SMTL ID : 9ffy.1

Cryo-EM structure of the alpha1beta3gamma2 GABA(A) receptor in complex with GABA and Nb38 in the short-lived asymmetric open1 state

Coordinates

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Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-1-1-mer

Ligands

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.1: 12 residues within 4Å: Chain A: N.164, T.166 Chain C: S.102, N.103, K.107, W.125, P.129 Chain D: A.162, N.164, P.168, K.170 Ligands: NAG-NAG-BMA-MAN-MAN.5 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.159, D:K.159

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.132, N.134, H.173 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain C: W.185, R.187, S.189, L.208, R.209, N.210 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain E: N.134, H.173 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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.3: 8 residues within 4Å: Chain B: N.203, R.246, V.248, S.249, R.250, S.265, F.266, R.267 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.7: 7 residues within 4Å: Chain E: N.203, R.246, V.248, S.249, R.250, S.265, R.267 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.246

1 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.5: 7 residues within 4Å: Chain A: S.145 Chain D: N.164, M.167, P.168 Chain E: Q.144 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.1 No protein-ligand interaction detected (PLIP)

1 x D3D: (19S,22R,25R)-22,25,26-trihydroxy-16,22-dioxo-17,21,23-trioxa-22lambda~5~-phosphahexacosan-19-yl (9E)-octadec-9-enoate(Non-covalent)

D3D.8: 11 residues within 4Å: Chain A: K.273, R.274, K.275, G.277, L.285, I.288, P.383, W.394 Chain B: N.319, M.340, F.343 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.383, A:W.394 Hydrogen bonds: A:R.274, A:G.277

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

ABU.9: 10 residues within 4Å: Chain A: F.118, R.120, T.183 Chain B: Y.151, E.209, S.210, Y.211, F.254, T.256, Y.259 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:F.118, B:F.254, B:Y.259 Hydrogen bonds: A:T.183, B:E.209, B:S.210, B:T.256, B:Y.259 Salt bridges: A:R.120 ABU.10: 11 residues within 4Å: Chain D: F.118, R.120, L.171, T.183 Chain E: Y.151, E.209, S.210, Y.211, F.254, T.256, Y.259 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:F.118 Salt bridges: D:R.120 Hydrogen bonds: E:S.210, E:T.256, E:T.256

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mihaylov, D.B. et al., Cryo-EM structure of the alpha1beta3gamma2 GABA(A) receptor in complex with GABA and Nb38 in the short-lived asymmetric open1 state. To Be Published

Release Date

2025-06-04

Peptides

Gamma-aminobutyric acid receptor subunit alpha-1: AD
Gamma-aminobutyric acid receptor subunit beta-3: BE
Isoform 1 of Gamma-aminobutyric acid receptor subunit gamma-2: C
Nanobody38: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

Membrane

We predict this structure to be a membrane protein.
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Gamma-aminobutyric acid receptor subunit alpha-1

Gamma-aminobutyric acid receptor subunit beta-3

Isoform 1 of Gamma-aminobutyric acid receptor subunit gamma-2

Nanobody38

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