9VSC | pdb_00009vsc

Structure of the phosphomimetic mutant CAX1 in Arabidopsis thaliana in the Calcium-bound state

• PDB DOI: https://doi.org/10.2210/pdb9VSC/pdb
• EM Map EMD-65300: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  MemProtMD


• Deposited: 2025-07-08 Released: 2025-09-03 
• Deposition Author(s): Sun, L., Wang, K.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of the phosphomimetic mutant CAX1 in Arabidopsis thaliana in the Calcium-bound state

Sun, L., Wang, K.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 154.08 kDa 
• Atom Count: 8,205 
• Modeled Residue Count: 1,074 
• Deposited Residue Count: 1,413 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar cation/proton exchanger 1	A, B, C	471	Arabidopsis thaliana	Mutation(s): 0  Gene Names: CAX1, RCI4, At2g38170, F16M14.10 Membrane Entity: Yes
UniProt
Find proteins for Q39253 (Arabidopsis thaliana) Explore Q39253  Go to UniProtKB:  Q39253

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA (Subject of Investigation/LOI)	D [auth A], E [auth B], F [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.13_2998:
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Sun, L., Wang, K.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	--

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release