Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C4  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.60 kDa 
• Atom Count: 2153 
• Modelled Residue Count: 275 
• Deposited Residue Count: 296 
• Unique protein chains: 1

3VOU

The crystal structure of NaK-NavSulP chimera channel

• DOI: 10.2210/pdb3VOU/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Bacillus mycoides KBAB4, Sulfitobacter sp. NAS-14.1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-02-10 Released: 2012-05-02 
• Deposition Author(s): Irie, K., Shimomura, T., Fujiyoshi, Y.

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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 

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

• PubMed: 22531178 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ion transport 2 domain protein, Voltage-gated sodium channel	A, B	148	Bacillus mycoides KBAB4, Sulfitobacter sp. NAS-14.1 This entity is chimeric	Mutation(s): 2  Gene Names: BcerKBAB4_0590, NAS141_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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO	D [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N
NA	C [auth A], E [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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 = 104.227	α = 90
b = 104.227	β = 90
c = 104.444	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-02-10 
• Released Date: 2012-05-02 
Deposition Author(s): Irie, K., Shimomura, T., Fujiyoshi, Y.

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