9UC2 | pdb_00009uc2

Crystal structure of voltage-gated sodium channel NavAb N49K/S178A mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.294 (Depositor), 0.294 (DCC) 
  • R-Value Work: 
    0.256 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 
    0.257 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure-function analysis of the lithium-ion selectivity of the voltage-gated sodium channel.

Maeda, Y.K.Kojima, K.Nakamura, T.Y.Nakatsu, T.Irie, K.

(2026) J Gen Physiol 158

  • DOI: https://doi.org/10.1085/jgp.202513855
  • Primary Citation of Related Structures:  
    9UC1, 9UC2, 9UC3, 9UC4

  • PubMed Abstract: 

    Voltage-gated sodium channels (Navs) selectively conduct Na+ to generate action potentials. Na+ permeates Navs with significantly higher efficiency than many other cations, but Li+ can also permeate Navs to an extent comparable with Na+. Li+ in the blood is known to enter cells via Navs and to have a beneficial effect on various neuropathies. However, the molecular basis of the high Li+ selectivity of Navs was unclear. In this study, using a prokaryotic Nav, we successfully created the first Nav mutant to be more selective for Li+ than for Na+. Electrophysiological and crystallographic analyses suggested the critical determinants of high Li+ selectivity: the strong electrostatic interaction between the ion pathway and hydrated ions, and the smaller number of hydration water exchanges within the ion pathway. Additionally, the extensive interactions around the ion pathway were shown to support monovalent cation selectivity. New drug directions based on the molecular basis for Li+ permeation may target various neurological disorders and could clarify the broader biological effects of lithium.


  • Organizational Affiliation
    • Department of Pharmacology, Faculty of Medicine, Wakayama Medical University, Wakayama, Japan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ion transport protein271Aliarcobacter butzleriMutation(s): 2 
Gene Names: Abu_1752
UniProt
Find proteins for A8EVM5 (Aliarcobacter butzleri (strain RM4018))
Explore A8EVM5 
Go to UniProtKB:  A8EVM5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8EVM5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PX4
Query on PX4

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A]
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C36 H73 N O8 P
CITHEXJVPOWHKC-UUWRZZSWSA-O
1N7
Query on 1N7

Download Ideal Coordinates CCD File 
E [auth A]CHAPSO
C32 H59 N2 O8 S
GUQQBLRVXOUDTN-XOHPMCGNSA-O
LMT
Query on LMT

Download Ideal Coordinates CCD File 
F [auth A]DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.294 (Depositor), 0.294 (DCC) 
  • R-Value Work:  0.256 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 0.257 (Depositor) 
Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.59α = 90
b = 126.59β = 90
c = 201.54γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan24K02168

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-18
    Type: Initial release
  • Version 1.1: 2026-03-04
    Changes: Database references