. Science 296:1091-1098.
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BtuCD-F Complex; BtuCD B12 Transporter + BtuF binding protein: Escherichia coli, 2.6 Å
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Hvorup et al. (2007)
Hvorup RN, Goetz BA, Niederer M, Hollenstein K, Perozo E, & Locher KP (2007). Asymmetry in the structure of the ABC transporter-binding protein complex BtuCD-BtuF. Science 317:1387-1390.
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Sav1866 Multidrug Transporter: Staphylococcus aureus, 3.0 Å
|
Dawson and Locher (2006)
Dawson RJP & Locher KP (2006). Structure of a bacterial multidrug ABC transporter. Nature 443:180-185.
|
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Hollenstein et al. (2007)
Hollenstein K, Frei DC, & Locher KP (2007). Structure of an ABC transporter in complex with its binding protein. Nature 446:213-216.
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ModBC Molybdate ABC Transporter in a trans-inhibited state: Methanosarcina acetivorans, 3.0 Å
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Gerber et al. (2008)
Gerber S, Comellas-Bigler M, Goetz BA, & Locher KP (2008). Structural basis of trans-inhibition in a molybdate/tungstate ABC transporter. Science 321:246-250.
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HI1470/1 Putative Metal-Chelate-type ABC Transporter: Haemophilus influenzae, 2.4 Å
First structure showing an inward-facing conformation of an ABC transporter |
Pinkett et al. (2007)
Pinkett HW, Lee AT, Lum P, Locher KP & Rees DC (2007). An inward-facing conformation of a putative metal-chelate-type ABC transporter. Science 315:373-377.
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MsbA Lipid "flippase" with bound AMPPNP: Salmonella typhimurium (expressed in E. coli), 3.7 Å
MsbA with bound AMPPNP used for initial model: 3B5Y, 4.5 Å ADP + Vanadate-bound conformation: 3B5Z, 4.2 Å Open apo-conformation (E. coli): 3B5W, 5.3 Å Closed apo-conformation (Vibrio cholerae expressed in E. coli): 3B5X, 5.5 Å |
Ward et al. (2007)
Ward A, Reyes CL, Yu J, Roth CB, & Chang G (2007). Flexibility in the ABC transporter MsbA: Alternating access with a twist. Proc Natl Acad Sci U S A 104:19005-19010.
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Aller et al. (2009)
Aller SG, Yu J, Ward A, Weng Y, Chittaboina S, Zhuo R, Harrell PM, Trinh YT, Zhang Q, Urbatsch IL, & Chang G. (2009). Structure of P-glycoprotein reveals a molecular basis for poly-specific drug binding. Science 323:1718-1722.
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MalFGK2-MBP Maltose uptake transporter complex: Escherichia coli, 2.8 Å
Complex includes maltose-binding protein (MBP), maltose, and ATP |
Oldham et al. (2007)
Oldham ML, Khare D, Quiocho FA, Davidson AL, & Chen J (2007). Crystal structure of a catalytic intermediate of the maltose transporter. Nature 450:515-521.
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MalFGK2 uptake transporter: Escherichia coli, 4.5 Å
Helix TM1 deleted. Shows transporter in the inward conformation in the resting state. |
Khare et al. (2009)
Khare D, Oldham ML, Orelle C, Davidson AL, & Chen J (2009). Alternating access in maltose transporter mediated by rigid-body rotations. Mol Cell 27:528-536.
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MalFGK2-MBP Maltose uptake transporter complex: Escherichia coli, 3.10 Å
The structure shows the transporter in the pretranslocation (pre-T) state using a mutant maltose binding protein MBPG69C/S337C that stabilizes the closed substrate-bound conformation. Complex with MBPG69C/S337C and AMP-PNP, 2.9 Å: 3PUZ Complex with wt. MBP and AMP-PNP, 3.1 Å: 3PUY |
Oldham & Chen (2011)
Oldham ML & Chen J (2011). Crystal structure of the maltose transporter in a pretranslocation intermediate State Science 332:1202-1205; doi:10.1126/science.1200767.
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Oldham & Chen (2011)
Oldham ML & Chen J (2011). Snapshots of the maltose transporter during ATP hydrolysis. Proc Natl Acad Sci USA 108:15152-15156; doi:10.1073/pnas.1108858108.
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MetNI Methionine uptake transporter complex: Escherichia coli, 3.7 Å
MetN-C2 domain 3DHX, 2.1 Å |
Kadaba et al. (2008)
Kadaba NS, Kaiser JT, Johnson E, Lee A, & Rees DC (2008). The high-affinity E. coli methionine ABC transporter: structure and allosteric regulation. Science 321:250-253.
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FbpC ferric iron-uptake transporter nucleotide-binding domain: Neisseria gonorrhoeae, 1.9 Å
A domain-swapped neucleotide-binding domain dimer |
Newstead et al. (2009)
Newstead S, Fowler PW, Bilton P, Carpenter EP, Sadler PJ, Campopiano DJ, Sansom MS, & Iwata S (2009). Insights into how nucleotide-binding domains power ABC transport. Structure 17:1213-1222.
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Heterodimeric ABC exporter TM287-TM288: Thermotoga maritima (expressed in E. coli), 2.90 Å
Protein is in the inward-facing conformation. |
Hohl et al. (2012)
Hohl M, Briand C, Grütter MG, & Seeger MA (2012). Crystal structure of a heterodimeric ABC transporter in its inward-facing conformation. Nature Struc Mol Biol 19:395-402; doi:10.1038/nsmb.2267.
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Methyltransferases
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Isoprenylcysteine carboxyl methyltransferase (ICMT): Methanosarcina acetivorans (expressed in E. coli), 3.40 Å
Catalyzes the final step of CAAX processing. The protein has 5 TM helices. |
Yang et al. (2011)
Yang J, Kulkarni K, Manolaridis I, Zhang Z, Dodd RB, Mas-Droux C, & Barford D (2011). Mechanism of Isoprenylcysteine Carboxyl Methylation from the Crystal Structure of the Integral Membrane Methyltransferase ICMT Mol Cell 44:997-1004; doi:10.1016/j.molcel.2011.10.020.
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Phosphoenolpyruvate-Dependent Phosphotransferases (PTSs)
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ChbC EIIC phosphorylation-coupled saccharide transporter: Bacillus cereus (expressed in E. coli), 3.30 Å
The protein is a homodimer. Each protomer contains a diacetylchitobiose. |
Cao et al. (2011)
Cao Y, Jin X, Levin EJ, Huang H, Zong Y, Quick M, Weng J, Pan Y, Love J, Punta M, Rost B, Hendrickson WA, Javitch JA, Rajashankar KR, & Zhou M (2011). Crystal structure of a phosphorylation-coupled saccharide transporter Nature 473:50-54; doi:10.1038/nature09939.
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Superfamily of K+ Transporters (SKT proteins)
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TrkH potassium ion transporter: Vibrio parahaemolyticus (expressed in E. coli), 3.51 Å
Lacking a Na+/K+-ATPase, non-animal cells require two different systems for K+ uptake, one of which is the SKT proteins. |
Cao et al. (2011)
Cao Y, Jin X, Huang H, Derebe MG, Levin EJ, Kabaleeswaran V, Pan Y, Punta M, Love J, Weng J, Quick M, Ye S, Kloss B, Bruni R, Martinez-Hackert E, Hendrickson WA, Rost B, Javitch JA, Rajashankar KR, Jiang Y, & Zhou M (2011). Crystal structure of a potassium ion transporter, TrkH. Nature 471:336-340.
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||
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P-type ATPase
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Calcium ATPase; rabbit sarcoplasmic reticulum. E1 state with bound calcium: Oryctolagus cuniculus, 2.4 Å
These ATPases are referred to as SERCA pumps; SERCA: Sarco(Endo)plasmic Reticulum CAlcium |
Toyoshima et al. (2000)
Toyoshima C, Nakasako M, Nomura H, & Ogawa H (2000). Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 Å resolution. Nature 405:647-655.
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||
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Calcium ATPase; rabbit sarcoplasmic reticulum. E1 state with bound calcium, magnesium, and an ATP analog: Oryctolagus cuniculus, 2.9 Å
|
Toyoshima & Mizutani (2004)
Toyoshima C & Mizutani T (2004). Crystal structure of the calcium pump with a bound ATP analogue. Nature 430:529-35.
|
||
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Calcium ATPase; rabbit sarcoplasmic reticulum. E2 state without bound calcium: Oryctolagus cuniculus, 3.1 Å
|
Toyoshima & Nomura (2002)
Toyoshima C & Nomura H (2002). Structural changes in the calcium pump accompanying the dissociation of calcium. Nature 418:605-611.
|
||
|
Calcium ATPase; rabbit sarcoplasmic reticulum. E2 state calcium-free with bound magnesium fluoride: Oryctolagus cuniculus, 2.3 Å
E1 state with bound AlFx and ADP, 2.40 Å: 2ZDB (supersedes 1WPE, which was superseded by 2Z9R) |
Toyoshima et al. (2004)
Toyoshima C, Nomura H, & Tsuda T (2004). Lumenal gating mechanism revealed in calcium pump crystal structures with phosphate analogues. Nature 432:361-368.
|
||
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Calcium ATPase; rabbit sarcoplamic reticulum. E1 state with bound calcium and AMPPC: Oryctolagus cuniculus, 2.6 Å
E1 state with bound calcium and ADP:AlF4–, 2.9 Å: 1T5T |
Sørensen et al. (2004)
Sørensen TL, Jensen AM Møller JV, & Nissen P (2004). Phosphoryl transfer and calcium ion occlusion in the calcium pump. Science 304:1672-1675.
|
||
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Calcium ATPase; rabbit sarcoplasmic reticulum. E2 state with bound AlF4– calcium-free: Oryctolagus cuniculus, 3.0 Å
|
Olesen et al. (2004)
Olesen C, Sørensen TL, Nielsen RC, Møller JV, & Nissen P (2004). Dephosphorylation of the calcium pump coupled to counterion occlusion. Science 306:2251-2255.
|
||
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Calcium ATPase; rabbit sarcoplasmic reticulum. Ca2+-free, with bound BHQ and thapsigargin: Oryctolagus cuniculus, 3.0 Å
|
Obara et al. (2005)
Obara K, Miyashita N, Xu C, Toyoshima I, Sugita Y, Inesi G, & Toyoshima C (2005). Structural role of countertransport revealed in Ca2+pump crystal structure in the absence of Ca2+. Proc Natl Acad Sci U S A 102:14489-14496.
|
||
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Calcium ATPase; rabbit sarcoplasmic reticulum. With bound synthesized derivative of thapsigargin: Oryctolagus cuniculus, 3.30 Å
|
Søhoel et al. (2006)
Søhoel H, Jensen AM, Møller JV, Nissen P, Denmeade SR, Isaacs JT, Olsen CE, Christensen SB (2006). Natural products as starting materials for development of second-generation SERCA inhibitors targeted towards prostate cancer cells. Bioorg Med Chem 14:2810-2815.
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Jensen et al. (2006)
Jensen AM, Sørensen TL, Olesen C, Møller JV, & Nissen P (2006). Modulatory and catalytic modes of ATP binding by the calcium pump. EMBO J 25:2305-2314.
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Calcium ATPase; rabbit sarcoplamic reticulum. Calcium-free with bound AlF4– and cyclopiazonic acid (CPA): Oryctolagus cuniculus, 2.65 Å
Calcium-free with bound CPA and ADP, 3.4 Å: 2OA0 |
Moncoq et al. (2007)
Moncoq K, Trieber CA, & Young HS (2007). The molecular basis for cyclopiazonic acid inhibition of the sarcoplasmic reticulum calcium pump. J Biol Chem 282:9748-9757.
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Takahashi et al. (2007)
Takahashi M, Kondou Y, & Toyoshima C (2007). Interdomain communication in calcium pump as revealed in the crystal structures with transmembrane inhibitors. Proc Natl Acad Sci USA 104:5800-5805.
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Olesen et al. (2007)
Olesen C, Picard M, Winther A-M L, Gyrup C, Morth JP, Oxvig C, Møller JV & Nissen P (2007). The structural basis of calcium transport by the calcium pump. Nature 450:1036-1042.
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Calcium ATPase; rabbit sarcoplamic reticulum. Ca2+-free E2 state with debutanoyl thapsigargin: Oryctolagus cuniculus, 3.10 Å
Structural analysis of the Type I crystal structure reveals the location and thickness of the lipid bilayer |
Sonntag et al. (2011)
Sonntag Y, Musgaard M, Olesen C, Schiφtt B, Mφller JV, Nissen P, & Thφgersen L. (2011). Mutual adaptation of a membrane protein and its lipid bilayer during conformational changes. Nat Commun 2:304; doi:10.1038/ncomms1307.
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Na,K-ATPase; pig kidney : Sus scrofa, 3.5 Å
|
Morth et al. (2007)
Morth JP, Pedersen BP, Kohl A,Toustrup-Jensen MS, Sørensen TL-M D, Petersen J, Petersen JP, Vilsen B, & Nissen P (2007). Crystal structure of the sodium-potassim pump. Nature 450:1043-1049.
|
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Na,K-ATPase; shark: Squalus acanthias, 2.4 Å
Includes α and β subunits plus FXYD regulatory protein. Reveals coordination of K+ in the transmembrane binding site. |
Shinoda et al. (2009)
Shinoda T, Ogawa H, Cornelius F, & Toyoshima C (2009). Crystal structure of the sodium-potassium pump at 2.4 Å resolution. Nature 459:446-450.
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Na,K-ATPase Regulatory Protein FXYD1: Homo sapiens (expressed in E. coli), NMR Structure
|
Teriete et al. (2007)
Teriete P, Franzin CM, Choi J, & Marassi FM (2007). Structure of the Na,K-ATPase regulatory protein FXYD1 in micelles. Biochemistry 46:6774-6783.
|
||
|
Oxenoid and Chou (2005)
Oxenoid K & Chou JJ (2005). The structure of phospholamban pentamer reveals a channel-like architecture in membranes. Proc Natl Acad Sci USA 102:10870-10875.
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Phospholamban homopentamer in T state: Homo sapiens (expressed in E. coli), NMR Structure
|
Verardi et al. (2011)
Verardi R, Shi L, Traaseth NJ, Walsh N, & Veglia G (2011). Structural topology of phospholamban pentamer in lipid bilayers by a hybrid solution and solid-state NMR method. Proc Natl Acad Sci USA 108:9101-9106; doi:10.1073/pnas.1016535108.
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Plasma Membrane H+-ATPase: Arabidopsis thaliana, 3.6 Å
|
Pedersen et al. (2007)
Pedersen BP, Buch-Pedersen MJ, Morth JP, Palmgren MG, Lauquin GJ, & Nissen P (2007). Crystal structure of the plasma membrane proton pump. Nature 450:1111-1114.
|
||
|
Copper-transporting ATPase type PIB: Legionella pneumophila (expressed in E. coli), 3.20 Å
The structure suggests a three-stage copper transport pathway |
Gourdon et al. (2011)
Gourdon P, Liu XY, Skjφrringe T, Morth JP, Mφller LB, Pedersen BP, & Nissen P (2011). Crystal structure of a copper-transporting PIB-type ATPase. Nature 475:59-64; doi:10.1038/nature10191.
|
||
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Bacterial V-type ATPase
Also called A-type ATPase |
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Rotor of V-type Na+-ATPase: Enterococcus hirae, 2.1 Å
|
Murata et al. (2005)
Murata T, Yamato I, Kakinuma Y, Leslie AG, & Walker JE (2005). Structure of the rotor of the V-Type Na+-ATPase from Enterococcus hirae. Science 308:654-659.
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V-ATPase central-axis DF complex: Enterococcus hirae (expressed in Cell-free synthesis), 2.00 Å
|
Saijo et al. (2011)
Saijo S, Arai S, Hossain KM, Yamato I, Suzuki K, Kakinuma Y, Ishizuka-Katsura Y, Ohsawa N, Terada T, Shirouzu M, Yokoyama S, Iwata S, & Murata T (2011). Crystal structure of the central axis DF complex of the prokaryotic V-ATPase. Proc Natl Acad Sci USA 108:19955-19960; doi:10.1073/pnas.1108810108.
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V1-ATPase atomic model derived from Cryo-EM reconstructions.: Thermus thermophilus, 9.7 Å
|
Lau & Rubinstein (2012)
Lau WC & Rubinstein JL (2012). Subnanometre-resolution structure of the intact Thermus thermophilus H+-driven ATP synthase. Nature 481:214-218; doi:10.1038/nature10699.
|
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V1-ATPase Complex (V-ATPase soluble domain) with bound nucleotide: Thermus thermophilus, 4.51 Å
Without nucleotide, 4.80 Å: 3A5D |
Numoto et al. (2009)
Numoto N, Hasegawa Y, Takeda K, & Miki K (2009). Inter-subunit interaction and quaternary rearrangement defined by the central stalk of prokaryotic V1-ATPase. EMBO Rep 10:1228-1234.
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A3B3 complex of V1-ATPase: Thermus thermophilus (expressed in E. coli), 2.8 Å
|
Maher et al. (2009)
Maher MJ, Akimoto S, Iwata M, Nagata K, Hori Y, Yoshida M, Yokoyama S, Iwata S, & Yokoyama K (2009). Crystal structure of A3B3complex of V-ATPase from Thermus thermophilus. EMBO J 28:3771-3779.
|
||
|
Peripheral stalk of H+-dependent V-ATP Synthase: Thermus thermophilus (expressed in E. coli), 3.10 Å
So-called PS1 structure. |
Lee et al. (2010)
Lee LK, Stewart AG, Donohoe M, Bernal RA, & Stock D (2010). The structure of the peripheral stalk of Thermus thermophilus H+-ATPase/synthase. Nat Struct Mol Biol 17:373-378.
|
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Peripheral stalk of H+-dependent V-ATP Synthase: Thermus thermophilus (expressed in E. coli), 2.25 Å
So-called PS2 structure. |
Stewart et al. (2012)
Stewart AG, Lee LK, Donohoe M, Chaston JJ, & Stock D (2012). The dynamic stator stalk of rotary ATPases. Nature Commun 3:687; doi:10.1038/ncomms1693.
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F-type ATPase
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|
F1-ATPase from bovine heart mitochondria: Bos taurus, 2.8 Å
|
Abrahams et al. (1994)
Abrahams JP, Leslie AG, Lutter R, & Walker JE (1994). Structure at 2.8 Å resolution of F1-ATPase from bovine heart mitochondria. Nature 370:621-628.
|
||
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F1-ATPase complexed with antibiotic inhibitor aurovertin B: Bos taurus, 3.10 Å
|
van Raaij et al. (1996)
van Raaij MJ, Abrahams JP, Leslie AG, & Walker JE (1996). The structure of bovine F1-ATPase complexed with the antibiotic inhibitor aurovertin B. Proc Natl Acad Sci USA 93:6913-6917.
|
||
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F1-ATPase complexed with peptide antibiotic efrapeptin: Bos taurus, 3.10 Å
|
Abrahams et al. (1996)
Abrahams JP, Buchanan SK, Van Raaij MJ, Fearnley IM, Leslie AG, & Walker JE (1996). The structure of bovine F1-ATPase complexed with the peptide antibiotic efrapeptin. Proc Natl Acad Sci USA 93:9420-9424.
|
||
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F1-ATPase complexed with azide: Bos taurus, 1.95 Å
|
Bowler et al. (2006)
Bowler MW, Montgomery MG, Leslie AG, & Walker JE (2006). How azide inhibits ATP hydrolysis by the F-ATPases. Proc Natl Acad Sci USA 103:8646-8649.
|
||
|
F1-ATPase, Ground State Structure: Bos taurus, 1.90 Å
|
Bowler et al. (2007)
Bowler MW, Montgomery MG, Leslie AG, & Walker JE (2007). Ground state structure of F1-ATPase from bovine heart mitochondria at 1.9 Å resolution. J Biol Chem 282:14238-14242.
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ATP Synthase Extrinsic Region: Bos taurus, 3.2 Å
|
Rees et al. (2009)
Rees DM, Leslie AG, Walker JE (2009). The structure of the membrane extrinsic region of bovine ATP synthase. Proc Natl Acad Sci USA 106:21597-21601.
|
||
|
F1-ATPase in an autoinhibited conformation: Escherichia coli, 3.26 Å
|
Cingolani & Duncan (2011)
Cingolani G & Duncan TM (2011). Structure of the ATP synthase catalytic complex (F1) from Escherichia coli in an autoinhibited conformation. Nat Struct Mol Biol 18:701-707; doi:10.1038/nsmb.2058.
|
||
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Stock et al. (1999)
Stock S, Leslie AGW, & Walker JE (1999). Molecular architecture of rotary motor in ATP synthase. Science 286:1700-1705.
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F1 ATPase: S. cerevisiae, 2.80 Å
|
Kabaleeswaran et al. (2006)
Kabaleeswaran V, Puri N, Walker JE, Leslie AG, & Mueller DM (2006). Novel features of the rotary catalytic mechanism revealed in the structure of yeast F1ATPase. EMBO J 25:5433-5442.
|
||
|
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Symersky et al. (2012)
Symersky J, Pagadala V, Osowski D, Krah A, Meier T, Faraldo-Gómez JD, & Mueller DM (2012). Structure of the c10 ring of the yeast mitochondrial ATP synthase in the open conformation. Nature Struc Mol Biol 19:485-491; doi:10.1038/nsmb.2284.
|
||
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Rotor (c11) of Na+-dependent F-ATP Synthase: Ilyobacter tartaricus, 2.4 Å
|
Meier et al. (2005)
Meier T, Polzer P, Diederichs K, Welte W, & Dimroth P (2005). Structure of the rotor ring of F-type Na-ATPase from Ilyobacter tartaricus. Science 308:659-662.
|
||
|
Rotor (c11) of Na+-dependent F-ATP Synthase with complete ion-coördination structure: Ilyobacter tartaricus, 2.35 Å
|
Meier et al. (2009)
Meier T, Krah A, Bond PJ, Pogoryelov D, Diederichs K, & Faraldo-Gómez JD (2009). Complete Ion-Coordination Structure in the Rotor Ring of Na+-Dependent F-ATP Synthases. J Mol Biol 391:498-507.
|
||
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Rotor (c14) of H+-dependent F-ATP Synthase of spinach chloroplasts: Spinacia oleracea, 3.80 Å
|
Vollmar et al. (2009)
Vollmar M, Schlieper D, Winn M, Büchner C, & Groth G (2009). Structure of the c14Rotor Ring of the Proton Translocating Chloroplast ATP Synthase. J Biol Chem 284:18228-18235.
|
||
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Rotor (c15) of H+-dependent F-ATP Synthase of an alkaliphilic cyanobacterium: Spirulina platensis, 2.1 Å
|
Pogoryelov et al. (2009)
Pogoryelov D, Yildiz O, Faraldo-Gómez JD, & Meier T (2009). High-resolution structure of the rotor ring of a proton-dependent ATP synthase. Nat Struct Mol Biol 16:1068-1073.
|
||
|
Rotor (c13) of H+-dependent F-ATP Synthase: Bacillus pseudofirmus OF4, 2.5 Å
|
Preiss et al. (2010)
Preiss L, Yildiz O, Hicks DB, Krulwich TA, & Meier T (2010). A New Type of Proton Coordination in an F1F0-ATP Synthase Rotor Ring. PLoS Biol 8; doi:e1000443.
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||
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Phosphotransferases
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|
Diacylglycerol kinase (DAGK): Escherichia coli, NMR structure (DPC micelles)
Domain-swapped homotrimer |
van Horn et al.. (2009)
van Horn WD, Kim HJ, Ellis CD, Hadziselimovic A, Sulistijo ES, Karra MD, Tian C, Sönnichsen FD, & Sanders CR (2009). Solution nuclear magnetic resonance structure of membrane-integral diacylglycerol kinase. Science 324:1726-1729.
|
||
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Hydrolases
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Estrone Sulfatase: Human placenta, 2.6 Å
|
Hernandez-Guzman et al. (2003)
Hernandez-Guzman FG, Higashiyama T, Pangborn W, Osawa Y, & Ghosh D (2003). Structure of human estrone sulfatase suggests functional roles of membrane association. J Biol Chem 278:22989-22997.
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Oxygenases
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Particulate methane monooxgenase (pMMO): Methylococcus capsulatus, 2.8 Å
|
Lieberman & Rosenzweig (2005)
Lieberman RL & Rosenzweig AC (2005). Crystal structure of a membrane-bound metalloenzyme that catalyses the biological oxidation of methane. Nature 434:177-181.
|
||
|
Particulate methane monooxgenase (pMMO): Methylosinus trichosporium OB3b, 3.90 Å
|
Hakemian et al. (2008)
Hakemian AS, Kondapalli KC, Telser J, Hoffman BM, Stemmler TL, & Rosenzweig AC (2008). The metal centers of particulate methane monooxygenase from Methylosinus trichosporium OB3b. Biochemistry 47:6793-6801.
|
||
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Oxidoreductases
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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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||
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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.
|
||
|
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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NarGHI Nitrate Reductase A: Escherichia coli, 1.9 Å
|
Bertero et al. (2003)
Bertero MG, Rothery RA, Palak M, Hou C, Lim D, Blasco F, Weiner JH, & Strynadka NC (2003). Insights into the respiratory electron transfer pathway from the structure of nitrate reductase A. Nature Structural Biol 10:681-687.
|
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NarGHI Nitrate Reductase A catalytic domain NarG with FS0 cluster: Escherichia coli, 2.2 Å
|
Rothery et al. (2004)
Rothery RA, Bertero MG, Cammack R, Palak M, Blasco F, Strynadka NC, & Weiner JH (2004). The catalytic subunit of Escherichia coli nitrate reductase A contains a novel [4Fe-4S] cluster with a high-spin ground state. Biochemistry 43:5324-5333.
|
||
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Bertero et al. (2005)
Bertero MG, Rothery RA, Boroumand N, Palak M, Blasco F, Ginet N, Weiner JH, Strynadka NC (2005). Structural and biochemical characterization of a quinol binding site of Escherichia coli nitrate reductase A. J Biol Chem 280:14836-14843.
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NrfH Cytochrome C Quinol Dehydrogenase: Desulfovibrio vulgaris, 2.3 Å
In complex with NrfA cytochrome c nitrite reductase. |
Rodrigues et al. (2006)
Rodrigues ML, Oliveira TF, Pereira AC & Archer M (2006). X-ray structure of the membrane-bound cytochrome c quinol dehydrogenase NrfH reveals novel haem coordination. EMBO J 25:5951-5960.
|
||
|
DsbB-DsbA Periplasmic Oxidase Complex: E. coli, 3.7 Å
DsbB is a four-helix bundle membrane protein that works with the periplasmic DsbA oxidase to introduce disulfide bonds into periplasmic proteins. |
Inaba et al. (2006)
Inaba K, Murakami S, Suzuki M, Nakagawa A, Yamashita E, Okada K, & Ito K (2006). Crystal structure of the DsbA-DsbB complex reveals a mechanism of disulfide bond generation. Cell 127:789-801.
|
||
|
DsbB-Fab complex: Eschericia coli, 3.4 Å
Shows the principal Cys104-Cys130 disulfide Updated DsbB-DsbA complex: 3.7 Å 2ZUP |
Inaba et al. (2009)
Inaba K, Murakami S, Nakagawa A, Iida H, Kinjo M, Ito K, & Suzuki M (2009). Dynamic nature of disulphide bond formation catalysts revealed by crystal structures of DsbB. EMBO J 28:779-791.
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wtDsbB-DsbA(Cys133A)-Q8 Complex: E. coli, 3.7 Å
|
Malojcic et al. (2008)
Malojcic G, Owen RL, Grimshaw JP, & Glockshuber R (2008). Preparation and structure of the charge-transfer intermediate of the transmembrane redox catalyst DsbB. FEBS Lett 582:3301-3307.
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Zhou et al. (2008)
Zhou Y, Cierpicki T, Jimenez RH, Lukasik SM, Ellena JF, Cafiso DS, Kadokura H, Beckwith J, & Bushweller JH (2008). NMR solution structure of the integral membrane enzyme DsbB: functional insights into DsbB-catalyzed disulfide bond formation. Mol Cell 31:896-908.
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Vitamin K epoxide reductase: Synechococcus sp. (expressed in E. coli), 3.60 Å
|
Li et al. (2010)
Li W, Schulman S, Dutton RJ, Boyd D, Beckwith J, Rapoport TA (2010). Structure of a bacterial homologue of vitamin K epoxide reductase. Nature 463:507-512.
|
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Mo/Wbis-MGD Oxidoreductases
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Jormakka et al. (2008)
Jormakka M, Yokoyama K, Yano T, Tamakoshi M, Akimoto S, Shimamura T, Curmi P, & Iwata S (2008). Molecular mechanism of energy conservation in polysulfide respiration. Nat Struct Mol Biol 15:730-737.
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Electron Transport Chain Complexes: Complex I
|
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Complex I membrane domain: Escherichia coli, 3.90 Å
|
Efremov et al. (2010)
Efremov RG, Baradaran R, & Sazanov LA (2010). High-resolution The architecture of respiratory complex I. Nature 465:441-445.
|
||
|
Complex I membrane domain: Escherichia coli, 3.00 Å
|
Efremov & Sazanov (2011)
Efremov RG & Sazanov LA (2011). Structure of the membrane domain of respiratory complex I. Nature 476:414-420; doi:10.1038/nature10330.
|
||
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Complex I complete: Thermus thermophilus, 4.50 Å
|
Efremov et al. (2010)
Efremov RG, Baradaran R, & Sazanov LA (2010). High-resolution The architecture of respiratory complex I. Nature 465:441-445.
|
||
|
Complex I soluble domain, oxidized (4 mol/ASU): Thermus thermophilus, 3.30 Å
|
Sazanov & Hinchliffe (2006)
Sazanov LA & Hinchliffe P (2006). Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus Science 311:1430-1436; doi:10.1126/science.1123809.
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Berrisford & Sazanov (2009)
Berrisford JM & Sazanov LA (2009). Structural basis for the mechanism of respiratory complex I J Biol Chem 284:29773-29783; doi:10.1074/jbc.M109.032144.
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Electron Transport Chain Complexes: Complex II
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Fumarate Reductase Complex: Escherichia coli, 3.3 Å
This structure has been replaced by 1L0V, below. |
Iverson et al. (1999)
Iverson TM, Luna-Chavez C, Cecchini G, & Rees DC (1999). Structure of the Escherichia coli fumerate reductase respiratory complex. Science 284:1961-1966.
|
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Iverson et al. (2002)
Iverson TM, Luna-Chavez C, Croal LR, Cecchini G, & Rees DC (2002). Crystallographic studies of the Escherichia coli quinol-fumarate reductase with inhibitors bound to the quinol-binding site. J Biol Chem 277:16124-16130.
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Fumarate Reductase Complex: Wolinella succinogenes, 1.78 Å
2BS2 has small unit cell. 1QLB, 2.2 Å, has a larger unit cell. |
Lancaster et al. (1999)
Lancaster CRD, Kröger A, Auer M, & Michel H (1999). Structure of fumarate reductase from Wolinella succinogenes at 2.2 Å resolution. Nature 402:377-385.
|
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Formate dehydrogenase-N: Escherichia coli, 1.6 Å (native structure)
HQNO complex, 2.8 Å: 1KQG |
Jormakka et al. (2002)
Jormakka M, Tornroth S, Byrne B, & Iwata S (2002). Molecular basis of proton motive force generation: structure of formate dehydrogenase-N. Science 295:1863-1868.
|
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Succinate:quinone oxidoreductase (SQR, Complex II): Escherichia coli, 2.6 Å
DNP-17 Complex, 2.9 Å: 1NEN |
Yankovskaya et al. (2003)
Yankovskaya V, Horsefield R, Törnroth S, Luna-Chavez C, Miyoshi H, Léger C, Byrne B, Cecchini G, & Iwata S (2003). Architecture of succinate dehydrogenase and reactive oxygen species generation. Science 299:700-704.
|
||
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Succinate:quinone oxidoreductase (SQR, Complex II) with Atpenin A5: Escherichia coli, 3.10 Å
|
Horsefield et al. (2006)
Horsefield R, Yankovskaya V, Sexton G, Whittingham W, Shiomi K, Omura S, Byrne B, Cecchini G, & Iwata S (2006). Structural and computational analysis of the quinone-binding site of complex II (succinate-ubiquinone oxidoreductase): a mechanism of electron transfer and proton conduction during ubiquinone reduction. J Biol Chem 281:7309-7316.
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Ruprecht et al. (2009)
Ruprecht J, Yankovskaya V, Maklashina E, Iwata S, & Cecchini G (2009). Structure of Escherichia coli succinate:quinone oxidoreductase with an occupied and empty quinone-binding site. J Biol Chem 284:29836-29846; doi:10.1074/jbc.M109.010058.
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Succinate:quinone oxidoreductase (SQR, Complex II), H207T SdhB mutant: Escherichia coli, 2.70 Å
|
Ruprecht et al. (2011)
Ruprecht J, Iwata S, Rothery RA, Weiner JH, Maklashina E, & Cecchini G (2011). Perturbation of the quinone-binding site of complex II alters the electronic properties of the proximal [3Fe-4S] iron-sulfur cluster J Biol Chem 286:12756-12765; doi:10.1074/jbc.M110.209874.
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Succinate:ubiquinone oxidoreductase (SQR, Complex II; pig heart): Sus scrofa, 2.4 Å
with inhibitors, 3.5 Å: 1ZP0 |
Sun et al. (2005)
Sun F, Huo X, Zhai Y, Wang A, Xu J, Su D, Bartlam M, & Rao Z (2005). Crystal structure of mitochondrial respiratory membrane protein complex II. Cell 121:1043-1057.
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Huang et al. (2006)
Huang LS, Sun G, Cobessi D, Wang AC, Shen JT, Tung EY, Anderson VE, & Berry EA (2006). 3-nitropropionic acid is a suicide inhibitor of mitochondrial respiration that, upon oxidation by complex II, forms a covalent adduct with a catalytic base arginine in the active site of the enzyme. J Biol Chem 281:5965-5972.
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Succinate:ubiquinone oxidoreductase (SQR, Complex II; chicken heart) with TEO at the active site: Gallus gallus , 1.74 Å
with bound malonate at the active site, 2.40 Å: 2H89 |
Huang et al. (2006)
Huang LS, Shen JT, Wang AC, & Berry EA (2006). Crystallographic studies of the binding of ligands to the dicarboxylate site of Complex II, and the identity of the ligand in the "oxaloacetate-inhibited" state. Biochim Biophys Acta 1757:1073-1083.
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Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Information about Cytochrome bc1 |
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Cytochrome bc1: Bos taurus, 2.7 Å
Bovine heart mitochondria, 5 subunits |
Xia et al. (1997)
Xia D, Yu C-A, Kim H, Xia J-Z, Kachurin AM, Zhang L, Yu L, & Deisenhofer, J (1997). Crystal structure of the cytochrome bc1complex from bovine heart mitochondria. Science 277:60-66.
|
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Cytochrome bc1: Bos taurus, 3.0 Å
Bovine Heart Mitochondria, 11 subunits. |
Iwata et al. (1998)
Iwata S, Lee JW, Okada K, Lee JK, Iwata M, Rasmussen B, Link TA, Ramaswamy S, & Jap BK (1998). Complete structure of the 11-subunit bovine mitochondrial cytochrome bc1complex. Science 281:64-71.
|
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Cytochrome bc1: Bos taurus, 2.26 Å
Bovine Heart Mitochondria, with jg144 inhibitor |
Esser et al. (2006)
Esser L, Gong X, Yang S, Yu L, Yu CA, & Xia D (2006). Surface-modulated motion switch: capture and release of iron-sulfur protein in the cytochrome bc1complex. Proc Natl Acad Sci U S A 103:13045-13050.
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Gao et al. (2003)
Gao X, Wen X, Esser L, Quinn B, Yu L, Yu CA, & Xia D. (2003). Structural basis for the quinone reduction in the bc1complex: a comparative analysis of crystal structures of mitochondrial cytochrome bc1with bound substrate and inhibitors at the Qisite. Biochemistry 42:9067-9080.
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Esser et al. (2004)
Esser L, Quinn B, Li YF, Zhang M, Elberry M, Yu L, Yu CA, & Xia D (2004). Crystallographic studies of quinol oxidation site inhibitors: a modified classification of inhibitors for the cytochrome bc1> complex. J Mol Biol 341:281-302.
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Huang et al. (2005)
Huang LS, Cobessi D, Tung EY, & Berry EA (2005). Binding of the respiratory chain inhibitor antimycin to the mitochondrial bc1complex: a new crystal structure reveals an altered intramolecular hydrogen-bonding pattern. J Mol Biol 351:573-597.
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|
Zhang et al. (1998)
Zhang ZL, Huang LS, Shulmeister VM, Chi Y-I, Kim K K, Hung L-W, Crofts AR, Berry EA, & Kim S-H (1998). Electron transfer by domain movement in cytochrome bc1. Nature 392:677-684.
|
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|
Cytochrome bc1: Sarcomyces cerevisiae, 2.3 Å
yeast, 9 subunits. |
Hunte et al. (2000)
Hunte C, Koepe J, Lange C, Rossmanith T, & Michel H (2000). Structure at 2.3 Å resolution of cytochrome bc1complex from the yeast Saccharomyces cerevisiae co-crystallized with an antibody Fv fragment. Structure 8:669-684.
|
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|
Cytochrome bc1: Sarcomyces cerevisiae, 2.3 Å
With phospholipids. |
Lange et al. (2001)
Lange C, Nett JH, Trumpower BL, & Hunte C (2001). Specific roles of protein-phospholipid interactions in the yeast cytochrome bc1complex structure. EMBO J 20:6591-6600.
|
||
|
Cytochrome bc1: Sarcomyces cerevisiae, 2.5 Å
With HHDBT inhibitor. |
Palsdottir et al. (2003)
Palsdottir H, Lojero CG, Trumpower BL, & Hunte C (2003). Structure of the yeast cytochrome bc1complex with a hydroxyquinone anion Qosite inhibitor bound. J Biol Chem 278:31303-31311.
|
||
|
Cytochrome bc1: Sarcomyces cerevisiae, 2.3 Å
With bound stigmatellin. |
Lancaster et al. (2007)
Lancaster CR, Hunte C, Kelley J 3rd, Trumpower BL, Ditchfield R (2007). A comparison of stigmatellin conformations, free and bound to the photosynthetic reaction center and the cytochrome bc1complex. J Mol Biol 368:197-208.
|
||
|
Cytochrome bc1: Sarcomyces cerevisiae, 1.9 Å
With bound isoform-1 cytochrome c. With bound isoform-2 cytochrome c, 2.50 Å: 3CXH |
Solmaz & Hunte (2008)
Solmaz SR & Hunte C (2008). Structure of complex III with bound cytochrome c in reduced state and definition of a minimal core interface for electron transfer. J Biol Chem 283:17452-17459.
|
||
|
Cytochrome bc1: Rhodobacter Sphaeroides, 3.20 Å
|
Esser et al. (2006)
Esser L, Gong X, Yang S, Yu L, Yu CA, & Xia D (2006). Surface-modulated motion switch: capture and release of iron-sulfur protein in the cytochrome bc1complex. Proc Natl Acad Sci U S A 103:13045-13050.
|
||
|
Cytochrome bc1: Rhodobacter capsulatus, 3.50 Å
|
Berry et al. (2004)
Berry EA, Huang LS, Saechao LK, Pon NG, Valkova-Valchanova M, & Daldal F (2004). X-Ray Structure of Rhodobacter Capsulatus Cytochrome bc (1): Comparison with its Mitochondrial and Chloroplast Counterparts. Photosynth Res 81:251-275.
|
||
|
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis
|
|||
|
Cytochrome b6f complex: Mastigocladus laminosus, 3.0 Å
(Original PDB file 1UM3 replaced by 1VF5) |
Kurisu et al. (2003)
Kurisu G, Zhang H, Smith JL, & Cramer WA (2003). Structure of the cytochrome b6f complex of oxygenic photosynthesis: tuning the cavity. Science 302:1009-1014.
|
||
|
Cytochrome b6f complex: Mastigocladus laminosus, 3.80 Å
In complex with quinone analogue inhibitor DBMIB. |
Yan et al. (2006)
Yan J, Kurisu G, & Cramer WA (2006). Intraprotein transfer of the quinone analogue inhibitor 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone in the cytochrome b6f complex. Proc Natl Acad Sci U S A 103:69-74.
|
||
|
Yamashita et al. (2007)
Yamashita E, Zhang H, & Cramer WA (2007). Structure of the cytochrome b6f complex: quinone analogue inhibitors as ligands of heme cn. J Mol Biol 370:39-52.
|
|||
|
Cytochrome b6f complex: Chlamydomonas reinhardtii, 3.1 Å
|
Stroebel et al. (2003)
Stroebel D, Choquet Y, Popot JL, & Picot D (2003). An atypical haem in the cytochrome b(6)f complex. Nature 426:413-418.
|
||
|
Cytochrome b6f complex: Nostoc sp. PCC 7120, 3.0 Å
|
Baniulis et al. (2010)
Baniulis D, Yamashita E, Whitelegge JP, Zatsman AI, Hendrich MP, Hasan SS, Ryan CM, & Cramer WA (2010). Structure-function, stability, and chemical modification of the cyanobacterial cytochrome b6f complex from Nostoc sp. PCC 7120. J Biol Chem 284:9861-9869.
|
||
|
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
( Information about cytochrome c oxidases) |
|||
|
Cytochrome C Oxidase, aa3: Bos taurus (bovine) heart mitochndria, 2.8 Å
|
Tsukihara et al. (1996)
Tsukihara T, Aoyama H, Yamashita E, Tomizaki T, Yamaguchi H, Shinzawa-Itoh K, Nakashima R, & Yoshikawa S (1996). The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 Å. Science 272:1136-1144.
|
||
|
Fully Oxidized Cytochrome C Oxidase, aa3: Bos taurus (bovine) heart mitochndria, 1.80 Å
Fully reduced form, 1.90 Å: 1V55 |
Tsukihara et al. (2003)
Tsukihara T, Shimokata K, Katayama Y, Shimada H, Muramoto K, Aoyama H, Mochizuki M, Shinzawa-Itoh K, Yamashita E, Yao M, Ishimura Y, Yoshikawa S (2003). The low-spin heme of cytochrome c oxidase as the driving element of the proton-pumping process. Proc Natl Acad Sci USA 100:15304-15309.
|
||
|
Cytochrome C Oxidase, aa3: Paracoccus denitrificans, 2.70 Å
|
Iwata et al. (1995)
Iwata S, Ostermeier C, Ludwig B, & Michel H (1995). Structure at 2.8 Å resolution of cytochrome c oxidase from Paracoccus denitrificans. Nature 376:660-669.
See also: Ostermeier et al. (1997) Ostermeier C, Harrenga A, Ermler U, & Michel H (1997). Structure at 2.7 Å resolution of the Paracoccus denitrificans two-subunit cytochrome c oxidase complexed with an antibody FV fragment. Proc Natl Acad Sci USA 94:10547-10553. |
||
|
Cytochrome C Oxidase, aa3, Fully Oxidized: Paracoccus denitrificans, 3.00 Å
|
Harrenga & Michel H (1999)
Harrenga A & Michel H (1999). The cytochrome c oxidase from Paracoccus denitrificans does not change the metal center ligation upon reduction. J Biol Chem 274:33296-33299.
|
||
|
Cytochrome C Oxidase, aa3, N131D variant: Paracoccus denitrificans, 2.32 Å
|
Dürr et al. (2008)
Dürr KL, Koepke J, Hellwig P, Müller H, Angerer H, Peng G, Olkhova E, Richter OM, Ludwig B, Michel H (2008). A D-pathway mutation decouples the Paracoccus denitrificans cytochrome c oxidase by altering the side-chain orientation of a distant conserved glutamate. J Mol Biol 384:865-877.
|
||
|
Cytochrome C Oxidase, aa3: Paracoccus denitrificans, 2.25 Å
|
Koepke et al. (2009)
Koepke J, Olkhova E, Angerer H, Müller H, Peng G, Michel H (2009). High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase: new insights into the active site and the proton transfer pathways. Biochim Biophys Acta 1787:635-645.
|
||
|
Cytochrome Oxidase, cbb3: Pseudomonas stutzeri, 3.2 Å
|
Buschmann et al. (2010)
Buschmann S, Warkentin E, Xie H, Langer JD, Ermler U, Michel H. (2010). The structure of cbb3cytochrome oxidase provides insights into proton pumping. Science 329:327-330.
|
||
|
Cytochrome ba3: Thermus thermophilus, 2.4 Å
|
Soulimane et al. (2000)
Soulimane T, Buse G, Bourenkov GP, Bartunik HD, Huber R, & Than ME (2000). Structure and mechanism of the aberrant ba(3)-cytochrome c oxidase from Thermus thermophilus. EMBO J 19:1766-1776.
|
||
|
Cytochrome ba3 with bound xenon: Thermus thermophilus, 3.37 Å
|
Luna et al. (2008)
Luna VM, Chen Y, Fee JA, & Stout CD (2008). Crystallographic studies of Xe and Kr binding within the large internal Cavity of Cytochrome ba3from Thermus thermophilus: Structural Analysis and Role of Oxygen Transport Channels in the Heme-Cu Oxidases. Biochemistry 47:4657-4665.
|
||
|
Cytochrome C Oxidase wild-type: Rhodobacter sphaeroides, 2.30 Å
EQ(I-286) mutant, 3.00 Å: 1M57 |
Svensson-Ek et al. (2002)
Svensson-Ek M, Abramson J, Larsson G, Törnroth S, Brzezinski P, & Iwata S (2002). The X-ray crystal structures of wild-type and EQ(I-286) mutant cytochrome c oxidases from Rhodobacter sphaeroides. J Mol Biol 321:329-339.
|
||
|
Cytochrome C Oxidase, two-subunit catalytic core: Rhodobacter sphaeroides, 2.0 Å
|
Qin et al. (2006)
Qin G, Hiser C, Mulichak A, Garavito RM, & Ferguson-Miller S (2006). Identification of conserved lipid/detergent-binding sites in a high-resolution structure of the membrane protein cytochrome c oxidase. Proc. Natl. Acad. Sci. USA 103:16117-16122.
|
||
|
Ubiquinol Oxidase, cytochrome bo3: E. coli, 3.5 Å
|
Abramson et al. (2000)
Abramson J, Riistama S, Larsson G, Jasaitis A, Svensson-Ek M, Laakkonen L, Puustinen A, Iwata S, & Wikstrom M (2000). The structure of the ubiquinol oxidase from Escherichia coli and its ubiquinone binding site. Nat Struct Biol 7:910-917.
|
||
|
Nitric Oxide Reductases
|
|||
|
Nitric Oxide Reductase: Pseudomonas aeruginosa, 2.70 Å
Crystallized with cNOR antibody (Fab) |
Hino et al. (2010)
Hino T, Matsumoto Y, Nagano S, Sugimoto H, Fukumori Y, Murata T, Iwata S, & Shiro Y (2010). Structural basis of biological N2O generation by bacterial nitric oxide reductase. Science 330:1666-1670.
|
||
|
Photosystems
|
|||
|
Photosystem I: Thermosynechococcus elongatus, 4.0 Å
|
Schubert et al. (1997)
Schubert W-D, Klukas O, Krauß N, Saenger W, Fromme P, & Witt HT (1997). Photosystem I of Synechococcus elongatus at 4 Å resolution: Comprehensive structure analysis. J Mol Biol 272:741-769.
|
||
|
Photosystem I: Thermosynechococcus elongatus, 2.5 Å
|
Jordan et al. (2001)
Jordan P, Fromme P, Witt HT, Klukas O, Saenger W, & Krauss N (2001). Three-dimensional structure of cyanobacterial photosystem I at 2.5 Å resolution. Nature 411:909-917.
|
||
|
Photosystem I (plant): Psium sativum, 3.4 Å
|
Amunts et al. (2007)
Amunts A, Drory O, & Nelson N (2007). The structure of a plant photosystem I supercomplex at 3.4 Å resolution. Nature 447:58-63.
|
||
|
Photosystem II: Thermosynechococcus elongatus, 3.8 Å
|
Zouni et al. (2001)
Zouni A, Horst-Tobias W, Kern J, Fromme P, Krauss N, Saenger W, & Orth P (2001). Crystal structure of photosystem II from Synechococcus elongatus at 3.8 Å resolution. Nature 409:739-743.
|
||
|
Photosystem II: Thermosynechococcus elongatus, 3.5 Å
Resolution sufficient to reveal oxygen-evolving center. |
Ferreira et al. (2004)
Ferreira KN, Iverson TM, Maghlaoui K, Barber J, & Iwata S (2004). Architecture of the photosynthetic oxygen-evolving center. Science 303:1831-1838.
|
||
|
Photosystem II: Thermosynechococcus elongatus, 3.0 Å
Shows locations of 77 cofactors per monomer and provides info on Mn4Ca cluster. |
Loll et al. (2005)
Loll B, Kern J, Saenger W, Zouni A, & Biesiadka J (2005). Towards complete cofactor arrangement in the 3.0 A resolution structure of photosystem II. Nature 438:1040-1044.
|
||
|
Photosystem II: Thermosynechococcus elongatus, 2.9 Å
Includes all 20 protein subunits and all 35 chlorophyll a molecules. Part 2 of coördinate file: 3BZ2 |
Guskov et al. (2009)
Guskov A, Kern J, Gabdulkhakov A, Broser M, Zouni A, & Saenger W (2009). Cyanobacterial photosystem II at 2.9-Å resolution and the role of quinones, lipids, channels and chloride. Nat Struct Mol Biol 16:334-342.
|
||
|
Photosystem II: Thermocynechococcus vulcanus, 3.7 Å
|
Kamiya & Shen (2003)
Kamiya N & Shen JR (2003). Crystal structure of oxygen-evolving photosystem II from Thermosynechococcus vulcanus at 3.7-Å resolution. Proc Natl Acad Sci USA 100:98-103.
|
||
|
Photosystem II, Br-substituted: Thermocynechococcus vulcanus, 3.7 Å
Br-substitution reveals location of chlorides. I-substituted, 4.0 Å: 3A0H |
Kawakami et al. (2009)
Kawakami K, Umena Y, Kamiya N, & Shen JR (2009). Location of chloride and its possible functions in oxygen-evolving photosystem II revealed by X-ray crystallography. Proc Natl Acad Sci USA 106:8567-8572.
|
||
|
Photosystem II: Thermosynechococcus vulcanus, 1.90 Å
Reveals the structure of the Mn4CaO5 cluster and all of their ligands. More than 1300 water molecules are observed in each monomer. |
Umena et al. (2011)
Umena Y, Kawakami K, Shen JR, & Kamiya N (2011). Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 Å; Nature 473:55-60; doi:10.1038/nature09913.
|
||
|
Light-Harvesting Complexes
|
|||
|
Light-Harvesting Complex: Rhodopseudomonas acidophila, 2.0 Å
R-free = 0.190. 1KZU, 2.5 Å R-free = 0.252 |
Papiz et al. (2003)
Papiz MZ, Prince SM, Howard T, Cogdell RJ, & Isaacs NW (2003). The structure and thermal motion of the B800-850 LH2 complex from Rps.acidophila at 2.0A resolution and 100K: new structural features and functionally relevant motions. J Mol Biol 278:31303-31311.
|
||
|
Light-Harvesting Complex: Rhodospirillum molischianum, 2.4 Å
|
Koepke et al. (1996)
Koepke J, Hu XC, Muenke C, Schulten K, & Michel H (1996). The crystal structure of the light-harvesting complex II (B800- 850) from Rhodospirillum molischianum. Structure 4:581-597.
|
||
|
Light-Harvesting Complex LHC-II, Spinach Photosystem II: Spinacia oleracia, 2.72 Å
|
Liu et al. (2004)
Liu Z, Yan H, Wang K, Kuang T, Zhang J, Gui L, An X, & Chang W (2004). Crystal structure of spinach major light-harvesting complex at 2.72 Å resolution. Nature 428:287-292.
|
||
|
Light-Harvesting Complex CP29, Spinach Photosystem II: Spinacia oleracia, 2.80 Å
|
Pan et al. (2011)
Pan X, Li M, Wan T, Wang L, Jia C, Hou Z, Zhao X, Zhang J, & Chang W (2011). Structural insights into energy regulation of light-harvesting complex CP29 from spinach. Nat Struc Mol Biol 18:309-315.
|
||
|
Light-Harvesting Complex LHC-II, Pea Photosystem II: Pisum sativum, 2.50 Å
|
Standfuss et al. (2005)
Standfuss J, Terwisscha van Scheltinga AC, Lamborghini M, Kühlbrandt W (2005). Mechanisms of photoprotection and nonphotochemical quenching in pea light-harvesting complex at 2.5 Å resolution. EMBO J 24:919-928.
|
||
|
Photosynthetic Reaction Centers
|
|||
|
Photosynthetic Reaction Center: Blastochloris viridis, 2.3 Å
The first high-resolution crystallographic structure of a membrane protein Former species name: Rhodopseudomonas virdis |
Deisenhofer et al. (1985)
Deisenhofer J, Epp O, Miki K, Huber R, & Michel H (1985). Structure of the protein subunits in the photosynthetic reaction centre of Rhodospeudomonas viridis at 3 Å resolution. Nature 318:618-624.
[not in PubMed]
|
||
|
Photosynthetic Reaction Center: Blastochloris viridis, 1.86 Å
Lipidic sponge-phase structure. Reveals lipids on protein surface. Low x-ray dose structure, 1.95 Å: 2WJM |
Wöhri et al. (2009)
Wöhri AB, Wahlgren WY, Malmerberg E, Johansson LC, Neutze R, & Katona G (2009). Lipidic sponge phase crystal structure of a photosynthetic reaction center reveals lipids on the protein surface. Biochemistry 48:9831-9838.
|
||
|
Photosynthetic Reaction Center: Rhodobacter sphaeroides, 3.0 Å
|
Yeates et al. (1987)
Yeates TO, Komiya H, Rees DC, Allen JP, & Feher G (1987). Structure of the reaction center from Rhodobacter sphaeroides R-26: Membrane-protein interactions. Proc. Natl. Acad. Sci. USA 84:6438-6442.
|
||
|
Photosynthetic Reaction Center: Rhodobacter sphaeroides, 3.1 Å
|
Chang et al. (1991)
Chang CH, Elkabbani O, Tiede D, Norris J, & Schiffer M. (1991). Structure of the membrane-bound protein photosynthetic reaction center from Rhodobacter sphaeroides. Biochemistry 30:5352-5360.
|
||
|
Photosynthetic Reaction Center: Rhodobacter sphaeroides (dark state), 2.2 Å
Illuminated state, 2.60 Å 1AIG |
Stowell et al. (1997)
Stowell MH, McPhillips TM, Rees DC, Soltis SM, Abresch E, & Feher G (1997). Light-induced structural changes in photosynthetic reaction center: implications for mechanism of electron-proton transfer. Science 276:812-816.
|
||
|
Photosynthetic Reaction Center: Rhodobacter sphaeroides, 2.35 Å
Lipidic cubic phase crystallization. |
Katona et al. (2003)
Katona K, Andréasson U, Landau EM, Andr?asson L-K, & Neutze R (2003). Lipidic cubic phase crystal structure of the photosynthetic reaction centre from Rhodobacter sphaeroides at 2.35 Å. J Mol Biol 331:681-692.
|
||
|
Photosynthetic Reaction Center: Rhodobacter sphaeroides, 1.87 Å
pH 8 neutral state. pH 8 charge-separated state, 2.07 Å: 2J8D |
Koepke et al. (2007)
Koepke J, Krammer EM, Klingen AR, Sebban P, Ullmann GM, & Fritzsch G. (2007). pH modulates the quinone position in the photosynthetic reaction center from Rhodobacter sphaeroides in the neutral and charge separated states. J Mol Biol 371:396-409.
|
||
|
Photosynthetic Reaction Center: Thermochromatium tepidum, 2.2 Å
|
Nogi et al. (2000)
Nogi T, Fathir I, Kobayashi M, Nozawa T, & Miki K (2000). Crystal structures of photosynthetic reaction center and high-potential iron-sulfur protein from Thermochromatium tepidum: thermostability and electron transfer. Proc Natl Acad Sci USA 97:6031-6036.
|
||
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The table provides useful information about integral membrane proteins whose crystallographic, or sometimes NMR, structures have been determined to a resolution sufficient to identify TM helices of helix-bundle membrane proteins (typically 4 - 4.5 Å). It is based upon Preusch et al. (1998) Preusch PC, Norvell JC, Cassatt JC, & Cassman M (1998). Progress away from 'no crystals, no grant'. Nature Struct. Biol. 5:12-14. as revised by White & Wimley (1999) White SH & Wimley WC (1999). Membrane protein folding and stability: Physical principles. Annu Rev Biophys Biomol Struct 28:319-365. . Reference is made to all of the protein types whose structures have been determined. We have attempted to make the database as inclusive as possible. If you find errors or omissions, please send a message to .
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This database emphasizes structures determined by diffraction methods, although some NMR structures are included. A comprehensive list of NMR-determined structures is available from Dror Warschawski.
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Structural Biology Knowledgebase Membrane Protein Hub
Research Collaboratory for Structural Bioinformatics (RCSB)
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Header Image: Photosystem I, 1JB0