8TQC

Structure of the human CDK8 kinase module


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structural basis of the human transcriptional Mediator regulated by its dissociable kinase module.

Chao, T.C.Chen, S.F.Kim, H.J.Tang, H.C.Tseng, H.C.Xu, A.Palao 3rd, L.Khadka, S.Li, T.Huang, M.F.Lee, D.F.Murakami, K.Boyer, T.G.Tsai, K.L.

(2024) Mol Cell 

  • DOI: https://doi.org/10.1016/j.molcel.2024.09.001
  • Primary Citation of Related Structures:  
    8TQ2, 8TQC, 8TQW, 8TRH

  • PubMed Abstract: 

    The eukaryotic transcriptional Mediator comprises a large core (cMED) and a dissociable CDK8 kinase module (CKM). cMED recruits RNA polymerase II (RNA Pol II) and promotes pre-initiation complex formation in a manner repressed by the CKM through mechanisms presently unknown. Herein, we report cryoelectron microscopy structures of the complete human Mediator and its CKM. The CKM binds to multiple regions on cMED through both MED12 and MED13, including a large intrinsically disordered region (IDR) in the latter. MED12 and MED13 together anchor the CKM to the cMED hook, positioning CDK8 downstream and proximal to the transcription start site. Notably, the MED13 IDR obstructs the recruitment of RNA Pol II/MED26 onto cMED by direct occlusion of their respective binding sites, leading to functional repression of cMED-dependent transcription. Combined with biochemical and functional analyses, these structures provide a conserved mechanistic framework to explain the basis for CKM-mediated repression of cMED function.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 12A [auth C]2,177Homo sapiensMutation(s): 0 
Gene Names: MED12
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Find proteins for Q93074 (Homo sapiens)
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PHAROS:  Q93074
GTEx:  ENSG00000184634 
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UniProt GroupQ93074
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 13B [auth D]2,174Homo sapiensMutation(s): 0 
Gene Names: MED13ARC250KIAA0593THRAP1TRAP240
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Find proteins for Q9UHV7 (Homo sapiens)
Explore Q9UHV7 
Go to UniProtKB:  Q9UHV7
PHAROS:  Q9UHV7
GTEx:  ENSG00000108510 
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UniProt GroupQ9UHV7
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase 8C [auth A]464Homo sapiensMutation(s): 0 
Gene Names: CDK8
EC: 2.7.11.23 (UniProt), 2.7.11.22 (UniProt)
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Find proteins for P49336 (Homo sapiens)
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PHAROS:  P49336
GTEx:  ENSG00000132964 
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UniProt GroupP49336
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-CD [auth B]283Homo sapiensMutation(s): 0 
Gene Names: CCNC
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Find proteins for P24863 (Homo sapiens)
Explore P24863 
Go to UniProtKB:  P24863
PHAROS:  P24863
GTEx:  ENSG00000112237 
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UniProt GroupP24863
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-09
    Type: Initial release