SMTL ID : 7qn6.1

Cryo-EM structure of human full-length beta3delta GABA(A)R in complex with nanobody Nb25

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-1-3-mer

Ligands

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

NAG-NAG.1: 2 residues within 4Å: Chain A: N.105, H.144 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain B: N.105, H.144 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain C: P.103, N.105, H.144 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain D: Y.91, N.105, H.144 No protein-ligand interaction detected (PLIP)

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.2: 7 residues within 4Å: Chain A: N.174, R.217, V.219, S.220, R.221, S.236, R.238 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.217, A:R.221 NAG-NAG-BMA-MAN-MAN.4: 12 residues within 4Å: Chain B: N.174, R.217, V.219, S.220, R.221, S.236, R.238 Chain F: N.28, Y.29, S.101, T.108, D.111 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain F Hydrogen bonds: B:R.217, B:R.221, F:Y.29, F:D.111 NAG-NAG-BMA-MAN-MAN.6: 12 residues within 4Å: Chain C: N.174, R.217, V.219, S.220, R.221, S.236, R.238 Chain G: N.28, Y.29, S.101, T.108, D.111 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain G Hydrogen bonds: C:R.217, C:R.221, G:Y.29, G:Y.29 NAG-NAG-BMA-MAN-MAN.8: 12 residues within 4Å: Chain D: N.174, R.217, V.219, S.220, R.221, S.236, R.238 Chain H: N.28, Y.29, S.101, T.108, D.111 5 PLIP interactions: 2 interactions with chain H, 3 interactions with chain D Hydrogen bonds: H:Y.29, H:D.111, D:R.217, D:R.221, D:S.234

3 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.9: 15 residues within 4Å: Chain A: N.66, I.67, D.68, Y.87, Q.89, M.140, T.201 Chain B: Y.122, E.180, S.181, Y.182, F.225, A.226, T.227, Y.230 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.122, B:E.180, A:T.201 pi-Cation interactions: B:Y.230 EPE.10: 12 residues within 4Å: Chain B: D.68, Y.87, Q.89, T.201 Chain C: Y.122, E.180, S.181, Y.182, F.225, A.226, T.227, Y.230 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:Y.122, C:E.180, C:A.226, C:T.227, B:D.68, B:D.68, B:T.201 pi-Cation interactions: C:Y.182 Salt bridges: B:D.68 EPE.11: 13 residues within 4Å: Chain C: D.68, Y.87, Q.89, M.140, T.201 Chain D: Y.122, E.180, S.181, Y.182, F.225, A.226, T.227, Y.230 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:Y.122, D:E.180, D:A.226, D:T.227, C:D.68, C:D.68, C:T.201 pi-Cation interactions: D:Y.230

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

NAG.12: 1 residues within 4Å: Chain E: N.103 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:N.103

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 beta-3: ABCD
Gamma-aminobutyric acid receptor subunit delta: E
Nanobody Nb25: FGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
K

G
L

H
M

Membrane

We predict this structure to be a membrane protein.
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Gamma-aminobutyric acid receptor subunit beta-3

Gamma-aminobutyric acid receptor subunit delta

Nanobody Nb25

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