9HIU | pdb_00009hiu

Cryo-EM structure of CDK2-cyclin A bound to a GMNC peptide

• PDB DOI: https://doi.org/10.2210/pdb9HIU/pdb
• EM Map EMD-52201: EMDB EMDataResource

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-11-27 Released: 2025-08-20 
• Deposition Author(s): de Martin Garrido, N., Ord, M., Cushing, V.I., Greber, B.J., Pryciak, P.M., Davey, N.E.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

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

Starting Model: in silico

Literature

Cryo-EM structure of CDK2-cyclin A bound to a GMNC peptide

Ord, M., Winters, M.J., Subbanna, M., de Martin Garrido, N., Cushing, V.I., Kliche, J., Benz, C., Ivarsson, Y., Greber, B.J., Pryciak, P.M., Davey, N.E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 83.94 kDa 
• Atom Count: 4,441 
• Modeled Residue Count: 551 
• Deposited Residue Count: 742 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-A2	A	432	Homo sapiens	Mutation(s): 1  Gene Names: CCNA2, CCN1, CCNA
UniProt & NIH Common Fund Data Resources
Find proteins for P20248 (Homo sapiens) Explore P20248  Go to UniProtKB:  P20248
PHAROS:  P20248 GTEx:  ENSG00000145386

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 2	B	297	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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Geminin coiled-coil domain-containing protein 1	C	13	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for A6NCL1 (Homo sapiens) Explore A6NCL1  Go to UniProtKB:  A6NCL1
PHAROS:  A6NCL1 GTEx:  ENSG00000205835

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
RECONSTRUCTION	RELION	5.0 beta
MODEL REFINEMENT	PHENIX	1.21.1_5286

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-20 
Deposition Author(s): de Martin Garrido, N., Ord, M., Cushing, V.I., Greber, B.J., Pryciak, P.M., Davey, N.E.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-08-20
  Type: Initial release