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: 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) ...

    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; Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA. Electronic address: rafael.casellas@nih.gov.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 1A382Mus musculusMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 4B100Mus musculusMutation(s): 0 
Gene Names: Med4Vdrip
UniProt
Find proteins for Q9CQA5 (Mus musculus)
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UniProt GroupQ9CQA5
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 6C246Mus musculusMutation(s): 0 
Gene Names: Med6
UniProt
Find proteins for Q921D4 (Mus musculus)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 7D157Mus musculusMutation(s): 0 
Gene Names: Med7Crsp9
UniProt
Find proteins for Q9CZB6 (Mus musculus)
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UniProt GroupQ9CZB6
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 8E180Mus musculusMutation(s): 0 
Gene Names: Med8MNCb-2386
UniProt
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UniProt GroupQ9D7W5
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 9F76Mus musculusMutation(s): 0 
Gene Names: Med9Med25
UniProt
Find proteins for Q8VCS6 (Mus musculus)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 10G155Mus musculusMutation(s): 0 
Gene Names: Med10
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IMPC:  MGI:106331
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UniProt GroupQ9CXU0
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 11H108Mus musculusMutation(s): 0 
Gene Names: Med11
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IMPC:  MGI:1913422
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UniProt GroupQ9D8C6
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 14I1,548Mus musculusMutation(s): 0 
Gene Names: Med14
UniProt
Find proteins for A2ABV5 (Mus musculus)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 15J167Mus musculusMutation(s): 0 
Gene Names: Med15Pcqap
UniProt
Find proteins for Q924H2 (Mus musculus)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 16K828Mus musculusMutation(s): 0 
Gene Names: Med16Thrap5
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IMPC:  MGI:2158394
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UniProt GroupQ6PGF3
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 17L631Mus musculusMutation(s): 0 
Gene Names: Med17Crsp6Trap80
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IMPC:  MGI:2182585
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UniProt GroupQ8VCD5
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 18M187Mus musculusMutation(s): 0 
Gene Names: Med18
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IMPC:  MGI:1914469
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UniProt GroupQ9CZ82
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Entity ID: 14
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Mediator of RNA polymerase II transcription subunit 19N243Mus musculusMutation(s): 0 
Gene Names: Med19
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IMPC:  MGI:1914234
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 20O198Mus musculusMutation(s): 0 
Gene Names: Med20Trfp
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IMPC:  MGI:1929648
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 21P126Mus musculusMutation(s): 0 
Gene Names: Med21Srb7Surb7
UniProt
Find proteins for Q9CQ39 (Mus musculus)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 22Q131Mus musculusMutation(s): 0 
Gene Names: Med22Surf5
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IMPC:  MGI:98446
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UniProt GroupQ62276
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 23R1,367Mus musculusMutation(s): 0 
Gene Names: Med23Crsp3Kiaa1216Sur2
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IMPC:  MGI:1917458
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UniProt GroupQ80YQ2
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 24S982Mus musculusMutation(s): 0 
Gene Names: Med24D11Ertd307eThrap4Trap100
UniProt
Find proteins for Q99K74 (Mus musculus)
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Entity ID: 20
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Mediator of RNA polymerase II transcription subunit 25T202Mus musculusMutation(s): 0 
Gene Names: Med25
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IMPC:  MGI:1922863
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 27U [auth V]297Mus musculusMutation(s): 0 
Gene Names: Med27Crsp8
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IMPC:  MGI:1916225
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 28V [auth W]118Mus musculusMutation(s): 0 
Gene Names: Med28Fksg20
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IMPC:  MGI:1914249
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 29W [auth X]134Mus musculusMutation(s): 0 
Gene Names: Med29Ixl
UniProt
Find proteins for Q9DB91 (Mus musculus)
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 30X [auth Y]152Mus musculusMutation(s): 0 
Gene Names: Med30Thrap6Trap25
UniProt
Find proteins for Q9CQI9 (Mus musculus)
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 31Y [auth Z]93Mus musculusMutation(s): 0 
Gene Names: Med31Soh1
UniProt
Find proteins for Q9CXU1 (Mus musculus)
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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