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 8J7M | pdb_00008j7m

ion channel


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8J7M

This is version 1.2 of the entry. See complete history. 

Literature

Structural mechanism of voltage-gated sodium channel slow inactivation.

Chen, H., Xia, Z., Dong, J., Huang, B., Zhang, J., Zhou, F., Yan, R., Shi, Y., Gong, J., Jiang, J., Huang, Z., Jiang, D.

(2024) Nat Commun 15: 3691-3691

  • DOI: https://doi.org/10.1038/s41467-024-48125-3
  • Primary Citation Related Structures: 
    8J7F, 8J7H, 8J7M

  • PubMed Abstract: 

    Voltage-gated sodium (Na V ) channels mediate a plethora of electrical activities. Na V channels govern cellular excitability in response to depolarizing stimuli. Inactivation is an intrinsic property of Na V channels that regulates cellular excitability by controlling the channel availability. The fast inactivation, mediated by the Ile-Phe-Met (IFM) motif and the N-terminal helix (N-helix), has been well-characterized. However, the molecular mechanism underlying Na V channel slow inactivation remains elusive. Here, we demonstrate that the removal of the N-helix of Na V Eh (Na V Eh ΔN ) results in a slow-inactivated channel, and present cryo-EM structure of Na V Eh ΔN in a potential slow-inactivated state. The structure features a closed activation gate and a dilated selectivity filter (SF), indicating that the upper SF and the inner gate could serve as a gate for slow inactivation. In comparison to the Na V Eh structure, Na V Eh ΔN undergoes marked conformational shifts on the intracellular side. Together, our results provide important mechanistic insights into Na V channel slow inactivation.


  • Organizational Affiliation: 
    • Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, China.

Macromolecule Content 

  • Total Structure Weight: 367.96 kDa 
  • Atom Count: 8,806 
  • Modeled Residue Count: 1,028 
  • Deposited Residue Count: 3,212 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ion channel,Voltage dependent ion channel,Green fluorescent protein (Fragment),Voltage dependent ion channel,Green fluorescent protein (Fragment),Voltage dependent ion channel,Green fluorescent protein (Fragment)A,
B [auth D],
C [auth B],
D [auth C]
803Homo sapiens, Aequorea victoriaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for R1EKX3 (Emiliania huxleyi)
Explore R1EKX3 
Go to UniProtKB:  R1EKX3
Find proteins for R1FVI4 (Emiliania huxleyi)
Explore R1FVI4 
Go to UniProtKB:  R1FVI4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsR1EKX3R1FVI4
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POV

Query on POV



Download:Ideal Coordinates CCD File
E [auth A],
H [auth D],
L [auth B],
O [auth C]
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
CLR

Query on CLR



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
I [auth D]
J [auth D]
K [auth D]
F [auth A],
G [auth A],
I [auth D],
J [auth D],
K [auth D],
M [auth B],
N [auth B],
P [auth C],
Q [auth C],
R [auth C]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil31971134

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-15
    Type: Initial release
  • Version 1.1: 2025-01-15
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2025-07-02
    Changes: Data collection