9VSD | pdb_00009vsd

Structure of the phosphomimetic mutant CAX1 in Arabidopsis thaliana in the apo state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • 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


Literature

Structural basis of CAX1 autoinhibition by its amino-terminal domain in Arabidopsis thaliana.

Wang, K.Ma, C.Chen, G.Yang, Z.Gao, Y.Zhang, Z.Liu, X.Sun, L.

(2025) Nat Plants 11: 2072-2083

  • DOI: https://doi.org/10.1038/s41477-025-02104-8
  • Primary Citation of Related Structures:  
    9VSD

  • PubMed Abstract: 

    Calcium homeostasis is tightly regulated due to the essential roles of calcium ions (Ca 2+ ) in various cellular processes. CAX1 in Arabidopsis thaliana (AtCAX1) serves as a Ca 2+ /H + exchanger transporting excess cytosolic Ca 2+ into the vacuole, which is modulated by kinase phosphorylation in response to diverse signals. However, the regulatory mechanism remains unclear. Here we present the structures of wild-type AtCAX1 in an inactivated state and a phosphomimetic mutant in an activated state. In the wild-type structure, the amino-terminal region forms an α-helix that blocks the transport tunnel, thus inhibiting its transport activity. In contrast, in the phosphomimetic mutant structure, this blocking helix is released from the tunnel, leading to AtCAX1 activation. Conformational changes are also observed in the transmembrane domain. Together, these findings provide insights into the transport mechanism of the Ca 2+ /H + exchangers and set up a basis for future studies of the regulation of calcium homeostasis in plants.


  • Organizational Affiliation
    • Department of Neurology, First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar cation/proton exchanger 1
A, B, C
471Arabidopsis thalianaMutation(s): 0 
Gene Names: CAX1RCI4At2g38170F16M14.10
Membrane Entity: Yes 
UniProt
Find proteins for Q39253 (Arabidopsis thaliana)
Explore Q39253 
Go to UniProtKB:  Q39253
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ39253
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.13_2998:
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-03
    Type: Initial release
  • Version 1.1: 2026-03-18
    Changes: Data collection, Database references