3VOU

The crystal structure of NaK-NavSulP chimera channel

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.292 

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

  • 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, ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ion transport 2 domain protein, Voltage-gated sodium channel
A, B
148Sulfitobacter sp. (strain NAS-14.1), Bacillus mycoides (strain KBAB4)
This entity is chimeric		Mutation(s): 2 
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))
Go to UniProtKB:  A3SUL8
Find proteins for A9VEV6 (Bacillus mycoides (strain KBAB4))
Go to UniProtKB:  A9VEV6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA
Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CO
Query on CO
Download SDF File 
Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.292 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 104.227α = 90.00
b = 104.227β = 90.00
c = 104.444γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement
HKL-2000data collection

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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