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)

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

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

Sun, L., Wang, K.

To be published.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q39253
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain E [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth C] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth C] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth B], F [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-09-03

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.