SMTL ID : 9g57.1

CryoEM structure of human rho1 GABAA receptor in complex with GABA and neurosteroid THDOC

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

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

ABU.1: 8 residues within 4Å: Chain A: E.217, S.218, Y.219, Y.262, T.265, Y.268 Chain B: R.125, S.189 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.189, B:S.189, A:S.218 Salt bridges: B:R.125 ABU.11: 9 residues within 4Å: Chain A: Y.123, R.125, S.189 Chain E: E.217, S.218, Y.219, Y.262, T.265, Y.268 5 PLIP interactions: 1 interactions with chain E, 4 interactions with chain A Hydrogen bonds: E:S.218, A:S.189, A:S.189 Hydrophobic interactions: A:Y.123 Salt bridges: A:R.125 ABU.12: 9 residues within 4Å: Chain B: E.217, S.218, Y.219, Y.262, T.265, Y.268 Chain C: Y.123, R.125, S.189 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:S.218, C:S.189, C:S.189 Hydrophobic interactions: C:Y.123 Salt bridges: C:R.125 ABU.22: 8 residues within 4Å: Chain C: E.217, S.218, Y.219, Y.262, T.265, Y.268 Chain D: R.125, S.189 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:S.218, D:S.189, D:S.189 Salt bridges: D:R.125 ABU.32: 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 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:S.189, E:S.189, D:S.218 Salt bridges: E:R.125

10 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(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: 2 residues within 4Å: Chain A: N.234, H.254 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:H.254 NAG.13: 1 residues within 4Å: Chain B: N.140 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.140 NAG.14: 2 residues within 4Å: Chain B: N.234, H.254 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:H.254 NAG.23: 1 residues within 4Å: Chain C: N.140 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.140 NAG.24: 2 residues within 4Å: Chain C: N.234, H.254 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:H.254 NAG.33: 1 residues within 4Å: Chain D: N.140 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.140 NAG.34: 2 residues within 4Å: Chain D: N.234, H.254 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:H.254 NAG.43: 1 residues within 4Å: Chain E: N.140 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.140 NAG.44: 2 residues within 4Å: Chain E: N.234, H.254 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:H.254

5 x A8Z: Tetrahydrodeoxycorticosterone(Non-covalent)

A8Z.4: 6 residues within 4Å: Chain A: L.285, Y.289, T.293, Y.347, W.475, S.479 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.285, A:W.475, A:W.475, A:W.475 Hydrogen bonds: A:Y.289 A8Z.15: 6 residues within 4Å: Chain B: L.285, Y.289, T.293, Y.347, W.475, S.479 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.285, B:W.475, B:W.475, B:W.475 Hydrogen bonds: B:Y.289 A8Z.25: 6 residues within 4Å: Chain C: L.285, Y.289, T.293, Y.347, W.475, S.479 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.285, C:W.475, C:W.475, C:W.475 Hydrogen bonds: C:Y.289 A8Z.35: 6 residues within 4Å: Chain D: L.285, Y.289, T.293, Y.347, W.475, S.479 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.285, D:W.475, D:W.475, D:W.475 Hydrogen bonds: D:Y.289 A8Z.45: 6 residues within 4Å: Chain E: L.285, Y.289, T.293, Y.347, W.475, S.479 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:L.285, E:W.475, E:W.475, E:W.475 Hydrogen bonds: E:Y.289

5 x D12: DODECANE(Non-covalent)

D12.5: 5 residues within 4Å: Chain A: Y.467, N.471, L.472, W.475, S.476 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.467, A:N.471, A:L.472, A:W.475 D12.16: 5 residues within 4Å: Chain B: Y.467, N.471, L.472, W.475, S.476 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.467, B:N.471, B:L.472, B:W.475 D12.26: 5 residues within 4Å: Chain C: Y.467, N.471, L.472, W.475, S.476 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.467, C:N.471, C:L.472, C:W.475 D12.36: 5 residues within 4Å: Chain D: Y.467, N.471, L.472, W.475, S.476 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:Y.467, D:N.471, D:L.472, D:W.475 D12.46: 5 residues within 4Å: Chain E: Y.467, N.471, L.472, W.475, S.476 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:Y.467, E:N.471, E:L.472, E:W.475

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

OCT.6: 3 residues within 4Å: Chain A: V.301, W.304 Chain E: A.364 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.301, A:W.304 OCT.17: 3 residues within 4Å: Chain A: A.364 Chain B: V.301, W.304 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:A.364, B:V.301, B:W.304 OCT.27: 3 residues within 4Å: Chain B: A.364 Chain C: V.301, W.304 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:V.301, C:W.304, B:A.364 OCT.37: 3 residues within 4Å: Chain C: A.364 Chain D: V.301, W.304 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:V.301, D:W.304, C:A.364 OCT.42: 3 residues within 4Å: Chain D: Y.367 Chain E: V.301, W.304 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:V.301, E:W.304, D:Y.367

15 x HEX: HEXANE(Non-covalent)

HEX.7: 2 residues within 4Å: Chain A: Y.458, S.459 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.458, A:Y.458 HEX.8: 1 residues within 4Å: Chain A: I.477 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.477 HEX.9: 3 residues within 4Å: Chain A: W.304, R.460, I.461 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.304, A:W.304 HEX.18: 2 residues within 4Å: Chain B: Y.458, S.459 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.458, B:Y.458 HEX.19: 1 residues within 4Å: Chain B: I.477 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.477 HEX.20: 3 residues within 4Å: Chain B: W.304, R.460, I.461 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.304, B:W.304 HEX.28: 2 residues within 4Å: Chain C: Y.458, S.459 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.458, C:Y.458 HEX.29: 1 residues within 4Å: Chain C: I.477 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.477 HEX.30: 3 residues within 4Å: Chain C: W.304, R.460, I.461 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.304, C:W.304 HEX.38: 2 residues within 4Å: Chain D: Y.458, S.459 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.458, D:Y.458 HEX.39: 1 residues within 4Å: Chain D: I.477 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.477 HEX.40: 3 residues within 4Å: Chain D: W.304, R.460, I.461 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:W.304, D:W.304 HEX.47: 2 residues within 4Å: Chain E: Y.458, S.459 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:Y.458, E:Y.458 HEX.48: 1 residues within 4Å: Chain E: I.477 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:I.477 HEX.49: 3 residues within 4Å: Chain E: W.304, R.460, I.461 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:W.304, E:W.304

5 x D10: DECANE(Non-covalent)

D10.10: 2 residues within 4Å: Chain A: L.285, F.290 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.285, A:F.290 D10.21: 2 residues within 4Å: Chain B: L.285, F.290 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.285, B:F.290 D10.31: 2 residues within 4Å: Chain C: L.285, F.290 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.285, C:F.290 D10.41: 2 residues within 4Å: Chain D: L.285, F.290 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.285, D:F.290 D10.50: 2 residues within 4Å: Chain E: L.285, F.290 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:L.285, E:F.290

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fan, C. et al., CryoEM structure of human rho1 GABAA receptor in complex with neurosteroid. To be published

Release Date

2025-07-30

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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