6LQA

voltage-gated sodium channel Nav1.5 with quinidine


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Basis for Pore Blockade of the Human Cardiac Sodium Channel Na v 1.5 by the Antiarrhythmic Drug Quinidine*.

Li, Z.Jin, X.Wu, T.Huang, G.Wu, K.Lei, J.Pan, X.Yan, N.

(2021) Angew Chem Int Ed Engl 60: 11474-11480

  • DOI: https://doi.org/10.1002/anie.202102196
  • Primary Citation of Related Structures:  
    6LQA

  • PubMed Abstract: 

    Na v 1.5, the primary voltage-gated Na + (Na v ) channel in heart, is a major target for class I antiarrhythmic agents. Here we present the cryo-EM structure of full-length human Na v 1.5 bound to quinidine, a class Ia antiarrhythmic drug, at 3.3 Å resolution. Quinidine is positioned right beneath the selectivity filter in the pore domain and coordinated by residues from repeats I, III, and IV. Pore blockade by quinidine is achieved through both direct obstruction of the ion permeation path and induced rotation of an invariant Tyr residue that tightens the intracellular gate. Structural comparison with a truncated rat Na v 1.5 in the presence of flecainide, a class Ic agent, reveals distinct binding poses for the two antiarrhythmics within the pore domain. Our work reported here, along with previous studies, reveals the molecular basis for the mechanism of action of class I antiarrhythmic drugs.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium channel protein type 5 subunit alphaA [auth B]2,059Homo 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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QDN
Query on QDN

Download Ideal Coordinates CCD File 
K [auth B]Quinidine
C20 H24 N2 O2
LOUPRKONTZGTKE-LHHVKLHASA-N
NAG
Query on NAG

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2016YFA0500402

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-24
    Type: Initial release
  • Version 1.1: 2021-05-05
    Changes: Database references
  • Version 1.2: 2021-05-19
    Changes: Database references