SMTL ID : 9ct0.1

Native human GABAA receptor of beta2-alpha1-beta2-alpha2-gamma2 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: 3 residues within 4Å: Chain C: P.78, N.80, H.119 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: P.78, N.80, H.119 No protein-ligand interaction detected (PLIP)

2 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: 8 residues within 4Å: Chain A: N.149, D.190, K.192, I.194, K.196, S.211, F.212, K.213 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 7 residues within 4Å: Chain C: N.149, K.192, I.194, T.195, K.196, S.211, K.213 No protein-ligand interaction detected (PLIP)

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.3: 13 residues within 4Å: Chain A: G.108 Chain B: N.111, M.112, T.113 Chain E: S.100, N.101, V.103, G.104, A.119, D.120, W.123, R.129 Ligands: NAG.11 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:A.119, A:G.108

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

ABU.6: 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 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:F.65, A:F.200, A:Y.205 Hydrogen bonds: B:T.130, A:S.156, A:T.202, A:Y.205 Salt bridges: B:R.67 ABU.9: 10 residues within 4Å: Chain C: Y.97, E.155, S.156, Y.157, T.202, Y.205 Chain D: F.64, R.66, L.117, T.129 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:Y.205, D:F.64 Hydrogen bonds: C:Y.157, C:T.202, C:Y.205 Salt bridges: D: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.7: 11 residues within 4Å: Chain B: R.249, T.306, F.310, K.312, R.313, N.387, S.388, S.390, K.391, I.392, S.396 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.392 Hydrogen bonds: B:R.249, B:R.249, B:F.310, B:N.387, B:S.388, B:S.388, B:K.391 Salt bridges: B:R.249, B:K.312, B:K.312, B:R.313 PIO.10: 7 residues within 4Å: Chain D: R.248, T.305, F.309, S.387, K.388, I.389, M.392 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:T.305, D:M.392 Hydrogen bonds: D:R.248, D:R.248, D:F.309, D:S.387, D:K.388, D:I.389 Salt bridges: D:R.248

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

POV.8: 19 residues within 4Å: Chain A: M.286, F.289, V.290 Chain B: D.192, K.222, I.223, G.224, V.227, I.228, L.232, P.233, I.235, M.236, I.239, P.401, F.404, N.408, W.412, L.416 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:V.227, B:I.228, B:P.233, B:I.239, B:F.404, B:W.412, B:W.412, B:L.416, A:M.286, A:F.289, A:V.290 Hydrogen bonds: B:I.223, B:G.224 Salt bridges: B:D.192 POV.12: 19 residues within 4Å: Chain C: T.262, N.265, M.286, F.289 Chain D: K.221, I.222, G.223, V.226, I.227, L.231, P.232, I.234, M.235, P.398, F.401, G.402, N.405, W.409, L.413 18 PLIP interactions: 4 interactions with chain C, 14 interactions with chain D Hydrophobic interactions: C:T.262, C:M.286, C:F.289, C:F.289, D:V.226, D:V.226, D:I.227, D:L.231, D:L.231, D:P.232, D:I.234, D:I.234, D:F.401, D:W.409, D:W.409 Hydrogen bonds: D:I.222, D:G.223 Salt bridges: D:K.221

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

NAG.11: 3 residues within 4Å: Chain D: A.108, N.110 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.3 No protein-ligand interaction detected (PLIP) NAG.13: 2 residues within 4Å: Chain E: S.187, N.208 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.187, E:S.187

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

F
I

G
J

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 alpha-2

Gamma-aminobutyric acid receptor subunit gamma-2

Kappa Fab_1F4 Light Chain

IgG2b Fab_1F4 Heavy Chain

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