Voltage-gated sodium channel beta3 subunit Ig domain

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Crystal Structure and Molecular Imaging of the Nav Channel beta 3 Subunit Indicates a Trimeric Assembly.

Namadurai, S.Balasuriya, D.Rajappa, R.Wiemhofer, M.Stott, K.Klingauf, J.Edwardson, J.M.Chirgadze, D.Y.Jackson, A.P.

(2014) J Biol Chem 289: 10797-10811

  • DOI: https://doi.org/10.1074/jbc.M113.527994
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The vertebrate sodium (Nav) channel is composed of an ion-conducting α subunit and associated β subunits. Here, we report the crystal structure of the human β3 subunit immunoglobulin (Ig) domain, a functionally important component of Nav channels in neurons and cardiomyocytes. Surprisingly, we found that the β3 subunit Ig domain assembles as a trimer in the crystal asymmetric unit. Analytical ultracentrifugation confirmed the presence of Ig domain monomers, dimers, and trimers in free solution, and atomic force microscopy imaging also detected full-length β3 subunit monomers, dimers, and trimers. Mutation of a cysteine residue critical for maintaining the trimer interface destabilized both dimers and trimers. Using fluorescence photoactivated localization microscopy, we detected full-length β3 subunit trimers on the plasma membrane of transfected HEK293 cells. We further show that β3 subunits can bind to more than one site on the Nav 1.5 α subunit and induce the formation of α subunit oligomers, including trimers. Our results suggest a new and unexpected role for the β3 subunits in Nav channel cross-linking and provide new structural insights into some pathological Nav channel mutations.

  • Organizational Affiliation

    Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium channel subunit beta-3
A, B, C
127Homo sapiensMutation(s): 0 
Gene Names: KIAA1158SCN3B
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NY72 (Homo sapiens)
Explore Q9NY72 
Go to UniProtKB:  Q9NY72
GTEx:  ENSG00000166257 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NY72
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.469α = 90
b = 81.469β = 90
c = 114.257γ = 120
Software Package:
Software NamePurpose
GDAdata collection
PHENIXmodel building
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2014-04-30
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Refinement description