SMTL ID : 8g4n.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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.1: 5 residues within 4Å: Chain D: W.221, R.223, S.225, L.244, N.246 No protein-ligand interaction detected (PLIP)

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.2: 2 residues within 4Å: Chain B: N.104, H.143 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.3: 6 residues within 4Å: Chain B: N.173, K.216, I.218, K.220, S.235, K.237 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.220 NAG-NAG-BMA-MAN-MAN.5: 5 residues within 4Å: Chain B: D.113, Q.114 Chain C: N.137, M.140 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.113, B:Q.114 NAG-NAG-BMA-MAN-MAN.6: 3 residues within 4Å: Chain E: L.103, N.104, H.143 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.7: 8 residues within 4Å: Chain E: N.173, D.214, K.216, I.218, K.220, K.221, S.235, K.237 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.220, E:K.221, E:K.221

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.4: 12 residues within 4Å: Chain A: N.137, M.138, T.139 Chain D: S.138, N.139, V.141, G.142, A.157, D.158, W.161, R.167 Ligands: NAG-NAG-BMA-MAN-MAN.5 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:A.157

2 x Y4B: allopregnanolone(Non-covalent)

Y4B.8: 11 residues within 4Å: Chain A: I.265, Q.268, V.269, W.272, P.427 Chain E: L.321, A.324, L.325, Y.328 Ligands: OCT.52, POV.53 11 PLIP interactions: 3 interactions with chain E, 8 interactions with chain A Hydrophobic interactions: E:L.321, E:A.324, E:Y.328, A:I.265, A:V.269, A:W.272, A:W.272, A:W.272, A:W.272, A:P.427 Hydrogen bonds: A:Q.268 Y4B.28: 11 residues within 4Å: Chain B: L.321, A.324, L.325, Y.328 Chain C: I.265, Q.268, V.269, W.272, P.427 Ligands: D12.18, POV.35 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:I.265, C:V.269, C:W.272, C:W.272, C:W.272, C:P.427, B:L.321, B:A.324, B:Y.328 Hydrogen bonds: C:Q.268

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: 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 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:T.332, A:K.417, A:L.421, A:L.421 Hydrogen bonds: A:R.275, A:R.275, A:N.413, A:S.414, A:K.417, A:I.418 Salt bridges: A:K.338, A:K.338, A:R.339, A:K.417, A:K.417 PIO.27: 12 residues within 4Å: Chain C: R.275, T.332, F.336, K.338, R.339, N.413, S.414, S.416, K.417, I.418, L.421 Ligands: OCT.34 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:K.417, C:I.418, C:L.421 Hydrogen bonds: C:R.275, C:R.275, C:N.413, C:S.414, C:K.417 Salt bridges: C:R.275, C:K.338, C:K.338, C:R.339

17 x D12: DODECANE(Non-covalent)(Non-functional Binders)

D12.10: 7 residues within 4Å: Chain A: S.296, A.317, Y.320, A.321, S.325 Chain B: M.251, L.255 Ligand excluded by PLIP D12.11: 6 residues within 4Å: Chain A: A.321, F.322, A.425, F.426, L.429, F.433 Ligand excluded by PLIP D12.17: 3 residues within 4Å: Ligands: D12.22, OCT.29, POV.36 Ligand excluded by PLIP D12.18: 5 residues within 4Å: Chain B: L.325, Y.328, I.329, G.332 Ligands: Y4B.28 Ligand excluded by PLIP D12.19: 6 residues within 4Å: Chain B: M.318, L.321, E.322, L.325, W.490, S.491 Ligand excluded by PLIP D12.20: 5 residues within 4Å: Chain B: I.254, F.499, N.503, W.507 Ligands: D12.21 Ligand excluded by PLIP D12.21: 6 residues within 4Å: Chain B: S.500, N.503, W.507, V.511 Ligands: D12.20, POV.24 Ligand excluded by PLIP D12.22: 7 residues within 4Å: Chain B: M.307, M.310, G.311, V.314, F.315 Ligands: D12.17, POV.36 Ligand excluded by PLIP D12.23: 5 residues within 4Å: Chain A: T.332, Y.335 Chain B: I.258, W.265 Ligands: POV.24 Ligand excluded by PLIP D12.32: 5 residues within 4Å: Chain C: S.296, A.317, A.321 Chain D: I.276, I.280 Ligand excluded by PLIP D12.33: 4 residues within 4Å: Chain C: F.322, F.426, L.429, F.433 Ligand excluded by PLIP D12.41: 5 residues within 4Å: Chain D: S.318, L.336, S.339, F.342 Chain E: L.247 Ligand excluded by PLIP D12.42: 3 residues within 4Å: Chain D: L.465, W.468 Ligands: OCT.43 Ligand excluded by PLIP D12.45: 7 residues within 4Å: Chain E: M.307, M.310, G.311, V.314, F.315, F.502 Ligands: OCT.46 Ligand excluded by PLIP D12.47: 6 residues within 4Å: Chain E: M.307, F.502, V.505, Y.506, Y.509, Y.510 Ligand excluded by PLIP D12.51: 7 residues within 4Å: Chain E: M.251, I.254, F.499, N.503, W.507, V.511 Ligands: OCT.50 Ligand excluded by PLIP D12.54: 5 residues within 4Å: Chain E: L.321, E.322, W.490, F.494, F.495 Ligand excluded by PLIP

17 x OCT: N-OCTANE(Non-covalent)(Non-functional Binders)

OCT.12: 2 residues within 4Å: Chain A: W.314, Y.441 Ligand excluded by PLIP OCT.13: 3 residues within 4Å: Chain A: L.258 Ligands: OCT.15, POV.16 Ligand excluded by PLIP OCT.14: 5 residues within 4Å: Chain A: L.435, W.438 Ligands: OCT.15, POV.16, POV.53 Ligand excluded by PLIP OCT.15: 2 residues within 4Å: Ligands: OCT.13, OCT.14 Ligand excluded by PLIP OCT.29: 3 residues within 4Å: Ligands: D12.17, OCT.31, POV.36 Ligand excluded by PLIP OCT.30: 4 residues within 4Å: Chain C: L.435, W.438 Ligands: OCT.31, POV.36 Ligand excluded by PLIP OCT.31: 2 residues within 4Å: Ligands: OCT.29, OCT.30 Ligand excluded by PLIP OCT.34: 5 residues within 4Å: Chain C: I.328, T.332, Y.335 Chain D: W.294 Ligands: PIO.27 Ligand excluded by PLIP OCT.38: 3 residues within 4Å: Chain D: R.453, I.454 Ligands: OCT.39 Ligand excluded by PLIP OCT.39: 2 residues within 4Å: Chain D: W.294 Ligands: OCT.38 Ligand excluded by PLIP OCT.40: 4 residues within 4Å: Chain D: S.329 Chain E: G.243, I.246 Ligands: OCT.50 Ligand excluded by PLIP OCT.43: 5 residues within 4Å: Chain D: T.283, F.460, N.464, W.468 Ligands: D12.42 Ligand excluded by PLIP OCT.46: 1 residues within 4Å: Ligands: D12.45 Ligand excluded by PLIP OCT.48: 6 residues within 4Å: Chain E: W.261, W.265, R.489, R.492, P.496 Ligands: OCT.49 Ligand excluded by PLIP OCT.49: 7 residues within 4Å: Chain D: V.350, G.353, T.354 Chain E: I.258, V.262, W.265 Ligands: OCT.48 Ligand excluded by PLIP OCT.50: 4 residues within 4Å: Chain E: I.242, I.246 Ligands: OCT.40, D12.51 Ligand excluded by PLIP OCT.52: 3 residues within 4Å: Chain E: I.329 Ligands: Y4B.8, POV.53 Ligand excluded by PLIP

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

POV.16: 16 residues within 4Å: Chain A: K.248, I.249, G.250, I.254, L.258, I.261, M.262, I.265, N.434, W.438, L.442 Chain E: V.302, F.313, V.314 Ligands: OCT.13, OCT.14 11 PLIP interactions: 4 interactions with chain E, 7 interactions with chain A Hydrophobic interactions: E:V.302, E:F.313, E:F.313, E:V.314, A:I.254, A:L.258, A:I.261, A:I.265, A:W.438, A:L.442 Hydrogen bonds: A:I.249 POV.24: 12 residues within 4Å: Chain A: I.328, Y.335 Chain B: L.255, W.265, R.489, R.492, I.493, P.496, V.497, S.500 Ligands: D12.21, D12.23 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:I.328, B:L.255, B:R.489, B:I.493, B:P.496, B:V.497 Hydrogen bonds: A:Y.335 Salt bridges: B:R.492 POV.35: 13 residues within 4Å: Chain B: L.321, Y.328 Chain C: W.272, R.420, R.423, I.424, P.427, L.428, G.431, I.432, L.435 Ligands: Y4B.28, POV.36 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.424, C:P.427, C:I.432, C:L.435 Salt bridges: C:R.420 Hydrogen bonds: B:Y.328 POV.36: 18 residues within 4Å: Chain B: P.300, M.310, F.313 Chain C: K.248, I.249, G.250, V.253, I.254, I.261, F.430, N.434, W.438, L.442 Ligands: D12.17, D12.22, OCT.29, OCT.30, POV.35 11 PLIP interactions: 1 interactions with chain B, 10 interactions with chain C Hydrophobic interactions: B:F.313, C:V.253, C:I.254, C:I.261, C:F.430, C:F.430, C:W.438, C:W.438, C:L.442 Hydrogen bonds: C:I.249, C:G.250 POV.53: 12 residues within 4Å: Chain A: W.272, R.420, R.423, I.424, P.427, G.431, I.432 Chain E: L.321, Y.328 Ligands: Y4B.8, OCT.14, OCT.52 8 PLIP interactions: 2 interactions with chain E, 6 interactions with chain A Hydrophobic interactions: E:L.321, E:Y.328, A:W.272, A:I.424, A:P.427, A:P.427, A:I.432 Salt bridges: A:R.420

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

ABU.25: 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 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:Y.181, B:Y.229, C:L.144 Hydrogen bonds: B:Y.121, B:Y.181, B:T.226, B:T.226 Salt bridges: C:R.93 ABU.44: 10 residues within 4Å: Chain A: F.91, R.93, L.144, T.156 Chain E: Y.121, E.179, S.180, Y.181, T.226, Y.229 8 PLIP interactions: 5 interactions with chain E, 3 interactions with chain A Hydrophobic interactions: E:Y.181, E:Y.229, A:F.91, A:L.144 Hydrogen bonds: E:E.179, E:Y.181, E:T.226 Salt bridges: A:R.93

1 x R5R: Zolpidem(Non-covalent)

R5R.26: 14 residues within 4Å: Chain C: F.126, H.128, Y.186, Q.230, S.231, S.232, T.233, Y.236 Chain D: D.94, M.95, Y.96, N.98, F.115, A.117 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:F.126, C:Y.236, C:Y.236, D:D.94, D:Y.96, D:F.115, D:F.115

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

NAG.37: 1 residues within 4Å: Chain D: N.128 No protein-ligand interaction detected (PLIP)

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: AC
Gamma-aminobutyric acid receptor subunit beta-2: BE
Gamma-aminobutyric acid receptor subunit gamma-2: D
Heavy Chain of 8E3 Fab: FG
Light Chain of 8E3 Fab: HI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

E
E

D
D

F
H

G
J

H
K

I
L

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

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