9HIW | pdb_00009hiw

Cryo-EM structure of CDK2-cyclin A bound to a SAMHD1 peptide

• PDB DOI: https://doi.org/10.2210/pdb9HIW/pdb
• EM Map EMD-52204: 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: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Cryo-EM structure of CDK2-cyclin A bound to a SAMHD1 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: 84.01 kDa 
• Atom Count: 4,425 
• Modeled Residue Count: 548 
• 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
Deoxynucleoside triphosphate triphosphohydrolase SAMHD1	C	13	Homo sapiens	Mutation(s): 0  EC: 3.1.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3Z3 (Homo sapiens) Explore Q9Y3Z3  Go to UniProtKB:  Q9Y3Z3
PHAROS:  Q9Y3Z3 GTEx:  ENSG00000101347

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286
RECONSTRUCTION	RELION	5.0 beta

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