6CNK

Structure of the 3alpha2beta stiochiometry of the human Alpha4Beta2 nicotinic receptor


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structural principles of distinct assemblies of the human alpha 4 beta 2 nicotinic receptor.

Walsh, R.M.Roh, S.H.Gharpure, A.Morales-Perez, C.L.Teng, J.Hibbs, R.E.

(2018) Nature 557: 261-265

  • DOI: https://doi.org/10.1038/s41586-018-0081-7
  • Primary Citation of Related Structures:  
    6CNJ, 6CNK

  • PubMed Abstract: 

    Fast chemical communication in the nervous system is mediated by neurotransmitter-gated ion channels. The prototypical member of this class of cell surface receptors is the cation-selective nicotinic acetylcholine receptor. As with most ligand-gated ion channels, nicotinic receptors assemble as oligomers of subunits, usually as hetero-oligomers and often with variable stoichiometries 1 . This intrinsic heterogeneity in protein composition provides fine tunability in channel properties, which is essential to brain function, but frustrates structural and biophysical characterization. The α4β2 subtype of the nicotinic acetylcholine receptor is the most abundant isoform in the human brain and is the principal target in nicotine addiction. This pentameric ligand-gated ion channel assembles in two stoichiometries of α- and β-subunits (2α:3β and 3α:2β). Both assemblies are functional and have distinct biophysical properties, and an imbalance in the ratio of assemblies is linked to both nicotine addiction 2,3 and congenital epilepsy 4,5 . Here we leverage cryo-electron microscopy to obtain structures of both receptor assemblies from a single sample. Antibody fragments specific to β2 were used to 'break' symmetry during particle alignment and to obtain high-resolution reconstructions of receptors of both stoichiometries in complex with nicotine. The results reveal principles of subunit assembly and the structural basis of the distinctive biophysical and pharmacological properties of the two different stoichiometries of this receptor.


  • Organizational Affiliation

    Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neuronal acetylcholine receptor subunit alpha-4
A, B, D
386Homo sapiensMutation(s): 0 
Gene Names: CHRNA4NACRA4
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P43681 (Homo sapiens)
Explore P43681 
Go to UniProtKB:  P43681
PHAROS:  P43681
GTEx:  ENSG00000101204 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43681
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Neuronal acetylcholine receptor subunit beta-2
C, E
403Homo 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
GTEx:  ENSG00000160716 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17787
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
IgG1 Kappa Light ChainF,
H [auth J]
238Mus musculusMutation(s): 0 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
IgG1 Heavy ChainG,
I [auth K]
462Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence
Oligosaccharides

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Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseJ [auth H],
K [auth I]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y01
Query on Y01

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth E]
M [auth A]
N [auth A]
S [auth B]
AA [auth E],
BA [auth E],
M [auth A],
N [auth A],
S [auth B],
T [auth B],
U [auth C],
V [auth C],
Y [auth D],
Z [auth D]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
L [auth A],
Q [auth B],
X [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
NCT
Query on NCT

Download Ideal Coordinates CCD File 
P [auth A],
R [auth B],
W [auth D]
(S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE
C10 H14 N2
SNICXCGAKADSCV-JTQLQIEISA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
O [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
NCT BindingDB:  6CNK Ki: min: 0.05, max: 150 (nM) from 77 assay(s)
IC50: min: 1.2, max: 430 (nM) from 9 assay(s)
EC50: min: 1, max: 1.00e+4 (nM) from 25 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.1
MODEL REFINEMENTPHENIX1.13-2988

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesNS095899
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesDA037492
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesDA042072

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-02
    Type: Initial release
  • Version 1.1: 2018-05-09
    Changes: Data collection, Structure summary
  • Version 1.2: 2018-05-16
    Changes: Data collection, Database references
  • Version 1.3: 2018-05-30
    Changes: Data collection, Database references
  • Version 1.4: 2018-07-18
    Changes: Data collection
  • Version 1.5: 2019-11-20
    Changes: Data collection, Database references
  • Version 1.6: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.7: 2019-12-18
    Changes: Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary