6UR8

CryoEM structure of human alpha4beta2 nicotinic acetylcholine receptor in complex with varenicline


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.71 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Synthetic antibodies against BRIL as universal fiducial marks for single-particle cryoEM structure determination of membrane proteins.

Mukherjee, S.Erramilli, S.K.Ammirati, M.Alvarez, F.J.D.Fennell, K.F.Purdy, M.D.Skrobek, B.M.Radziwon, K.Coukos, J.Kang, Y.Dutka, P.Gao, X.Qiu, X.Yeager, M.Eric Xu, H.Han, S.Kossiakoff, A.A.

(2020) Nat Commun 11: 1598-1598

  • DOI: https://doi.org/10.1038/s41467-020-15363-0
  • Primary Citation of Related Structures:  
    6CBV, 6UR8, 6USF

  • PubMed Abstract: 

    We propose the concept of universal fiducials based on a set of pre-made semi-synthetic antibodies (sABs) generated by customized phage display selections against the fusion protein BRIL, an engineered variant of apocytochrome b562a. These sABs can bind to BRIL fused either into the loops or termini of different GPCRs, ion channels, receptors and transporters without disrupting their structure. A crystal structure of BRIL in complex with an affinity-matured sAB (BAG2) that bound to all systems tested delineates the footprint of interaction. Negative stain and cryoEM data of several examples of BRIL-membrane protein chimera highlight the effectiveness of the sABs as universal fiducial marks. Taken together with a cryoEM structure of sAB bound human nicotinic acetylcholine receptor, this work demonstrates that these anti-BRIL sABs can greatly enhance the particle properties leading to improved cryoEM outcomes, especially for challenging membrane proteins.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA. koss@bsd.uchicago.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chimera of soluble cytochrome b562 (BRIL) and neuronal acetylcholine receptor subunit alpha-4
A, D
487Homo sapiensEscherichia coliMutation(s): 0 
Gene Names: CHRNA4NACRA4cybC
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Find proteins for P43681 (Homo sapiens)
Explore P43681 
Go to UniProtKB:  P43681
PHAROS:  P43681
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0ABE7P43681
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Neuronal acetylcholine receptor subunit beta-2
B, C, E
397Homo sapiensMutation(s): 0 
Gene Names: CHRNB2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P17787 (Homo sapiens)
Explore P17787 
Go to UniProtKB:  P17787
PHAROS:  P17787
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17787
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A]
H [auth B]
I [auth B]
K [auth C]
L [auth C]
F [auth A],
H [auth B],
I [auth B],
K [auth C],
L [auth C],
N [auth D],
P [auth E],
Q [auth E]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
QMR (Subject of Investigation/LOI)
Query on QMR

Download Ideal Coordinates CCD File 
G [auth A],
O [auth D]
VARENICLINE
C13 H13 N3
JQSHBVHOMNKWFT-DTORHVGOSA-N
BMA
Query on BMA

Download Ideal Coordinates CCD File 
J [auth B],
M [auth C],
R [auth E]
beta-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.71 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0-beta
MODEL REFINEMENTPHENIX1.16-3549

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2020-05-06
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary