SMTL ID : 8si9.1

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

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 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.89, 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: 26 residues within 4Å: Chain A: R.86, V.106, G.108, K.112 Chain B: N.111, M.112, T.113, M.114 Chain D: N.28, S.92, K.93, 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 No protein-ligand interaction detected (PLIP)

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 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.222

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.9: 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 Y4B: allopregnanolone(Non-covalent)

Y4B.7: 10 residues within 4Å: Chain A: L.297, A.300, L.301, Y.304, I.305 Chain B: I.239, Q.242, V.243, W.246, P.330 13 PLIP interactions: 4 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:L.297, A:A.300, A:L.301, A:Y.304, B:I.239, B:Q.242, B:V.243, B:V.243, B:W.246, B:W.246, B:W.246, B:W.246, B:P.330 Y4B.11: 10 residues within 4Å: Chain C: F.293, L.297, A.300, L.301, Y.304 Chain D: I.239, Q.242, V.243, W.246, P.330 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:A.300, C:L.301, C:Y.304, D:W.246, D:W.246, D:W.246, D:P.330

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

ABU.8: 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 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:F.65 Salt bridges: B:R.67 Hydrogen bonds: A:Y.97, A:S.156, A:Y.157, A:T.202, A:T.202 ABU.10: 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 8 PLIP interactions: 2 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:F.65, C:Y.205 Salt bridges: D:R.67 Hydrogen bonds: C:Y.97, C:E.155, C:S.156, C:T.202, C:T.202

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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