SMTL ID : 9cx7.1

Native human GABAA receptor of beta3-alpha1-gamma2-beta3-alpha2 assembly

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

3 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.3: 4 residues within 4Å: Chain A: D.89 Chain B: N.111, P.115 Ligands: NAG-NAG-BMA-MAN-MAN.4 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain G: 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: 7 residues within 4Å: Chain A: N.149, R.192, V.194, R.196, S.211, F.212, R.213 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.194 NAG-NAG-BMA.6: 7 residues within 4Å: Chain G: N.149, R.192, V.194, R.196, S.211, F.212, R.213 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:V.194, G:R.196 Hydrogen bonds: G:R.192, G:R.196

1 x NAG- NAG- BMA- MAN- MAN: 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.4: 7 residues within 4Å: Chain C: A.119, D.120, W.123 Chain D: N.110, T.112 Chain G: G.108 Ligands: NAG-NAG.3 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G: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 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.200, A:Y.205, B:F.65, B:L.118 Hydrogen bonds: A:Y.97, A:S.156, A:T.202, B:T.130 Salt bridges: B:R.67 ABU.11: 10 residues within 4Å: Chain D: F.64, R.66, T.129 Chain G: Y.97, E.155, S.156, Y.157, F.200, T.202, Y.205 7 PLIP interactions: 2 interactions with chain D, 5 interactions with chain G Hydrophobic interactions: D:F.64, G:F.200, G:Y.205 Salt bridges: D:R.66 Hydrogen bonds: G:Y.97, G:S.156, G:T.202

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: 7 residues within 4Å: Chain B: R.249, T.306, F.310, S.388, S.390, K.391, I.392 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:T.306, B:I.392 Hydrogen bonds: B:R.249, B:R.249, B:S.388, B:S.390, B:K.391 Salt bridges: B:R.249 PIO.10: 10 residues within 4Å: Chain D: R.248, E.302, T.305, F.309, K.311, V.386, S.387, K.388, I.389, M.392 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:E.302, D:T.305, D:K.388, D:I.389, D:M.392 Hydrogen bonds: D:R.248, D:R.248, D:S.387, D:K.388 Salt bridges: D:R.248, D:R.248, D:K.311, D:K.311, D:K.388

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

NAG.9: 5 residues within 4Å: Chain C: K.184, R.185, S.187, N.208, T.209 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.185, C:S.187, C:S.187, C:T.210

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-3: AG
Gamma-aminobutyric acid receptor subunit alpha-1: B
Gamma-aminobutyric acid receptor subunit gamma-2: C
Gamma-aminobutyric acid receptor subunit alpha-2: D
IgG2b Fab_1F4 Heavy Chain: E
Kappa Fab_1F4 Light Chain: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

G
D

B
B

C
C

D
E

E
K

F
L

Membrane

We predict this structure to be a membrane protein.
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Gamma-aminobutyric acid receptor subunit beta-3

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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