SMTL ID : 7sms.1

Cryo-EM structure of Torpedo acetylcholine receptor in complex with d-tubocurarine

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.18 Å

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: 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 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.202 Hydrogen bonds: A:H.186 NAG-NAG-BMA-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 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.189, 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: 8 residues within 4Å: Chain B: N.143, K.198, N.200, Y.218, P.482, P.485, F.486, E.487 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: 9 residues within 4Å: Chain C: W.139, N.141, T.143, R.194, N.196, Y.210, P.464, P.467, F.468 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.194, C:R.194, C:N.196

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.6: 5 residues within 4Å: Chain A: I.291, V.294, F.316, W.399, I.406 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.291, A:F.316, A:I.406, A:I.406 CLR.12: 8 residues within 4Å: Chain C: L.297, V.300, L.304, R.307, I.318, F.439 Chain D: Y.234, T.328 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.297, C:L.304, C:F.439, C:F.439 Hydrogen bonds: C:R.307, C:R.307 CLR.14: 9 residues within 4Å: Chain D: V.294, T.298, R.301, V.312, F.316, W.399, I.406, L.410 Ligands: POV.15 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:V.294, D:V.312, D:F.316, D:W.399, D:I.406, D:L.410

4 x TC9: D-TUBOCURARINE(Non-covalent)

TC9.7: 15 residues within 4Å: Chain A: Y.93, W.149, T.150, D.152, Y.190, C.192, Y.198 Chain B: S.36, T.38, W.57, D.59, R.81, L.111, L.121, I.178 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.121, A:Y.198, A:Y.198 Hydrogen bonds: B:S.36, B:R.81 pi-Stacking: B:W.57, A:Y.190 pi-Cation interactions: A:W.149 TC9.8: 6 residues within 4Å: Chain A: V.259 Chain B: Q.276 Chain C: L.265, D.268 Chain E: F.267, Q.271 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: C:D.268, A:V.259 Salt bridges: D:E.262 Hydrogen bonds: B:Q.276 TC9.13: 12 residues within 4Å: Chain D: L.223, S.226, F.227, Y.277, F.280, T.281, F.284, F.414, I.417, C.418, G.421, S.424 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:Y.277, D:F.280, D:F.414, D:I.417 Hydrogen bonds: D:S.424, D:S.424 TC9.16: 15 residues within 4Å: Chain D: Y.93, W.149, T.150, Y.190, C.192, C.193, Y.198 Chain E: K.34, W.55, R.79, L.109, Y.111, Y.117, L.119, E.163 11 PLIP interactions: 5 interactions with chain D, 6 interactions with chain E Hydrophobic interactions: D:W.149, D:Y.198, E:W.55, E:L.109, E:L.119 Hydrogen bonds: D:T.150, D:Y.190, E:K.34, E:R.79 pi-Stacking: D:W.149 pi-Cation interactions: E:Y.117

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

POV.9: 6 residues within 4Å: Chain B: L.283, V.285, F.294, S.297 Chain C: I.226, L.230 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:F.294, C:I.226, C:L.230 Salt bridges: B:K.290 POV.10: 5 residues within 4Å: Chain B: R.315 Chain C: L.237, Y.240, R.437, Y.441 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C Salt bridges: B:R.315, C:R.437 Hydrophobic interactions: C:L.237, C:Y.240 Hydrogen bonds: C:Y.240 POV.11: 8 residues within 4Å: Chain C: V.277, R.282, M.285, F.286, I.289, I.449, G.450, I.454 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.286, C:I.289, C:I.449, C:I.454 POV.15: 11 residues within 4Å: Chain D: V.294, N.297, R.301, H.306 Chain E: S.235, V.238, L.239, F.242, K.449, L.456 Ligands: CLR.14 8 PLIP interactions: 3 interactions with chain D, 5 interactions with chain E Hydrophobic interactions: D:V.294, E:V.238, E:L.239, E:F.242, E:L.456 Hydrogen bonds: D:H.306 Salt bridges: D:R.301, E:K.449 POV.17: 13 residues within 4Å: Chain A: Y.234, T.328 Chain E: Y.241, L.296, N.300, I.303, R.310, K.320, I.321, L.324, I.447, C.451, A.455 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:L.296, E:N.300, E:I.303, E:I.447, E:A.455 Salt bridges: E:R.310

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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