8TQW

Structure of human transcriptional Mediator complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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 84: 3932-3949.e10

  • 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 27A [auth 0]311Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000160563 
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UniProt GroupQ6P2C8
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 28B [auth 1]178Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000118579 
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UniProt GroupQ9H204
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 29C [auth 2]200Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000063322 
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UniProt GroupQ9NX70
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 30D [auth 3]178Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164758 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 31E [auth 4]131Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108590 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 1F [auth A]1,581Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125686 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown ChainG [auth B]20Homo sapiensMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 4H [auth D]270Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136146 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 6I [auth F]246Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000133997 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 7J [auth G]233Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000155868 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 8K [auth H]268Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000159479 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 9L [auth I]146Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000141026 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 10M [auth J]135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000133398 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 11N [auth K]117Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161920 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 14O [auth N]1,454Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000180182 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 15P [auth O]788Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000099917 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 16Q [auth P]877Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175221 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 17R [auth Q]651Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000042429 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 18S [auth R]208Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130772 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 19T [auth S]244Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000156603 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 20U [auth T]212Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000124641 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 21V [auth U]144Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000152944 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 22W [auth V]200Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000148297 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 23X [auth W]1,368Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112282 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 24Y [auth X]989Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000008838 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase 8Z [auth a]464Homo sapiensMutation(s): 0 
EC: 2.7.11.23 (UniProt), 2.7.11.22 (UniProt)
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GTEx:  ENSG00000132964 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-CAA [auth b]283Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112237 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 12BA [auth c]2,177Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000184634 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 13CA [auth d]2,174Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108510 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.20 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
  • Version 1.1: 2024-11-06
    Changes: Data collection, Database references