SMTL ID : 8foi.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-1-2-2-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: 18 residues within 4Å: Chain A: N.137, M.138, T.139, M.140 Chain D: S.138, N.139, M.140, V.141, G.142, A.157, D.158, W.161, P.165, R.167 Chain E: V.130, G.132, K.136 Ligands: NAG-NAG-BMA-MAN-MAN.4 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: 3 residues within 4Å: Chain B: L.103, N.104, H.143 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.3: 10 residues within 4Å: Chain B: N.173, T.175, D.214, Y.215, K.216, I.218, K.220, S.235, F.236, K.237 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.220 NAG-NAG-BMA-MAN-MAN.4: 10 residues within 4Å: Chain A: S.118 Chain B: I.49, D.113, Q.114 Chain C: L.115, N.137, T.139, M.140, P.141 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.1 No protein-ligand interaction detected (PLIP) 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: 12 residues within 4Å: Chain E: N.173, T.175, D.214, Y.215, K.216, I.218, T.219, K.220, K.221, S.235, F.236, K.237 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.221, E:K.221, E: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.5: 7 residues within 4Å: Chain D: W.221, K.222, R.223, S.225, L.244, R.245, N.246 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.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 Ligands: D12.10, D12.25 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.421 Hydrogen bonds: A:R.275, A:R.275, A:N.413, A:S.414, A:S.414, A:S.414, A:S.416, A:K.417, A:I.418 Salt bridges: A:K.338, A:K.338, A:R.339, A:K.417, A:K.417 PIO.26: 18 residues within 4Å: Chain C: R.275, S.325, I.328, E.329, T.332, V.333, F.336, K.338, R.339, N.413, S.414, S.416, K.417, I.418, L.421, S.422, A.425, F.426 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:T.332, C:K.417 Hydrogen bonds: C:R.275, 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

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

D12.9: 13 residues within 4Å: Chain A: S.296, I.316, A.317, Y.320, A.321, F.324, S.325, I.328 Chain B: L.247, M.251, P.252, L.255 Ligands: POV.15 Ligand excluded by PLIP D12.10: 10 residues within 4Å: Chain A: V.318, A.321, F.322, S.325, A.425, F.426, L.429, I.432, F.433 Ligands: PIO.8 Ligand excluded by PLIP D12.19: 4 residues within 4Å: Chain B: V.314 Ligands: D12.24, OCT.27, POV.33 Ligand excluded by PLIP D12.20: 7 residues within 4Å: Chain B: L.325, Y.328, I.329, D.483 Ligands: Y4B.18, D12.21, POV.32 Ligand excluded by PLIP D12.21: 13 residues within 4Å: Chain B: M.318, L.321, E.322, L.325, A.486, I.487, W.490, S.491, F.494, F.495 Ligands: Y4B.18, D12.20, POV.32 Ligand excluded by PLIP D12.22: 12 residues within 4Å: Chain B: I.242, I.246, I.254, I.258, W.261, Y.308, F.499, S.500, N.503, W.507, V.511 Ligands: D12.23 Ligand excluded by PLIP D12.23: 8 residues within 4Å: Chain B: S.500, N.503, I.504, W.507, L.508, V.511 Ligands: POV.15, D12.22 Ligand excluded by PLIP D12.24: 9 residues within 4Å: Chain B: V.302, M.307, M.310, G.311, V.314, F.315, F.502 Ligands: D12.19, POV.33 Ligand excluded by PLIP D12.25: 11 residues within 4Å: Chain A: I.328, A.331, T.332, Y.335, F.336 Chain B: I.258, W.261, V.262, W.265 Ligands: PIO.8, POV.15 Ligand excluded by PLIP D12.30: 12 residues within 4Å: Chain C: T.293, S.296, I.316, A.317, Y.320, A.321, F.324, I.328 Chain D: I.276, I.280, P.281, L.284 Ligand excluded by PLIP D12.31: 10 residues within 4Å: Chain C: V.318, A.321, F.322, S.325, A.425, F.426, L.429, I.432, F.433, V.436 Ligand excluded by PLIP D12.39: 12 residues within 4Å: Chain D: T.315, S.318, V.331, L.336, V.338, S.339, F.342 Chain E: L.247, M.251, P.252, L.255 Ligands: OCT.37 Ligand excluded by PLIP D12.40: 6 residues within 4Å: Chain D: C.461, N.464, L.465, W.468, V.469 Ligands: OCT.41 Ligand excluded by PLIP D12.44: 11 residues within 4Å: Chain E: V.302, M.307, M.310, G.311, V.314, F.315, V.498, F.502 Ligands: POV.16, OCT.45, D12.46 Ligand excluded by PLIP D12.46: 8 residues within 4Å: Chain E: V.302, M.307, F.502, V.505, Y.506, Y.509, Y.510 Ligands: D12.44 Ligand excluded by PLIP D12.50: 13 residues within 4Å: Chain E: L.169, I.242, I.246, M.251, I.254, I.258, W.261, F.499, S.500, N.503, W.507, V.511 Ligands: OCT.49 Ligand excluded by PLIP D12.53: 11 residues within 4Å: Chain E: M.318, L.321, E.322, L.325, I.487, W.490, S.491, F.494, F.495 Ligands: OCT.51, POV.52 Ligand excluded by PLIP

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

OCT.11: 8 residues within 4Å: Chain A: E.170, W.314, F.433, V.436, Y.437, T.440, Y.441, R.444 Ligand excluded by PLIP OCT.12: 6 residues within 4Å: Chain A: V.253, L.258, I.261, M.262 Ligands: OCT.14, POV.16 Ligand excluded by PLIP OCT.13: 9 residues within 4Å: Chain A: G.431, N.434, L.435, W.438, A.439, L.442 Ligands: OCT.14, POV.16, POV.52 Ligand excluded by PLIP OCT.14: 4 residues within 4Å: Ligands: OCT.12, OCT.13, POV.16, POV.52 Ligand excluded by PLIP OCT.27: 8 residues within 4Å: Chain C: V.253, L.258, I.261, M.262, I.265 Ligands: D12.19, OCT.29, POV.33 Ligand excluded by PLIP OCT.28: 9 residues within 4Å: Chain C: G.431, N.434, L.435, W.438, A.439, L.442 Ligands: OCT.29, POV.32, POV.33 Ligand excluded by PLIP OCT.29: 3 residues within 4Å: Ligands: OCT.27, OCT.28, POV.33 Ligand excluded by PLIP OCT.35: 5 residues within 4Å: Chain D: W.294, R.453, I.454, P.457 Ligands: OCT.36 Ligand excluded by PLIP OCT.36: 4 residues within 4Å: Chain C: Y.335 Chain D: W.294 Ligands: OCT.35, OCT.38 Ligand excluded by PLIP OCT.37: 9 residues within 4Å: Chain D: S.329, Y.330, V.331 Chain E: G.243, I.246, L.247, M.251 Ligands: D12.39, OCT.49 Ligand excluded by PLIP OCT.38: 8 residues within 4Å: Chain C: I.328, A.331, T.332, Y.335, F.336 Chain D: V.291, W.294 Ligands: OCT.36 Ligand excluded by PLIP OCT.41: 9 residues within 4Å: Chain D: T.275, Y.279, T.283, W.290, F.460, C.461, N.464, W.468 Ligands: D12.40 Ligand excluded by PLIP OCT.45: 4 residues within 4Å: Chain E: V.314 Ligands: POV.16, D12.44, POV.52 Ligand excluded by PLIP OCT.47: 7 residues within 4Å: Chain E: I.258, W.261, W.265, R.492, I.493, P.496 Ligands: OCT.48 Ligand excluded by PLIP OCT.48: 9 residues within 4Å: Chain D: V.350, G.353, T.354, Y.357 Chain E: I.258, W.261, V.262, W.265 Ligands: OCT.47 Ligand excluded by PLIP OCT.49: 6 residues within 4Å: Chain E: I.242, G.243, I.246, M.251 Ligands: OCT.37, D12.50 Ligand excluded by PLIP OCT.51: 6 residues within 4Å: Chain E: L.325, Y.328, I.329 Ligands: Y4B.42, POV.52, D12.53 Ligand excluded by PLIP

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

POV.15: 17 residues within 4Å: Chain A: F.324, I.328, Y.335 Chain B: M.251, L.255, I.258, W.265, R.489, R.492, I.493, P.496, V.497, S.500, F.501 Ligands: D12.9, D12.23, D12.25 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.258, B:W.265, B:R.492, B:I.493, B:P.496, B:V.497 Hydrogen bonds: A:Y.335 POV.16: 31 residues within 4Å: Chain A: D.218, R.247, K.248, I.249, G.250, V.253, I.254, L.258, P.259, I.261, M.262, I.265, F.430, G.431, N.434, W.438, L.442 Chain E: T.286, N.289, P.300, Y.301, V.302, M.310, F.313, V.314 Ligands: OCT.12, OCT.13, OCT.14, D12.44, OCT.45, POV.52 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:I.254, A:I.261, A:F.430, A:W.438, A:L.442, E:F.313, E:F.313 Hydrogen bonds: A:I.249, A:G.250 Salt bridges: A:D.218 POV.32: 19 residues within 4Å: Chain B: F.317, M.318, L.321, Y.328 Chain C: I.265, W.272, R.420, R.423, I.424, P.427, L.428, G.431, I.432, L.435 Ligands: Y4B.18, D12.20, D12.21, OCT.28, POV.33 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:P.427, C:I.432, B:L.321 Salt bridges: C:R.420 POV.33: 30 residues within 4Å: Chain B: T.286, N.289, P.300, V.302, M.310, F.313, V.314 Chain C: K.248, I.249, G.250, V.253, I.254, L.258, P.259, I.261, M.262, I.265, P.427, F.430, G.431, N.434, W.438, L.442 Ligands: Y4B.18, D12.19, D12.24, OCT.27, OCT.28, OCT.29, POV.32 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:V.253, C:I.254, C:L.258, C:I.261, C:F.430, C:N.434, C:W.438, B:F.313 Hydrogen bonds: C:I.249, C:G.250 POV.52: 21 residues within 4Å: Chain A: I.265, W.272, R.420, R.423, I.424, P.427, L.428, G.431, I.432, L.435 Chain E: F.317, M.318, L.321, Y.328 Ligands: OCT.13, OCT.14, POV.16, Y4B.42, OCT.45, OCT.51, D12.53 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.420

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

ABU.17: 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 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:Y.181, B:Y.229 Hydrogen bonds: B:E.179, B:T.226, B:T.226 Salt bridges: C:R.93 ABU.43: 12 residues within 4Å: Chain A: F.91, R.93, L.144, T.156 Chain E: Y.121, E.179, S.180, Y.181, G.182, F.224, T.226, Y.229 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain E Hydrophobic interactions: A:F.91, E:Y.181, E:F.224, E:Y.229 Salt bridges: A:R.93 Hydrogen bonds: E:Y.121, E:Y.181, E:T.226

2 x Y4B: allopregnanolone(Non-covalent)

Y4B.18: 13 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: D12.20, D12.21, POV.32, POV.33 11 PLIP interactions: 3 interactions with chain B, 8 interactions with chain C Hydrophobic interactions: B:L.321, B:A.324, B:Y.328, C:I.265, C:V.269, C:W.272, C:W.272, C:W.272, C:W.272, C:P.427 Hydrogen bonds: C:Q.268 Y4B.42: 13 residues within 4Å: Chain A: I.265, Q.268, V.269, W.272, P.427 Chain E: F.317, L.321, A.324, L.325, Y.328, I.329 Ligands: OCT.51, POV.52 10 PLIP interactions: 3 interactions with chain E, 7 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 Hydrogen bonds: A:Q.268

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

NAG.34: 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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