9QCX | pdb_00009qcx

Cryo-EM structure of apo-CAK-CDK2-cyclin A2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of T-loop-independent recognition and activation of CDKs by the CDK-activating kinase.

Cushing, V.I.McGeoch, A.J.S.Williams, S.L.Roumeliotis, T.I.Feng, J.Dan, L.M.Choudhary, J.S.Davey, N.E.Greber, B.J.

(2025) Science : eadw0053-eadw0053

  • DOI: https://doi.org/10.1126/science.adw0053
  • Primary Citation of Related Structures:  
    9I9I, 9I9J, 9I9K, 9QCV, 9QCX, 9SKQ

  • PubMed Abstract: 

    Cyclin-dependent kinases (CDKs) are prototypical regulators of the cell cycle. The CDK-activating kinase (CAK) acts as a master regulator of CDK activity by catalyzing the activating phosphorylation of CDKs on a conserved threonine residue within the regulatory T-loop. However, structural data illuminating the mechanism by which the CAK recognizes and activates CDKs have remained elusive. Here, we determine high-resolution structures of the CAK in complex with CDK2 and CDK2-cyclin A2 by cryogenic electron microscopy. Our structures reveal a T-loop-independent kinase-kinase interface with contributions from both kinase lobes. Computational analysis and structures of CAK in complex with CDK1-cyclin B1 and CDK11 indicate that these structures represent the general architecture of CAK-CDK complexes. These results advance our mechanistic understanding of cell cycle regulation and kinase signaling cascades.


  • Organizational Affiliation
    • Division of Structural Biology, The Institute of Cancer Research, 237 Fulham Road, London, UK.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CDK-activating kinase assembly factor MAT1A [auth H]328Homo sapiensMutation(s): 0 
Gene Names: MNAT1CAP35MAT1RNF66
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PHAROS:  P51948
GTEx:  ENSG00000020426 
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UniProt GroupP51948
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-HB [auth I]324Homo sapiensMutation(s): 1 
Gene Names: CCNH
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Find proteins for P51946 (Homo sapiens)
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PHAROS:  P51946
GTEx:  ENSG00000134480 
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UniProt GroupP51946
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase 7C [auth J]391Homo sapiensMutation(s): 0 
Gene Names: CDK7CAKCAK1CDKN7MO15STK1
EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (PDB Primary Data)
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Find proteins for P50613 (Homo sapiens)
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PHAROS:  P50613
GTEx:  ENSG00000134058 
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UniProt GroupP50613
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase 2D [auth K]301Homo sapiensMutation(s): 0 
Gene Names: CDK2CDKN2
EC: 2.7.11.22
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Find proteins for P24941 (Homo sapiens)
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PHAROS:  P24941
GTEx:  ENSG00000123374 
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UniProt GroupP24941
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-A2E [auth L]435Homo sapiensMutation(s): 1 
Gene Names: CCNA2CCN1CCNA
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Find proteins for P20248 (Homo sapiens)
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PHAROS:  P20248
GTEx:  ENSG00000145386 
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UniProt GroupP20248
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION5.0
MODEL REFINEMENTPHENIX1.21-5207

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/V009354/1
The Institute of Cancer Research (ICR)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-15
    Type: Initial release
  • Version 1.1: 2025-10-29
    Changes: Data collection, Database references