SMTL ID : 9crv.1

Native human GABAA receptor of beta2-alpha1-gamma2-beta2-alpha2 assembly

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-1-1-1-mer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 2 residues within 4Å: Chain A: N.80, H.119 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain D: P.78, N.80, H.119 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 7 residues within 4Å: Chain A: N.149, K.192, I.194, T.195, K.196, S.211, K.213 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.195 NAG-NAG-BMA.3: 3 residues within 4Å: Chain A: D.89 Chain B: N.111 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.6 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 7 residues within 4Å: Chain D: N.149, K.192, I.194, T.195, K.196, S.211, K.213 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.195

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN.6: 13 residues within 4Å: Chain C: S.100, N.101, V.103, G.104, A.119, D.120, W.123, P.127, R.129 Chain D: G.108 Chain E: N.110, T.112 Ligands: NAG-NAG-BMA.3 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:A.119, D:G.108

2 x ABU: GAMMA-AMINO-BUTANOIC ACID(Non-covalent)

ABU.7: 11 residues within 4Å: Chain A: Y.97, E.155, S.156, Y.157, F.200, T.202, Y.205 Chain B: F.65, R.67, L.118, T.130 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.118, A:F.200, A:Y.205 Salt bridges: B:R.67 Hydrogen bonds: A:E.155, A:S.156, A:T.202 ABU.11: 9 residues within 4Å: Chain D: Y.97, E.155, S.156, Y.157, F.200, T.202, Y.205 Chain E: R.66, T.129 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:F.200, D:Y.205 Hydrogen bonds: D:S.156, D:T.202, D:Y.205, D:Y.205, E:T.129 Salt bridges: E:R.66

2 x PIO: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate(Non-covalent)

PIO.8: 9 residues within 4Å: Chain B: R.249, T.306, F.310, K.312, R.313, S.388, S.390, K.391, I.392 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:T.306, B:I.392 Hydrogen bonds: B:R.249, B:R.249, B:R.313, B:S.388, B:S.388, B:S.390, B:K.391, B:I.392 Salt bridges: B:R.249, B:K.312, B:K.312 PIO.12: 9 residues within 4Å: Chain E: R.248, F.309, K.311, R.312, S.385, S.387, K.388, I.389, M.392 15 PLIP interactions: 15 interactions with chain E Hydrophobic interactions: E:K.388, E:I.389, E:I.389, E:M.392 Hydrogen bonds: E:R.248, E:R.248, E:S.385, E:S.385, E:S.387, E:K.388 Salt bridges: E:R.248, E:K.311, E:K.311, E:R.312, E:K.388

1 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.9: 17 residues within 4Å: Chain A: N.265, V.278, M.286, F.289 Chain B: K.222, I.223, G.224, V.227, I.228, L.232, P.233, I.235, M.236, P.401, F.404, N.408, L.416 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.223, B:V.227, B:I.228, B:L.232, B:P.233, B:I.235, B:F.404, A:V.278 Hydrogen bonds: B:I.223

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.10: 5 residues within 4Å: Chain C: W.183, K.184, R.185, N.208, T.210 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:T.210 Hydrogen bonds: C:W.183

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, J. et al., Resolving native GABA A receptor structures from the human brain. Nature (2025)

Release Date

2025-01-22

Peptides

Gamma-aminobutyric acid receptor subunit beta-2: AD
Gamma-aminobutyric acid receptor subunit alpha-1: B
Gamma-aminobutyric acid receptor subunit gamma-2: C
Gamma-aminobutyric acid receptor subunit alpha-2: E
IgG2b Fab_1F4 Heavy Chain: F
Kappa Fab_1F4 Light Chain: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

C
C

E
E

F
K

G
L

Membrane

We predict this structure to be a membrane protein.
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Gamma-aminobutyric acid receptor subunit beta-2

Gamma-aminobutyric acid receptor subunit alpha-1

Gamma-aminobutyric acid receptor subunit gamma-2

Gamma-aminobutyric acid receptor subunit alpha-2

IgG2b Fab_1F4 Heavy Chain

Kappa Fab_1F4 Light Chain

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