SMTL ID : 7smm.1

Cryo-EM structure of Torpedo acetylcholine receptor in apo form

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.50 Å

Oligo State

hetero-2-1-1-1-mer

Ligands

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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-MAN-MAN.1: 10 residues within 4Å: Chain A: N.141, T.143, W.184, K.185, H.186, W.187, Y.189, T.202, H.204, I.206 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.186 NAG-NAG-BMA-MAN-MAN-MAN-MAN.4: 10 residues within 4Å: Chain D: N.141, T.143, W.184, K.185, H.186, W.187, Y.189, T.202, H.204, I.206 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.186, D:T.202 Water bridges: D:W.184

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.2: 8 residues within 4Å: Chain B: W.141, N.143, K.198, N.200, Y.218, P.482, F.486, E.487 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.198, B:K.198, B:E.487, B:E.487

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.3: 8 residues within 4Å: Chain C: W.139, N.141, R.194, N.196, Y.210, P.464, P.467, F.468 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.210, C:Y.210

1 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.5: 11 residues within 4Å: Chain E: N.141, K.192, N.194, W.197, I.210, F.212, P.476, F.478, P.479, F.480, P.481 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:I.210 Hydrogen bonds: E:K.192

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

POV.6: 11 residues within 4Å: Chain A: V.271, K.276, L.279, F.280, I.283, F.284, S.287, I.417 Chain B: I.230, L.238 Ligands: CLR.7 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.279, A:I.283, A:F.284, A:I.417, B:L.238 Hydrogen bonds: A:V.271 Salt bridges: A:K.276 POV.10: 5 residues within 4Å: Chain B: R.315, R.325 Chain C: L.237, Y.240, R.437 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C Salt bridges: B:R.315, C:R.437 Hydrophobic interactions: C:Y.240, C:Y.240 Hydrogen bonds: C:Y.240 POV.11: 8 residues within 4Å: Chain B: L.135, A.284, V.285, K.290, F.294, S.297 Chain C: L.218, L.230 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:L.230, B:F.294 Hydrogen bonds: B:V.285 Salt bridges: B:K.290, B:K.290 POV.13: 7 residues within 4Å: Chain C: V.277, R.282, M.285, F.286, I.289, G.450 Chain D: I.220 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.286, C:I.289 POV.16: 11 residues within 4Å: Chain D: V.271, K.276, L.279, F.280, I.283, F.284, S.287, F.414, I.417, V.425 Ligands: CLR.15 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.280, D:I.283, D:I.283, D:F.284, D:F.414, D:I.417, D:V.425 Salt bridges: D:K.276 POV.18: 16 residues within 4Å: Chain A: Y.234, T.328 Chain E: Y.241, I.297, M.299, N.300, I.303, V.307, R.310, I.321, L.324, F.325, I.447, C.451, A.455, L.458 11 PLIP interactions: 10 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:I.297, E:N.300, E:I.303, E:F.325, E:I.447, E:I.447, E:A.455, E:L.458, A:Y.234 Hydrogen bonds: E:R.310 Salt bridges: E:R.310 POV.19: 8 residues within 4Å: Chain A: L.212 Chain E: L.278, N.279, V.280, K.285, I.288, F.289, F.292 7 PLIP interactions: 6 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:K.285, E:I.288, E:F.292, A:L.212 Hydrogen bonds: E:V.280 Salt bridges: E:K.285, E:K.285 POV.20: 9 residues within 4Å: Chain D: V.294, N.297, R.301, H.306 Chain E: V.238, L.239, F.242, L.456 Ligands: CLR.15 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:V.294, E:L.456 Salt bridges: D:R.301

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.7: 12 residues within 4Å: Chain A: I.291, V.294, T.298, R.301, P.309, F.316, W.399, I.406, L.410, V.413, F.414 Ligands: POV.6 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.291, A:F.316, A:F.316, A:W.399, A:I.406, A:I.406, A:L.410, A:V.413, A:F.414 CLR.14: 9 residues within 4Å: Chain C: V.300, L.304, R.307, I.318, F.322, F.439, V.442 Chain D: Y.234, T.328 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:V.300, C:L.304, C:I.318, C:F.322, C:F.439, C:F.439, C:V.442 Hydrogen bonds: C:R.307, C:R.307, D:T.328 CLR.15: 12 residues within 4Å: Chain D: I.291, V.294, T.298, R.301, P.309, V.312, F.316, W.399, I.406, L.410 Ligands: POV.16, POV.20 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:I.291, D:F.316, D:F.316, D:I.406, D:I.406, D:I.406, D:L.410 Hydrogen bonds: D:R.301

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

NAG.8: 3 residues within 4Å: Chain B: N.70, S.72, E.73 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.73 NAG.9: 3 residues within 4Å: Chain B: F.206, N.208 Chain C: Q.111 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.208 NAG.17: 3 residues within 4Å: Chain E: N.68, S.70, E.71 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.68

1 x DD9: nonane(Non-covalent)

DD9.12: 1 residues within 4Å: Chain D: M.386 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rahman, M.M. et al., Structural mechanism of muscle nicotinic receptor desensitization and block by curare. Nat.Struct.Mol.Biol. (2022)

Release Date

2022-03-09

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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