9VSA | pdb_00009vsa

Structure of the wild-type CAX1 in Arabidopsis thaliana in the apo state

PDB DOI: https://doi.org/10.2210/pdb9VSA/pdb
EM Map EMD-65299: 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: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Structure of the wild-type CAX1 in Arabidopsis thaliana in the apo state

Sun, L., Wang, K.

To be published.

Macromolecule Content

Total Structure Weight: 153.63 kDa
Atom Count: 9,048
Modeled Residue Count: 1,182
Deposited Residue Count: 1,413
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q39253
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

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

Structure Validation

View Full Validation Report

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

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.