8S0T | pdb_00008s0t

Cryo-EM structure of CAK in complex with SY-5609


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

TFIIH kinase CDK7 drives cell proliferation through a common core transcription factor network.

Jones, T.Feng, J.Luyties, O.Cozzolino, K.Sanford, L.Rimel, J.K.Ebmeier, C.C.Shelby, G.S.Watts, L.P.Rodino, J.Rajagopal, N.Hu, S.Brennan, F.Maas, Z.L.Alnemy, S.Richter, W.F.Koh, A.F.Cronin, N.B.Madduri, A.Das, J.Cooper, E.Hamman, K.B.Carulli, J.P.Allen, M.A.Spencer, S.Kotecha, A.Marineau, J.J.Greber, B.J.Dowell, R.D.Taatjes, D.J.

(2025) Sci Adv 11: eadr9660-eadr9660

  • DOI: https://doi.org/10.1126/sciadv.adr9660
  • Primary Citation of Related Structures:  
    8S0R, 8S0T

  • PubMed Abstract: 

    How cyclin-dependent kinase 7 (CDK7) coordinately regulates the cell cycle and RNA polymerase II transcription remains unclear. Here, high-resolution cryo-electron microscopy revealed how two clinically relevant inhibitors block CDK7 function. In cells, CDK7 inhibition rapidly suppressed transcription, but constitutively active genes were disproportionately affected versus stimulus-responsive. Distinct transcription factors (TFs) regulate constitutive versus stimulus-responsive genes. Accordingly, stimulus-responsive TFs were refractory to CDK7 inhibition whereas constitutively active "core" TFs were repressed. Core TFs (n = 78) are predominantly promoter associated and control cell cycle and proliferative gene expression programs across cell types. Mechanistically, rapid suppression of core TF function can occur through CDK7-dependent phosphorylation changes in core TFs and RB1. Moreover, CDK7 inhibition depleted core TF protein levels within hours, consistent with durable target gene suppression. Thus, a major but unappreciated biological function for CDK7 is regulation of a TF cohort that drives proliferation, revealing an apparent universal mechanism by which CDK7 coordinates RNAPII transcription with cell cycle CDK regulation.


  • Organizational Affiliation
    • Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CDK-activating kinase assembly factor MAT1A [auth H]93Homo sapiensMutation(s): 0 
Gene Names: MNAT1CAP35MAT1RNF66
UniProt & NIH Common Fund Data Resources
Find proteins for P51948 (Homo sapiens)
Explore P51948 
Go to UniProtKB:  P51948
PHAROS:  P51948
GTEx:  ENSG00000020426 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51948
Sequence Annotations
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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
UniProt & NIH Common Fund Data Resources
Find proteins for P51946 (Homo sapiens)
Explore P51946 
Go to UniProtKB:  P51946
PHAROS:  P51946
GTEx:  ENSG00000134480 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51946
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase 7C [auth J]349Homo sapiensMutation(s): 0 
Gene Names: CDK7CAKCAK1CDKN7MO15STK1
EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P50613 (Homo sapiens)
Explore P50613 
Go to UniProtKB:  P50613
PHAROS:  P50613
GTEx:  ENSG00000134058 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50613
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YNK (Subject of Investigation/LOI)
Query on YNK

Download Ideal Coordinates CCD File 
D [auth J]7-dimethylphosphoryl-3-[2-[[(3~{S})-6,6-dimethylpiperidin-3-yl]amino]-5-(trifluoromethyl)pyrimidin-4-yl]-1~{H}-indole-6-carbonitrile
C23 H26 F3 N6 O P
JDJOUBVVSQDIRC-AWEZNQCLSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1
RECONSTRUCTIONRELION4.0 beta

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-25
    Type: Initial release
  • Version 1.1: 2025-07-09
    Changes: Data collection, Database references