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Cumulative MP structures, 2008
  • Bulletin Board for Unpublished MP Structures Now Available: We have created a bulletin board service for unpublished MP structures released by the Protein Data Bank.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).
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Latest new protein entered: 26 Jan 2012 at 19:20 PST.
Last database update: 26 Jan 2012 at 19:20 PST

New Structures:

Unique proteins in database = 310;  number of coördinate files in database = 928.
(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):
 

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Links to the Protein Data Bank Site
Links to the Structural Biology Knowledgebase Site
Membrane Proteins of Known 3D Structure
(Table description)
Protein PDB Code Links Reference
(links are to PubMed)
MONOTOPIC MEMBRANE PROTEINS
Cyclooxygenases
Ram Prostaglandin H2 synthase-1 (cyclooxygenase-1 or COX-1): Ovis aries, 3.5 Å
1PRH
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.
Ram Prostaglandin H2 synthase-1 (COX-1): Ovis aries, 3.4 Å
In complex with bromoaspirin.
1PTH
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.
Ram Prostaglandin H2 synthase-1 (COX-1): Ovis aries, 3.1 Å
In complex with flurbiprofen.
1CQE
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.
Ram Prostaglandin H2 synthase-1 (COX-1): Ovis aries, 2.61 Å
1EQG is complex with ibuprofen.
Complex with flurbiprofen, 2.70 Å: 1EQH
Complex with flurbiprofen methyl ester, 2.75 Å: 1HT5
Complex with alclofenac, 2.69 Å: 1HT8
1EQG
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.
Ram Prostaglandin H2 synthase-1 (COX-1): Ovis aries, 3.2 Å
In complex with O-actylsalicylhydroxamic acid.
1EBV
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.
Ram Prostaglandin H2 synthase-1 (COX-1): Ovis aries, 2.00 Å
In complex with alpha-methyl-4-biphenyl acetic acid.
1Q4G
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.
Ram Prostaglandin H2 synthase-1 (COX-1): Ovis aries, 2.00 Å
In complex with flurbiprofen + Mn(III) PPIX cofactor.
2AYL
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.
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
3N8V
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.
Cyclooxygenase-2: Mus Musculus, 3.0 Å
1CX2
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.
Squalene-Hopene Cyclases
Squalene-hopene cyclase: Alicyclobacillus acidocaldarius, 2.0 Å
2SQC is space group P43212. 3SQC, 2.8 Å is P3221.
2SQC
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.
Monoamine Oxidases
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.
1GOS
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.
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
1OJA
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.
Monoamine Oxidase A: Rat mitochondrial outer membrane (expressed in S. cerevisiae), 3.20 Å
1O5W
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.
Monoamine Oxidase A with bound Clorglycine: Human mitochondrial outer membrane (expressed in Pichia pastoris), 3.00 Å
crystal form B, 3.15 Å: 2BXS
Monoamine Oxidase B with bound Deprenyl, 2.20 Å: 2BYB
2BXR
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.
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
2Z5X
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.
Hydrolases
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.
1MT5
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.
Oxidoreductases (Monotopic)
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).
3HYW
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.
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).
2GMH
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.
Peptidoglycan Glycosyltransferases
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.
2OLV
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.
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.
2OQO
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.
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
3FWM
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.
Peptidases
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.
1B12
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.
Signal Peptidase (SPase), apoprotein: Escherichia coli, 2.40 Å
Δ2-75 protein lacking the two transmembrane helices
1KN9
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.
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.
1T7D
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.
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.
3BF0
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.
Dehydrogenases
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.
2QCU
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.
Dihydroorotate Dehydrogenases (DHODH, class 2)
Class 1 DHODHs are soluble proteins. Class 2 are membrane associated proteins.
Dihydroorotate Dehydrogenase: Escherichia coli, 1.70 Å
1J79
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.
Dihydroorotate Dehydrogenase: Escherichia coli, 1.90 Å
1XGE
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.
Dihydroorotate Dehydrogenase in complex with atovaquone: Rattus rattus (expressed in E. coli), 2.30 Å
DHO in complex with brequinar, 2.40 Å: 1UUO
1UUM
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.
Dihydroorotate Dehydrogenase, apo form: Homo sapiens (expressed in E. coli), 3.00 Å
DHODH in complex with brequinar analogue, 2.40 Å: 2PRH
DHODH in complex with 'a novel inhibitor', 3.00 Å: 2PRL
2PRM
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.
Dihydroorotate Dehydrogenase with triazolopyrimidine-based inhibitor DSM1: Plasmodium falciparum 3d7 (expressed in E. coli), 2.00 Å
With bound triazolopyrimidine-based inhibitor DSM2, 2.40 Å: 3I68
With bound triazolopyrimidine-based inhibitor DSM74, 2.50 Å: 3I6R
3I65
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.
Polymerases
TagF teichoic acid polymerase: Staphylococcus epidermidis (expressed in E. coli), 2.70 Å
H444N mutant, 2.81 Å: 3L7J
H444N + CDPG, 15' soak, 3.10 Å: 3L7K
H444N + CDPG, 30' soak, 2.95 Å: 3L7L
H584A mutant, 2.85 Å: 3L7M
3L7I
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.
ADP-Ribosylation Factors
ADP-ribosylation factor (ARF1), myristoylated: Saccharomyces cerevisiae (expressed in E. coli), NMR Structure
2K5U
Liu et al. (2009) Liu Y, Kahn RA, & Prestegard JH (2009). Structure and Membrane Interaction of Myristoylated ARF1. Structure 17:79-87.
ADP-ribosylation factor (ARF1*GTP), myristoylated: Saccharomyces cerevisiae (expressed in E. coli), NMR Structure
2KSQ
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.
Isomerases
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.
3FSN
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.
TRANSMEMBRANE PROTEINS: BETA-BARREL
Beta-Barrel Membrane Proteins: Multimeric
(Porins and Relatives)
Porin: Rhodobacter capsulatus, 1.8 Å
2POR
Weiss & Schulz (1992) Weiss MS & Schulz GE (1992). Structure of porin refined at 1.8 Å resolution. J. Mol. Biol. 227:493-509.
Porin: Rhodopeudomonas blastica, 1.96 Å
1PRN
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.
OmpK36 osmoporin: Klebsiella pneumoniae, 3.2 Å
1OSM
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.
Omp32 anion-selective porin: Comamonas acidovorans, 2.1 Å
1E54
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.
Omp32 anion-selective porin: Delftia acidovorans, 1.5 Å
With bound malate, 1.45 Å: 2FGQ
2FGR
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.
OmpF Matrix Porin: Escherichia coli, 2.4 Å
Note: Also see BtuB with bound colicin E3 R-domain, below.
2OMF
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.
OmpF Matrix Porin: Escherichia coli, 1.6 Å
With inserted 83 residue N-terminal peptide of colicin E3, 3.0 Å: 2ZLD
2ZFG
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.
OmpF Matrix Porin in complex with colicin peptide OBS1: Escherichia coli, 3.01 Å
Shows colicin bound within porin lumen spanning the membrane bilayer
3O0E
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.
OmpC Osmoporin: Escherichia coli, 2.0 Å
2J1N
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.
OmpG *monomeric* porin: Escherichia coli, 2.3 Å
2F1C
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.
OmpG *monomeric* porin in open state: Escherichia coli, 2.3 Å
OmpG in closed state, 2.73 Å: 2IWW
2IWV
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.
OmpG *monomeric* porin: Escherichia coli, NMR Structure (DPC micelles)
2JQY
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.
PhoE: Escherihia coli, 3.0 Å
1PHO
Cowan et al. (1992) Cowan SW, Schirmer T, Rummel G, Steiert M, Ghosh R, Pauptit RA, Jansonius JN, & Rosenbusch JP (1992). Crystal structures explain functional properties of two Escherichia coli porins. Nature 358:727-733.
LamB Maltoporin: Salmonella typhimurium, 2.4 Å
2MPR
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.
LamB Maltoporin: Escherichia coli, 3.1 Å
1MAL
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.
LamB Maltoporin in complex with maltose: Escherichia coli, 2.6 Å
In complex with maltotriose, 3.20 Å: 1MPN
In complex with maltohexaose, 2.80 Å: 1MPO
1MPM
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.
LamB Maltoporin in complex with sucrose: Escherichia coli, 2.4 Å
In complex with trehalose, 3.0 Å: 1MPQ
1AF6
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.
ScrY sucrose-specific porin: Salmonella typhimurium, 2.4 Å
Complexed Form, 1A0T.
Uncomplexed form, 1A0S.
1A0T
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.
MspA mycobacterial porin: Mycobacterium smegmatis, 2.5 Å
Homooctamer
1UUN
Faller et al. (2004) Faller M, Niederweis M, & Schulz GE (2004). The structure of a mycobacterial outer-membrane channel. Science 303:1189-1192.
OprP phosphate-specific transporter: Pseudomonas aeruginosa, 1.9 Å
Contains a novel nine-residue arginine ladder
2O4V
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.
OprD basic amino acid uptake channel: Pseudomonas aeruginosa, 2.9 Å
Like OprP, contains a basic ladder
2ODJ
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.
OpdK hydrocarbon transporter: Pseudomonas aeruginosa, 2.8 Å
Binds vanillate. Forms labile trimer.
2QTK
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.
PorB outer membrane protein, native structure: Neisseria meningitidis (expressed in E. coli), 2.30 Å
The second most common OMP of Neisseria, PorB is required for pathogenesis.
In complex with sucrose, 2.20 Å: 3A2S
In complex with galactose, 3.20 Å: 3A2T
In complex with AMP-PNP, 2.90 Å: 3A2U
3A2R
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.
Beta-Barrel Membrane Proteins: Monomeric/Dimeric
TolC outer membrane protein: Escherichia coli, 2.1 Å
NOTE: Functional protein is a homotrimer. Each monomer contributes 4 strands to a single barrel.
1EK9
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.
TolC outer membrane protein, ligand blocked: Escherichia coli, 2.75 Å
1TQQ
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.
TolC outer membrane protein (Y362F, R367E), partially open state: Escherichia coli, 3.2 Å
2VDE is P212121 form. C2 form, 3.30 Å: 2VDD
2VDE
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.
VceC outer membrane protein: Vibrio cholerae, 1.8 Å
NOTE: Functional protein is a homotrimer. Each monomer contributes 4 strands to a single barrel.
1YC9
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.
OprM drug discharge outer membrane protein: Pseudomonas aeruginosa, 2.56 Å
NOTE: Functional protein is a homotrimer. Each monomer contributes 4 strands to a single barrel. H32 space group.
1WP1
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.
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.
3PIK
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.
CusBA heavy-metal efflux complex outer membrane protein: Escherichia coli, 2.90 Å
CusA, present as a trimer, interacts with six CusB protomers. The CusA trimer is an inner-membrane protein. The CusB hexamer spans the periplasmic space to interact with CusC.
3NE5
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.
BenF-like Porin (putative): Pseudomonas fluorescens, 2.60 Å
3JTY
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.
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
3D5K
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.
apo BtuB cobalamin transporter: Escherichia coli, 2.0 Å
Related structures:
1NQF (SeMet-BtuB),
1NQG (Ca2+-BtuB),
1NQH (Ca2+-B12-BtuB).
1NQE
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.
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).
1UJW
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.
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.
2GUF
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.
BtuB in complex with TonB: Escherichia coli, 2.1 Å
2GSK
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.
BtuB with bound colicin E2 R-domain: Escherichia coli, 3.50 Å
2YSU
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.
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
2HDI
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.
OmpA: Escherichia coli, x-ray diffraction, 2.5 Å
1BXW
Pautsch & Schulz (1998) Pautsch A & Schulz GE (1998). Structure of the outer membrane protein A transmembrane domain. Nature Struct Biol 5:1013-1017.
OmpA: Escherichia coli, x-ray diffraction, 1.6 Å
1QJP
Pautsch & Schulz (2000) Pautsch A & Schulz GE (2000). High-resolution structure of the OmpA membrane domain. J Mol Biol 298:273-282.
OmpA: Escherichia coli, NMR (in DPC micelles)
1G90
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.
OmpA with four shortened loops: Escherichia coli, NMR (in DHPC micelles)
Called β-barrel platform (BBP)
2JMM
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.
OmpA: Klebsiella pneumoniae (expressed in E. coli), NMR Structure (DHPC micelles)
2K0L
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.
OmpT outer membrane protease: Escherichia coli, 2.6 Å
1I78
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.
Pla Plasminogen activator (native 1): Yersinia pestis (Expressed in E. coli), 1.90 Å
Wild-type (Native 2), 2.30 Å: 2X56
D86A mutant, 2.55 Å: 2X4M
2X55
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.
OmpW outer membrane protein: Escherichia coli, 2.7 Å
2F1V is orthorhomibic form. Trigonal form, 3.0 Å: 2F1T
2F1V
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.
OprG outer membrane protein: Pseudomonas aeruginosa (expressed in E. coli), 2.4 Å
Potential channel for hydrophobic molecule transport
2X27
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.
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.
2LHF
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.
OmpX: Escherichia coli, 1.9 Å
Structure at 2.1 Å, 1QJ9
1QJ8
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.
OmpX: Escherichia coli, NMR (DHPC micelles)
1ORM
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.
OmpX: Escherichia coli, NMR (DPC micelles, with H-bond constraints)
For structure without H-bond constraints, see 1Q9G
1Q9F
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.
Ail adhesion protein: Yersinia pestis (expressed in E. coli), 1.80 Å
In complex with sucrose octasulfate (SOS), 1.85 Å: 3QRC
3QRA
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.
TtoA Outer Membrane Protein (OMP): Thermus thermophilus HB27, 2.8 Å
First structure of an OMP from a thermophile
3DZM
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.
OmpLA (PldA) outer membrane phospholipase A monomer: Escherichia coli, 2.17 Å
Dimer, 2.10 Å: 1QD6
1QD5
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.
OmpLA (PldA) outer membrane phospholipase A monomer with Ca++: Escherichia coli, 2.60 Å
Dimer, 2.80 Å: 1FW3
1FW2
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.
OmpLA (PldA) active-site mutant (N156A), pH 6.1: Escherichia coli, 2.50 Å
pH 4.6, 2.80 Å: 1ILD
pH 8.3, 2.98 Å: 1IM0
1ILZ
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.
OpcA adhesin protein: Neisseria meningitidis, 2.0 Å
1K24
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.
NspA surface protein: Neisseria meningitidis, 2.55 Å
1P4T
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.
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.
2WJR
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.
PagP outer membrane palimitoyl transferease: Escherichia coli, NMR
1MM4 is Structure in DPC micelles. Structure in OG micelles: 1MM5
1MM4
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.
PagP outer membrane palimitoyl transferease: Escherichia coli, x-ray, 1.9 Å
1THQ
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.
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)
3GP6
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.
FadL long-chain fatty acid transporter: Escherichia coli, 2.6 Å
1T16 is from Monoclinic crystals. From hexagonal crystals, 2.8 Å: 1T1L
1T16
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.
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
3DWN
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.
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
3PGR
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.
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.
3DWO
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.
FauA alcaligin outer membrane transporter: Bordetella pertusssis (expressed in E. coli), 2.3 Å
3EFM
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.
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
3BS0
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.
TbuX hydrocarbon transporter: Ralstonia pickettii, 3.2 Å
3BRY
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.
Tsx nucleoside transporter (apoprotein): Eschericia coli, 3.0 Å
Protein + thymidine, 3.10 Å: 1TLW
Protein + uridine, 3.10 Å: 1TLZ
1TLY
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.
FhuA, Ferrichrome-iron receptor without ligand: Escherichia coli, 2.7 Å
With ligand: 1BY5
1BY3
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.
FhuA: Escherichia coli, 2.50 Å
Includes the structure of a bound lipopolysaccharide (LPS) molecule
In complex with ferrichrome-iron, 2.70 Å: 1FCP
2FCP
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.
FhuA-AW140-LPS: Escherichia coli, 2.5 Å
Structure of lipopolysaccharide (LPS) in complex with FhuA.
FhuA-DL41-LPS-ferricrocin, 2.7 Å: 1QFF
1QFG
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
1QKC
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
1FI1
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
2GRX
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
1FEP
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
1KMO
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.
FecA, siderophore transporter (no ligand): Escherichia coli, 2.5 Å
FecA with iron-free dicitrate, 2.15 Å: : 1PO0
FecA with diferric dicitrate, 3.4 Å: : 1PO3
1PNZ
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
2D1U
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.
HasR heme-uptake receptor in complex with HasA hemophore and heme: Serratia marcescens (expressed in E. coli), 2.7 Å
HasA~HasR, 3.0 Å: 3CSN
HasA~HasR[I671G]~heme, 2.8 Å: 3DDR
3CSL
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
1XKW
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
1XKH
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.
FpvA, Pyoverdine receptor (apo form): Pseudomonas aeruginosa, 2.77 Å
2O5P
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
2IAH
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.
3RBH
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.
P pilus usher translocation domain, PapC130-640: Escherichia coli, 3.2 Å
2VQI
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
3RFZ
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.
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.
1UYN
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
2GR8
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
2QOM
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.
EspP autotransporter, pre-cleavage state (N1023A mutant): Escherichia coli, 2.48 Å
Pre-cleavage structure (N1023D mutant), 2.52 Å: 3SLO
Pre-cleavage structure (N1023S mutant), 2.46 Å: 3SLT
3SLJ
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.
3SZE
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.
3AEH
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.
1WXR
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.
3KVN
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
2QDZ
Clantin et al. (2007) Clantin B, Delattre AS, Rucktooa P, Saint N, Meli AC, Locht C, Jacob-Dubuisson F, & Villeret V (2007). Structure of the membrane protein FhaC: a member of the Omp85-TpsB transporter superfamily. Science 317:957-961.
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.
2X8X
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
3MC9
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
2QCZ
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.
3EFC
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.
2V9H
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.
3OG5
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.
3Q6B
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.
BamB component of the Bam β-barrel assembly machine: Escherichia coli, 1.80 Å
3PRW
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.
BamB component of the Bam β-barrel assembly machine: Escherichia coli, 2.60 Å
3P1L
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.
BamB component of the Bam β-barrel assembly machine, I222 space group: Escherichia coli, 1.65 Å
P212121 space group, 1.77 Å: 3Q7N
P213 space group, 2.09 Å: 3Q7O
3Q7M
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.
BamB component of the Bam β-barrel assembly machine: Escherichia coli, 2.60 Å
2YH3
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
2YH6
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
2YH5
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
2LAF
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
3SNS
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.
3QKY
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
2YHC
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.
BamE component of the Bam β-barrel assembly machine: Escherichia coli, NMR structure
2KM7
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.
BamE component of the Bam β-barrel assembly machine: Escherichia coli, 1.80 Å
2YH9
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.
3TGO
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.
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.
2K4T
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.
2JK4
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.
3EMN
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
7AHL
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
3B07
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.
LukF component of γ-hemolysin: Staphylococcus aureus (expressed in E. coli), 1.9 Å
The structure is of the water soluble form of the protein.
At 2.5 Å: 2LKF. With bound phosphocholine, 1.9 Å: 3LKF
1LKF
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.
1PFO
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.
3KWV
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.
3NSJ
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.
3O44
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
1XEZ
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
2WCD
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
3LIM
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.
2J58
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.
Porin B monomer: Corynebacterium glutamicum (expressed in Escherichia coli), 1.82 Å
Putative helical porin, probably comprised of five monomers. Crystal form I.
Crystal form II, 2.89 Å: 2VQH
Crystal form IV, 4.20 Å: 2VQK
Crystal form III, 3.16 Å: 2VQL
2VQG
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.
3JQO
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.
Bacterial and Algal Rhodopsins
Bacteriorhodopsin (BR): Halobacterium salinarium, 3.5 Å
Electron Diffraction. The first atomic-resolution structure of bacteriorhodopsin
2BRD
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.
Bacteriorhodopsin (BR): Halobacterium salinarium, 3.0 Å
Electron Diffraction
1AT9
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.
Bacteriorhodopsin (BR): Halobacterium salinarium, 2.35 Å
The first x-ray structure of bacteriorhodopsin
1AP9
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.
Bacteriorhodopsin (BR): Halobacterium salinarium, 2.90 Å
1BRR
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.
Bacteriorhodopsin (BR): Halobacterium salinarium, 2.30 Å
1BRX
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.
Bacteriorhodopsin (BR), K intermediate: Halobacterium salinarium, 2.10 Å
R-free = O.255. R-free = 0.303, 2.1 Å: 1QKO
1QKP
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.
Bacteriorhodopsin (BR), K intermediate (illuminated): Halobacterium salinarium, 1.43 Å
Non-illuminated, 1.47 Å: 1M0L
1M0K
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.
Bacteriorhodopsin (BR): Halobacterium salinarium, 1.90 Å
1QHJ
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.
Bacteriorhodopsin (BR): Halobacterium salinarium, 1.55 Å
1C3W
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.
Bacteriorhodopsin (BR), D96N in bR state: Halobacterium salinarium, 1.80 Å
D96N in M-state, 2.00 Å: 1C8S.
1C8R
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.
Bacteriorhodopsin in ground state: Halobacterium salinarium, 1.78 Å
Ground state, after x-ray modification, 1.78 Å: 3NSB
3NS0
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.
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.
3T45
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.
Halorhodopsin (HR): Halobacterium salinarium, 1.8 Å
1E12
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.
Halorhodopsin (HR): Natronomonas pharaonis, 2.0 Å
3A7K
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.
Sensory Rhodopsin I (SRI): Anabaena (Nostoc) sp. PCC7120, 2.0 Å
1XIO
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.
Sensory Rhodopsin II (SRII): Natronomonas pharaonis, 2.40 Å
1JGJ
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.
Sensory Rhodopsin II (SRII): Natronomonas pharaonis (expressed in E. coli), 2.10 Å
1H68
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.
Sensory Rhodopsin II (SRII) with transducer: Natronomonas pharaonis (expressed in E. coli), 1.93 Å
1H2S
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.
Sensory Rhodopsin II (SRII): Natronomonas pharaonis (expressed in E. coli), NMR structure
2KSY
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.
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
3QDC
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.
Archaerhodopsin-1 (aR-1): Halorubrum sp. aus-1, 3.4 Å
1UAZ
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.
Archaerhodopsin-2 (aR-2): Haloroubrum sp. aus-2, 2.5 Å
1VGO
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.
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.
2EI4
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.
Xanthorhodopsin: Salinibacter ruber, 1.9 Å
Contains bound carotenoid.
3DDL
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.
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
3AM6
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.
G Protein-Coupled Receptors (GPCRs)
Rhodopsin: Bovine Rod Outer Segment (Bos taurus), 2.80 Å
See also 1HZX and RPE65 retinoid isomerase
1F88
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.
Rhodopsin: Bovine Rod Outer Segment, 2.6 Å
1L9H
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.
Rhodopsin: Bovine Rod Outer Segment, 2.65 Å
1GZM
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.
Rhodopsin: Bovine Rod Outer Segment, 2.2 Å
1U19
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.
Rhodopsin: Bovine Rod Outer Segment (expressed in COS cells), 3.4 Å
Recombinant rhodopsin mutant, N2C/D282C
2J4Y
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.
Rhodopsin, photoactivated: Bovine Rod Outer Segment, 4.15 Å
Ground state, rhombohedral crystals, 3.8 Å 2I35.
Ground state, trigonal crystals, 4.1 Å 2I36.
2I37
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.
Rhodopsin in ligand-free state (opsin): Bovine Rod Outer Segment, 2.9 Å
2 molecules in asymmetric unit.
3CAP
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.
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
3PXO
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.
Rhodopsin, Ops*-GαCT peptide complex: Bovine Rod Outer Segment, 3.2 Å
3DQB
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.
Rhodopsin in constitutively active meta-II state: Bos taurus (expressed in HEK2935-GnTl- cells), 3.30 Å
M257Y mutant in complex with GαCT.
4A4M
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.
Rhodopsin, Squid: Todarodes pacificus, 2.50 Å
2Z73
Murakami & Kouyama (2008) Murakami M & Kouyama T (2008). Crystal structure of squid rhodopsin. Nature 453:363-367.
Rhodopsin, Squid: Todarodes pacificus, 3.7 Å
Shows intracellularly extended cytoplasmic region.
2ZIY
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.
Rhodopsin, Squid; 9-cis isorhodopsin (Iso): Todarodes pacificus, 2.70 Å
Batho intermediate state, 2.80 Å: 3AYM
3AYN
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.
β1 adrenergic receptor (engineered): Meleagris gallopavo (turkey) (expressed in Trichoplusia ni), 2.7 Å
2VT4
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.
β1 adrenergic receptor (engineered) with bound dobutamine: Meleagris gallopavo (turkey) (expressed in Trichoplusia ni), 2.50 Å
With bound dobutamine, 2.65 Å:2Y01
With bound carmoterol, 2.65 Å:2Y02
With bound isoprenaline, 2.85 Å:2Y03
With bound salbutamol, 3.05 Å:2Y04
2Y00
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.
β1 adrenergic receptor (engineered) with bound carazolol (t1118): Meleagris gallopavo (turkey) (expressed in Trichoplusia ni), 3.00 Å
With bound cyanopindolol (t148), 3.25 Å:2YCX
With bound cyanopindolol (t468), 3.15 Å:2YCY
With bound lodocyanopindolol (t756), 3.65 Å:2YCZ
2YCW
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.
β2 adrenergic receptor: Homo sapiens (Expressed in Spodoptera frugiperda), 3.4/3.7 Å
from β2AR365-Fab5 complex. From β2AR24/365-Fab5 complex: 2R4S
2R4R
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.
Methylated β2 adrenergic receptor: Homo sapiens (Expressed in S. frugiperda), 3.4 Å
from β2AR365-Fab5 complex.
3KJ6
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.
β2 adrenergic receptor (engineered): Homo sapiens (Expressed in S. frugiperda), 2.4 Å
T4 lysozyme replaces third intracellular loop. Reveals close association with cholesterol.
2RH1
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.
β2 adrenergic receptor (engineered): Homo sapiens (Expressed in S. frugiperda), 2.8 Å
T4 lysozyme replaces third intracellular loop. Reveals specific cholesterol binding site.
3D4S
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.
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.
3P0G
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.
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.
3PDS
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.
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.
3SN6
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.
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.
3EML
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.
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.
3QAK
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.
A2A adenosine receptor (engineered) with bound adenosine: Homo sapiens (expressed in Trichoplusia ni), 3.00 Å
With synthetic agonist NECA, 2.6 Å:2YDV
2YDO
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.
A2A adenosine receptor in complex with caffeine: Homo sapiens (expressed in S. frugiperda), 3.60 Å
Engineered protein, designated A2A-StaR2: A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A
In complex with ZM241385, 3.30 Å: 3PWH
In complex with XAC, 3.31 Å: 3REY
3RFM
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.
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
3ODU
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.
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.
3PBL
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.
Histamine H1 receptor, complexed with doxepin: Homo sapiens (expressed in Pichia pastoris), 3.10 Å
3RZE
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.
Autonomously Folding "Membrane Proteins" (Sec-independent)
Mistic membrane-integrating protein: Bacillus subtilis, NMR structure
Note: This is not a constitutive membrane protein. It is included here because of general interest.
1YGM
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.
Glycoproteins
Glycophorin A transmembrane-domain dimer: Homo sapiens (expressed in E. coli), NMR Structure
1AFO
MacKenzie et al. (1997) MacKenzie KR, Prestegard JH, & Engelman DM (1997). A transmembrane helix dimer: structure and implications. Science 276:131-133.
SNARE Protein Family
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.
3HD7
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
2KOG
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.
Integrin Adhesion Receptors
Human Integrin αIIbβ3 transmembrane-cytoplasmic heterodimer: Homo sapiens (expressed in E. coli), NMR Structure
2KNC
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.
Histidine Kinase Receptors
ArcB (1-115) Aerobic Respiration Control sensor membrane domain: Escherichia coli (cell-free expression), NMR Structure
2KSD
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.
QseC (1-185) Sensor protein membrane domain: Escherichia coli (cell-free expression), NMR Structure
2KSE
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.
KdpD (397-502) Sensor protein membrane domain: Escherichia coli (cell-free expression), NMR Structure
2KSF
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
2HAC
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
2L35
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
1BL8
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
1K4C
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
3EFF
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
3PJS
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
3IGA
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.
KcsA Potassium channel in the open inactivated state. Open 32 Å conformer: Streptomyces lividans (expressed in E. coli), 3.30 Å
Open 23 Å conformer, 3.20 Å: 3F7V
Open 17 Å conformer, 3.40 Å: 3F7Y
Open 16 Å conformer, 3.00 Å: 3FB6
Open 14.5 Å conformer, 2.80 Å: 3FB5
3F5W
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
3HPL
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
3OR7
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.
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
1ORQ
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.
KvAP Voltage-gated potassium Channel in complex with Fv fragments: Aeropyrum pernix (Expressed in E. coli), 3.9 Å
2A0L
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
2KYH
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
2A79
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
3LUT
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.
2R9R
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.
3LNM
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
1LNQ
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.
K+ pore of the MthK Potassium channel (residues 28-99): Methanothermobacter thermautotrophicus (expressed in E. coli), 1.45 Å
3LDC crystallized in 100 mM KCl. S68H/V77C mutant.
99 mM NaCl + 1 mM KCl; S68R, V77C mutant; 1.45 Å: 3LDD
100 mM NaCl; S68H, V77C mutant; 2.21 Å: 3LDE
3LDC
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
3RBZ
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.
3MT5
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.
3NAF
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.
BK Channel Ca2+ gating ring from zebra fish in the open state: Danio rerio (expressed in S. frugiperda), 3.61 Å
3U6N
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
3JYC
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.
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
3SPI
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.
GIRK1 (Kir3.1) cytoplasmic domain: Mus musculus (expressed in E. coli), 1.8 Å
GIRK = G-Protein-Gated Inward Rectifying Potassium Channel
1N9P
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.
Kir3.1-Prokaryotic Kir Chimera: Mus musculus & Burkholderia xenovornas (expressed in Escherichia coli), 2.2 Å
2QKS
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.
Kir3.1 cytoplasmic domain: Mus musculus (expressed in E. coli), 2.0 Å
3K6N
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.
GIRK2 (Kir3.2) G-protein-gated K+ channel: Mus musculus (expressed in Pichia pastoris), 3.60 Å
First complete structure of a G-protein-gated potassium-selective channel.
Wild-type protein + PIP2, 3.00 Å: 3SYA
D228N mutant, 3.4 Å: 3SYC
R201A mutant, 3.1 Å: 3SYP
R201A mutant + PIP2, 3.45 Å: 3SYQ
3SYO
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.
KirBac1.1 Inward-Rectifier Potassium channel (closed state): Burkholderia pseudomallei, 3.65 Å
For re-refined structure, see 2WLL
1P7B
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.
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
2WLJ
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.
MlotiK1 cyclic nucleotide-regulated K+-channel: Mesorhizobium loti (expressed in E. coli), 3.1 Å
3BEH
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.
NaK channel (Na+complex): Bacillus cereus (expressed in E. coli), 2.4 Å
K+ complex, 2.8 Å: 2AHZ.
2AHY
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.
NaK channel with bound calcium, D66A mutant: Bacillus cereus (expressed in E. coli), 2.30 Å
D66A/S70E mutant, 2.50 Å: 2Q68. D66N mutant, 2.40 Å: 2Q69. D66E mutant, 2.60 Å: 2Q6A.
2Q67
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.
NaK channel in open state (NΔ19 mutant): Bacillus cereus (expressed in E. coli), 1.60 Å
3E86
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
3K0D
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.
NaK channel; K+ selective mutant (NaK2K): Bacillus cereus (expressed in E. coli), 1.55 Å
CNG-mimicking mutant; NaK-DTPP/K+ complex, 1.62 Å: 3K03
MthK channel T59A mutant, 1.75 Å: 3OUS
3OUF
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.
NaK/NaK2K channel mutants; NaK-D66Y: Bacillus cereus (expressed in E. coli), 1.80 Å
NaK-N68D, 1.95 Å: 3T2M
NaK2K-Y66F, 1.90 Å: 3TET
NaK2K-Y55W, 1.90 Å: 3T4Z
NaK2K-Y55F, 1.70 Å: 3T4D
NaK2K-D68E, 1.75 Å: 3TCU
3T1C
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.
Voltage-Gated Sodium Channel (Nav), I217C mutant: Arcobacter butzleri (expressed in Trichoplusia ni), 2.70 Å
NavAb is the first structure of a voltage-dependent sodium channel. It is a member of the NaChBac family.
I217C mutant, 2.80 Å: 3RVZ
M221C mutant, 2.95 Å: 3RW0
3RVY
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.
Channels: Other Ion Channels
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
3KG2
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
3BKD
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
2RLF
Schnell & Chou. (2008) Schnell JR & Chou JJ (2008). Structure and mechanism of the M2 proton channel of influenza A virus. Nature 451:591-595.
M2 proton channel (AM2) in a hydrated lipid bilayer: Influenza A (expressed in E. coli), NMR structure
2L0J
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
2KIX
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.
M2A-M2B chimeric proton channel (AM2-BM2): Influenza A/Influenza B (expressed in E. coli), NMR Structure
With rimantadine inhibitor, NMR structure: 2LJC
2LJB
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.
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
2QTS
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.
ASIC1 Acid-Sensing Ion Channel (ASIC1mfc; minimal functional channel): Gallus gallus (expressed in SF9 cells), 3.0 Å
Desensitized State
3HGC
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.
MscL Mechanosensitive channel: Mycobacterium tuberculosis, 3.5 Å
2OAR
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.
MscL Mechanosensitive channel, Δ95-120: Staphylococcus aureus, 3.8 Å
Shows MscL in an expanded intermediate state.
3HZQ
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.
MscS voltage-modulated mechanosensitive channel: Escherichia coli, 3.7 Å
2OAU
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.
MscS mechanosensitive channel in the open form: Escherichia coli, 3.45 Å
2VV5
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.
MgtE Mg2+ Transporter: Thermus thermophilus (expressed in E. coli), 3.5 Å
Cytoplasmic domains w. bound Mg2+, 2.30 Å: 2YVY
Cytoplasmic domains without Mg2+, 3.90 Å: 2YVZ
2YVX
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.
MgtE Mg2+ Transporter: Thermus thermophilus (expressed in E. coli), 2.9 Å
2ZY9
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.
SLAC1 anion channel, TehA homolog (wild-type): Haemophilus influenzae (expressed in E. coli), 1.2 Å
F262A mutant, 1.15 Å: 3M73
F262L mutant, 1.65 Å: 3M74
F262V mutant, 1.60 Å: 3M75
G15D mutant, 1.50 Å: 3M76
3M71
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.
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
3H9V
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.
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)
Nicotinic Acetylcholine Receptor Pore (closed state): Torpedo marmorata, 4.0 Å
Electron Diffraction
1OED
Miyazawa et al. (2003) Miyazawa A, Fujiyoshi Y, & Unwin N (2003). Structure and gating mechanism of the acetylcholine receptor pore. Nature 423:949-955.
Nicotinic Acetylcholine Receptor, refined structure: Torpedo marmorata, 4.0 Å
Electron Diffraction
2BG9
Unwin (2005) Unwin N. (2005). Refined structure of the nicotinic acetylcholine receptor at 4 Å resolution. J Mol Biol 346:967-989.
Prokaryotic pentameric ligand-gated ion channel (pLGIC): Erwinia chrysanthemi (expressed in E. coli), 3.3 Å
First high-resolution x-ray structure of an AChR-like channel.
2VL0
Hilf & Dutzler (2008) Hilf RJC & Dutzler R (2008). X-ray structure of a prokaryotic pentameric ligand-gated ion channel. Nature 452:375-379.
Prokaryotic pentameric ligand-gated ion channel (GLIC): Gloebacter violaceus (expressed in E. coli), 3.1 Å
Related to pLGIC (above), this pentameric channel is apparently in an open state. E221A mutant, 3.50 Å: 3EI0
3EHZ
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.
Prokaryotic pentameric ligand-gated ion channel (GLIC): Gloebacter violaceus (expressed in E. coli), 2.9 Å
Related to pLGIC (above), this pentameric channel is apparently in an open state.
3EAM
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.
Prokaryotic "pentameric" ligand-gated ion channel (GLIC) with hexameric quaternary structure: Gloebacter violaceus (expressed in E. coli), 2.3 Å
3IGQ
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.
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
2XQA
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.
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
3P50
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.
GluClα anion-selective receptor (Fab-invermectin complex): Caenorhabditis elegans (expressed in S. frugiperda), 3.26 Å
With glutamate, 3.35 Å:3RIF
With picrotoxin, 3.40 Å:3RI5
With iodide, 3.80 Å:3RIA
3RHW
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.
Channels: Aquaporins and Glyceroporins
AQP0 aquaporin water channel: Bovine lens, 2.24 Å
1YMG
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.
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.
1SOR
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.
AQP0 aquaporin sheep lens junction: Ovis aries, 1.90 Å
Electron Diffraction
Non-junctional form, 2.4 Å: 2B6P
2B6O
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.
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
3M9I
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.
AQP1 red blood cell aquaporin water channel: Homo sapiens, 3.8 Å
Electron Diffraction. Resolution shown is in-plane.
1FQY
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.
AQP1 red blood cell aquaporin water channel: Homo sapiens, 3.7 Å
Electron Diffraction. Protein in vitreous ice.
1IH5
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.
AQP1 aquaporin red blood cell water channel: Bos taurus, 2.20 Å
X-ray Diffraction
1J4N
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.
AQP4 aquaporin rat glial cell water channel: Rattus norvegicus (expressed in S. frugiperda), 3.2 Å
Electron Diffraction.
2D57
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.
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.
2ZZ9
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.
AQP4 aquaporin water channel: Human (expressed in Pichia pastoris), 1.8 Å
3GD8
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.
AQP5 aquaporin water channel (HsAQP5): human (expressed in Pichia pastoris), 2.0 Å
3D9S
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.
AqpM aquaporin water channel: Methanothermobacter marburgensis (expressed in E. coli), 1.68 Å
Initial structure, 2.3 Å: 2EVU
2F2B
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.
AqpZ aquaporin water channel: Escherichia coli, 2.5 Å
1RC2
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.
AqpZ aquaporin showing two conformations of Arg-189: Escherichia coli, 3.2 Å
2ABM
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.
AqpZ aquaporin (C9S/C20S), T183C mutant without Hg: Escherichia coli, 2.30 Å
T183C with Hg, 2.20 Å: 2O9E. L170C without Hg, 2.55 Å: 2O9F. L170C with Hg, 1.90 Å: 2O9G.
2O9D
Savage & Stroud (2007) Savage DF & Stroud RM (2007). Structural basis of aquaporin inhibition by mercury. J Mol Biol 368:607-617.
AqpZ aquaporin mutant F43W: Escherichia coli, 2.40 Å
H174G/T183F mutant, 2.50 Å: 3NKA. F43W/H174G/T183F mutant, 3.10 Å: 3NKC.
3NK5
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.
SoPIP2;1 plant aquaporin (closed conformation): Spinacia oleracea (expressed in Pichia pastoris), 2.1 Å
Open conformation, 3.9 Å: 2B5F
1Z98
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.
GlpF glycerol facilitator channel: Escherichia coli, 2.2 Å
1FX8
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.
GlpF glycerol facilitator channel, W84F/F200T-mutant: Escherichia coli, 2.1 Å
GlpF with non-transported xylose replacing glycerol: (GlpF - G)A, 2.7 Å: 1LDI
GlpF with non-transported xylose replacing glycerol: (GlpF - G)B, 2.8 Å: 1LDA
1LDF
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.
PfAQP aquaglyceroporin: Plasmodium falciparum, 2.05 Å
Transports water and glycerol equally well.
3C02
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.
Aqy1 yeast aquaporin (pH 3.5): Pischia pastoris, 1.15 Å
pH 8.0, 1.40 Å: 2W1P
2W2E
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.
Channels : Formate Nitrate Transporter (FNT) Family
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
3KCU
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.
FocA formate transporter without formate: Vibrio cholerae (expressed in E. coli), 2.10 Å
FocA with bound formate: 3KLZ, 2.50 Å
3KLY
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.
FocA formate transporter at pH 4.0: Salmonela typhimurium, 2.80 Å
Three different conformations are observed in the asymmetric unit: Open, Intermediate, & closed
3Q7K
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.
Channels: Urea Transporters
Urea transporter: Desulfovibrio vulgaris (expressed in E. coli), 2.30 Å
Structure with bound dimethyl urea: 3K3G, 2.40 Å
3K3F
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.
Channels: Gap Junctions
Connexin 26 (Cx26; GJB2) gap junction: Human (expressed in Sf9 cells), 3.5 Å
2ZW3
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.
Channels: Amt/Rh proteins
AmtB ammonia channel (mutant): Escherichia coli, 1.40 Å
1U7G is Protein + ammonia. Apoprotein, 2.0 Å: 1U77
Protein + methylammonia, 1.85 Å: 1U7C
1U7G
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.
AmtB ammonia channel (wild-type): Escherichia coli, 1.8 Å (P63 crystal form)
R3 crystal form: 1XQE, 2.1 Å resolution
1XQF
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.
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
2NMR
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.
AmtB ammonia channel in complex with GlnK: Escherichia coli, 2.5 Å
2NUU
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.
AmtB ammonia channel in complex with inhibitory GlnK: Escherichia coli, 1.96 Å
2NS1
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.
Amt-1 ammonium channel: Archaeoglobus fulgidus (expressed in E. coli), 1.72 Å
Native protein: 2B2F.
Protein + 20 mM Ammonium Sulfate: 2B2H
Protein + 80 mM Ammonium Sulfate: 2B2I
Protein+xenon: 2B2J
2B2F
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.
Rh protein, possible ammonia or CO2 channel: Nitrosomonas europaea (expressed in Methylococcus capsulatus), 1.85 Å
CO2 pressurized protein, 1.85 Å: 3B9Z
3B9Y
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.
Rh protein, possible ammonia or CO2 channel: Nitrosomonas europaea (expressed in E. coli), 1.30 Å
3B9W
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.
Human Rh C glycoprotein ammonia transporter: Homo sapiens (expressed in HEK293s cells), 2.10 Å
3HD6
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.
Sec Proteins
Membrane Proteins Involved with Protein Insertion and Secretion
formerly listed as "Channels: Protein-Conducting"
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).
1RHZ
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.
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).
2YXR
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.
SecYEβ "primed" protein-conducting channel: Pyrococcus furiosus (expressed in E. coli), 3.1 Å
3MP7
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.
SecYEG protein-conducting channel in complex with SecA: Thermotoga maritima (expressed in E. coli), 4.5 Å
3DIN
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.
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).
2ZJS
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.
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
3AQP
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.
Oligosaccharyltransferases (OST)
Catalyses Asparagine-linked (N-linked) Glycosylation
PglB OST in complex with acceptor peptide: Campylobacter lari (expressed in E. coli), 3.40 Å
3RCE
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.
Intramembrane Proteases
( NSMB News & Views on three GlpG Structures)
GlpG rhomboid-family intramembrane protease: Eschericia coli, 2.1 Å
P32 space group. One molecule in asymmetric unit.
2IC8
Wang et al. (2006) Wang Y, Zhang Y, & Ha Y (2006). Crystal structure of a rhomboid family intramembrane protease. Nature 444:179-183.
GlpG rhomboid-family intramembrane protease: Eschericia coli, 1.90 Å
W136A mutant, 1.70 Å: 3B44
3B45
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.
GlpG rhomboid-family intramembrane protease: Eschericia coli, 2.5 Å
Shows GlpG in a more open conformation.
2O7L
Wang & Ha (2007) Wang Y & Ha Y (2007). Open-cap conformation of intramembrane protease GlpG. Proc Natl Acad Sci USA 104:2098-2102.
GlpG rhomboid-family intramembrane protease: Eschericia coli, 2.6 Å
P31 space group. Two anti-parallel molecules in asymmetric unit.
2NRF
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.
GlpG rhomboid-family intramembrane protease: Eschericia coli, 2.3 Å
P21 space group. Two anti-parallel molecules in asymmetric unit.
2IRV
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.
GlpG rhomboid-family intramembrane protease: Eschericia coli, 1.65 Å
Acyl GlpG: GlpG with covalently bound isocoumarin inhibitor, 2.09 Å: 2XOW
2XOV
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.
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
2XTV
Vinothkumar (2011) Vinothkumar KR (2011). Structure of Rhomboid Protease in a Lipid Environment. J Mol Biol 407:232-247.
GlpG rhomboid-family intramembrane peptidase: Haemophilus influenzae (Expressed in E. coli), 2.2 Å
Shows three bound lipid molecules. Monoclinic C2 space group.
2NR9
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.
GlpG rhomboid-family intramembrane peptidase: Haemophilus influenzae (expressed in E. coli), 2.84 Å
Reveals disorder in loops 4 and 5 and helix 5.
3ODJ
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.
Site-2 Protease (S2P). Intramembrane Metalloprotease: Methanocaldococcus jannaschii, 3.3 Å
Structure is of the transmembrane core only.
3B4R
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.
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.
3BF0
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.
FlaK preflagellin aspartyl protease: Methanococcus maripaludis (expressed in E. coli), 3.60 Å
This is a GXGD protease related to presenilln.
3S0X
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.
Membrane-Bound Metalloproteases
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.
3KDS
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.
H+/Cl-Exchange Transporters
H+/Cl- Exchange Transporter: Salmonella typhimurium (Expressed in E. coli), 3.0 Å
Formerly ClC Chloride Channel. Eschericia coli protein, 3.5 Å: 1KPK
1KPL
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.
H+/Cl- Exchange Transporter: Escherichia coli, 2.51 Å
Formerly ClC Chloride Channel. Structure reveals gating by a glutamate residue
E148A mutant, 3.00 Å: 1OTT.
E148Q mutant, 3.30 Å: 1OTU.
1OTS
Dutzler et al. (2003) Dutzler R, Campbell EB, & MacKinnon R (2003). Gating the selectivity filter in ClC chloride channels. Science 300:108-112.
H+/Cl- Exchange Transporter without bound ions: Escherichia coli, 3.20 Å
E148Q mutant without bound ions, 3.1 Å: 2EXY.
S107A/E148Q/Y445A mutant with bound Br-, 3.54 Å: 2EZ0.
2EXW
Lobet & Dutzler (2006) Lobet S & Dutzler R (2006). Ion-binding properties of the ClC chloride selectivity filter. EMBO J 25:24-33.
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.
3NMO
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.
H+/Cl- Eukaryotic Exchange Transporter: Cyanidioschyzon merolae (Expressed in Trichoplusia ni), 3.50 Å
3ORG
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.
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
3ND0
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.
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.
CorA Mg2+ Transporter: Thermotoga maritima (expressed in E. coli), 3.9 Å
Cytoplasmic domain alone, 1.85 Å: 2BBH
2BBJ
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.
CorA Mg2+ Transporter: Thermotoga maritima (expressed in E. coli), 2.9 Å
2IUB
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.
CorA Mg2+ Transporter: Thermotoga maritima (expressed in E. coli), 3.7 Å
2HN2
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.
ZntB Zn+2 transporter cytoplasmic domain: Vibrio parahemolyticus (expressed in E. coli), 1.90 Å
3CK6
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.
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
3NVO
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.
Bacterial Mercury Detoxification Proteins
MerF Hg(II) transporter: Morganella morganii/ (Expressed in E. coli), NMR structure
Structure of truncated protein (AAs 13-72) determined in aligned bicelles.
2H3O
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.
MerF Hg(II) transporter: Morganella morganii (Expressed in E. coli), NMR structure
Structure of truncated protein (AAs 13-72) determined in SDS micelles.
1WAZ
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.
Multi-Drug Efflux Transporters
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.
1IWG
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.
AcrB bacterial multi-drug efflux transporter: Escherichia coli, 3.7 Å
With substrates:
rhodamine 6G, 3.63 Å: 1OY8. ethidium, 3.80 Å: 1OY9. dequalinium, 3.80 Å: 1OYD. ciprofloxacin, 3.48 Å: 1OYE.
1OY6
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.
AcrB bacterial multi-drug efflux transporter, apo protein, N109A mutant: Escherichia coli, 3.23 Å
With substrates:
ciprofloxacin, 3.11 Å: 1T9U. rhodamine 6G, 3.80 Å: 1T9V. nafcillin, 3.23 Å: 1T9W. ethidium, 3.08 Å: 1T9X. Phe-Arg-β-naphthylamide, 3.64 Å: 1T9Y.
1T9T
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.
AcrB bacterial multi-drug efflux transporter, D407A mutant: Escherichia coli, 3.56 Å
D408A, 3.65 Å: 2HQD. K940A, 3.38 Å: 2HQF. T978A, 3.38 Å: 2HQG.
2HQC
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.
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.
2GIF
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.
AcrB bacterial multi-drug efflux transporter without ligands: Escherichia coli, 2.8 Å
With minocycline, 3.1 Å: 2DRD. With doxorubicin, 3.3 Å: 2DR6
2DHH
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.
AcrB bacterial multi-drug efflux transporter with YajC subunit: Escherichia coli, 3.5 Å
2RDD
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.
AcrB bacterial multi-drug efflux transporter in complex with bile acid: Escherichia coli, 3.85 Å
2W1B
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.
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
3AOB
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.
MexB bacterial multi-drug efflux transporter: Pseudomonas aeruginosa (expressed in E. coli), 3.0 Å
2V50
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.
CusA metal-ion efflux pump: Escherichia coli, 3.52 Å
3K07
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.
EmrE bacterial multi-drug efflux transporter with bound TPP substrate: Escherichia coli, 3.8 Å
3B5D is C2 crystal form. P21 form with TPP, 4.5 Å: 3B62
3B5D and 3B62 expressed in cell-free system. Ligand-free structure expressed in vivo, 4.5 Å: 3B61
3B5D
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.
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
3MKT
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.
Membrane-Associated Proteins in Eicosanoid and Glutathione Metabolism (MAPEG)
Microsomal Glutathione Transferase 1: Rattus norvegicus, 3.2 Å
Electron Diffraction
2H8A
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.
Microsomal Prostaglandin E Synthase 1: Homo sapiens (expressed in E. coli), 3.5 Å
Electron Diffraction. In complex with glutathione.
3DWW
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.
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.
2Q7M
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.
Leukotriene LTC4 Synthase in complex with glutathione: Human (expressed in Shizosaccharomyces pombe), 3.3 Å
2PNO
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.
Leukotriene LTC4 Synthase in complex with glutathione: Human (expressed in Pichia pastoris.), 2.15 Å
apo form: 2UUI, 2.00 Å.
2UUH
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.
Major Facilitator Superfamily (MFS) Transporters
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).
1PV7
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.
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).
2CFQ
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.
LacY Lactose Permease (wild-type) with TDG: Escherichia coli, 3.6 Å
2V8N
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.
LacY Lactose Permease with covalently bound MTS-gal: Escherichia coli, 3.4 Å
methanethiosulfonyl-galactopyranoside (MTS-gal) is a 'suicide' substrate.
2Y5Y
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.
FucP Fucose Transporter in outward-facing conformation: Escherichia coli, 3.1 Å
N162A mutant, 3.2 Å: 3O7P
3O7Q
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.
GlpT Glycerol-3-Phosphate Transporter: Escherichia coli, 3.3 Å
1PW4
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.
EmrD Multidrug Transporter: Escherichia coli, 3.5 Å
2GFP
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.
PepTSo Oligopeptide-proton symporter: Shewanella oneidensis (expressed in E. coli), 3.6 Å
2XUT
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.
Solute Sodium Symporter (SSS) Family
vSGLT Sodium Galactose Transporter: Vibrio parahaemolyticus (expressed in E. coli), 2.70 Å
Galactose-bound inward-occuluded conformation
3DH4
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.
vSGLT Sodium Galactose Transporter, K294A mutant: Vibrio parahaemolyticus (expressed in E. coli), 2.70 Å
inward-open conformation
2XQ2
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.
Nucleobase-Cation-Symport-1 (NCS1) Family
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.
2JLN
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.
Mhp1 Benzyl-hydantoin transporter; inward-facing conformation: Microbacterium liquefaciens (expressed in E. coli), 3.8 Å
2X79
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.
Nucleobase-Cation-Symport-2 (NCS2) Family
also known as nucleobase/ascorbate transporter (NAT)
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.
3QE7
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.
Betaine/Choline/Carnitine Transporter (BCCT) Family
BetP glycine betaine transporter: Corynebacterium glutamicum (expressed in E. coli), 3.35 Å
A Na+-coupled symporter in an intermediate state. Formerly PDB 2W8A.
2WIT
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.
CaiT carnitine transporter: Escherichia coli, 3.15 Å
This is a precursor/product antiporter that catalyzes the exchange of L-carnitine wtih ?-butyrobetaine. The protein is a homotrimer with each monomer containing 12 transmembrane helices.
3HFX
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.
CaiT carnitine transporter: Escherichia coli, 3.50 Å
Fully-open inward-facing conformation.
2WSX
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.
CaiT carnitine transporter: Proteus mirabilis, 2.3 Å
Fully-open inward-facing conformation.
2WSW
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.
Amino Acid/Polyamine/Organocation (APC) Superfamily
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).
3LRB
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.
AdiC Arginine:Agmatine Antiporter (N22A, L123W mutant) with bound Arginine: Escherichia coli, 3.0 Å
Outward-facing occluded state
3L1L
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.
AdiC Arginine:Agmatine Antiporter (N101A mutant) with bound Arginine: Escherichia coli, 3.0 Å
Reveals AdiC in the open-to-out conformation.
3OB6
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.
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.
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.
apo ApcT Na+-independent Amino Acid Transporter: Methanocaldococcus jannaschii (expressed in E. coli), 2.35 Å
ApcT-7F11 Fab complex, 2.50 Å: 3GI9
ApcT-K158A/7F11 Fab complex, 2.60 Å: 3GI8
3GIA
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.
Amino Acid Secondary Transporters
LeuTAa Leucine transporter: Aquifex aeolicus (expressed in E. coli), 1.65 Å
2A65
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.
LeuT Leucine transporter with bound inhibitors: Aquifex aeolicus (expressed in E. coli), 1.85 Å
Alanine-Sodium-Clomipramine
Leucine-Sodium-Clomipramine, 2Q6H
Leucine-Sodium-Imipramine, 2Q72
Leucine-Sodium-Desipramine, 2QB4
2QEI
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.
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
3F3A
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.
LeuT Leucine Transporter with Bound Desipramine: Aquifex aeolicus (expressed in E. coli), 2.9 Å
2QJU
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.
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
3GJD
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.
Mutant LeuT transporter with Nitroxide Spin Label (F177R1): Aquifex aeolicus (expressed in E. coli), 2.25 Å
I204R1 mutant, 2.25 Å: 3MPQ
3MPN
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.
LeuT engineered to transport tryptophan (F259V): Aquifex aeolicus (expressed in E. coli), 2.63 Å
All structures are with protein-bound Na+ & L-Trp
I359Q mutant, 2.60 Å: 3QS5
F259V,I359Q mutant, 2.80 Å:3QS6
3QS4
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.
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)
3TT1
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.
Glutamate Transporter Homologue (GltPh): Pyrococcus horikoshii (expressed in E. coli), 3.50 Å
Outward-facing state
1XFH
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.
Glutamate Transporter Homologue (GltPh): Pyrococcus horikoshii (expressed in E. coli), 3.51 Å
Inward-facing state
3KBC
Reyes et al. (2009) Reyes N, Ginter C, & Boudker O (2009). Transport mechanism of a bacterial homologue of glutamate transporters. Nature 462:880-885.
Aspartate Transporter Li+-Bound State(GltPh): Pyrococcus horikoshii (expressed in E. coli), 2.96 Å
TBOA-bound, 3.20 Å: 2NWW
Sodium-bound, 3.29 Å: 2NWX
2NWL
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.
Cation Diffusion Facilitator (CDF) Family
YiiP Zinc Transporter: Escherichia coli, 3.8 Å
9-18, 2005)
2QFI
Lu & Fu (2007) Lu M & Fu D (2007). Structure of the zinc transporter YiiP. Science 317:1746-1748.
YiiP Zinc Transporter: Escherichia coli, 2.9 Å
9-18, 2005)
3H90
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.
Antiporters
NhaA Na+/H+ antiporter: Escherichia coli, 3.45 Å
1ZCD
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.
NhaA Na+/H+ antiporter: Escherichia coli, by electron crystallography
Difference maps show structural changes with changes in pH.
3FI1
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.
Mitochondrial ADP/ATP Carrier: Bovine heart mitochondria, 2.2 Å
Monomeric, in complex with carboxyatractyloside inhibitor.
1OKC
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.
Mitochondrial ADP/ATP Carrier: Bovine heart mitochondria, 2.8 Å
Biological dimer with endogenous cardiolipins.
2C3E
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.
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.
2LCK
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.
Apical Sodium-Dependent Bile Acid Transporters (ASBT)
Bacterial homologue of ASBT (ASBTNM) with bound taurocholate: Neisseria meningitidis (expressed in E. coli), 2.20 Å
Derivatized Cys mutant soaked in mercury acetate, 2.20 Å: 3ZUX
The protein is structurally similar to the NhaA Na+/H+ antiporter 1ZCD
3ZUY
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.
Energy-Coupling Factor (ECF) Transporters
RibU, S Component of the Riboflavin Transporter: Staphylococcus aureus (Expressed in E. coli), 3.6 Å
3P5N
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.
ThiT, S component of the Thiamin Transporter: Lactococcus lactis, 2.00 Å
3RLB
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.
ATP Binding Cassette (ABC) Transporters
BtuCD Vitamin B12 Transporter: Escherichia coli, 3.2 Å
1L7V
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.
BtuCD-F Complex; BtuCD B12 Transporter + BtuF binding protein: Escherichia coli, 2.6 Å
2QI9
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.
Sav1866 Multidrug Transporter: Staphylococcus aureus, 3.0 Å
2HYD
Dawson and Locher (2006) Dawson RJP & Locher KP (2006). Structure of a bacterial multidrug ABC transporter. Nature 443:180-185.
Molybdate Transporter ModB2C2 Complexed with ModA: Archaeoglobus fulgidus, 3.1 Å
ModA with bound MoO4, 1.60 Å 2ONR
ModA with bound WO4, 1.55 Å 2ONS
2ONK
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.
ModBC Molybdate ABC Transporter in a trans-inhibited state: Methanosarcina acetivorans, 3.0 Å
3D31
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.
HI1470/1 Putative Metal-Chelate-type ABC Transporter: Haemophilus influenzae, 2.4 Å
First structure showing an inward-facing conformation of an ABC transporter
2NQ2
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.
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
3B60
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.
P-Glycoprotein: Mus musculus (mouse) (expressed in Pichia pastoris), 3.8 Å
With bound QZ59-RRR: 3G60, 4.40 Å
With bound QZ59-SSS: 3G61, 4.35 Å
3G5U
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.
MalFGK2-MBP Maltose uptake transporter complex: Escherichia coli, 2.8 Å
Complex includes maltose-binding protein (MBP), maltose, and ATP
2R6G
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.
MalFGK2 uptake transporter: Escherichia coli, 4.5 Å
Helix TM1 deleted. Shows transporter in the inward conformation in the resting state.
3FH6
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.
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
3PV0
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.
MalFGK2-MBP Maltose uptake transporter complex with bound MgAMPPNP: Escherichia coli, 2.20 Å
The protein is in the outward-facing conformation.
With bound ADP-BeF3, 2.30 Å: 3PUX
With bound ADP-VO4, 2.40 Å: 3PUV
With bound ADP-AlF4, 2.30 Å: 3PUW
3RLF
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.
MetNI Methionine uptake transporter complex: Escherichia coli, 3.7 Å
MetN-C2 domain 3DHX, 2.1 Å
3DHW
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.
FbpC ferric iron-uptake transporter nucleotide-binding domain: Neisseria gonorrhoeae, 1.9 Å
A domain-swapped neucleotide-binding domain dimer
3FVQ
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.
Methyltransferases
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.
4A2N
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.
Phosphoenolpyruvate-Dependent Phosphotransferases (PTSs)
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.
3QNQ
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.
Superfamily of K+Transporters (SKT proteins)
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.
3PJZ
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.
P-type ATPase
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
1SU4
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.
Calcium ATPase; rabbit sarcoplasmic reticulum. E1 state with bound calcium, magnesium, and an ATP analog: Oryctolagus cuniculus, 2.9 Å
1VFP
Toyoshima & Mizutani (2004) Toyoshima C & Mizutani T (2004). Crystal structure of the calcium pump with a bound ATP analogue. Nature 430:529-35.
Calcium ATPase; rabbit sarcoplasmic reticulum. E2 state without bound calcium: Oryctolagus cuniculus, 3.1 Å
1IWO
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)
1WPG
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.
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
1T5S
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.
Calcium ATPase; rabbit sarcoplasmic reticulum. E2 state with bound AlF4– calcium-free: Oryctolagus cuniculus, 3.0 Å
1XP5
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.
Calcium ATPase; rabbit sarcoplasmic reticulum. Ca2+-free, with bound BHQ and thapsigargin: Oryctolagus cuniculus, 3.0 Å
2AGV
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.
Calcium ATPase; rabbit sarcoplasmic reticulum. With bound synthesized derivative of thapsigargin: Oryctolagus cuniculus, 3.30 Å
2BY4
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.
Calcium ATPase; rabbit sarcoplamic reticulum. Ca2+-free E2 state with thapsigargin and AMPPCP: Oryctolagus cuniculus, 3.10 Å
With partially occupied AMPPCP site, 2.80 Å: 2C8K
With thapsigargin, 3.10 Å: 2C8L
In the Ca2+ E1 state solved in a P1 crystal form, 3.00 Å: 2C9M
2C88
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.
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
2O9J
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.
Calcium ATPase; rabbit sarcoplamic reticulum. P21 crystal form with bound thapsigargin: Oryctolagus cuniculus, 3.10 Å
With bound CPA, 3.4 Å: 3EAS
With bound CPA and thapsigargin, 2.90 Å: 3EAT
With bound CPA in the presence of curcumin, 2.80 Å: 3EAU
3EAR
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.
Calcium ATPase; rabbit sarcoplamic reticulum. Ca2+E1~P (Ca2+E1~P.AMPPN): Oryctolagus cuniculus, 2.8 Å
E2P (E2-BeF3–), 2.65 Å: 3B9B
E2-P* (E2-AlF4–), 3.0 Å: 3B9R
3BA6
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.
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
2YFY
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.
Na,K-ATPase; pig kidney : Sus scrofa, 3.5 Å
3B8E
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.
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.
2ZXE
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.
Na,K-ATPase Regulatory Protein FXYD1: Homo sapiens (expressed in E. coli), NMR Structure
2JO1
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.
Phospholamban homopentamer: Homo sapiens (expressed in E. coli), NMR structure
See also 1FJK and 1FJP.
1ZLL
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.
Phospholamban homopentamer in T state: Homo sapiens (expressed in E. coli), NMR Structure
2KYV
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.
Plasma Membrane H+-ATPase: Arabidopsis thaliana, 3.6 Å
3B8C
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
3RFU
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.
V-type ATPase
Rotor of V-type Na+-ATPase: Enterococcus hirae, 2.1 Å
2BL2
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.
V-ATPase central-axis DF complex: Enterococcus hirae (expressed in Cell-free synthesis), 2.00 Å
3AON
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.
V1-ATPase atomic model derived from Cryo-EM reconstructions.: Thermus thermophilus, 9.7 Å
3J0J
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.
V1-ATPase Complex (V-ATPase soluble domain) with bound nucleotide: Thermus thermophilus, 4.51 Å
Without nucleotide, 4.80 Å: 3A5D
3A5C
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.
A3B3 complex of V1-ATPase: Thermus thermophilus (expressed in E. coli), 2.8 Å
3GQB
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.
F-type ATPase
F1-ATPase from bovine heart mitochondria: Bos taurus, 2.8 Å
1BMF
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.
F1-ATPase complexed with antibiotic inhibitor aurovertin B: Bos taurus, 3.10 Å
1COW
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.
F1-ATPase complexed with peptide antibiotic efrapeptin: Bos taurus, 3.10 Å
1EFR
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.
F1-ATPase complexed with azide: Bos taurus, 1.95 Å
2CK3
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
2JDI
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.
ATP Synthase Extrinsic Region: Bos taurus, 3.2 Å
2WSS
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
3OAA
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.
ATP synthase (F1c10): S. cerevisiae, 3.9 Å
NOTE: X-ray structure is a C-alpha model derived from composite of 1BMF, 1A91, & 1AQT
1QO1
Stock et al. (1999) Stock S, Leslie AGW, & Walker JE (1999). Molecular architecture of rotary motor in ATP synthase. Science 286:1700-1705.
F1 ATPase: S. cerevisiae, 2.80 Å
2HLD
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.
Rotor (c11) of Na+-dependent F-ATP Synthase: Ilyobacter tartaricus, 2.4 Å
1YCE
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
2WGM
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.
Rotor (c14) of H+-dependent F-ATP Synthase of spinach chloroplasts: Spinacia oleracea, 3.80 Å
2W5J
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.
Rotor (c15) of H+-dependent F-ATP Synthase of an alkaliphilic cyanobacterium: Spirulina platensis, 2.1 Å
2WIE
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
2X2V
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.
Peripheral stalk of H+-dependent F-ATP Synthase: Thermus thermophilus (expressed in E. coli), 3.10 Å
3K5B
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.
Phosphotransferases
Diacylglycerol kinase (DAGK): Escherichia coli, NMR structure (DPC micelles)
Domain-swapped homotrimer
2KDC
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.
Hydrolases
Estrone Sulfatase: Human placenta, 2.6 Å
1P49
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.
Oxygenases
Particulate methane monooxgenase (pMMO): Methylococcus capsulatus, 2.8 Å
1YEW
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
3CHX
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.
Oxidoreductases
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).
3HYW
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.
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).
2GMH
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.
2QCU
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.
NarGHI Nitrate Reductase A: Escherichia coli, 1.9 Å
1Q16
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.
NarGHI Nitrate Reductase A catalytic domain NarG with FS0 cluster: Escherichia coli, 2.2 Å
1SIW
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.
NarGHI Nitrate Reductase with pentachlorophenol (PCP): Escherichia coli, 2.0 Å
K86A mutant, 1.90 Å : 1Y5I. K86A w. PCP, 2.50 Å : 1Y5N. H66Y mutant, 2.50 Å : 1Y5L.
1Y4Z
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.
NrfH Cytochrome C Quinol Dehydrogenase: Desulfovibrio vulgaris, 2.3 Å
In complex with NrfA cytochrome c nitrite reductase.
2J7A
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.
2HI7
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
2ZUQ
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.
wtDsbB-DsbA(Cys133A)-Q8 Complex: E. coli, 3.7 Å
3E9J
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.
DsbB in DPC micelles: E. coli, NMR Structure
w. bound ubiquinone: 2K74
2K73
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.
Vitamin K epoxide reductase: Synechococcus sp. (expressed in E. coli), 3.60 Å
3KP9
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.
Mo/Wbis-MGD Oxidoreductases
Polysulfide Reductase PsrABC (native): Thermus thermophilus, 2.4 Å
w. bound quinone inhibitor PCP, 2.5 Å: 2PVY
w. bound menaquinone, 3.1 Å: 2PVW
w. bound quinone, 3.1 Å: 2PVX
2VPZ
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.
Electron Transport Chain Complexes: Complex I
Complex I membrane domain: Escherichia coli, 3.90 Å
3M9C
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
3RKO
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.
Complex I complete: Thermus thermophilus, 4.50 Å
3M9S
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
2FUG
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.
Complex I soluble domain, oxidized (2 mol/ASU): Thermus thermophilus, 3.10 Å
oxidized (4 mol/ASU), 3.15 Å: 3IAS
reduced (2 mol/ASU) with bound NADH, 3.10 Å: 3IAM
3I9V
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.
Electron Transport Chain Complexes: Complex II
Fumarate Reductase Complex: Escherichia coli, 3.3 Å
This structure has been replaced by 1L0V, below.
1FUM
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.
Native Fumarate Reductase Complex: Escherichia coli, 3.3 Å
+HQNO, 2.7 Å, 1KF6. +DNP-19, 3.6 Å, 1KFY
1L0V
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.
Fumarate Reductase Complex: Wolinella succinogenes, 1.78 Å
2BS2 has small unit cell. 1QLB, 2.2 Å, has a larger unit cell.
2BS2
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.
Formate dehydrogenase-N: Escherichia coli, 1.6 Å (native structure)
HQNO complex, 2.8 Å: 1KQG
1KQF
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.
Succinate:quinone oxidoreductase (SQR, Complex II): Escherichia coli, 2.6 Å
DNP-17 Complex, 2.9 Å: 1NEN
1NEK
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.
Succinate:quinone oxidoreductase (SQR, Complex II) with Atpenin A5: Escherichia coli, 3.10 Å
2ACZ
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.
Succinate:quinone oxidoreductase (SQR, Complex II) with carboxin in Q-site: Escherichia coli, 2.40 Å
with pentachlorophenol in Q-site, 3.20 Å: 2WDR
with empty Q-site, 3.20 Å: 2WDV
2WDQ
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.
Succinate:quinone oxidoreductase (SQR, Complex II), H207T SdhB mutant: Escherichia coli, 2.70 Å
2WP9
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.
Succinate:ubiquinone oxidoreductase (SQR, Complex II; pig heart): Sus scrofa, 2.4 Å
with inhibitors, 3.5 Å: 1ZP0
1ZOY
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.
Succinate:ubiquinone oxidoreductase (SQR, Complex II; chicken heart) w. carboxin inhibitor: Gallus gallus, 2.1 Å
with 3-nitropropionic acid (3-NP) inhibitor, 2.33 Å: 1YQ4
with OAA inhibitor, 2.2 Å: 1YQ3
2FBW
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.
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
2H88
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.
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Information about Cytochrome bc1
Cytochrome bc1: Bos taurus, 2.7 Å
Bovine heart mitochondria, 5 subunits
1QCR
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.
Cytochrome bc1: Bos taurus, 3.0 Å
Bovine Heart Mitochondria, 11 subunits.
1BGY
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.
Cytochrome bc1: Bos taurus, 2.26 Å
Bovine Heart Mitochondria, with jg144 inhibitor
2FYU
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: Bos taurus, 2.40 Å
Bovine Heart Mitochondria, without ubiquinone.
w. ubiquinone, 2.60 Å: 1NTZ
w. antimycin A1, 2.60 Å: 1NTK
w. NQNO, 3.2 Å: 1NU1
1NTM
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.
Cytochrome bc1: Bos taurus, 2.60 Å
Bovine Heart Mitochondria, w. stigmatellin
w. azoxystrobin, 2.69 Å: 1SQB
w. myxothiazol, 2.70 Å: 1SQP
w. MOAS, 3.00 Å: 1SQQ
w. UHDBT, 2.85 Å: 1SQV
1SQX
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.
Cytochrome bc1: Bos taurus, 2.10 Å
Bovine Heart Mitochondria, w. bound antimycin
without antimycin, 2.10 Å: 1PP9
with bound stigmatellin, 2.10 Å: 2A06
1PPJ
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.
Cytochrome bc1: Gallus gallus, 3.16 Å
Chicken Heart Mitochondria (native structure)
w. bound stigmatellin, 3.5 Å: 2BCC
w. bound stigmatellin and antimycin, 3.7 Å: 3BCC
1BCC
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.
Cytochrome bc1: Sarcomyces cerevisiae, 2.3 Å
yeast, 9 subunits.
1EZV
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.
Cytochrome bc1: Sarcomyces cerevisiae, 2.3 Å
With phospholipids.
1KB9
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.
1P84
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.
2IBZ
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
3CX5
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
2FYN
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
1ZRT
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)
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.
2D2C
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.
Cytochrome b6f complex, native structure: Mastigocladus laminosus, 3.00 Å
In complex with NQNO, 3.55 Å: 2E75
In complex with TDS, 3.41 Å: 2E76
2E74
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
1Q90
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
2ZT9
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
1OCC
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
1V54
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
1AR1
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
1QLE
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
3EHB
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
3HB3
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
3MK7
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
1EHK
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
3BVD
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
1M56
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
2GSM
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
1FFT
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)
3O0R
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
2PPS
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
1JB0
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
2O01
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
1FE1
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.
1S5L
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.
2AXT
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
3BZ1
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
1IZL
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
3A0B
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.
3ARC
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
1NKZ
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
1LGH
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
1RWT
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
3PL9
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
2BHW
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
1PRC
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
2WJN
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
1PSS
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
2RCR
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
1AIJ
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.
1OGV
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
2J8C
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
1EYS
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.

Description of Table

The table above 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 .

Search the PDB at the Research Collaboratory for Structural Bioinformatics (RCSB)

 

The figure at the top right of the page shows the progress of membrane protein structure determination. The figure may be used freely in seminar presentations provided that the URL and lab information on the image are not removed. We thank Ahmed Bakan for bringing some counting errors to our attention, and Tony Crofts, Kenneth Rudd, and Ilan Samish for bringing missing structures to our attention. If structures are missing, please let us know. Send comments and suggestions to

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.