5FEB

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

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

(2016) Elife 5: --

  • DOI: 10.7554/eLife.10960
  • Primary Citation of Related Structures:  

  • 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 functiona ...

    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 Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sodium channel subunit beta-2
A
125Homo sapiensMutation(s): 1 
Gene Names: SCN2B
Find proteins for O60939 (Homo sapiens)
Go to Gene View: SCN2B
Go to UniProtKB:  O60939
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 28.700α = 90.00
b = 59.420β = 90.00
c = 71.260γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-06-22
    Type: Structure summary
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence, Derived calculations