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Cumulative MP structures, 2008

Last database update: 3 July 2009

New Structures:
AdiC Amino acid antiporter
yeast Aqy1 aquaporin at 1.15 Å resolution
Sulfide:quinone oxidoreductase
Photosystem II. Br-substitution shows location of chlorides

Unique proteins* in database = 196.

Number of coördinate files in database = 480.

*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. The figure to the right 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.

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.

 
 
Membrane Proteins of Known 3D Structure
(Table description)
Protein PDB Code Get File Get Image Reference
(links are to PubMed)
MONOTOPIC MEMBRANE PROTEINS
Prostaglandin  H2  synthase-1: Ram (Ovine) seminal vesicle, 3.5 Å
Cyclooxygenase-2: Mus Musculus, 3.0Å
Squalene-hopene cyclase: Alicyclobacillus acidocaldarius, 2.0 Å
2SQC is space group P43212. 3SQC, 2.8 Å is P3221.
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.
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
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
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
Monoamine Oxidase A: Rat mitochondrial outer membrane (expressed in S. cerevisiae), 3.20 Å
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.
Flavoprotein-ubiquinone oxidoreductase (ETF-QO) with bound UQ: Sus scrofa, 2.5 Å
UQ-free structure, 2.6 Å: 2GMJ
Sulfide:quinone oxidoreductase in complex with decylubiquinone: Aquifex aeolicus, 2.0 Å
"as-purified" protein, 2.30 Å: 3H27
in complex with aurachin C, 2.9 Å: 3H29
This monotopic membrane protein is thought to be buried about 12 Å in the bilayer interface. Also listed under Respiratory Proteins.
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.
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.
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
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.
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.
ADP-ribosylation factor (ARF1), myristoylated: Saccharomyces cerevisiae (Expressed in E. coli), NMR Structure
TRANSMEMBRANE PROTEINS: BETA-BARREL
Beta-Barrel Membrane Proteins: Multimeric
(Porins and Relatives)
Porin: Rhodobacter capsulatus, 1.8 Å
Porin: Rhodopeudomonas blastica, 1.96 Å
OmpK36 osmoporin: Klebsiella pneumoniae, 3.2 Å
Omp32 anion-selective porin: Comamonas acidovorans, 2.1 Å
Omp32 anion-selective porin: Delftia acidovorans, 1.5 Å
With bound malate, 1.45 Å: 2FGQ
OmpF Matrix Porin: Escherichia coli, 2.4 Å
Note: Also see BtuB with bound colicin E3 R-domain, below.
OmpF Matrix Porin: Escherichia coli, 1.6 Å
With inserted 83 residue N-terminal peptide of colicin E3, 3.0 Å: 2ZLD
OmpC Osmoporin: Escherichia coli, 2.0 Å
OmpG *monomeric* porin: Escherichia coli, 2.3 Å
OmpG *monomeric* porin in open state: Escherichia coli, 2.3 Å
OmpG in closed state, 2.73 Å: 2IWW
OmpG *monomeric* porin: Escherichia coli, NMR Structure (DPC micelles)
PhoE: Escherihia coli, 3.0 Å
LamB Maltoporin : Salmonella typhimurium, 2.4 Å
LamB Maltoporin: Escherichia coli, 3.1 Å
ScrY sucrose-specific porin: Salmonella typhimurium, 2.4 Å
Complexed Form, 1AOT.
Uncomplexed form, 1A0S.
MspA mycobacterial porin: Mycobacterium smegmatis, 2.5 Å
Homooctamer
OprP phosphate-specific transporter: Pseudomonas aeruginosa, 1.9 Å
Contains a novel nine-residue arginine ladder
OprD basic amino acid uptake channel: Pseudomonas aeruginosa, 2.9 Å
Like OprP, contains a basic ladder
OpdK hydrocarbon transporter: Pseudomonas aeruginosa, 2.8 Å
Binds vanillate. Forms labile trimer.
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.
VceC outer membrane protein: Vibrio cholerae, 1.8 Å
NOTE: Functional protein is a homotrimer. Each monomer contributes 4 strands to a single barrel.
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.
apo BtuB cobalamin transporter: Escherichia coli, 2.0 Å
Related structures:
1NQF (SeMet-BtuB),
1NQG (Ca2+-BtuB),
1NQH (Ca2+-B12-BtuB).
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.
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).
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).
BtuB in complex with TonB: Escherichia coli, 2.1 Å
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
OmpA: Escherichia coli, x-ray diffraction, 2.5 Å
OmpA: Escherichia coli, x-ray diffraction, 1.6 Å
OmpA: Escherichia coli, NMR (in DPC micelles)
OmpA with four shortened loops: Escherichia coli, NMR (in DHPC micelles)
Called β-barrel platform (BBP)
OmpT outer membrane protease: Escherichia coli, 2.6 Å
OmpW outer membrane protein: Escherichia coli, 2.7 Å
2F1V is orthorhomibic form. Trigonal form, 3.0 Å: 2F1T
OmpX: Escherichia coli, 1.9 Å
Structure at 2.1 Å, 1QJ9
OmpX: Escherichia coli, NMR (DHPC micelles)
OmpX: Escherichia coli, NMR (DPC micelles, with H-bond constraints)
For structure without H-bond constraints, see 1Q9G
TtoA Outer Membrane Protein (OMP): Thermus thermophilus HB27, 2.8 Å
First structure of an OMP from a thermophile
OmpLA outer membrane phospholipase A monomer: Escherichia coli, 2.17 Å Dimer, 2.10 Å: 1QD6
OpcA adhesin protein: Neisseria meningitidis, 2.0 Å
NspA surface protein: Neisseria meningitidis, 2.55 Å
NalP autotransporter translocator domain: Neisseria meningitidis, 2.60 Å
p6122 space group. See also 1UYO, C2221 space group, 3.2 Å resolution.
Hia1022-1098 trimeric autotransporter: Haemophilus influenzae, 2.0 Å
Hia992-1098, 2.3 Å: 2GR7
EspP autotransporter, postcleavage state: Escherichia coli, 2.7 Å
PagP outer membrane palimitoyl transferease: Escherichia coli, NMR
1MM4 is Structure in DPC micelles. Structure in OG micelles:  1MM5
PagP outer membrane palimitoyl transferease: Escherichia coli, x-ray, 1.9 Å
FadL long-chain fatty acid transporter: Escherichia coli, 2.6 Å
1T16 is from Monoclinic crystals. From hexagonal crystals, 2.8 Å: 1T1L
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.
P34A mutant, 3.3 Å: 2R4L
N33A mutant, 3.2 Å: 2R4N
ΔNPA mutant, 3.6 Å: 2R4O
G212E mutant, 2.9 Å: 2R4P
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.
FauA alcaligin outer membrane transporter: Bordetella pertusssis (expressed in E. coli), 2.3 Å
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
TbuX hydrocarbon transporter: Ralstonia pickettii, 3.2 Å
Tsx nucleoside transporter (apoprotein): Eschericia coli, 3.0 Å
Protein + thymidine, 3.10 Å: 1TLW
Protein + uridine, 3.10 Å: 1TLZ
FhuA, Ferrichrome-iron receptor without ligand: Escherichia coli, 2.7 Å
With ligand: 1BY5
FhuA-AW140-LPS: Escherichia coli, 2.5 Å
Detailed examination of the structure of lipopolysaccharide (LPS) in complex with FhuA.
FhuA-DL41-LPS-ferricrocin, 2.7 Å: 1QFF
FhuA in complex with lipopolysaccharide and rifamycin CGP4832 Escherichia coli, 2.90 Å
FhuA: Escherichia coli, 2.5 Å
FhuA + ferrichrome-iron: Escherichia coli, 2.7 Å
FhuA in complex withTonB: Escherichia coli, 3.3  Å
FepA, Ferric enterobactin receptor: Escherichia coli, 2.4 Å
FecA, siderophore transporter: Escherichia coli, 2.0 Å
Structure at 2.5 Å: 1KMP
FecA, siderophore transporter periplasmic signalling domain: Escherichia coli, NMR Structure
Shows the signalling domain not seen x-ray structures
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
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
FptA, pyochelin outer membrane receptor: Pseudomonas aeruginosa, 2.0 Å
FpvA, Pyoverdine receptor: Pseudomonas aeruginosa, 3.6 Å
FpvA, Pyoverdine receptor (apo form): Pseudomonas aeruginosa, 2.77 Å
P pilus usher translocation domain, PapC130-640: Escherichia coli, 3.2 Å
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.
VDAC-1 voltage dependent anion channel (Human expressed in E. coli): 4 Å
Structure determined by combining x-ray and NMR data.
VDAC-1 voltage dependent anion channel (Murine expressed in E. coli): 2.3 Å
Reveals the voltage-sensing N-terminal α-helix.
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
YaeT21-351 POTRA domains (periplasmic fragment): Escherichia coli, 2.2 Å
The polypeptide transport-associated (POTRA) domains link to a transmembrane β-barrel, which is absent in this structure.
YaeT21-410 POTRA domains (periplasmic fragment): Escherichia coli, 3.3 Å
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.
Non-constitutive. Pore-forming Toxins, etc.
Alpha-hemolysin: Staphylococcus aureus, 1.9 Å
LukF: Staphylococcus aureus, 1.9 Å
NOTE: The structure is of the water soluble form of the protein. It is included here because it is similar to alpha-hemolysin in behavior, and may be taken as representative of the protomeric state of alpha-hemolysin. 
At 2.5 Å: 2LKF. With bound phosphocholine, 1.9 Å: 3LKF
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Non-constitutive. Alpha-helical Pore-forming Toxins, etc.
Cytolysin A (ClyA, aka HlyE): Escherichia coli, 3.29 Å
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.
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
Bacterial Rhodopsins
Halobacterium salinarium if not noted otherwise.
Bacteriorhodopsin (BR)
2D crystals, electron diffraction, 3.5 Å
 
2D crystals, electron diffraction, 3.0 Å
 
3D crystals,  X-ray,  2.35 Å
 
3D crystals, X-ray, 1.9 Å
K intermediate: 3D crystals, X-ray, 2.1 Å
R-free = O.255. 1QKO, 2.1 Å has R-free = 0.303
3D crystals, X-ray, 2.3 Å
3D crystals, X-ray, 1.55 Å
D96N mutant in bR state: 3D crystals, X-ray, 1.80 Å
D96N mutant in M-state, 2.00 Å: 1C8S.
3D crystals, X-ray, 2.9 Å
Halorhodopsin (HR)
3D crystals, X-ray, 1.8 Å
Sensory Rhodopsin I (SRI)
3D crystals, X-ray, 2.0 Å, Anabaena (Nostoc) sp. PCC7120
Sensory Rhodopsin II (SRII)
3D crystals, X-ray, 2.4 Å, N. pharaonis
3D crystals, X-ray, 2.1 Å, N. pharaonis
Sensory Rhodopsin II with Transducer
3D crystals, X-ray, 1.93 Å, N. pharaonis
Archaerhdopsins
Archaerhodopsin-1 (aR-1), x-ray, 3.4 Å, Halorubrum sp. aus -1
Archaerhodopsin-2 (aR-2), x-ray, 2.5 Å, Haloroubrum sp. aus -2
Archaerhodopsin-2 (aR-2), x-ray, 2.10 Å, Haloroubrum sp. aus-2
Crystallized with the carotenoid bacterioruberin. 2EI4 is space group P321. Space group P63: 2Z55, 2.50 Å.
Xanthorhodopsin
Xanthorhodopsin with bound carotenoid, x-ray, 1.9 Å, Salinibacter ruber
G Protein-Coupled Receptors
Rhodopsin: Bovine Rod Outer Segment, 2.8 Å.
See also 1HZX
Rhodopsin: Bovine Rod Outer Segment, 2.6 Å
Rhodopsin: Bovine Rod Outer Segment, 2.65 Å
Rhodopsin:  Bovine Rod Outer Segment, 2.2 Å
Rhodopsin:  Bovine Rod Outer Segment (expressed in COS cells), 3.4 Å
Recombinant rhodopsin mutant, N2C/D282C
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.  
Rhodopsin in ligand-free state (opsin):  Bovine Rod Outer Segment, 2.9 Å
2 molecules in asymmetric unit.
Rhodopsin, Ops*-GαCT peptide complex:  Bovine Rod Outer Segment, 3.2 Å
Rhodopsin: Squid (Todarodes pacificus),  2.5 Å
Rhodopsin: Squid (Todarodes pacificus),  3.7 Å
Shows intracellularly extended cytoplasmic region.
Turkey β1 adrenergic receptor (engineered), 2.7 Å
Expressed in baculovirus.
Human β2 adrenergic receptor, 3.4/3.7 Å
from β2AR365-Fab5 complex. From β2AR24/365-Fab5 complex: 2R4S
Engineered human β2 adrenergic receptor, 2.4 Å
T4 lysozyme replaces third intracellular loop. Reveals close association with cholesterol.
Engineered human β2 adrenergic receptor, 2.8 Å
T4 lysozyme replaces third intracellular loop. Reveals specific cholesterol binding site.
Human A2A adenosine receptor, 2.6 Å
In complex with a high-affinity subtype-selective antagonist ZM241385.
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.
Ion Channels
(more information)
KcsA Potassium channel, H+ gated: Streptomyces lividans (Expressed in E. coli), 3.2 Å
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
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
NaK channel (Na+complex):  Bacillus cereus (expressed in E. coli), 2.4 Å
K+ complex, 2.8 Å: 2AHZ.
NaK (NΔ19) channel in the open state:  Bacillus cereus (expressed in E. coli), 1.6 Å
MthK Potassium channel, Ca++ gated: Methanobacterium thermoautotrophicum, 3.3 Å
Jiang et al. (2002) Crystal structure and mechanism.
Jiang et al. (2002) Open pore conformation.
KvAP Voltage-gated potassium Channel: Aeropyrum pernix, 3.2 Å
Voltage sensor domain, 1.9 Å: 1ORS
Jiang et al (2003) Crystal structures.
Jiang et al (2003) Voltage sensor mechanism.
KirBac1.1 Inward-Rectifier Potassium channel (closed state): Burkholderia pseudomallei, 3.65 Å
Kir3.1-Prokaryotic Kir Chimera: Mus musculus & Burkholderia xenovornas, 2.2 Å
Expressed in Escherichia coli.
KirBac3.1 Inward-Rectifier Potassium channel (intermediate states): Magnetospirillum magnetotacticum, 2.6 Å
1XL4 is "intermediate state" 1. "Intermediate state" 2, 2.85 Å: 1XL6
Gulbis, J.M., Kuo, A., Smith, B., Doyle, D.A., Edwards, A., Arrowsmith, C., Sundstrom, M., in preparation
Kv1.2 Voltage-gated potassium Channel: Rattus norvegicus (expressed in Pichia pastoris) , 2.9 Å
Kv1.2/Kv2.1 Voltage-gated potassium channel chimera: Rattus norvegicus (expressed in Pichia pastoris) , 2.4 Å
First Kv channel with resolved lipids.
MlotiK1 cyclic nucleotide-regulated K+-channel: Mesorhizobium loti (expressed in E. coli) , 3.1 Å
Influenza M2 proton channel (synthesized), 2.05 Å
with amantadine inhibitor, 3.50 Å: 3C9J
Influenza M2 proton channel (bacterial expression system), NMR structure
with rimantadine inhibitor
mGIRK1 G-Protein Gated Inward Rectifying Potassium Channel: Mus musculus, 1.8 Å
NOTE: This is not strictly an integral membrane protein, because it is the cytoplasmic channel domain located external to the membrane. It is included here for completeness.
ASIC1 Acid-Sensing Ion Channel: Gallus gallus, 1.9 Å
Nicotinic Acetylcholine Receptor Pore (closed state): Torpedo marmorata, electron diffraction, 4.0 Å
Nicotinic Acetylcholine Receptor, refined structure: Torpedo marmorata, electron diffraction, 4.0 Å
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.
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
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.
MscL Mechanosensitive channel: Mycobacterium tuberculosis, 3.5 Å
MscS voltage-modulated mechanosensitive channel: Escherichia coli, 3.7 Å
MscS mechanosensitive channel in the open form: Escherichia coli, 3.45 Å
CorA Mg2+ Transporter: Thermotoga maritima, 3.9 Å
Soluble domain, 1.85 Å. 2BBH
CorA Mg2+ Transporter: Thermotoga maritima, 2.9 Å
MgtE Mg2+ Transporter: Thermus thermophilus, 3.5 Å
Cytoplasmic domains w. bound Mg2+, 2.30  Å: 2YVY
Cytoplasmic domains without Mg2+, 3.90  Å: 2YVZ
Other 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).
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).
SecYEG protein-conducting channel in complex with SecA: Thermotoga maritima (expressed in E. coli), 4.5 Å
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).
Other Channels: Aquaporins and Glyceroporins
AQP0 aquaporin water channel: Bovine lens, 2.24 Å
AQP0 aquaporin water channel: Ovine lens, electron diffraction, 3.0 Å (plane) by 3.5 Å (normal)
AQP0 organized as a membrane junction.
AQP0 aquaporin lens junction: Ovine lens, electron diffraction, 1.9 Å
Non-junctional form, 2.4 Å: 2B6P
AQP1 aquaporin water channel: Human red blood cell, electron diffraction, 3.8 Å
(in membrane plane)
AQP1 aquaporin water channel: Human red blood cell, in vitreous ice by electron diffraction, 3.7 Å
AQP1 aquaporin water channel: Bovine red blood cell, X-ray diffraction, 2.2 Å
AQP4 aquaporin water channel: rat glial cells (expressed in insect cells), electron diffraction, 3.2 Å
AQP4 aquaporin water channel: rat glial cells (expressed in insect cells), electron diffraction, 2.8 Å
S180D mutant. Structure reveals five lipids associated with AQP4.
AQP4 aquaporin water channel: Human (expressed in Pichia pastoris), 1.8 Å
AQP5 aquaporin water channel (HsAQP5): human (expressed in Pichia pastoris): 2.0 Å
AQPZ aquaporin water channel: Escherichia coli, 2.5 Å
AQPZ aquaporin showing two conformations of Arg-189: Escherichia coli, 3.2 Å
SoPIP2;1 plant aquaporin: Spinacia oleracea (expressed in Pichia pastoris) 2.1 Å
1Z98 is closed conformation. Open conformation, 3.9 Å: 2B5F
GlpF glycerol facilitator channel: Escherichia coli, 2.2 Å
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
PfAQP aquaglyceroporin: Plasmodium falciparum, 2.05 Å
Transports water and glycerol equally well.
Aqy1 yeast aquaporin (pH 3.5): Pischia pastoris, 1.15 Å
pH 8.0, 1.40 Å: 2W1P
Other Channels: Gap Junctions
Connexin 26 (Cx26; GJB2) gap junction: Human (expressed in Sf9 cells), 3.5 Å
Other 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
AmtB ammonia channel (wild-type): Escherichia coli, 1.8 Å (P63 crystal form)
R3 crystal form: 1XQE, 2.1 Å resolution
AmtB ammonia channel in complex with GlnK: Escherichia coli, 2.5 Å
AmtB ammonia channel in complex with inhibitory GlnK: Escherichia coli, 1.96 Å
Amt-1 ammonium channel: Archaeoglobus fulgidus, 1.54 Å
Native protein: 2B2F.
Protein + 20 mM Ammonium Sulfate:   2B2H
Protein + 80 mM Ammonium Sulfate:   2B2I
Protein+xenon:  2B2J
Rh protein, possible ammonia or CO2 channel: Nitrosomonas europaea, 1.85 Å
CO2 pressurized protein, 1.85 Å: 3B9Z
Rh protein, possible ammonia or CO2 channel: Nitrosomonas europaea, 1.30 Å
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.
GlpG rhomboid-family intramembrane protease:  Eschericia coli, 2.5 Å
Shows GlpG in a more open conformation.
GlpG rhomboid-family intramembrane protease:  Eschericia coli, 2.6 Å
P31 space group. Two anti-parallel molecules in asymmetric unit.
GlpG rhomboid-family intramembrane protease:  Eschericia coli, 2.3 Å
P21 space group. Two anti-parallel molecules in asymmetric unit.
GlpG rhomboid-family intramembrane peptidase:  Haemophilus influenzae, 2.2 Å
Shows three bound lipid molecules. Monoclinic C2 space group.
Site-2 Protease (S2P). Intramembrane Metalloprotease:  Methanocaldococcus jannaschii, 3.3 Å
Structure is of the transmembrane core only.
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 Monotopic Membrane Proteins.
H+/Cl- Exchange Transporters
H+/Cl- Exchange Transporter (formerly ClC Chloride Channel), Salmonella typhimurium, 3.0 Å
Eschericia coli, 3.5 Å: 1KPK
H+/Cl- Exchange Transporter (formerly ClC Chloride Channel)
Gating by a glutamate residue: Escherichia coli, 2.51 Å
Glu148Ala mutant, 1OTT.
Glu148Gln mutant, 1OTU.
Multi-Drug Efflux Transporters
AcrB bacterial multi-drug efflux transporter: Escherichia coli, 3.5 Å
AcrB bacterial multi-drug efflux transporter in complex with bile acid: Escherichia coli, 3.85 Å
AcrB bacterial multi-drug efflux transporter: Escherichia coli, 3.7 Å
With substrates: 1OY8, 1OY9, 1OYD, 1OYE
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.
AcrB bacterial multi-drug efflux transporter with substrates: Escherichia coli, 2.8 Å
2DHH is without ligand
w. minocycline: 2DRD, 3.1 Å
w. doxorubicin: 2DR6, 3.3 Å
AcrB bacterial multi-drug efflux transporter with YajC subunit: Escherichia coli, 3.5 Å
MexB bacterial multi-drug efflux transporter: Pseudomonas aeruginosa (expressed in E. coli), 3.0 Å
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
Membrane-Associated Proteins in Eicosanoid and Gluththione Metabolism (MAPEG)
Microsomal Glutathione Transferase 1: Rattus norvegicus, 3.2 Å (Electron Diffraction)
Microsomal Prostaglandin E Synthase 1: Human (Expressed in E. coli), 3.5 Å (Electron Diffraction)
In complex with glutathione.
5-Lipoxygenase-Activating Protein (FLAP) with Bound MK-591 Inhibitor: Human, 4.0 Å
FLAP with iodinated MK-591 analog:  2Q7R. Expressed in E. coli.
Leukotriene LTC4 Synthase in complex with glutathione: Human, 3.3 Å
Expressed in Shizosaccharomyces pombe.
Leukotriene LTC4 Synthase in complex with glutathione: Human, 2.15 Å
apo form:  2UUI, 2.00 Å. Expressed in Pichia pastoris.
Major Facilitator Superfamily (MSF) 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).
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).
LacY Lactose Permease (wild-type) with TDG: Escherichia coli, 3.6 Å
GlpT Glycerol-3-Phosphate Transporter: Escherichia coli, 3.3 Å
EmrD Multidrug Transporter: Escherichia coli, 3.5 Å
Solute Sodium Symporter (SSS) Family
vSGLT Sodium Galactose Transporter: Vibrio parahaemolyticus, 2.70 Å
Nucleobase-Cation-Symport-1 (NCS1) Family
Mhp1 Benzyl-hydantoin transporter (without substrate): Microbacterium liquefaciens (Expressed in E. coli), 2.85 Å
With hydantion substrate 2JLO (4.0 Å).
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.
Amino Acid/Polyamine/Organocation (APC) Superfamily
AdiC Arginine:Agmatine Antiporter (P212121 space group): Escherichia coli, 3.6 Å
P1 space group: 3H6B, 4.1 Å.
Amino Acid Secondary Transporters
LeuTAa Leucine transporter: Aquifex aeolicus (expressed in E. coli), 1.65 Å
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
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
LeuT Leucine Transporter with Bound Desipramine: Aquifex aeolicus (expressed in E. coli), 2.9 Å
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: 3JGC
Glutamate Transporter Homologue (GltPh): Pyrococcus horikoshii (expressed in E. coli), 3.5 Å
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
Cation Diffusion Facilitator (CDF) Family
YiiP Zinc Transporter: Escherichia coli, 3.8 Å
Renamed FieF iron & zinc transporter (see Grass et al. Arch. Microbiol. 183:9-18, 2005)
Antiporters
NhaA Na+/H+ antiporter: Escherichia coli, 3.45 Å
NhaA Na+/H+ antiporter: Escherichia coli by electron crystallography
Difference maps show structural changes with changes in pH.
Mitochondrial ADP/ATP Carrier: Bovine heart mitochondria, 2.2 Å
Monomeric, in complex with carboxyatractyloside inhibitor. Also listed under Respiratory Proteins.
Mitochondrial ADP/ATP Carrier: Bovine heart mitochondria, 2.8 Å
Biological dimer with endogenous cardiolipins. Also listed under Respiratory Proteins.
ATP Binding Cassette Transporters
BtuCD Vitamin B12 Transporter: Escherichia coli, 3.2 Å
Sav1866 Multidrug Transporter: Staphylococcus aureus, 3.0 Å
BtuCD-F Complex; BtuCD B12 Transporter + BtuF binding protein: Escherichia coli, 2.6 Å
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
ModBC Molybdate ABC Transporter in a trans-inhibited state: Methanosarcina acetivorans, 3.0 Å
HI1470/1 Putative Metal-Chelate-type ABC Transporter: Haemophilus influenzae, 2.4 Å
First structure showing an inward-facing conformation of an ABC transporter
MsbA Lipid "flippase" with bound AMPPNP: Salmonella typhimurium (expressed on 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
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
MalFGK2-MBP Maltose uptake transporter complex: Escherichia coli, 2.8 Å
Complex includes maltose-binding protein (MBP), maltose, and ATP
MalFGK2 uptake transporter: Escherichia coli, 4.5 Å
Helix TM1 deleted. Shows transporter in the inward conformation in the resting state.
MetNI Methionine uptake transporter complex: Escherichia coli, 3.7 Å
MetN-C2 domain 3DHX, 2.1 Å
Hydrolases
Estrone Sulfatase: Human placenta, 2.6 Å
Oxygenases
Particulate methane monooxgenase (pMMO): Methylococcus capsulatus, 2.8 Å
Photosynthetic Reaction Centers
Rhodopseudomonas virdis, 2.3 Å
The first high-resolution crystallographic structure of a membrane protein