SMTL ID : 8rhg.1

CryoEM structure of human rho1 GABAA receptor in complex with GABA and pregnenolone sulfate

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

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

ABU.1: 9 residues within 4Å: Chain A: F.159, E.217, S.218, Y.219, T.265, Y.268 Chain B: R.125, M.177, S.189 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.219, B:S.189 Salt bridges: B:R.125 ABU.5: 8 residues within 4Å: Chain A: R.125, S.189 Chain E: E.217, S.218, Y.219, Y.262, T.265, Y.268 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:S.218, E:T.265, A:S.189 Salt bridges: A:R.125 ABU.7: 8 residues within 4Å: Chain B: E.217, S.218, Y.219, T.265, Y.268 Chain C: Y.123, R.125, S.189 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:Y.219, B:T.265, C:S.189 Hydrophobic interactions: C:Y.123 Salt bridges: C:R.125 ABU.12: 9 residues within 4Å: Chain C: E.217, S.218, Y.219, Y.262, T.265, Y.268 Chain D: Y.123, R.125, S.189 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Y.123 Hydrogen bonds: D:S.189, C:Y.219, C:T.265 Salt bridges: D:R.125 ABU.17: 10 residues within 4Å: Chain D: E.217, S.218, Y.219, Y.262, T.265, Y.268 Chain E: Y.123, R.125, M.177, S.189 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:Y.123 Hydrogen bonds: E:S.189, D:Y.219 Salt bridges: E:R.125

10 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)

NAG.2: 1 residues within 4Å: Chain A: N.140 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.140 NAG.3: 1 residues within 4Å: Chain A: N.234 No protein-ligand interaction detected (PLIP) NAG.8: 1 residues within 4Å: Chain B: N.140 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.140 NAG.9: 1 residues within 4Å: Chain B: N.234 No protein-ligand interaction detected (PLIP) NAG.13: 1 residues within 4Å: Chain C: N.140 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.140 NAG.14: 1 residues within 4Å: Chain C: N.234 No protein-ligand interaction detected (PLIP) NAG.18: 1 residues within 4Å: Chain D: N.140 No protein-ligand interaction detected (PLIP) NAG.19: 1 residues within 4Å: Chain D: N.234 No protein-ligand interaction detected (PLIP) NAG.22: 1 residues within 4Å: Chain E: N.140 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.140 NAG.23: 1 residues within 4Å: Chain E: N.234 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.234

5 x OCT: N-OCTANE(Non-covalent)(Non-functional Binders)

OCT.4: 2 residues within 4Å: Chain A: L.285, W.475 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.285 OCT.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) OCT.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) OCT.20: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) OCT.24: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x A8W: Pregnenolone sulfate(Non-covalent)

A8W.6: 4 residues within 4Å: Chain A: P.315, T.319 Chain D: L.322 Ligands: CL.26 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.315, A:P.315, A:T.319

4 x HEX: HEXANE(Non-functional Binders)(Non-covalent)

HEX.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.16: 1 residues within 4Å: Chain C: I.477 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.477 HEX.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.25: 3 residues within 4Å: Chain E: F.470, I.473, I.477 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:F.470, E:I.473, E:I.477

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.26: 3 residues within 4Å: Chain D: P.311 Chain E: P.311 Ligands: A8W.6 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, F. et al., Divergent mechanisms of steroid inhibition in the human rho1 GABAA receptor. Nat Commun (2024)

Release Date

2024-08-28

Peptides

Gamma-aminobutyric acid receptor subunit rho-1: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Membrane

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

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