24JT | pdb_000024jt

Crystal structure of voltage-gated sodium channel NavAb N49K mutant

• PDB DOI: https://doi.org/10.2210/pdb24JT/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Aliarcobacter butzleri RM4018
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2026-03-06 Released: 2026-05-20 
• Deposition Author(s): Irie, K.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.10 Å
• R-Value Free: 
  0.375 (Depositor), 0.374 (DCC) 
• R-Value Work: 
  0.354 (Depositor), 0.358 (DCC) 
• R-Value Observed: 
  0.355 (Depositor) 

Starting Model: experimental

Literature

The structural dynamics and molecular coupling in the slow inactivation of a prokaryotic voltage-gated sodium channel

Irie, K., Han, S., Applewhite, S., Maeda, Y.K., Vance, J., Wang, S.

(2026) bioRxiv 

• DOI: https://doi.org/10.1101/2025.08.14.670348

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)

Macromolecule Content 

• Total Structure Weight: 27.75 kDa 
• Atom Count: 1,779 
• Modeled Residue Count: 208 
• Deposited Residue Count: 229 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ion transport protein	A	229	Aliarcobacter butzleri RM4018	Mutation(s): 1  Gene Names: Abu_1752
UniProt
Find proteins for A8EVM5 (Aliarcobacter butzleri (strain RM4018)) Explore A8EVM5  Go to UniProtKB:  A8EVM5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1N7	C [auth A]	CHAPSO C32 H59 N2 O8 S GUQQBLRVXOUDTN-XOHPMCGNSA-O
LMT	B [auth A]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
CA (Subject of Investigation/LOI)	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.10 Å
• R-Value Free:  0.375 (Depositor), 0.374 (DCC) 
• R-Value Work:  0.354 (Depositor), 0.358 (DCC) 
• R-Value Observed: 0.355 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.28	α = 90
b = 128.28	β = 90
c = 202.36	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
DIALS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-05-20 
Deposition Author(s): Irie, K.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	17K17795
Japan Society for the Promotion of Science (JSPS)	Japan	20K09193
Japan Society for the Promotion of Science (JSPS)	Japan	24K02168

Revision History  

• Version 1.0: 2026-05-20
  Type: Initial release