Membrane Proteins of Known Structure

News

Last database update: 15 April 08

Monoamine Oxidase Structures Updated

New Structure:
Prokaryotic pentameric ligand-gated ion channel

Unique proteins* in database = 157.

Number of coördinate files in database = 368.

*Includes 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.

Comments on the progress of membrane protein structure determination

Hartmut Michel's Database of Membrane Protein Crystallization

Martin Caffrey's Membrane Protein Data Bank (University of Limerick)

Protein Data Bank of Transmembrane Proteins (Institute of Enzymology, Budapest)

Membrane Proteins of Known 3D Structure
(Table description)
Protein	PDB Code	Reference (links are to PubMed)
MONOTOPIC MEMBRANE PROTEINS
*Prostaglandin H2 synthase-1: Ram (Ovine) seminal vesicle, 3.5 Å*	1PRH	Picot et al. (1994)
*Cyclooxygenase-2: Mus Musculus, 3.0Å*	1CX2	Kurumbail et al. (1996)
*Squalene-hopene cyclase: Alicyclobacillus acidocaldarius, 2.0 Å* 2SQC is space group P4₃2₁2. 3SQC, 2.8 Å is P3₂21.	2SQC	Wendt et al. (1999)
*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 outside of the membrane.	1GOS	Binda et al. (2002)
*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)
*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)
*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)
*Monoamine Oxidase A: Rat mitochondrial outer membrane (expressed in S. cerevisiae), 3.20 Å*	1O5W	Ma et al. (2004)
*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)
*Flavoprotein-ubiquinone oxidoreductase (ETF-QO) with bound UQ: Sus scrofa, 2.5 Å* UQ-free structure, 2.6 Å: 2GMJ	2GMH	Zhang et al. (2006)
*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)
*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. Also listed under Intramembrane Proteases.	3BF0	Kim et al. (2008)
*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 Also listed under Respiratory Proteins.	2QCU AUTH	Yeh et al. (2008)
TRANSMEMBRANE PROTEINS: BETA-BARREL
Beta-Barrel Membrane Proteins: Multimeric (Porins and Relatives)
*Porin: Rhodobacter capsulatus, 1.8 Å*	2POR	Weiss & Schulz (1992)
*Porin: Rhodopeudomonas blastica,* 1.96 Å**	1PRN	Kreutsch et al. (1994)
*OmpK36 osmoporin: Klebsiella pneumoniae, 3.2 Å*	1OSM	Dutzler et al. (1999)
*Omp32 anion-selective porin: Comamonas acidovorans, 2.1 Å*	1E54	Zeth et al. (2000)
*Omp32 anion-selective porin: Delftia acidovorans, 1.5 Å* With bound malate, 1.45 Å: 2FGQ	2FGR	Zachariae et al. (2006)
*OmpF Matrix Porin: Escherichia coli, 2.4 Å* Note: Also see BtuB with bound colicin E3 R-domain, below.	2OMF	Cowan et al. (1992)
*OmpC Osmoporin: Escherichia coli, 2.0 Å*	2J1N	Baslé et al. (2006)
*OmpG monomeric* porin: Escherichia coli, 2.3 Å**	2F1C	Subbarao and van den Berg (2006)
*OmpG monomeric* porin in open state: Escherichia coli, 2.3 Å** OmpG in closed state, 2.73 Å: 2IWW	2IWV	Yildiz et al. (2006)
*OmpG monomeric* porin: Escherichia coli, NMR Structure (DPC micelles)**	2JQY	Liang & Tamm (2007)
*PhoE: Escherihia coli, 3.0 Å*	1PHO	Cowan et al. (1992)
*Maltoporin: Salmonella typhimurium, 2.4 Å*	2MPR	Meyer et al. (1997)
*Maltoporin: Escherichia coli,* 3.1 Å**	1MAL	Schirmer et al. (1995)
*ScrY sucrose-specific porin: Salmonella typhimurium, 2.4 Å* Complexed Form, 1AOT. Uncomplexed form, 1A0S.	1A0T	Forst et al. (1998)
*MspA mycobacterial porin: Mycobacterium smegmatis, 2.5 Å* Homooctamer	1UUN	Faller et al. (2004)
*OprP phosphate-specific transporter: Pseudomonas aeruginosa, 1.9 Å* Contains a novel nine-residue arginine ladder	2O4V	Moraes et al. (2007)
*OprD basic amino acid uptake channel: Pseudomonas aeruginosa, 2.9 Å* Like OprP, contains a basic ladder	2ODJ	Biswas et al. (2007)
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)
*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)
*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.	1WP1	Akama et al. (2004)
*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)
*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)
*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)
*BtuB with bound colicin E2 R-domain: Escherichia coli, 3.50 Å* NOTE: The 135-residue coiled-coil R-domain is believed to deliver the colicin to OmpF or OmpC (above).	2YSU	Sharma et al. (2007)
*BtuB in complex with TonB: Escherichia coli, 2.1 Å*	2GSK	Shultis et al. (2006)
*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)
*OmpA: Escherichia coli, x-ray diffraction, 2.5 Å*	1BXW	Pautsch & Schulz (1998)
*OmpA: Escherichia coli, NMR (in DPC micelles)*	1G90	Arora et al. (2001)
*OmpA with four shortened loops: Escherichia coli, NMR (in DHPC micelles)* Called β-barrel platform (BBP)	2jmm	Johansson et al. (2007)
*OmpT outer membrane protease: Escherichia coli, 2.6 Å*	1I78	Vandeputte-Rutten et al. (2001)
*OmpW outer membrane protein: Escherichia coli, 2.7 Å* 2F1V is orthorhomibic form. Trigonal form, 3.0 Å: 2F1T	2F1V	Hong et al. (2006)
*OmpX: Escherichia coli, 1.9 Å*	1QJ8	Vogt & Schulz (1999)
*OmpX: Escherichia coli, NMR (DPC micelles, with H-bond constraints)* For structure without H-bond constraints, see 1Q9G	1Q9F	Fernández et al. (2004)
*OmpLA outer membrane phospholipase A monomer: Escherichia coli,* 2.17 Å** Dimer, 2.10 Å: 1QD6	1QD5	Snijder et al.(1999)
*OpcA adhesin protein: Neisseria meningitidis, 2.0 Å*	1K24	Prince et al. (2002)
NspA surface protein: Neisseria meningitidis, 2.55 Å	1P4T	Vandeputte-Rutten et al. (2003)
*NalP autotransporter translocator domain: Neisseria meningitidis, 2.60 Å* p6₁22 space group. See also 1UYO, C222₁ space group, 3.2 Å resolution.	1UYN	Oomen et al.(2004)
*Hia_1022-1098 trimeric autotransporter: Haemophilus influenzae, 2.0 Å* Hia_992-1098, 2.3 Å: 2GR7	2GR8	Meng et al. (2006)
*EspP autotransporter, postcleavage state: Escherichia coli, 2.7 Å*	2QOM	Barnard et al. (2007)
*PagP outer membrane palimitoyl transferease: Escherichia coli, NMR* 1MM4 is Structure in DPC micelles. Structure in OG micelles: 1MM5	1MM4	Hwang et al. (2002)
*PagP outer membrane palimitoyl transferease: Escherichia coli, x-ray, 1.9 Å*	1THQ	Ahn et al. (2004)
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)
*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)
*FhuA, Ferrichrome-iron receptor without ligand: Escherichia coli, 2.7 Å* With ligand: 1BY5

from the Stephen White laboratory at UC Irvine

News

Comments on the progress of membrane protein structure determination

Hartmut Michel's Database of Membrane Protein Crystallization

Martin Caffrey's Membrane Protein Data Bank (University of Limerick)

Protein Data Bank of Transmembrane Proteins (Institute of Enzymology, Budapest)