9VDR | pdb_00009vdr

Crystal structure of voltage-gated sodium channel NavAb N49K/L176F mutant

PDB DOI: https://doi.org/10.2210/pdb9VDR/pdb

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

Deposited: 2025-06-09 Released: 2026-05-20
Deposition Author(s): Irie, K.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.70 Å
R-Value Free:
0.327 (Depositor), 0.328 (DCC)
R-Value Work:
0.298 (Depositor), 0.298 (DCC)
R-Value Observed:
0.299 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 34.51 kDa
Atom Count: 2,044
Modeled Residue Count: 223
Deposited Residue Count: 269
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ion transport protein	A	269	Aliarcobacter butzleri RM4018	Mutation(s): 2 Gene Names: Abu_1752
UniProt
Find proteins for A8EVM5 (Aliarcobacter butzleri (strain RM4018)) Explore A8EVM5 Go to UniProtKB: A8EVM5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A8EVM5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PX4 Query on PX4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	F [auth A], G [auth A], H [auth A]	1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₃₆ H₇₃ N O₈ P CITHEXJVPOWHKC-UUWRZZSWSA-O		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
1N7 Query on 1N7 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CHAPSO C₃₂ H₅₉ N₂ O₈ S GUQQBLRVXOUDTN-XOHPMCGNSA-O		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
LMT Query on LMT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
NA (Subject of Investigation/LOI) Query on NA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.70 Å
R-Value Free: 0.327 (Depositor), 0.328 (DCC)
R-Value Work: 0.298 (Depositor), 0.298 (DCC)
R-Value Observed: 0.299 (Depositor)

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.32	α = 90
b = 125.32	β = 90
c = 202.38	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
d*TREK	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-05-20

Deposition Author(s):

Irie, K.

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