5YUA

Crystal structure of voltage-gated sodium channel NavAb in high-pH condition

• PDB DOI: https://doi.org/10.2210/pdb5YUA/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Aliarcobacter butzleri
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTM


• Deposited: 2017-11-21 Released: 2017-12-27 
• Deposition Author(s): Irie, K., Shimomura, T., Fujiyoshi, Y.
• Funding Organization(s): Toyoaki Scholarship Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.262 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 

Literature

Structural insight on the voltage dependence of prokaryotic voltage gated sodium channel NavAb.

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

(2017) FEBS Lett 

• PubMed: 29274127 
• DOI: https://doi.org/10.1002/1873-3468.12955
• Primary Citation of Related Structures:  
  5YUA, 5YUB, 5YUC


• PubMed Abstract: 
  

  Voltage-gated sodium channels are crucial for electro-signalling in living systems. Analysis of the molecular mechanism requires both fine electrophysiological evaluation and high-resolution channel structures. Here, we optimized a dual expression system of NavAb, which is a well-established standard of prokaryotic voltage-gated sodium channels, for E. coli and insect cells using a single plasmid vector to analyse high-resolution protein structures and measure large ionic currents. Using this expression system, we evaluated the voltage dependence and determined the crystal structures of NavAb wild-type and two mutants, E32Q and N49K, whose voltage dependence were positively shifted and essential interactions were lost in voltage sensor domain. The structural and functional comparison elucidated the molecular mechanisms of the voltage dependence of prokaryotic voltage-gated sodium channels.

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Organizational Affiliation: 

Cellular and Structural Physiology Institute (CeSPI), Nagoya University, Japan.

Biological Assembly 1  

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

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

Biological Assembly Evidence: cross-linking

Macromolecule Content

• Total Structure Weight: 37.15 kDa 
• Atom Count: 2,248 
• Modelled Residue Count: 228 
• Deposited Residue Count: 271 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ion transport protein	A	271	Aliarcobacter butzleri	Mutation(s): 0  Gene Names: SAMEA4475700_01771 Membrane Entity: Yes
UniProt
Find proteins for A8EVM5 (Aliarcobacter butzleri (strain RM4018)) Explore A8EVM5  Go to UniProtKB:  A8EVM5

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PX4	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C36 H73 N O8 P CITHEXJVPOWHKC-UUWRZZSWSA-O
1N7	E [auth A]	CHAPSO C32 H59 N2 O8 S GUQQBLRVXOUDTN-XOHPMCGNSA-O
LMT	C [auth A], D [auth A]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.262 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.45	α = 90
b = 126.45	β = 90
c = 201.658	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-12-27 
Deposition Author(s): Irie, K., Shimomura, T., Fujiyoshi, Y.

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Funding Organization	Location	Grant Number
Toyoaki Scholarship Foundation	Japan	--

Revision History  

• Version 1.0: 2017-12-27
  Type: Initial release
  
• Version 1.1: 2018-01-17
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description