SMTL ID : 8rh7.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: T.138, N.140 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.138, A:N.140 NAG.2: 1 residues within 4Å: Chain A: N.234 No protein-ligand interaction detected (PLIP) NAG.17: 2 residues within 4Å: Chain B: T.138, N.140 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.138, B:N.140 NAG.18: 1 residues within 4Å: Chain B: N.234 No protein-ligand interaction detected (PLIP) NAG.27: 2 residues within 4Å: Chain C: T.138, N.140 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.138, C:N.140 NAG.28: 1 residues within 4Å: Chain C: N.234 No protein-ligand interaction detected (PLIP) NAG.39: 2 residues within 4Å: Chain D: T.138, N.140 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.138, D:N.140 NAG.40: 1 residues within 4Å: Chain D: N.234 No protein-ligand interaction detected (PLIP) NAG.54: 2 residues within 4Å: Chain E: T.138, N.140 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.138, E:N.140 NAG.55: 1 residues within 4Å: Chain E: N.234 No protein-ligand interaction detected (PLIP)

25 x OCT: N-OCTANE

OCT.3: 3 residues within 4Å: Chain A: L.285, L.286, F.290 Ligand excluded by PLIP OCT.6: 2 residues within 4Å: Chain A: I.455, S.459 Ligand excluded by PLIP OCT.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OCT.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OCT.12: 3 residues within 4Å: Chain A: F.470, I.473, I.477 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.16: 3 residues within 4Å: Chain B: F.470, I.473, I.477 Ligand excluded by PLIP OCT.19: 3 residues within 4Å: Chain B: L.285, L.286, F.290 Ligand excluded by PLIP OCT.22: 2 residues within 4Å: Chain B: I.455, S.459 Ligand excluded by PLIP OCT.29: 3 residues within 4Å: Chain C: L.285, L.286, F.290 Ligand excluded by PLIP OCT.32: 2 residues within 4Å: Chain C: I.455, S.459 Ligand excluded by PLIP OCT.35: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OCT.36: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OCT.37: 3 residues within 4Å: Chain C: F.470, I.473, I.477 Ligand excluded by PLIP OCT.41: 3 residues within 4Å: Chain D: L.285, L.286, F.290 Ligand excluded by PLIP OCT.44: 2 residues within 4Å: Chain D: I.455, S.459 Ligand excluded by PLIP OCT.47: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OCT.48: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OCT.49: 3 residues within 4Å: Chain D: F.470, I.473, I.477 Ligand excluded by PLIP OCT.50: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OCT.51: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OCT.52: 3 residues within 4Å: Chain E: F.470, I.473, I.477 Ligand excluded by PLIP OCT.56: 3 residues within 4Å: Chain E: L.285, L.286, F.290 Ligand excluded by PLIP OCT.59: 2 residues within 4Å: Chain E: I.455, S.459 Ligand excluded by PLIP

15 x HEX: HEXANE

HEX.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.7: 1 residues within 4Å: Chain A: I.455 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.455 HEX.20: 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.23: 1 residues within 4Å: Chain B: I.455 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.455 HEX.30: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.31: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.33: 1 residues within 4Å: Chain C: I.455 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.455 HEX.42: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.43: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.45: 1 residues within 4Å: Chain D: I.455 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.455 HEX.57: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.58: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.60: 1 residues within 4Å: Chain E: I.455 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:I.455

5 x EST: ESTRADIOL

EST.8: 7 residues within 4Å: Chain A: E.113, R.279, Q.287, S.334 Chain B: N.332, R.337, S.339 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Q.287, B:N.332 Hydrogen bonds: A:E.113, A:R.279, A:S.334 pi-Cation interactions: B:R.337 EST.24: 7 residues within 4Å: Chain B: E.113, R.279, Q.287, S.334 Chain E: N.332, R.337, S.339 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain E Hydrophobic interactions: B:Q.287, E:N.332 Hydrogen bonds: B:E.113, B:R.279, B:S.334 pi-Cation interactions: E:R.337 EST.34: 7 residues within 4Å: Chain A: N.332, R.337, S.339 Chain C: E.113, R.279, Q.287, S.334 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:Q.287, A:N.332 Hydrogen bonds: C:E.113, C:R.279, C:S.334 pi-Cation interactions: A:R.337 EST.46: 7 residues within 4Å: Chain C: N.332, R.337, S.339 Chain D: E.113, R.279, Q.287, S.334 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Q.287, C:N.332 Hydrogen bonds: D:E.113, D:R.279, D:S.334 pi-Cation interactions: C:R.337 EST.61: 7 residues within 4Å: Chain D: N.332, R.337, S.339 Chain E: E.113, R.279, Q.287, S.334 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain E Hydrophobic interactions: D:N.332, E:Q.287 pi-Cation interactions: D:R.337 Hydrogen bonds: E:E.113, E:R.279, E:S.334

5 x ABU: GAMMA-AMINO-BUTANOIC ACID

ABU.9: 8 residues within 4Å: Chain A: R.125, S.189 Chain B: E.217, S.218, Y.219, Y.262, T.265, Y.268 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:E.217, B:S.218, B:T.265, A:S.189, A:S.189 Salt bridges: A:R.125 ABU.25: 8 residues within 4Å: Chain B: R.125, S.189 Chain E: E.217, S.218, Y.219, Y.262, T.265, Y.268 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain E Hydrogen bonds: B:S.189, B:S.189, E:E.217, E:S.218, E:T.265 Salt bridges: B:R.125 ABU.26: 9 residues within 4Å: Chain A: E.217, S.218, Y.219, Y.262, T.265, Y.268 Chain C: R.125, M.177, S.189 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:S.189, C:S.189, A:E.217, A:S.218, A:T.265 Salt bridges: C:R.125 ABU.38: 8 residues within 4Å: Chain C: E.217, S.218, Y.219, Y.262, T.265, Y.268 Chain D: R.125, S.189 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:S.189, D:S.189, C:E.217, C:S.218, C:T.265 Salt bridges: D:R.125 ABU.53: 9 residues within 4Å: Chain D: E.217, S.218, Y.219, Y.262, T.265, Y.268 Chain E: R.125, M.177, S.189 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:S.189, E:S.189, D:E.217, D:S.218, D:T.265 Salt bridges: E:R.125

1 x CL: CHLORIDE ION

CL.13: 0 residues within 4Å: (No contacts) 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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