SMTL ID : 8f6y.1

Cryo-EM structure of Torpedo nicotinic acetylcholine receptor in complex with etomidate, desensitized-like state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-1-mer

Ligands

3 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 8 residues within 4Å: Chain A: N.141, T.143, W.184, K.185, H.186, W.187, T.202, I.206 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.186 NAG-NAG-BMA-MAN-MAN.4: 8 residues within 4Å: Chain D: N.141, T.143, W.184, K.185, H.186, W.187, T.202, I.206 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.186 NAG-NAG-BMA-MAN-MAN.5: 12 residues within 4Å: Chain E: W.139, N.141, K.192, N.194, W.197, F.212, I.214, P.476, P.479, F.480, P.481, G.482 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.192, E:G.482

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 7 residues within 4Å: Chain B: W.141, N.143, K.198, N.200, Y.218, P.482, F.486 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 7 residues within 4Å: Chain C: W.139, N.141, R.194, N.196, Y.210, P.467, F.468 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.194, C:N.196, C:Y.210

2 x V8D: Etomidate(Non-covalent)

V8D.6: 9 residues within 4Å: Chain A: S.226, F.227, Y.277, F.280, F.284, F.414, I.417, C.418, G.421 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.280, A:F.284, A:F.414, A:F.414, A:I.417 V8D.14: 12 residues within 4Å: Chain D: S.226, F.227, Y.277, F.280, T.281, F.284, F.414, I.417, C.418, G.421, T.422, V.425 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:F.227, D:F.280, D:F.284, D:F.284, D:F.414, D:I.417, D:V.425

2 x CHT: CHOLINE ION(Non-covalent)

CHT.7: 7 residues within 4Å: Chain A: Y.93, W.149, Y.190, C.192, Y.198 Chain B: W.57, L.121 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:W.149 CHT.15: 5 residues within 4Å: Chain D: Y.93, W.149, Y.190 Chain E: W.55, L.119 1 PLIP interactions: 1 interactions with chain D pi-Cation interactions: D:W.149

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.8: 6 residues within 4Å: Chain A: I.291, V.294, F.316, I.406, L.410, V.413 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.316, A:F.316, A:I.406, A:L.410, A:V.413 CLR.13: 7 residues within 4Å: Chain C: V.300, R.307, I.318, F.322, F.439 Chain D: Y.234, T.328 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:V.300, C:F.322, C:F.322, C:F.439, C:F.439 Hydrogen bonds: C:R.307, C:R.307 CLR.16: 9 residues within 4Å: Chain D: I.291, V.294, T.298, R.301, F.316, W.399, I.406, L.410 Ligands: POV.17 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:I.291, D:I.291, D:F.316, D:F.316, D:I.406, D:I.406, D:I.406

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.9: 1 residues within 4Å: Chain B: N.208 No protein-ligand interaction detected (PLIP) NAG.19: 2 residues within 4Å: Chain E: N.68, S.70 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.68

6 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.10: 9 residues within 4Å: Chain B: L.135, L.283, A.284, V.285, K.290, F.294, S.297 Chain C: I.226, L.230 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.226, C:L.230, B:F.294 POV.11: 5 residues within 4Å: Chain B: R.315 Chain C: L.237, Y.240, W.331, R.437 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.237, C:Y.240 Hydrogen bonds: C:Y.240 Salt bridges: C:R.437, B:R.315, B:R.315 POV.12: 7 residues within 4Å: Chain C: V.277, R.282, F.286, I.289, I.449, G.450, I.454 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.286, C:F.286, C:I.289, C:I.449, C:I.454 POV.17: 9 residues within 4Å: Chain D: V.294, N.297, R.301, H.306 Chain E: S.235, L.239, F.242, K.449 Ligands: CLR.16 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain E Salt bridges: D:R.301, E:K.449 Hydrophobic interactions: E:L.239, E:F.242 POV.20: 14 residues within 4Å: Chain A: Y.234, T.328 Chain E: Y.241, I.297, N.300, I.303, V.307, R.310, I.321, F.325, I.447, C.451, A.455, L.458 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:I.297, E:I.303, E:A.455, E:L.458 Hydrogen bonds: E:R.310 POV.21: 7 residues within 4Å: Chain A: L.212, I.220 Chain E: L.278, N.279, V.280, K.285, F.292 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain E Hydrophobic interactions: A:I.220, E:F.292 Hydrogen bonds: E:V.280 Salt bridges: E:K.285

1 x DD9: nonane(Non-covalent)

DD9.18: 1 residues within 4Å: Chain D: M.386 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goswami, U. et al., Structural interplay of anesthetics and paralytics on muscle nicotinic receptors. Nat Commun (2023)

Release Date

2023-06-07

Peptides

Acetylcholine receptor subunit alpha: AD
Acetylcholine receptor subunit delta: B
Acetylcholine receptor subunit beta: C
Acetylcholine receptor subunit gamma: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

C
C

E
E

Membrane

We predict this structure to be a membrane protein.
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Acetylcholine receptor subunit alpha

Acetylcholine receptor subunit delta

Acetylcholine receptor subunit beta

Acetylcholine receptor subunit gamma

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