7X5V

NaVEh Sodium channel, and NaVEh from the coccolithophore Emiliania huxleyi


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.83 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


Literature

N-type fast inactivation of a eukaryotic voltage-gated sodium channel.

Zhang, J.Shi, Y.Fan, J.Chen, H.Xia, Z.Huang, B.Jiang, J.Gong, J.Huang, Z.Jiang, D.

(2022) Nat Commun 13: 2713-2713

  • DOI: https://doi.org/10.1038/s41467-022-30400-w
  • Primary Citation of Related Structures:  
    7X5V

  • PubMed Abstract: 

    Voltage-gated sodium (Na V ) channels initiate action potentials. Fast inactivation of Na V channels, mediated by an Ile-Phe-Met motif, is crucial for preventing hyperexcitability and regulating firing frequency. Here we present cryo-electron microscopy structure of Na V Eh from the coccolithophore Emiliania huxleyi, which reveals an unexpected molecular gating mechanism for Na V channel fast inactivation independent of the Ile-Phe-Met motif. An N-terminal helix of Na V Eh plugs into the open activation gate and blocks it. The binding pose of the helix is stabilized by multiple electrostatic interactions. Deletion of the helix or mutations blocking the electrostatic interactions completely abolished the fast inactivation. These strong interactions enable rapid inactivation, but also delay recovery from fast inactivation, which is ~160-fold slower than human Na V channels. Together, our results provide mechanistic insights into fast inactivation of Na V Eh that fundamentally differs from the conventional local allosteric inhibition, revealing both surprising structural diversity and functional conservation of ion channel inactivation.


  • Organizational Affiliation

    College of Life Science and Technology, Key Laboratory of Molecular Biophysics of MOE, Huazhong University of Science and Technology, Wuhan, Hubei, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ion channel,GFP-TwinStrep
A, B, C, D
815Emiliania huxleyiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for R1EKX3 (Emiliania huxleyi)
Explore R1EKX3 
Go to UniProtKB:  R1EKX3
Find proteins for P42212 (Aequorea victoria)
Explore P42212 
Go to UniProtKB:  P42212
Find proteins for R1FVI4 (Emiliania huxleyi)
Explore R1FVI4 
Go to UniProtKB:  R1FVI4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsR1EKX3P42212R1FVI4
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ion channel17Emiliania huxleyiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for R1DBK9 (Emiliania huxleyi)
Explore R1DBK9 
Go to UniProtKB:  R1DBK9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupR1DBK9
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31971134

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-01
    Type: Initial release
  • Version 1.1: 2024-06-26
    Changes: Data collection