SMTL ID : 7qna.1

Cryo-EM structure of human full-length alpha4beta3gamma2 GABA(A)R in complex with GABA and nanobody Nb25

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-3-1-1-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: 3 residues within 4Å: Chain A: M.122, N.144, P.148 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:M.122 NAG-NAG-BMA-MAN-MAN.3: 7 residues within 4Å: Chain B: N.174, R.217, V.219, S.220, R.221, S.236, R.238 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.217, B:R.221 NAG-NAG-BMA-MAN-MAN.5: 7 residues within 4Å: Chain D: N.174, R.217, V.219, S.220, R.221, S.236, R.238 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.217, D:R.221 NAG-NAG-BMA-MAN-MAN.7: 12 residues within 4Å: Chain E: 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 F, 2 interactions with chain E Hydrogen bonds: F:D.111, F:D.111, E:R.217, E:R.221

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

2 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:T.159, A:T.159 NAG.10: 6 residues within 4Å: Chain C: W.214, K.215, R.216, S.218, N.239, T.241 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.216, C:S.218, C:T.241

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

ABU.9: 10 residues within 4Å: Chain A: F.98, R.100, T.163 Chain B: Y.122, E.180, S.181, Y.182, F.225, T.227, Y.230 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Y.122, B:S.181, B:T.227, A:T.163 Hydrophobic interactions: A:F.98 Salt bridges: A:R.100

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: BDE
Gamma-aminobutyric acid receptor subunit gamma-2: C
Nanobody Nb25: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
D

E
E

C
C

F
N

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 gamma-2

Nanobody Nb25

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