SMTL ID : 8g5h.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.89 Å

Oligo State

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

Ligands

5 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.1: 6 residues within 4Å: Chain A: D.113, Q.114 Chain B: N.137, M.140 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-FUC.4, NAG-NAG-BMA-MAN-MAN-MAN-FUC.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.114 NAG-NAG-BMA-MAN-MAN.2: 3 residues within 4Å: Chain D: N.104, H.143, D.145 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.3: 8 residues within 4Å: Chain D: N.173, Y.215, K.216, I.218, T.219, K.220, S.235, K.237 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.216, D:K.220, D:K.220 NAG-NAG-BMA-MAN-MAN.5: 3 residues within 4Å: Chain A: N.104, H.143, P.144 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.6: 6 residues within 4Å: Chain A: N.173, K.216, I.218, K.220, S.235, K.237 No protein-ligand interaction detected (PLIP)

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.4: 7 residues within 4Å: Chain C: A.157, W.161 Chain G: N.163, M.164, T.165 Ligands: NAG-NAG-BMA-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN.1 No protein-ligand interaction detected (PLIP)

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.7: 4 residues within 4Å: Chain C: W.221, R.223, S.225, N.246 No protein-ligand interaction detected (PLIP)

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

ABU.8: 10 residues within 4Å: Chain A: Y.121, S.180, Y.181, F.224, T.226, Y.229 Chain B: F.91, R.93, L.144, T.156 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.181, A:Y.229, B:F.91, B:L.144 Hydrogen bonds: A:S.180, A:T.226, A:T.226 Salt bridges: B:R.93 ABU.12: 11 residues within 4Å: Chain D: Y.121, E.179, S.180, Y.181, F.224, T.226, Y.229 Chain G: F.117, R.119, L.170, T.182 7 PLIP interactions: 2 interactions with chain G, 5 interactions with chain D Hydrophobic interactions: G:F.117, D:F.224, D:Y.229 Salt bridges: G:R.119 Hydrogen bonds: D:E.179, D:Y.181, D:T.226

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.9: 12 residues within 4Å: Chain B: R.275, E.329, T.332, F.336, K.338, R.339, F.412, S.414, S.416, K.417, I.418, L.421 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:T.332, B:I.418 Hydrogen bonds: B:R.275, B:R.275, B:S.414, B:S.414, B:S.416, B:S.416, B:K.417, B:I.418 Salt bridges: B:K.338, B:K.338, B:R.339 PIO.13: 10 residues within 4Å: Chain G: R.301, E.355, F.362, K.364, R.365, S.451, S.453, K.454, V.455, I.458 10 PLIP interactions: 10 interactions with chain G Hydrophobic interactions: G:V.455, G:I.458 Hydrogen bonds: G:R.301, G:R.301, G:S.451, G:K.454, G:V.455 Salt bridges: G:K.364, G:K.364, G:R.365

1 x R5R: Zolpidem(Non-covalent)

R5R.10: 14 residues within 4Å: Chain B: F.126, H.128, Y.186, Q.230, S.231, S.232, T.233, Y.236 Chain C: D.94, Y.96, F.115, A.117, T.180, E.227 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:D.94, C:Y.96, C:F.115, C:F.115, C:A.117, C:T.180, B:F.126, B:Y.236, B:Y.236

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

NAG.11: 1 residues within 4Å: Chain C: N.128 No protein-ligand interaction detected (PLIP)

1 x Y4B: allopregnanolone(Non-covalent)

Y4B.14: 8 residues within 4Å: Chain D: A.324, L.325, Y.328 Chain G: I.291, Q.294, V.295, W.298, P.464 8 PLIP interactions: 2 interactions with chain D, 6 interactions with chain G Hydrophobic interactions: D:A.324, D:Y.328, G:I.291, G:V.295, G:W.298, G:W.298, G:W.298 Hydrogen bonds: G:Q.294

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 beta-2: AD
Gamma-aminobutyric acid receptor subunit alpha-1: B
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
B

D
E

B
C

C
D

E
J

F
K

G
A

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

Heavy Chain of 8E3 Fab

Light Chain of 8E3 Fab

Gamma-aminobutyric acid receptor subunit alpha-3

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