SMTL ID : 6uwz.1

Cryo-EM structure of Torpedo acetylcholine receptor in complex with alpha-bungarotoxin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-1-2-mer

Ligands

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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-MAN-MAN-MAN-MAN-MAN.1: 11 residues within 4Å: Chain A: N.141, T.143, W.184, K.185, H.186, W.187, T.202, H.204, I.206 Chain F: T.6, A.7 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:T.6, A:H.186 Water bridges: F:E.41, F:E.41 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.4: 13 residues within 4Å: Chain D: N.141, T.143, W.184, K.185, H.186, W.187, V.188, T.202, H.204, I.206 Chain G: T.6, A.7, E.41 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain G Hydrogen bonds: D:H.186, G:T.6, G:T.6, D:H.186, D:H.186 Hydrophobic interactions: D:T.202

2 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, N.200, Y.218, P.482, P.485, F.486, E.487 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 7 residues within 4Å: Chain C: W.139, N.141, R.194, N.196, Y.210, P.467, F.468 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.194, C:N.196

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

NAG-NAG-NAG-MAN-MAN.5: 11 residues within 4Å: Chain E: W.139, N.141, K.192, N.194, W.197, F.212, I.214, P.479, F.480, P.481, G.482 No protein-ligand interaction detected (PLIP)

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

POV.6: 10 residues within 4Å: Chain A: F.227, Y.234, F.326, S.327, T.328, H.408, L.411, C.412, M.415 Chain E: R.310 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:F.227, A:Y.234, A:M.415 Hydrogen bonds: A:Y.234, A:Y.234 Salt bridges: A:H.408, E:R.310 POV.10: 11 residues within 4Å: Chain B: F.312, R.315, H.320 Chain C: I.236, L.237, Y.240, W.331, I.332, Q.333, R.437, F.444 9 PLIP interactions: 2 interactions with chain B, 7 interactions with chain C Hydrophobic interactions: B:F.312, C:I.236, C:L.237, C:Y.240, C:Y.240, C:F.444 Salt bridges: B:R.315, C:R.437 Hydrogen bonds: C:R.437 POV.11: 8 residues within 4Å: Chain C: V.277, R.282, M.285, F.286, I.289, G.450, I.454 Chain D: L.212 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.454 POV.12: 9 residues within 4Å: Chain D: V.293, V.294, N.297, R.301, H.306 Chain E: L.239, F.242, K.449, L.456 7 PLIP interactions: 4 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:L.239, E:F.242, E:L.456, D:V.294 Salt bridges: E:K.449, D:R.301, D:R.301 POV.13: 11 residues within 4Å: Chain C: R.307 Chain D: F.227, Y.234, F.326, S.327, T.328, M.329, H.408, L.411, C.412, M.415 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.227, D:L.411 Hydrogen bonds: D:Y.234, D:T.328, D:M.329 Salt bridges: D:H.408, C:R.307

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

NAG.7: 3 residues within 4Å: Chain B: N.70, S.72, E.73 No protein-ligand interaction detected (PLIP) NAG.8: 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.14: 3 residues within 4Å: Chain E: N.68, S.70, E.71 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.71

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

OCT.9: 1 residues within 4Å: Chain B: I.429 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.429

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rahman, M.M. et al., Structure of the Native Muscle-type Nicotinic Receptor and Inhibition by Snake Venom Toxins. Neuron (2020)

Release Date

2020-04-15

Peptides

Acetylcholine receptor subunit alpha: AD
Acetylcholine receptor subunit delta: B
Acetylcholine receptor subunit beta: C
Acetylcholine receptor subunit gamma: E
Alpha-bungarotoxin: FG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

C
C

E
E

F
F

G
G

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

Alpha-bungarotoxin

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