3VOU

The crystal structure of NaK-NavSulP chimera channel

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.292 
  • R-Value Observed: 0.293 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

The C-terminal helical bundle of the tetrameric prokaryotic sodium channel accelerates the inactivation rate

Irie, K., Shimomura, T., Fujiyoshi, Y.

(2012) Nat Commun 3: 793-793

  • DOI: 10.1038/ncomms1797
  • Primary Citation of Related Structures:  
    3VOU

  • PubMed Abstract: 

    • Most tetrameric channels have cytosolic domains to regulate their functions, including channel inactivation. Here we show that the cytosolic C-terminal region of NavSulP, a prokaryotic voltage-gated sodium channel cloned from Sulfitobacter pontiacus, accelerates channel inactivation ...

    Most tetrameric channels have cytosolic domains to regulate their functions, including channel inactivation. Here we show that the cytosolic C-terminal region of NavSulP, a prokaryotic voltage-gated sodium channel cloned from Sulfitobacter pontiacus, accelerates channel inactivation. The crystal structure of the C-terminal region of NavSulP grafted into the C-terminus of a NaK channel revealed that the NavSulP C-terminal region forms a four-helix bundle. Point mutations of the residues involved in the intersubunit interactions of the four-helix bundle destabilized the tetramer of the channel and reduced the inactivation rate. The four-helix bundle was directly connected to the inner helix of the pore domain, and a mutation increasing the rigidity of the inner helix also reduced the inactivation rate. These findings suggest that the NavSulP four-helix bundle has important roles not only in stabilizing the tetramer, but also in accelerating the inactivation rate, through promotion of the conformational change of the inner helix.

    Organizational Affiliation: 

    Department of Biophysics, Graduate School of Science, Kyoto University, Oiwake, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ion transport 2 domain protein, Voltage-gated sodium channelA, B148Bacillus mycoides KBAB4, Sulfitobacter sp. NAS-14.1
This entity is chimeric		Mutation(s): 2 
Gene Names: BcerKBAB4_0590, NAS141_12386
Membrane Entity: Yes 
UniProt
Find proteins for A3SUL8 (Sulfitobacter sp. (strain NAS-14.1))
Explore A3SUL8 
Go to UniProtKB:  A3SUL8
Find proteins for A9VEV6 (Bacillus mycoides (strain KBAB4))
Explore A9VEV6 
Go to UniProtKB:  A9VEV6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsA9VEV6A3SUL8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CO
Query on CO
Download Ideal Coordinates CCD File 
D [auth A]COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.292 
  • R-Value Observed: 0.293 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.227α = 90
b = 104.227β = 90
c = 104.444γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-02
    Type: Initial release
  • Version 1.1: 2013-08-07
    Changes: Database references, Derived calculations
  • Version 1.2: 2017-08-16
    Changes: Refinement description, Source and taxonomy