SMTL ID : 8g5f.1

Native GABA-A receptor from the mouse brain, ortho-alpha1-alpha3-beta2-gamma2 subtype, in complex with GABA and allopregnanolone

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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-MAN-MAN-MAN-FUC.1: 12 residues within 4Å: Chain A: N.163, M.164, T.165, T.166, P.167, K.169 Chain D: A.157, D.158, W.161 Chain E: V.130, G.132 Ligands: NAG-NAG.4 No protein-ligand interaction detected (PLIP)

4 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: 4 residues within 4Å: Chain B: P.102, L.103, N.104, H.143 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 10 residues within 4Å: Chain B: N.173, D.214, Y.215, K.216, I.218, T.219, K.220, S.235, F.236, K.237 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.220 NAG-NAG-BMA.6: 3 residues within 4Å: Chain E: N.104, H.143, P.144 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 8 residues within 4Å: Chain E: N.173, T.175, K.216, I.218, K.220, S.233, S.235, K.237 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.216, E:K.220

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.4: 6 residues within 4Å: Chain B: I.49, D.113 Chain C: N.137, M.140, P.141 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-FUC.1 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:D.113 NAG-NAG.5: 7 residues within 4Å: Chain D: W.221, R.223, S.225, L.244, R.245, N.246, T.247 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.223

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: 19 residues within 4Å: Chain A: R.301, S.351, I.354, E.355, T.358, V.359, F.362, K.364, R.365, N.450, S.451, V.452, S.453, K.454, V.455, I.458, S.459, I.462, F.463 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:E.355, A:V.455, A:I.458 Hydrogen bonds: A:R.301, A:R.301, A:N.450, A:S.451, A:S.451, A:S.451, A:S.453, A:K.454, A:V.455 Salt bridges: A:R.301, A:K.364, A:K.364, A:R.365, A:K.454, A:K.454 PIO.12: 17 residues within 4Å: Chain C: R.275, S.325, I.328, E.329, T.332, F.336, K.338, R.339, N.413, S.414, S.416, K.417, I.418, L.421, S.422, A.425, F.426 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:I.328, C:I.418, C:L.421 Hydrogen bonds: C:R.275, C:S.414, C:S.414, C:K.417 Salt bridges: C:R.275, C:K.338, C:K.338, C:R.339, C:K.417, C:K.417

2 x Y4B: allopregnanolone(Non-covalent)

Y4B.9: 10 residues within 4Å: Chain A: I.291, Q.294, V.295, W.298, P.464 Chain E: L.321, A.324, L.325, Y.328, I.329 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:A.324, E:L.325, E:Y.328, A:V.295 Hydrogen bonds: A:Q.294 Y4B.11: 11 residues within 4Å: Chain B: F.317, L.321, A.324, L.325, Y.328, I.329 Chain C: I.265, Q.268, V.269, W.272, P.427 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:V.269, C:W.272, B:L.321, B:A.324, B:Y.328 Hydrogen bonds: C:Q.268

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

ABU.10: 11 residues within 4Å: Chain B: Y.121, E.179, S.180, Y.181, F.224, T.226, Y.229 Chain C: F.91, R.93, L.144, T.156 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:Y.229, C:F.91 Hydrogen bonds: B:Y.121, B:E.179, B:T.226, C:T.156 Salt bridges: C:R.93 ABU.13: 11 residues within 4Å: Chain A: F.117, R.119, L.170, T.182 Chain E: Y.121, E.179, S.180, Y.181, F.224, T.226, Y.229 8 PLIP interactions: 6 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:Y.181, E:F.224, E:Y.229, A:F.117 Hydrogen bonds: E:E.179, E:T.226, E:Y.229 Salt bridges: A:R.119

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
E

C
C

D
D

F
J

G
K

Membrane

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

Gamma-aminobutyric acid receptor subunit beta-2

Gamma-aminobutyric acid receptor subunit alpha-1

Gamma-aminobutyric acid receptor subunit gamma-2

Heavy Chain of 8E3 Fab

Light Chain of 8E3 Fab

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