structure of a channel

Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


Open-state structure and pore gating mechanism of the cardiac sodium channel.

Jiang, D.Banh, R.Gamal El-Din, T.M.Tonggu, L.Lenaeus, M.J.Pomes, R.Zheng, N.Catterall, W.A.

(2021) Cell 184: 5151

  • DOI: https://doi.org/10.1016/j.cell.2021.08.021
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The heartbeat is initiated by voltage-gated sodium channel Na V 1.5, which opens rapidly and triggers the cardiac action potential; however, the structural basis for pore opening remains unknown. Here, we blocked fast inactivation with a mutation and captured the elusive open-state structure. The fast inactivation gate moves away from its receptor, allowing asymmetric opening of pore-lining S6 segments, which bend and rotate at their intracellular ends to dilate the activation gate to ∼10 Å diameter. Molecular dynamics analyses predict physiological rates of Na + conductance. The open-state pore blocker propafenone binds in a high-affinity pose, and drug-access pathways are revealed through the open activation gate and fenestrations. Comparison with mutagenesis results provides a structural map of arrhythmia mutations that target the activation and fast inactivation gates. These results give atomic-level insights into molecular events that underlie generation of the action potential, open-state drug block, and fast inactivation of cardiac sodium channels, which initiate the heartbeat.

  • Organizational Affiliation

    Department of Pharmacology, University of Washington, Seattle, WA 98195, USA; Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China. Electronic address: jiangdh@iphy.ac.cn.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium channel protein type 5 subunit alpha,Sodium channel protein type 5 subunit alpha,Sodium channel protein type 5 subunit alpha,G protein/GFP fusion protein1,838Rattus norvegicusRecombinant vesicular stomatitis Indiana virus rVSV-G/GFPMutation(s): 3 
Gene Names: Scn5aGGFP
Membrane Entity: Yes 
Find proteins for B7UCZ6 (Recombinant vesicular stomatitis Indiana virus rVSV-G/GFP)
Explore B7UCZ6 
Go to UniProtKB:  B7UCZ6
Find proteins for P15389 (Rattus norvegicus)
Explore P15389 
Go to UniProtKB:  P15389
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP15389B7UCZ6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 6OU

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [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],
P [auth A]
[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
C39 H76 N O8 P
Query on 9Z9

Download Ideal Coordinates CCD File 
Q [auth A],
R [auth A]
C34 H56 O5
4Y4 (Subject of Investigation/LOI)
Query on 4Y4

Download Ideal Coordinates CCD File 
O [auth A]1-[2-[(2R)-2-oxidanyl-3-(propylamino)propoxy]phenyl]-3-phenyl-propan-1-one
C21 H27 N O3
Query on NAG

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
C8 H15 N O6
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR01 HL112808

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-22
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references