9M3V | pdb_00009m3v

Arabidopsis thaliana CDC48A, nucleotide-free (Apo)

PDB DOI: https://doi.org/10.2210/pdb9M3V/pdb
EM Map EMD-63608: EMDB EMDataResource

Classification: PLANT PROTEIN
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-03-03 Released: 2025-10-29
Deposition Author(s): Huntington, B., Arold, S.T.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.90 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

Plant-specific adaptations of the CDC48 unfoldase

Huntington, B., Sandholu, A., Wang, J., Zhang, J., Zhao, L., Qureshi, B.M., Hameed, U.F.S., Arold, S.T.

To be published.

Macromolecule Content

Total Structure Weight: 539.54 kDa
Atom Count: 35,280
Modeled Residue Count: 4,518
Deposited Residue Count: 4,884
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division control protein 48 homolog A	A, B, C, D, E A, B, C, D, E, F	814	Arabidopsis thaliana	Mutation(s): 0 Gene Names: CDC48A, CDC48, At3g09840, F8A24.11
UniProt
Find proteins for P54609 (Arabidopsis thaliana) Explore P54609 Go to UniProtKB: P54609
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P54609
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	dev_4694
RECONSTRUCTION	RELION

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private	Saudi Arabia	URF/1/4039-01-01
Other private	Saudi Arabia	URF/1/4080-01-01

Revision History (Full details and data files)

Version 1.0: 2025-10-29
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.