SMTL ID : 8rh4.1

CryoEM structure of human rho1 GABAA receptor in complex with estradiol

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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.234, A:T.255 NAG.17: 3 residues within 4Å: Chain B: T.138, N.139, N.140 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.138, B:N.140 NAG.18: 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.27: 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.28: 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.40: 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.41: 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.54: 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.55: 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

15 x OCT: N-OCTANE

OCT.3: 1 residues within 4Å: Ligands: OCT.4 No protein-ligand interaction detected (PLIP) OCT.4: 3 residues within 4Å: Chain A: Y.458, S.459 Ligands: OCT.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.458, A:Y.458 OCT.8: 2 residues within 4Å: Chain A: V.350 Ligands: D10.32 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.350 OCT.19: 1 residues within 4Å: Ligands: OCT.20 No protein-ligand interaction detected (PLIP) OCT.20: 3 residues within 4Å: Chain B: Y.458, S.459 Ligands: OCT.19 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.458, B:Y.458 OCT.24: 2 residues within 4Å: Chain B: V.350 Ligands: D10.6 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.350 OCT.29: 1 residues within 4Å: Ligands: OCT.30 No protein-ligand interaction detected (PLIP) OCT.30: 3 residues within 4Å: Chain C: Y.458, S.459 Ligands: OCT.29 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.458, C:Y.458 OCT.34: 2 residues within 4Å: Chain C: V.350 Ligands: D10.45 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.350 OCT.42: 1 residues within 4Å: Ligands: OCT.43 No protein-ligand interaction detected (PLIP) OCT.43: 3 residues within 4Å: Chain D: Y.458, S.459 Ligands: OCT.42 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.458, D:Y.458 OCT.47: 3 residues within 4Å: Chain D: V.350 Chain E: F.290 Ligands: D10.59 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:V.350, E:F.290 OCT.56: 1 residues within 4Å: Ligands: OCT.57 No protein-ligand interaction detected (PLIP) OCT.57: 3 residues within 4Å: Chain E: Y.458, S.459 Ligands: OCT.56 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:Y.458, E:Y.458 OCT.61: 2 residues within 4Å: Chain E: V.350 Ligands: D10.22 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:V.350

25 x HEX: HEXANE

HEX.5: 1 residues within 4Å: Chain A: R.460 Ligand excluded by PLIP HEX.7: 3 residues within 4Å: Chain A: F.470, I.473, I.477 Ligand excluded by PLIP HEX.9: 3 residues within 4Å: Chain A: W.475, S.479 Ligands: D10.6 Ligand excluded by PLIP HEX.10: 2 residues within 4Å: Chain A: Y.367 Chain C: W.304 Ligand excluded by PLIP HEX.12: 2 residues within 4Å: Chain A: W.304 Chain B: Y.367 Ligand excluded by PLIP HEX.13: 2 residues within 4Å: Chain A: Y.367 Chain C: W.304 Ligand excluded by PLIP HEX.16: 2 residues within 4Å: Chain A: W.304 Chain B: Y.367 Ligand excluded by PLIP HEX.21: 1 residues within 4Å: Chain B: R.460 Ligand excluded by PLIP HEX.23: 3 residues within 4Å: Chain B: F.470, I.473, I.477 Ligand excluded by PLIP HEX.25: 3 residues within 4Å: Chain B: W.475, S.479 Ligands: D10.22 Ligand excluded by PLIP HEX.26: 2 residues within 4Å: Chain B: W.304 Chain E: Y.367 Ligand excluded by PLIP HEX.31: 1 residues within 4Å: Chain C: R.460 Ligand excluded by PLIP HEX.33: 3 residues within 4Å: Chain C: F.470, I.473, I.477 Ligand excluded by PLIP HEX.35: 3 residues within 4Å: Chain C: W.475, S.479 Ligands: D10.32 Ligand excluded by PLIP HEX.36: 2 residues within 4Å: Chain C: Y.367 Chain D: W.304 Ligand excluded by PLIP HEX.39: 2 residues within 4Å: Chain C: Y.367 Chain D: W.304 Ligand excluded by PLIP HEX.44: 1 residues within 4Å: Chain D: R.460 Ligand excluded by PLIP HEX.46: 3 residues within 4Å: Chain D: F.470, I.473, I.477 Ligand excluded by PLIP HEX.48: 3 residues within 4Å: Chain D: W.475, S.479 Ligands: D10.45 Ligand excluded by PLIP HEX.49: 2 residues within 4Å: Chain D: Y.367 Chain E: W.304 Ligand excluded by PLIP HEX.51: 2 residues within 4Å: Chain B: W.304 Chain E: Y.367 Ligand excluded by PLIP HEX.53: 2 residues within 4Å: Chain D: Y.367 Chain E: W.304 Ligand excluded by PLIP HEX.58: 1 residues within 4Å: Chain E: R.460 Ligand excluded by PLIP HEX.60: 3 residues within 4Å: Chain E: F.470, I.473, I.477 Ligand excluded by PLIP HEX.62: 3 residues within 4Å: Chain E: W.475, S.479 Ligands: D10.59 Ligand excluded by PLIP

5 x D10: DECANE

D10.6: 8 residues within 4Å: Chain A: F.282, L.285, F.290, T.293, Y.347 Chain B: I.341 Ligands: HEX.9, OCT.24 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.282, A:F.290, B:I.341 D10.22: 8 residues within 4Å: Chain B: F.282, L.285, F.290, T.293, Y.347 Chain E: I.341 Ligands: HEX.25, OCT.61 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: B:F.282, B:F.290, E:I.341 D10.32: 8 residues within 4Å: Chain A: I.341 Chain C: F.282, L.285, F.290, T.293, Y.347 Ligands: OCT.8, HEX.35 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:I.341, C:F.282, C:F.290 D10.45: 8 residues within 4Å: Chain C: I.341 Chain D: F.282, L.285, F.290, T.293, Y.347 Ligands: OCT.34, HEX.48 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:I.341, D:F.282, D:F.290 D10.59: 8 residues within 4Å: Chain D: I.341 Chain E: F.282, L.285, F.290, T.293, Y.347 Ligands: OCT.47, HEX.62 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:F.282, E:F.290, D:I.341

5 x EST: ESTRADIOL

EST.11: 10 residues within 4Å: Chain A: E.113, Q.247, Q.287, V.331, S.334, M.335, P.336 Chain B: N.332, R.337, S.339 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Q.287, B:N.332 Hydrogen bonds: A:E.113, B:S.339 pi-Cation interactions: B:R.337 EST.14: 10 residues within 4Å: Chain A: N.332, R.337, S.339 Chain C: E.113, Q.247, Q.287, V.331, S.334, M.335, P.336 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:Q.287, A:N.332, A:R.337 Hydrogen bonds: C:E.113, A:S.339 pi-Cation interactions: A:R.337 EST.37: 10 residues within 4Å: Chain C: N.332, R.337, S.339 Chain D: E.113, Q.247, Q.287, V.331, S.334, M.335, P.336 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:N.332, C:R.337, D:Q.287 Hydrogen bonds: C:S.339, D:E.113 pi-Cation interactions: C:R.337 EST.50: 10 residues within 4Å: Chain D: N.332, R.337, S.339 Chain E: E.113, Q.247, Q.287, V.331, S.334, M.335, P.336 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:N.332, E:Q.287 Hydrogen bonds: D:S.339, E:E.113 pi-Cation interactions: D:R.337 EST.52: 10 residues within 4Å: Chain B: E.113, Q.247, Q.287, V.331, S.334, M.335, P.336 Chain E: N.332, R.337, S.339 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain E Hydrophobic interactions: B:Q.287, E:N.332, E:R.337 Hydrogen bonds: B:E.113, E:S.339 pi-Cation interactions: E:R.337

2 x CL: CHLORIDE ION

CL.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.38: 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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