SMTL ID : 8sgo.1

Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus pregnenolone sulfate

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

3 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: 8 residues within 4Å: Chain A: N.149, D.190, Y.191, K.192, I.194, K.196, S.211, K.213 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.192 NAG-NAG-BMA.3: 10 residues within 4Å: Chain C: N.149, T.151, D.190, Y.191, K.192, I.194, K.196, S.211, F.212, K.213 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.196 NAG-NAG-BMA.4: 9 residues within 4Å: Chain C: I.25, D.89 Chain D: L.89, N.111, M.114, P.115 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.2 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.89

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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-MAN-MAN-MAN.2: 24 residues within 4Å: Chain A: R.86, V.106, G.108, K.112 Chain B: N.111, M.112, T.113 Chain D: N.28, S.92, A.109, N.111, P.115, K.117 Chain E: S.137, N.138, M.139, V.140, G.141, K.142, D.157, W.160, P.164, R.166 Ligands: NAG-NAG-BMA.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.112, A:G.108

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.5: 6 residues within 4Å: Chain E: W.220, K.221, R.222, L.243, R.244, N.245 No protein-ligand interaction detected (PLIP)

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

NAG.6: 4 residues within 4Å: Chain A: P.78, L.79, N.80, H.119 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.80, A:H.119 NAG.11: 4 residues within 4Å: Chain C: P.78, L.79, N.80, H.119 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.80, C:H.119

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

ABU.7: 11 residues within 4Å: Chain A: Y.97, E.155, S.156, Y.157, F.200, T.202, Y.205 Chain B: F.65, R.67, L.118, T.130 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:F.65, A:Y.157 Salt bridges: B:R.67 Hydrogen bonds: A:Y.97, A:S.156, A:Y.157, A:Y.157, A:T.202 ABU.12: 11 residues within 4Å: Chain C: Y.97, E.155, S.156, Y.157, F.200, T.202, Y.205 Chain D: F.65, R.67, L.118, T.130 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Y.97, C:E.155, C:S.156, C:T.202, C:T.202 Hydrophobic interactions: D:F.65 Salt bridges: D:R.67

6 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.8: 23 residues within 4Å: Chain A: T.262, N.265, P.276, M.286, F.289, V.290 Chain B: K.222, I.223, G.224, V.227, I.228, L.232, P.233, I.235, M.236, T.237, I.239, P.330, F.333, G.334, N.337, W.341 Ligands: PTY.10 18 PLIP interactions: 6 interactions with chain A, 12 interactions with chain B Hydrophobic interactions: A:T.262, A:M.286, A:F.289, A:F.289, A:F.289, A:V.290, B:V.227, B:V.227, B:I.228, B:L.232, B:P.233, B:I.235, B:M.236, B:F.333, B:W.341, B:W.341 Hydrogen bonds: B:I.223, B:G.224 PTY.9: 19 residues within 4Å: Chain B: V.292, Y.294, A.295, F.296, F.298, S.299, I.302, E.303, T.306, F.310, R.317, I.321, S.325, A.328, F.329, L.332, I.335, F.336 Chain C: L.231 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:V.292, B:Y.294, B:A.295, B:F.296, B:F.296, B:F.298, B:F.298, B:E.303, B:A.328, B:F.329, B:L.332, B:L.332, B:I.335, B:F.336 Hydrogen bonds: B:T.306, B:R.317 PTY.10: 9 residues within 4Å: Chain A: Y.304 Chain B: W.246, R.323, R.326, I.327, P.330, L.331, G.334 Ligands: PTY.8 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.246, B:W.246, B:R.326, B:I.327, B:I.327, B:L.331, A:Y.304 Salt bridges: B:R.326 Hydrogen bonds: A:Y.304 PTY.14: 23 residues within 4Å: Chain C: T.262, N.265, P.276, V.278, M.286, F.289, V.290 Chain D: K.222, I.223, G.224, V.227, I.228, L.232, P.233, I.235, M.236, T.237, I.239, F.333, G.334, N.337, W.341 Ligands: Q3G.13 14 PLIP interactions: 5 interactions with chain C, 9 interactions with chain D Hydrophobic interactions: C:V.278, C:M.286, C:F.289, C:F.289, C:V.290, D:V.227, D:I.228, D:P.233, D:P.233, D:I.235, D:W.341, D:W.341 Hydrogen bonds: D:I.223, D:G.224 PTY.15: 21 residues within 4Å: Chain D: A.291, V.292, Y.294, A.295, F.296, F.298, S.299, I.302, E.303, T.306, F.310, R.317, I.321, L.324, S.325, A.328, F.329, L.332, I.335, F.336 Chain E: L.283 19 PLIP interactions: 17 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:V.292, D:Y.294, D:A.295, D:F.296, D:F.298, D:F.298, D:E.303, D:I.321, D:L.324, D:A.328, D:F.329, D:F.329, D:F.329, D:L.332, D:I.335, D:F.336, E:L.283, E:L.283 Salt bridges: D:R.317 PTY.16: 9 residues within 4Å: Chain C: Y.304 Chain D: W.246, R.249, R.323, R.326, I.327, P.330, L.331, G.334 8 PLIP interactions: 1 interactions with chain C, 7 interactions with chain D Hydrogen bonds: C:Y.304, D:R.326, D:R.326 Hydrophobic interactions: D:W.246, D:W.246, D:W.246, D:L.331 Salt bridges: D:R.326

1 x Q3G: O-[(R)-[(2S)-2-(hexadecanoyloxy)-3-(octadecanoyloxy)propoxy](hydroxy)phosphoryl]-D-serine(Non-covalent)

Q3G.13: 18 residues within 4Å: Chain C: R.141, P.276, Y.277, V.278, M.283, M.286, G.287, V.290, F.291, M.294, V.327, F.330, F.331, V.334, Y.335, Y.338, Y.339 Ligands: PTY.14 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:M.286, C:F.291, C:F.291, C:F.331, C:V.334, C:Y.338, C:Y.338 Hydrogen bonds: C:V.278 Salt bridges: C:R.141

1 x A8W: Pregnenolone sulfate(Non-covalent)

A8W.17: 16 residues within 4Å: Chain A: A.248, A.252, T.256, L.259 Chain B: V.257, T.261 Chain C: A.248, A.252 Chain D: P.253, V.257 Chain E: P.300, A.301, S.304, I.307, T.308, L.311 7 PLIP interactions: 3 interactions with chain E, 1 interactions with chain C, 1 interactions with chain D, 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: E:P.300, E:I.307, E:T.308, C:A.252, D:V.257, B:V.257, A:A.252

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Legesse, D.H. et al., Structural insights into opposing actions of neurosteroids on GABA A receptors. Nat Commun (2023)

Release Date

2023-08-30

Peptides

Gamma-aminobutyric acid receptor subunit beta-2: AC
Gamma-aminobutyric acid receptor subunit alpha-1: BD
Gamma-aminobutyric acid receptor subunit gamma-2: E
Kappa Fab Light Chain: FH
IgG2b Fab Heavy Chain: GI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

F
I

H
L

G
J

I
K

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

Kappa Fab Light Chain

IgG2b Fab Heavy Chain

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