SMTL ID : 8rh9.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

10 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose

NAG.1: 3 residues within 4Å: Chain A: T.138, N.139, N.140 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.138, A:N.140 NAG.2: 3 residues within 4Å: Chain A: N.234, H.254, T.255 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.255 NAG.12: 3 residues within 4Å: Chain B: T.138, N.139, N.140 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.138 NAG.13: 3 residues within 4Å: Chain B: N.234, H.254, T.255 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.234, B:T.255 NAG.22: 3 residues within 4Å: Chain C: T.138, N.139, N.140 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.138, C:N.140 NAG.23: 3 residues within 4Å: Chain C: N.234, H.254, T.255 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.234, C:T.255 NAG.32: 3 residues within 4Å: Chain D: T.138, N.139, N.140 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.138, D:N.140 NAG.33: 3 residues within 4Å: Chain D: N.234, H.254, T.255 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.234, D:T.255 NAG.42: 3 residues within 4Å: Chain E: T.138, N.139, N.140 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.138, E:N.140 NAG.43: 3 residues within 4Å: Chain E: N.234, H.254, T.255 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.234, E:T.255

16 x OCT: N-OCTANE

OCT.3: 1 residues within 4Å: Ligands: D10.5 Ligand excluded by PLIP OCT.7: 2 residues within 4Å: Chain A: F.470, I.473 Ligand excluded by PLIP OCT.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OCT.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OCT.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OCT.18: 1 residues within 4Å: Chain B: L.472 Ligand excluded by PLIP OCT.24: 2 residues within 4Å: Chain C: W.475 Ligands: D10.26 Ligand excluded by PLIP OCT.25: 1 residues within 4Å: Chain C: I.477 Ligand excluded by PLIP OCT.28: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OCT.29: 1 residues within 4Å: Chain C: L.472 Ligand excluded by PLIP OCT.31: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OCT.34: 2 residues within 4Å: Chain D: W.475, S.479 Ligand excluded by PLIP OCT.44: 1 residues within 4Å: Chain E: S.479 Ligand excluded by PLIP OCT.47: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OCT.50: 1 residues within 4Å: Chain E: L.472 Ligand excluded by PLIP OCT.51: 3 residues within 4Å: Chain E: Y.458, I.462, F.463 Ligand excluded by PLIP

7 x D10: DECANE

D10.4: 1 residues within 4Å: Chain A: I.461 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.461 D10.5: 4 residues within 4Å: Chain A: F.282, L.286, F.290 Ligands: OCT.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.282, A:L.286, A:F.290 D10.26: 5 residues within 4Å: Chain C: F.282, L.286, Y.289, F.290 Ligands: OCT.24 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.282, C:L.286, C:Y.289, C:F.290 D10.40: 1 residues within 4Å: Chain D: L.472 No protein-ligand interaction detected (PLIP) D10.41: 2 residues within 4Å: Chain E: V.301, W.304 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:V.301, E:W.304 D10.46: 3 residues within 4Å: Chain E: W.304, I.461, A.465 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:W.304, E:I.461, E:A.465 D10.48: 1 residues within 4Å: Chain E: I.477 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:I.477

3 x D12: DODECANE

D12.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) D12.10: 1 residues within 4Å: Chain A: L.472 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.472 D12.38: 1 residues within 4Å: Chain D: F.463 No protein-ligand interaction detected (PLIP)

13 x HEX: HEXANE

HEX.9: 2 residues within 4Å: Chain A: S.459, I.462 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.462 HEX.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.27: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.30: 1 residues within 4Å: Chain C: S.459 No protein-ligand interaction detected (PLIP) HEX.35: 1 residues within 4Å: Chain D: I.461 No protein-ligand interaction detected (PLIP) HEX.36: 1 residues within 4Å: Chain D: I.477 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.477 HEX.37: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.39: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.45: 1 residues within 4Å: Chain A: W.304 No protein-ligand interaction detected (PLIP) HEX.49: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x A8W: Pregnenolone sulfate

A8W.19: 13 residues within 4Å: Chain A: P.311, T.319, L.322 Chain B: P.311, L.322 Chain C: P.315, T.319, L.322 Chain D: P.311, P.315 Chain E: P.311, P.315, T.319 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E, 2 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: D:P.315, E:P.315, C:P.315, C:L.322, A:T.319

1 x CL: CHLORIDE ION

CL.20: 2 residues within 4Å: Chain B: P.311 Chain C: P.311 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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