8JGL | pdb_00008jgl

Cryo-EM structure of mClC-3 with AMP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8JGL

This is version 1.2 of the entry. See complete history

Literature

Structural basis of adenine nucleotides regulation and neurodegenerative pathology in ClC-3 exchanger.

Wan, Y.Guo, S.Zhen, W.Xu, L.Chen, X.Liu, F.Shen, Y.Liu, S.Hu, L.Wang, X.Ye, F.Wang, Q.Wen, H.Yang, F.

(2024) Nat Commun 15: 6654-6654

  • DOI: https://doi.org/10.1038/s41467-024-50975-w
  • Primary Citation Related Structures: 
    8JEV, 8JGJ, 8JGK, 8JGL, 8JGS, 8JGV

  • PubMed Abstract: 

    The ClC-3 chloride/proton exchanger is both physiologically and pathologically critical, as it is potentiated by ATP to detect metabolic energy level and point mutations in ClC-3 lead to severe neurodegenerative diseases in human. However, why this exchanger is differentially modulated by ATP, ADP or AMP and how mutations caused gain-of-function remains largely unknow. Here we determine the high-resolution structures of dimeric wildtype ClC-3 in the apo state and in complex with ATP, ADP and AMP, and the disease-causing I607T mutant in the apo and ATP-bounded state by cryo-electron microscopy. In combination with patch-clamp recordings and molecular dynamic simulations, we reveal how the adenine nucleotides binds to ClC-3 and changes in ion occupancy between apo and ATP-bounded state. We further observe I607T mutation induced conformational changes and augments in current. Therefore, our study not only lays the structural basis of adenine nucleotides regulation in ClC-3, but also clearly indicates the target region for drug discovery against ClC-3 mediated neurodegenerative diseases.


  • Organizational Affiliation
    • Department of Biophysics and Disease Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.

Macromolecule Content 

  • Total Structure Weight: 182.61 kDa 
  • Atom Count: 10,794 
  • Modeled Residue Count: 1,368 
  • Deposited Residue Count: 1,636 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
H(+)/Cl(-) exchange transporter 3
A, B
818Mus musculusMutation(s): 2 
Gene Names: Clcn3Clc3
Membrane Entity: Yes 
UniProt
Find proteins for P51791 (Mus musculus)
Explore P51791 
Go to UniProtKB:  P51791
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51791
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32122040

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-11
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-07-02
    Changes: Data collection