Crystal structure of the Voltage-gated Sodium Channel Beta 2 subunit extracellular domain

Experimental Data Snapshot

  • Resolution: 1.35 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

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This is version 1.3 of the entry. See complete history


Binary architecture of the Nav1.2-beta 2 signaling complex.

Das, S.Gilchrist, J.Bosmans, F.Van Petegem, F.

(2016) Elife 5

  • DOI: https://doi.org/10.7554/eLife.10960
  • Primary Citation of Related Structures:  
    5FDY, 5FEB

  • PubMed Abstract: 

    To investigate the mechanisms by which β-subunits influence Nav channel function, we solved the crystal structure of the β2 extracellular domain at 1.35Å. We combined these data with known bacterial Nav channel structural insights and novel functional studies to determine the interactions of specific residues in β2 with Nav1.2. We identified a flexible loop formed by (72)Cys and (75)Cys, a unique feature among the four β-subunit isoforms. Moreover, we found that (55)Cys helps to determine the influence of β2 on Nav1.2 toxin susceptibility. Further mutagenesis combined with the use of spider toxins reveals that (55)Cys forms a disulfide bond with (910)Cys in the Nav1.2 domain II pore loop, thereby suggesting a 1:1 stoichiometry. Our results also provide clues as to which disulfide bonds are formed between adjacent Nav1.2 (912/918)Cys residues. The concepts emerging from this work will help to form a model reflecting the β-subunit location in a Nav channel complex.

  • Organizational Affiliation

    Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium channel subunit beta-2125Homo sapiensMutation(s): 1 
Gene Names: SCN2BUNQ326/PRO386
UniProt & NIH Common Fund Data Resources
Find proteins for O60939 (Homo sapiens)
Explore O60939 
Go to UniProtKB:  O60939
PHAROS:  O60939
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60939
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GOL

Download Ideal Coordinates CCD File 
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.35 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 28.7α = 90
b = 59.42β = 90
c = 71.26γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-06-22
    Changes: Structure summary
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Refinement description