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, acc ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ion transport 2 domain protein, Voltage-gated sodium channel AB148Bacillus mycoides KBAB4Sulfitobacter sp. NAS-14.1
This entity is chimeric
Mutation(s): 2 
Gene Names: BcerKBAB4_0590NAS141_12386
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Potassium, Sodium, & Proton Ion-Selective
Protein: 
NaK channel chimera with grafted C-terminal region of a NaV channel
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
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 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
A, 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



Entry History 

Deposition Data

Revision History 

  • 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