SMTL ID : 9fg6.1

Cryo-EM structure of the full-length alpha1beta3 GABA(A) receptor in complex with GABA and HSM in the long-lived symmetric desensitised state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-3-mer

Ligands

5 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: 6 residues within 4Å: Chain A: N.146, M.149, P.150 Chain B: D.114 Ligands: NAG-NAG-BMA-MAN-MAN.6, NAG-NAG-BMA-MAN-MAN.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.114 NAG-NAG-BMA-MAN-MAN.2: 7 residues within 4Å: Chain B: N.174, R.217, V.219, S.220, R.221, S.236, R.238 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.217, B:R.217, B:R.221 NAG-NAG-BMA-MAN-MAN.4: 7 residues within 4Å: Chain C: N.174, R.217, V.219, S.220, R.221, S.236, R.238 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.222, C:R.217 NAG-NAG-BMA-MAN-MAN.6: 6 residues within 4Å: Chain D: N.146, T.148, M.149 Chain E: K.137 Ligands: NAG-NAG-BMA-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN.1 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.137 NAG-NAG-BMA-MAN-MAN.7: 7 residues within 4Å: Chain E: N.174, R.217, V.219, S.220, R.221, S.236, R.238 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.217

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.3: 3 residues within 4Å: Chain B: P.103, N.105, H.144 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain C: P.103, L.104, N.105, H.144 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain E: P.103, N.105, H.144 No protein-ligand interaction detected (PLIP)

2 x PIO: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate(Non-covalent)

PIO.9: 11 residues within 4Å: Chain A: R.284, T.341, F.345, K.347, R.348, N.422, S.423, S.425, K.426, I.427, L.430 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:T.341, A:I.427, A:L.430 Hydrogen bonds: A:R.284, A:R.284, A:S.423, A:S.423, A:S.423, A:K.426 Salt bridges: A:R.284, A:K.347, A:K.347, A:R.348, A:K.426, A:K.426 PIO.12: 11 residues within 4Å: Chain D: R.284, T.341, F.345, K.347, R.348, N.422, S.423, S.425, K.426, I.427, L.430 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:I.427, D:L.430 Hydrogen bonds: D:R.284, D:R.284, D:F.345, D:S.423, D:K.426 Salt bridges: D:R.284, D:K.347, D:K.347, D:R.348, D:K.426, D:K.426

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

ABU.10: 10 residues within 4Å: Chain A: F.100, R.102, T.165 Chain B: Y.122, E.180, S.181, Y.182, F.225, T.227, Y.230 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.225, B:Y.230, A:F.100 Hydrogen bonds: B:Y.122, B:E.180 Salt bridges: A:R.102 ABU.11: 11 residues within 4Å: Chain C: Y.122, E.180, S.181, Y.182, F.225, T.227, Y.230 Chain D: F.100, R.102, L.153, T.165 7 PLIP interactions: 2 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:F.100, C:Y.230 Salt bridges: D:R.102 Hydrogen bonds: C:Y.122, C:E.180, C:Y.182, C:Y.230

1 x HSM: HISTAMINE(Non-covalent)

HSM.13: 8 residues within 4Å: Chain C: Y.87, Q.89 Chain E: Y.122, E.180, S.181, Y.182, T.227, Y.230 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:Y.122, E:E.180, C:Q.89 Hydrophobic interactions: C:Y.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mihaylov, D.B. et al., Cryo-EM structure of the full-length alpha1beta3 GABA(A) receptor in complex with GABA and HSM in the long-lived symmetric desensitised 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: BCE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

C
C

E
E

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

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