SMTL ID : 6usf.1

CryoEM structure of human alpha4beta2 nicotinic acetylcholine receptor with varenicline in complex with anti-BRIL synthetic antibody BAK5

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-3-2-2-mer

Ligands

2 x NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-BMA.1: 2 residues within 4Å: Chain B: R.186 Ligands: NAG.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.186, B:R.186 NAG-BMA.2: 3 residues within 4Å: Chain C: R.186, N.188 Ligands: NAG.7 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.186, C:N.188

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: 3 residues within 4Å: Chain E: N.143, R.186 Ligands: BMA.10 No protein-ligand interaction detected (PLIP)

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

NAG.4: 1 residues within 4Å: Chain A: N.148 No protein-ligand interaction detected (PLIP) NAG.6: 2 residues within 4Å: Chain B: N.143 Ligands: NAG-BMA.1 No protein-ligand interaction detected (PLIP) NAG.7: 4 residues within 4Å: Chain C: N.143, R.186, D.202 Ligands: NAG-BMA.2 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.143 NAG.8: 1 residues within 4Å: Chain D: N.148 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.148

2 x QMR: VARENICLINE(Non-covalent)

QMR.5: 9 residues within 4Å: Chain A: Y.100, W.156, T.157, C.199, C.200, Y.204 Chain B: V.111, F.119, L.121 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:W.156 Hydrophobic interactions: B:L.121 pi-Stacking: B:F.119 QMR.9: 10 residues within 4Å: Chain D: Y.100, W.156, T.157, Y.197, C.199, C.200, Y.204 Chain E: V.111, F.119, L.121 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:L.121 Hydrogen bonds: D:W.156, D:T.157 pi-Stacking: D:W.156

1 x BMA: beta-D-mannopyranose(Non-functional Binders)

BMA.10: 1 residues within 4Å: Ligands: NAG-NAG.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mukherjee, S. et al., Synthetic antibodies against BRIL as universal fiducial marks for single-particle cryoEM structure determination of membrane proteins. Nat Commun (2020)

Release Date

2020-04-29

Peptides

chimera of soluble cytochrome b562 (BRIL) and neuronal acetylcholine receptor subunit alpha-4: AD
Neuronal acetylcholine receptor subunit beta-2: BCE
Fab heavy chain: FH
Fab light chain: GI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

C
C

E
E

F
H

H
K

G
L

I
M

Membrane

We predict this structure to be a membrane protein.
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chimera of soluble cytochrome b562 (BRIL) and neuronal acetylcholine receptor subunit alpha-4

Neuronal acetylcholine receptor subunit beta-2

Fab heavy chain

Fab light chain

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