8ROZ

Cryo-EM structure of CDK2-cyclin A in complex with CDC25A

PDB DOI: https://doi.org/10.2210/pdb8ROZ/pdb
EM Map EMD-19408: EMDB EMDataResource

Classification: CELL CYCLE
Organism(s): Homo sapiens, Bos taurus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-01-12 Released: 2024-05-29
Deposition Author(s): Rowland, R.J., Noble, M.E.M., Endicott, J.A.
Funding Organization(s): Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.70 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

Cryo-EM structure of the CDK2-cyclin A-CDC25A Complex

Rowland, R.J., Korolchuk, S., Salamina, M., Ault, J.R., Hart, S., Turkenburg, J.P., Blaza, J.N., Noble, M.E.M., Endicott, J.A.

To be published.

Macromolecule Content

Total Structure Weight: 86.79 kDa
Atom Count: 6,079
Modelled Residue Count: 751
Deposited Residue Count: 751
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 2	A	298	Homo sapiens	Mutation(s): 0 Gene Names: CDK2, CDKN2 EC: 2.7.11.22
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens) Explore P24941 Go to UniProtKB: P24941
PHAROS: P24941 GTEx: ENSG00000123374
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P24941
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-A2	B	263	Bos taurus	Mutation(s): 0 Gene Names: CCNA2
UniProt
Find proteins for P30274 (Bos taurus) Explore P30274 Go to UniProtKB: P30274
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P30274
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
M-phase inducer phosphatase 1	C	190	Homo sapiens	Mutation(s): 1 Gene Names: CDC25A EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P30304 (Homo sapiens) Explore P30304 Go to UniProtKB: P30304
PHAROS: P30304 GTEx: ENSG00000164045
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P30304
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR Query on PTR	A	L-PEPTIDE LINKING	C₉ H₁₂ N O₆ P		TYR
TPO Query on TPO	A	L-PEPTIDE LINKING	C₄ H₁₀ N O₆ P		THR

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-05-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/V029142/1
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/N009738/1

Revision History (Full details and data files)

Version 1.0: 2024-05-29
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 R01GM133198.