SMTL ID : 7smq.1

Cryo-EM structure of Torpedo acetylcholine receptor in apo form with added cholesterol

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.74 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 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.186, D:T.202

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

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: 7 residues within 4Å: Chain C: W.139, N.141, R.194, Y.210, P.464, P.467, F.468 No protein-ligand interaction detected (PLIP)

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: 9 residues within 4Å: Chain E: N.141, K.192, N.194, W.197, F.212, P.476, P.479, F.480, P.481 1 PLIP interactions: 1 interactions with chain E 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: 9 residues within 4Å: Chain A: V.271, L.279, F.280, I.283, F.284, S.287 Chain B: I.230 Ligands: CLR.7, CLR.8 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.279, A:F.280, A:F.284 Hydrogen bonds: A:V.271 Salt bridges: A:K.276 POV.11: 5 residues within 4Å: Chain B: R.315, R.325 Chain C: L.237, Y.240, R.437 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:L.237, C:L.237, C:Y.240 Salt bridges: C:R.437, B:R.315 POV.12: 12 residues within 4Å: Chain B: L.135, L.283, A.284, V.285, K.290, F.294, S.297 Chain C: L.218, I.226, L.230 Ligands: CLR.14, CLR.18 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:F.294, C:I.226, C:L.230 Hydrogen bonds: B:V.285 Salt bridges: B:K.290, B:K.290 POV.19: 7 residues within 4Å: Chain C: S.276, V.277, R.282, I.289 Chain D: L.212, I.220 Ligands: CLR.16 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.289 POV.22: 14 residues within 4Å: Chain D: S.269, A.270, V.271, K.276, L.279, F.280, I.283, F.284, S.287, F.414 Chain E: I.224 Ligands: CLR.20, CLR.21, CLR.27 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:K.276, D:F.280, D:F.280, D:F.284, D:F.414 Salt bridges: D:K.276, D:K.276 POV.23: 6 residues within 4Å: Chain D: V.294, N.297 Chain E: V.238, F.242, L.456 Ligands: CLR.20 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:V.238, E:F.242, E:L.456 POV.25: 13 residues within 4Å: Chain A: Y.234, T.328 Chain E: Y.241, M.299, N.300, I.303, V.307, R.310, K.320, I.321, F.325, I.454, A.455 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:N.300, E:I.303, E:F.325, E:I.454, E:A.455 Salt bridges: E:R.310, E:K.320 POV.26: 8 residues within 4Å: Chain A: L.212 Chain E: L.278, N.279, V.280, K.285, I.288, F.289, F.292 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:K.285, E:I.288, E:F.289, E:F.292 Hydrogen bonds: E:V.280 Salt bridges: E:K.285

11 x CLR: CHOLESTEROL(Non-covalent)

CLR.7: 6 residues within 4Å: Chain A: K.276, F.280, I.420, G.421, S.424 Ligands: POV.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.276, A:F.280, A:I.420 CLR.8: 11 residues within 4Å: Chain A: I.291, V.294, T.298, R.301, P.309, F.316, W.399, I.406, V.413, I.417 Ligands: POV.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.316, A:F.316, A:I.406, A:I.406, A:V.413, A:I.417 CLR.13: 7 residues within 4Å: Chain B: F.139, V.229, I.233, V.237, L.238, F.473, N.477 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.139, B:V.229, B:V.229, B:I.233, B:V.237, B:V.237, B:L.238, B:F.473, B:N.477 CLR.14: 7 residues within 4Å: Chain B: K.290, F.294, L.467, G.468, F.471, I.472 Ligands: POV.12 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:K.290, B:F.294, B:F.471, B:F.471, B:I.472 CLR.16: 7 residues within 4Å: Chain C: R.282, V.445, I.446, I.449, G.450, I.454 Ligands: POV.19 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.445, C:I.446, C:I.449, C:I.454 CLR.17: 7 residues within 4Å: Chain C: V.300, R.307, I.318, F.439, V.442 Chain D: Y.234, T.328 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:V.300, C:I.318, C:F.439, C:F.439, C:V.442 Hydrogen bonds: C:R.307, D:Y.234 CLR.18: 6 residues within 4Å: Chain C: F.137, I.221, I.226, F.455, S.459 Ligands: POV.12 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.137, C:I.221, C:I.221, C:I.226, C:F.455 CLR.20: 11 residues within 4Å: Chain D: I.291, V.294, T.298, R.301, P.309, V.312, F.316, L.410 Ligands: CLR.21, POV.22, POV.23 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:I.291, D:V.294, D:F.316, D:F.316, D:L.410 Hydrogen bonds: D:R.301 CLR.21: 7 residues within 4Å: Chain D: K.276, V.413, I.417, S.424, V.425 Ligands: CLR.20, POV.22 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:V.413, D:I.417, D:I.417 Hydrogen bonds: D:K.276 CLR.27: 7 residues within 4Å: Chain E: F.137, I.223, I.227, V.231, F.467, H.471 Ligands: POV.22 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:F.137, E:I.223, E:I.227, E:V.231, E:V.231, E:F.467, E:H.471 Hydrogen bonds: E:H.471 CLR.28: 6 residues within 4Å: Chain E: K.285, F.289, L.458, G.462, A.465, I.466 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:K.285, E:F.289, E:I.466

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

NAG.9: 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.10: 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.24: 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)

DD9.15: 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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