SMTL ID : 8rh8.1

CryoEM structure of human rho1 GABAA receptor in complex with GABA and estradiol in desensitized state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

5 x ABU: GAMMA-AMINO-BUTANOIC ACID

ABU.1: 9 residues within 4Å: Chain A: F.159, E.217, S.218, Y.219, Y.262, T.265 Chain C: Y.123, R.125, S.189 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:S.189, A:E.217, A:S.218 Salt bridges: C:R.125 Hydrophobic interactions: A:Y.262 ABU.11: 9 residues within 4Å: Chain A: Y.123, R.125, S.189 Chain B: F.159, E.217, S.218, Y.219, Y.262, T.265 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.189, B:E.217, B:S.218 Salt bridges: A:R.125 Hydrophobic interactions: B:Y.262 ABU.19: 9 residues within 4Å: Chain C: F.159, E.217, S.218, Y.219, Y.262, T.265 Chain D: Y.123, R.125, S.189 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:S.189, C:E.217, C:S.218 Salt bridges: D:R.125 Hydrophobic interactions: C:Y.262 ABU.27: 9 residues within 4Å: Chain D: F.159, E.217, S.218, Y.219, Y.262, T.265 Chain E: Y.123, R.125, S.189 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:Y.262 Hydrogen bonds: D:E.217, D:S.218, E:S.189 Salt bridges: E:R.125 ABU.35: 9 residues within 4Å: Chain B: Y.123, R.125, S.189 Chain E: F.159, E.217, S.218, Y.219, Y.262, T.265 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain B Hydrophobic interactions: E:Y.262 Hydrogen bonds: E:E.217, E:S.218, B:S.189 Salt bridges: B:R.125

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

NAG.2: 1 residues within 4Å: Chain A: N.140 No protein-ligand interaction detected (PLIP) NAG.3: 4 residues within 4Å: Chain A: N.234, H.254, T.255, T.256 No protein-ligand interaction detected (PLIP) NAG.12: 1 residues within 4Å: Chain B: N.140 No protein-ligand interaction detected (PLIP) NAG.13: 4 residues within 4Å: Chain B: N.234, H.254, T.255, T.256 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:H.254 NAG.20: 1 residues within 4Å: Chain C: N.140 No protein-ligand interaction detected (PLIP) NAG.21: 4 residues within 4Å: Chain C: N.234, H.254, T.255, T.256 No protein-ligand interaction detected (PLIP) NAG.28: 1 residues within 4Å: Chain D: N.140 No protein-ligand interaction detected (PLIP) NAG.29: 4 residues within 4Å: Chain D: N.234, H.254, T.255, T.256 No protein-ligand interaction detected (PLIP) NAG.36: 1 residues within 4Å: Chain E: N.140 No protein-ligand interaction detected (PLIP) NAG.37: 4 residues within 4Å: Chain E: N.234, H.254, T.255, T.256 No protein-ligand interaction detected (PLIP)

15 x HEX: HEXANE

HEX.4: 1 residues within 4Å: Chain B: Y.367 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.367 HEX.6: 1 residues within 4Å: Chain A: W.475 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.475 HEX.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.14: 1 residues within 4Å: Chain E: Y.367 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.367 HEX.16: 1 residues within 4Å: Chain B: W.475 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.475 HEX.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.22: 1 residues within 4Å: Chain A: Y.367 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.367 HEX.24: 1 residues within 4Å: Chain C: W.475 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.475 HEX.26: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.30: 1 residues within 4Å: Chain C: Y.367 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.367 HEX.32: 1 residues within 4Å: Chain D: W.475 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:W.475 HEX.34: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.38: 1 residues within 4Å: Chain D: Y.367 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.367 HEX.40: 1 residues within 4Å: Chain E: W.475 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:W.475 HEX.42: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

10 x OCT: N-OCTANE

OCT.5: 4 residues within 4Å: Chain A: L.285, F.290, T.293, W.475 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.285, A:F.290, A:F.290, A:W.475 OCT.7: 3 residues within 4Å: Chain A: F.470, I.473, I.477 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.470, A:I.473 OCT.15: 4 residues within 4Å: Chain B: L.285, F.290, T.293, W.475 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.285, B:F.290, B:F.290, B:W.475 OCT.17: 3 residues within 4Å: Chain B: F.470, I.473, I.477 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.470, B:I.473 OCT.23: 4 residues within 4Å: Chain C: L.285, F.290, T.293, W.475 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.285, C:F.290, C:F.290, C:W.475 OCT.25: 3 residues within 4Å: Chain C: F.470, I.473, I.477 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.470, C:I.473 OCT.31: 4 residues within 4Å: Chain D: L.285, F.290, T.293, W.475 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.285, D:F.290, D:F.290, D:W.475 OCT.33: 3 residues within 4Å: Chain D: F.470, I.473, I.477 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.470, D:I.473 OCT.39: 4 residues within 4Å: Chain E: L.285, F.290, T.293, W.475 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:L.285, E:F.290, E:F.290, E:W.475 OCT.41: 3 residues within 4Å: Chain E: F.470, I.473, I.477 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:F.470, E:I.473

2 x CL: CHLORIDE ION

CL.9: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: P.311 Chain B: P.311 Chain E: 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
E

C
B

D
C

E
D

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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