6W1S

Atomic model of the mammalian Mediator complex

  • Classification: GENE REGULATION
  • Organism(s): Mus musculus
  • Mutation(s): No 

  • Deposited: 2020-03-04 Released: 2021-03-10 
  • Deposition Author(s): Zhao, H., Young, N., Asturias, F.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.02 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

A Pliable Mediator Acts as a Functional Rather Than an Architectural Bridge between Promoters and Enhancers.

El Khattabi, L.Zhao, H.Kalchschmidt, J.Young, N.Jung, S.Van Blerkom, P.Kieffer-Kwon, P.Kieffer-Kwon, K.R.Park, S.Wang, X.Krebs, J.Tripathi, S.Sakabe, N.Sobreira, D.R.Huang, S.C.Rao, S.S.P.Pruett, N.Chauss, D.Sadler, E.Lopez, A.Nobrega, M.A.Aiden, E.L.Asturias, F.J.Casellas, R.

(2019) Cell 178: 1145-1158.e20

  • DOI: https://doi.org/10.1016/j.cell.2019.07.011
  • Primary Citation of Related Structures:  
    6W1S

  • PubMed Abstract: 

    While Mediator plays a key role in eukaryotic transcription, little is known about its mechanism of action. This study combines CRISPR-Cas9 genetic screens, degron assays, Hi-C, and cryoelectron microscopy (cryo-EM) to dissect the function and structure of mammalian Mediator (mMED). Deletion analyses in B, T, and embryonic stem cells (ESC) identified a core of essential subunits required for Pol II recruitment genome-wide. Conversely, loss of non-essential subunits mostly affects promoters linked to multiple enhancers. Contrary to current models, however, mMED and Pol II are dispensable to physically tether regulatory DNA, a topological activity requiring architectural proteins. Cryo-EM analysis revealed a conserved core, with non-essential subunits increasing structural complexity of the tail module, a primary transcription factor target. Changes in tail structure markedly increase Pol II and kinase module interactions. We propose that Mediator's structural pliability enables it to integrate and transmit regulatory signals and act as a functional, rather than an architectural bridge, between promoters and enhancers.


  • Organizational Affiliation

    Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 1382Mus musculusMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 4100Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9CQA5 (Mus musculus)
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UniProt GroupQ9CQA5
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 6246Mus musculusMutation(s): 0 
UniProt
Find proteins for Q921D4 (Mus musculus)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 7157Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9CZB6 (Mus musculus)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 8180Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9D7W5 (Mus musculus)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 976Mus musculusMutation(s): 0 
UniProt
Find proteins for Q8VCS6 (Mus musculus)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 10155Mus musculusMutation(s): 0 
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IMPC:  MGI:106331
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UniProt GroupQ9CXU0
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 11108Mus musculusMutation(s): 0 
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Find proteins for Q9D8C6 (Mus musculus)
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IMPC:  MGI:1913422
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UniProt GroupQ9D8C6
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 141,548Mus musculusMutation(s): 0 
UniProt
Find proteins for A2ABV5 (Mus musculus)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 15167Mus musculusMutation(s): 0 
UniProt
Find proteins for Q924H2 (Mus musculus)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 16828Mus musculusMutation(s): 0 
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Find proteins for Q6PGF3 (Mus musculus)
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IMPC:  MGI:2158394
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UniProt GroupQ6PGF3
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 17631Mus musculusMutation(s): 0 
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IMPC:  MGI:2182585
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 18187Mus musculusMutation(s): 0 
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Find proteins for Q9CZ82 (Mus musculus)
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IMPC:  MGI:1914469
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UniProt GroupQ9CZ82
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 19243Mus musculusMutation(s): 0 
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IMPC:  MGI:1914234
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 20198Mus musculusMutation(s): 0 
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IMPC:  MGI:1929648
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 21126Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9CQ39 (Mus musculus)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 22131Mus musculusMutation(s): 0 
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Find proteins for Q62276 (Mus musculus)
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IMPC:  MGI:98446
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 231,367Mus musculusMutation(s): 0 
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Find proteins for Q80YQ2 (Mus musculus)
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IMPC:  MGI:1917458
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UniProt GroupQ80YQ2
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 24982Mus musculusMutation(s): 0 
UniProt
Find proteins for Q99K74 (Mus musculus)
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UniProt GroupQ99K74
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 25202Mus musculusMutation(s): 0 
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Find proteins for Q8VCB2 (Mus musculus)
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IMPC:  MGI:1922863
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UniProt GroupQ8VCB2
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 27U [auth V]297Mus musculusMutation(s): 0 
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IMPC:  MGI:1916225
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UniProt GroupQ9DB40
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 28V [auth W]118Mus musculusMutation(s): 0 
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IMPC:  MGI:1914249
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UniProt GroupQ920D3
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 29W [auth X]134Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9DB91 (Mus musculus)
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UniProt GroupQ9DB91
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 30X [auth Y]152Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9CQI9 (Mus musculus)
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UniProt GroupQ9CQI9
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 31Y [auth Z]93Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9CXU1 (Mus musculus)
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UniProt GroupQ9CXU1
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.02 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 StatesR01-67167
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-10
    Type: Initial release