cryo-EM structure of the NavCt voltage-gated sodium channel

Experimental Data Snapshot

  • Resolution: 9.00 Å
  • R-Value Free: 0.473 
  • R-Value Work: 0.497 
  • R-Value Observed: 0.497 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Two Alternative Conformations of a Voltage-Gated Sodium Channel.

Tsai, C.J.Tani, K.Irie, K.Hiroaki, Y.Shimomura, T.Mcmillan, D.G.Cook, G.M.Schertler, G.Fujiyoshi, Y.Li, X.D.

(2013) J Mol Biol 425: 4074

  • DOI: https://doi.org/10.1016/j.jmb.2013.06.036
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Activation and inactivation of voltage-gated sodium channels (Navs) are well studied, yet the molecular mechanisms governing channel gating in the membrane remain unknown. We present two conformations of a Nav from Caldalkalibacillus thermarum reconstituted into lipid bilayers in one crystal at 9Å resolution based on electron crystallography. Despite a voltage sensor arrangement identical with that in the activated form, we observed two distinct pore domain structures: a prominent form with a relatively open inner gate and a closed inner-gate conformation similar to the first prokaryotic Nav structure. Structural differences, together with mutational and electrophysiological analyses, indicated that widening of the inner gate was dependent on interactions among the S4-S5 linker, the N-terminal part of S5 and its adjoining part in S6, and on interhelical repulsion by a negatively charged C-terminal region subsequent to S6. Our findings suggest that these specific interactions result in two conformational structures.

  • Organizational Affiliation

    Paul Scherrer Institute, 5232 Villigen, Switzerland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
298Caldalkalibacillus thermarumMutation(s): 0 
Membrane Entity: Yes 
Find proteins for F5L478 (Caldalkalibacillus thermarum (strain TA2.A1))
Explore F5L478 
Go to UniProtKB:  F5L478
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF5L478
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 9.00 Å
  • R-Value Free: 0.473 
  • R-Value Work: 0.497 
  • R-Value Observed: 0.497 
  • Space Group: P 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115α = 90
b = 115β = 90
c = 118γ = 90
Software Package:
Software NamePurpose
MRCmodel building
MRCdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-10
    Type: Initial release
  • Version 1.1: 2013-07-17
    Changes: Database references
  • Version 1.2: 2013-11-13
    Changes: Database references