SMTL ID : 8ci1.1

Human alpha7 nicotinic receptor in complex with the E3 nanobody and nicotine

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-5-5-mer

Ligands

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

NAG-NAG.1: 3 residues within 4Å: Chain A: N.110, S.112, H.114 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain B: N.110, S.112, H.114 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain C: N.110, S.112, H.114 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain D: N.110, S.112, H.114 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain E: N.110, S.112, H.114 No protein-ligand interaction detected (PLIP)

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

NAG.6: 4 residues within 4Å: Chain A: N.23, S.25, Q.26 Chain F: R.56 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.23 NAG.7: 2 residues within 4Å: Chain A: N.67, S.69 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.67 NAG.9: 4 residues within 4Å: Chain B: N.23, S.25, Q.26 Chain G: R.56 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.23 NAG.10: 2 residues within 4Å: Chain B: N.67, S.69 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.67 NAG.12: 4 residues within 4Å: Chain C: N.23, S.25, Q.26 Chain H: R.56 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.23 NAG.13: 2 residues within 4Å: Chain C: N.67, S.69 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.67 NAG.15: 4 residues within 4Å: Chain D: N.23, S.25, Q.26 Chain I: R.56 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.23 NAG.16: 2 residues within 4Å: Chain D: N.67, S.69 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.67 NAG.18: 4 residues within 4Å: Chain E: N.23, S.25, Q.26 Chain J: R.56 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.23 NAG.19: 2 residues within 4Å: Chain E: N.67, S.69 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.67

5 x NCT: (S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE(Non-covalent)

NCT.8: 10 residues within 4Å: Chain A: Y.92, S.147, W.148, Y.187, C.189, C.190, Y.194 Chain B: W.54, L.108, L.118 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.54, A:W.148 NCT.11: 10 residues within 4Å: Chain B: Y.92, S.147, W.148, Y.187, C.189, C.190, Y.194 Chain C: W.54, L.108, L.118 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:W.54, B:W.148 NCT.14: 10 residues within 4Å: Chain C: Y.92, S.147, W.148, Y.187, C.189, C.190, Y.194 Chain D: W.54, L.108, L.118 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:W.148, D:W.54 NCT.17: 10 residues within 4Å: Chain D: Y.92, S.147, W.148, Y.187, C.189, C.190, Y.194 Chain E: W.54, L.108, L.118 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:W.148, E:W.54 NCT.20: 10 residues within 4Å: Chain A: W.54, L.108, L.118 Chain E: Y.92, S.147, W.148, Y.187, C.189, C.190, Y.194 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:W.148, A:W.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prevost, M.S. et al., An original potentiating mechanism revealed by the cryo-EM structures of the human alpha 7 nicotinic receptor in complex with nanobodies. Nat Commun (2023)

Release Date

2023-10-11

Peptides

Neuronal acetylcholine receptor subunit alpha-7: ABCDE
Nanobody E3: FGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

Neuronal acetylcholine receptor subunit alpha-7

Nanobody E3

Related Entries With Identical Sequence