9ITH | pdb_00009ith

Nav1.5 in complex with TTX


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9ITH

This is version 1.0 of the entry. See complete history

Literature

Critical role of extracellular loops in differential modulations of TTX-sensitive and TTX-resistant Na v channels.

Wu, T.Yang, X.Jin, X.Yan, N.Li, Z.

(2025) Proc Natl Acad Sci U S A 122: e2510355122-e2510355122

  • DOI: https://doi.org/10.1073/pnas.2510355122
  • Primary Citation Related Structures: 
    9ITH, 9ITI

  • PubMed Abstract: 

    The cardiac voltage-gated sodium channel Na v 1.5 is resistant to tetrodotoxin (TTXr). Here, we report a cryo-electron microscopy (cryo-EM) structure of wild-type human Na v 1.5, coexpressed with the β1 auxiliary subunit and treated with high-concentration TTX, at 3.4 Å resolution. Structural comparison reveals the molecular determinants for the distinct responses to TTX as well as β subunits between TTXr and TTX-sensitive (TTXs) Na v channels. A conserved cation-π interaction between the guanidinium group of TTX and Tyr or Phe on the P2 I helix in TTXs Na v channels is lost in all TTXr subtypes owing to the replacement by Cys/Ser at the corresponding locus, explaining their differential TTX sensitivities. The β1 subunit is invisible in the EM map. Comparison of Na v 1.5 with Na v 1.7 and Na v 1.8, which are, respectively, TTXs and TTXr, identifies four sites on the extracellular loops (ECLs) that may account for their different β1-binding abilities. When the corresponding residues in TTXs Na v 1.7 are replaced with those from Na v 1.5, the modulatory effects of β1 on channel activation and inactivation are diminished. Consistently, β1 is absent in the 3D EM reconstruction of this Na v 1.7 mutant. Together with our previous structure-guided discovery that TTXr channels lack a Cys on the ECL II for disulfide bond formation with β2 or β4, the structure-function relationship studies underscore the importance of the ECLs in the mechanistic distinctions between TTXs and TTXr Na v channels. The ECLs may be further explored for the development of subtype-specific drugs.


  • Organizational Affiliation
    • State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.

Macromolecule Content 

  • Total Structure Weight: 234.6 kDa 
  • Atom Count: 9,424 
  • Modeled Residue Count: 1,151 
  • Deposited Residue Count: 2,059 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Sodium channel protein type 5 subunit alpha2,059Homo sapiensMutation(s): 0 
Gene Names: SCN5A
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q14524 (Homo sapiens)
Explore Q14524 
Go to UniProtKB:  Q14524
PHAROS:  Q14524
GTEx:  ENSG00000183873 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14524
Glycosylation
Glycosylation Sites: 9Go to GlyGen: Q14524-1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9Z9

Query on 9Z9



Download:Ideal Coordinates CCD File
L [auth A](3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en
C34 H56 O5
CEEBZAXXSRFQIC-GZSGZGDASA-N
9SR
(Subject of Investigation/LOI)

Query on 9SR



Download:Ideal Coordinates CCD File
K [auth A](1R,5R,6R,7R,9S,11S,12S,13S,14S)-3-amino-14-(hydroxymethyl)-8,10-dioxa-2,4-diazatetracyclo[7.3.1.1~7,11~.0~1,6~]tetradec-3-ene-5,9,12,13,14-pentol (non-preferred name)
C11 H17 N3 O8
CFMYXEVWODSLAX-QOZOJKKESA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32330052

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-20
    Type: Initial release