SMTL ID : 7qnc.1

Cryo-EM structure of human full-length extrasynaptic alpha4beta3delta GABA(A)R in complex with THIP (gaboxadol), histamine and nanobody Nb25

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-3-1-2-mer

Ligands

4 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: 5 residues within 4Å: Chain A: M.122, T.125, N.144, P.148 Chain C: D.114 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:M.122, A:T.125 NAG-NAG-BMA-MAN-MAN.3: 8 residues within 4Å: Chain B: N.174, R.217, V.219, S.220, R.221, S.236, F.237, R.238 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.217, B:R.221 NAG-NAG-BMA-MAN-MAN.5: 11 residues within 4Å: Chain C: N.174, R.217, V.219, S.220, R.221, S.236, R.238 Chain F: N.28, Y.29, S.101, D.111 6 PLIP interactions: 3 interactions with chain F, 3 interactions with chain C Hydrogen bonds: F:T.108, C:R.217, C:R.217, C:R.221, F:Y.29, F:Y.29, F:D.111 NAG-NAG-BMA-MAN-MAN.7: 11 residues within 4Å: Chain D: N.174, R.217, V.219, S.220, R.221, S.236, R.238 Chain G: N.28, Y.29, S.101, D.111 6 PLIP interactions: 3 interactions with chain G, 3 interactions with chain D Hydrogen bonds: G:T.108, D:R.217, D:R.217, D:R.221, G:Y.29, G:Y.29, G:D.111

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

NAG-NAG.2: 3 residues within 4Å: Chain B: P.103, N.105, H.144 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain C: P.103, N.105, H.144 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain D: P.103, N.105, H.144 No protein-ligand interaction detected (PLIP)

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

NAG.8: 4 residues within 4Å: Chain A: I.104, M.155, N.157, T.159 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.104 Hydrogen bonds: A:N.157, A:T.159 NAG.10: 4 residues within 4Å: Chain B: N.33, S.35, F.36, E.39 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.33, B:E.39 NAG.13: 4 residues within 4Å: Chain C: N.33, S.35, F.36, E.39 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.33, C:E.39 NAG.16: 4 residues within 4Å: Chain D: N.33, S.35, F.36, E.39 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.33, D:E.39 NAG.18: 4 residues within 4Å: Chain E: N.65, V.193, Y.194, Y.195 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.65, E:Y.194 NAG.20: 1 residues within 4Å: Chain E: N.103 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.103

3 x D10: DECANE(Non-covalent)

D10.9: 3 residues within 4Å: Chain B: I.255, N.464, W.468 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:N.464, B:W.468, B:W.468 D10.12: 2 residues within 4Å: Chain C: N.464, W.468 No protein-ligand interaction detected (PLIP) D10.15: 2 residues within 4Å: Chain D: N.464, W.468 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:W.468

2 x EI7: 4,5,6,7-tetrahydro-[1,2]oxazolo[5,4-c]pyridin-3-one(Non-covalent)

EI7.11: 10 residues within 4Å: Chain A: F.98, R.100, L.151, T.163 Chain B: Y.122, E.180, S.181, Y.182, F.225, T.227 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.98, B:F.225 Hydrogen bonds: A:R.100, A:T.163, A:T.163, B:Y.122, B:Y.182 pi-Stacking: A:F.98, B:Y.182 EI7.19: 8 residues within 4Å: Chain D: D.68, Y.87, Q.89 Chain E: F.125, E.183, Y.185, K.229, F.234 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:Y.87, E:K.229 Hydrogen bonds: D:D.68, E:E.183 pi-Stacking: D:Y.87

2 x HSM: HISTAMINE(Non-covalent)

HSM.14: 8 residues within 4Å: Chain B: D.68, Q.89 Chain C: Y.122, E.180, S.181, Y.182, F.225, T.227 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:Q.89, C:Y.122, C:E.180 pi-Stacking: B:Y.87, C:F.225 HSM.17: 9 residues within 4Å: Chain C: D.68, Q.89 Chain D: Y.122, E.180, S.181, Y.182, F.225, T.227, Y.230 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Y.122, D:E.180 pi-Stacking: C:Y.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sente, A. et al., Differential assembly diversifies GABA A receptor structures and signalling. Nature (2022)

Release Date

2022-04-13

Peptides

Gamma-aminobutyric acid receptor subunit alpha-4: A
Gamma-aminobutyric acid receptor subunit beta-3: BCD
Gamma-aminobutyric acid receptor subunit delta: E
Nanobody Nb25: FG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

Membrane

We predict this structure to be a membrane protein.
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Gamma-aminobutyric acid receptor subunit alpha-4

Gamma-aminobutyric acid receptor subunit beta-3

Gamma-aminobutyric acid receptor subunit delta

Nanobody Nb25

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