SMTL ID : 8g5g.1

Native GABA-A receptor from the mouse brain, meta-alpha1-alpha3-beta2-gamma2 subtype, in complex with GABA, Zolpidem, and endogenous neurosteroid

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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.1: 16 residues within 4Å: Chain A: N.137, M.138, T.139 Chain C: S.138, N.139, V.141, G.142, K.143, A.157, D.158, W.161, P.165, R.167 Ligands: NAG-NAG-BMA-FUC.7, NAG-NAG-BMA-FUC.7, NAG-NAG-BMA-FUC.7 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.157

4 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.2: 4 residues within 4Å: Chain B: P.102, L.103, N.104, H.143 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.3: 5 residues within 4Å: Chain B: N.173, K.216, I.218, S.235, K.237 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.5: 4 residues within 4Å: Chain D: P.102, L.103, N.104, H.143 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.6: 8 residues within 4Å: Chain D: N.173, K.216, I.218, T.219, K.220, K.221, S.235, K.237 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.221, D:K.221, D:K.221, D:K.216, D:K.216, D:K.220

1 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.4: 4 residues within 4Å: Chain C: W.221, S.225, L.244, N.246 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-FUC.7: 8 residues within 4Å: Chain G: A.161, N.163, T.165, T.166, P.167 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN-MAN.1 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:A.161

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: 11 residues within 4Å: Chain A: R.275, T.332, F.336, K.338, R.339, N.413, S.414, S.416, K.417, I.418, L.421 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:T.332, A:K.417, A:I.418, A:L.421, A:L.421 Hydrogen bonds: A:R.275, A:R.275, A:N.413, A:S.414, A:S.414, A:K.417, A:I.418 Salt bridges: A:R.275, A:K.338, A:K.338, A:R.339 PIO.14: 12 residues within 4Å: Chain G: R.301, T.358, F.362, K.364, R.365, N.450, S.451, S.453, K.454, V.455, I.458, I.462 17 PLIP interactions: 17 interactions with chain G Hydrophobic interactions: G:T.358, G:V.455, G:V.455, G:I.458, G:I.458, G:I.462 Hydrogen bonds: G:R.301, G:N.450, G:N.450, G:S.451, G:S.453, G:K.454, G:V.455 Salt bridges: G:K.364, G:K.364, G:R.365, G:K.454

1 x Y4B: allopregnanolone(Non-covalent)

Y4B.9: 8 residues within 4Å: Chain A: I.265, Q.268, V.269, W.272, P.427 Chain D: A.324, L.325, Y.328 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:I.265, A:V.269, A:W.272, D:A.324, D:L.325, D:Y.328, D:Y.328 Hydrogen bonds: A:Q.268

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

ABU.10: 8 residues within 4Å: Chain B: Y.121, S.180, Y.181, F.224, T.226, Y.229 Chain G: F.117, R.119 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain G Hydrophobic interactions: B:Y.229, G:F.117 Hydrogen bonds: B:Y.121, B:Y.181, B:T.226 Salt bridges: G:R.119 ABU.12: 11 residues within 4Å: Chain A: F.91, R.93, L.144, T.156 Chain D: Y.121, E.179, S.180, Y.181, F.224, T.226, Y.229 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:F.224, D:Y.229, A:F.91, A:L.144 Hydrogen bonds: D:E.179, D:Y.181, D:T.226, D:Y.229 Salt bridges: A:R.93

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

NAG.11: 2 residues within 4Å: Chain C: K.126, N.128 No protein-ligand interaction detected (PLIP)

1 x R5R: Zolpidem(Non-covalent)

R5R.13: 16 residues within 4Å: Chain C: D.94, M.95, Y.96, F.115, A.117, M.168, T.180 Chain G: F.152, H.154, S.211, Y.212, R.256, S.257, S.258, T.259, Y.262 8 PLIP interactions: 4 interactions with chain G, 4 interactions with chain C Hydrophobic interactions: G:F.152, G:Y.262, C:Y.96, C:Y.96, C:F.115, C:F.115 Hydrogen bonds: G:S.257 pi-Stacking: G:Y.212

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sun, C. et al., Cryo-EM structures reveal native GABA A receptor assemblies and pharmacology. Nature (2023)

Release Date

2023-09-20

Peptides

Gamma-aminobutyric acid receptor subunit alpha-1: A
Gamma-aminobutyric acid receptor subunit beta-2: BD
Gamma-aminobutyric acid receptor subunit gamma-2: C
Heavy Chain of 8E3 Fab: E
Light Chain of 8E3 Fab: F
Gamma-aminobutyric acid receptor subunit alpha-3: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
E

C
D

E
H

F
L

G
C

Membrane

We predict this structure to be a membrane protein.
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Gamma-aminobutyric acid receptor subunit alpha-1

Gamma-aminobutyric acid receptor subunit beta-2

Gamma-aminobutyric acid receptor subunit gamma-2

Heavy Chain of 8E3 Fab

Light Chain of 8E3 Fab

Gamma-aminobutyric acid receptor subunit alpha-3

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