6VSV

Crystal structure of a disease mutant of the Voltage-gated Sodium Channel Beta 4 subunit extracellular domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

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This is version 1.2 of the entry. See complete history


Literature

Biophysical Investigation of Sodium Channel Interaction with beta-Subunit Variants Associated with Arrhythmias.

Llongueras, J.P.Das, S.De Waele, J.Capulzini, L.Sorgente, A.Van Petegem, F.Bosmans, F.

(2020) Bioelectricity 2: 269-278

  • DOI: https://doi.org/10.1089/bioe.2020.0030
  • Primary Citation of Related Structures:  
    6VRR, 6VSV

  • PubMed Abstract: 

    Background: Voltage-gated sodium (Na V ) channels help regulate electrical activity of the plasma membrane. Mutations in associated subunits can result in pathological outcomes. Here we examined the interaction of Na V channels with cardiac arrhythmia-linked mutations in SCN2B and SCN4B , two genes that encode auxiliary β-subunits. Materials and Methods: To investigate changes in SCN2B R137H and SCN4B I80T function, we combined three-dimensional X-ray crystallography with electrophysiological measurements on Na V 1.5, the dominant subtype in the heart. Results: SCN4B I80T alters channel activity, whereas SCN2B R137H does not have an apparent effect. Structurally, the SCN4B I80T perturbation alters hydrophobic packing of the subunit with major structural changes and causes a thermal destabilization of the folding. In contrast, SCN2B R137H leads to structural changes but overall protein stability is unaffected. Conclusion: SCN4B I80T data suggest a functionally important region in the interaction between Na V 1.5 and β4 that, when disrupted, could lead to channel dysfunction. A lack of apparent functional effects of SCN2B R137H on Na V 1.5 suggests an alternative working mechanism, possibly through other Na V channel subtypes present in heart tissue. Indeed, mapping the structural variations of SCN2B R137H onto neuronal Na V channel structures suggests altered interaction patterns.


  • Organizational Affiliation

    Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium channel subunit beta-4129Homo sapiensMutation(s): 1 
Gene Names: SCN4B
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IWT1 (Homo sapiens)
Explore Q8IWT1 
Go to UniProtKB:  Q8IWT1
PHAROS:  Q8IWT1
GTEx:  ENSG00000177098 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IWT1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.123α = 90
b = 43.123β = 90
c = 107.492γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-26
    Type: Initial release
  • Version 1.1: 2021-09-15
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Refinement description