5U0S

Cryo-EM structure of the Mediator-RNAPII complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Mediator structure and rearrangements required for holoenzyme formation.

Tsai, K.L.Yu, X.Gopalan, S.Chao, T.C.Zhang, Y.Florens, L.Washburn, M.P.Murakami, K.Conaway, R.C.Conaway, J.W.Asturias, F.J.

(2017) Nature 544: 196-201

  • DOI: https://doi.org/10.1038/nature21393
  • Primary Citation of Related Structures:  
    5U0P, 5U0S

  • PubMed Abstract: 

    The conserved Mediator co-activator complex has an essential role in the regulation of RNA polymerase II transcription in all eukaryotes. Understanding the structure and interactions of Mediator is crucial for determining how the complex influences transcription initiation and conveys regulatory information to the basal transcription machinery. Here we present a 4.4 Å resolution cryo-electron microscopy map of Schizosaccharomyces pombe Mediator in which conserved Mediator subunits are individually resolved. The essential Med14 subunit works as a central backbone that connects the Mediator head, middle and tail modules. Comparison with a 7.8 Å resolution cryo-electron microscopy map of a Mediator-RNA polymerase II holoenzyme reveals that changes in the structure of Med14 facilitate a large-scale Mediator rearrangement that is essential for holoenzyme formation. Our study suggests that access to different conformations and crosstalk between structural elements are essential for the Mediator regulation mechanism, and could explain the capacity of the complex to integrate multiple regulatory signals.


  • Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla California, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator complex subunit 6A [auth F]216Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q9US45 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator complex subunit 8B [auth H]200Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O94646 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator complex subunit 17C [auth Q]545Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P87306 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator complex subunit 18D [auth R]207Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O14198 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator complex subunit 20E [auth T]193Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q10317 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator complex subunit 11F [auth K]116Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q9P6Q0 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator complex subunit 22G [auth V]136Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O14010 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator complex subunit 14H [auth N]931Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q9P7Y4 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator complex subunit 4I [auth D]239Schizosaccharomyces pombeMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator complex subunit 7J [auth G]376Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator complex subunit 21K [auth U]138Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O94376 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator complex subunit 31L [auth 3]139Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q9USH1 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator complex subunit 27M [auth 2]273Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q10477 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator complex subunit 9N [auth I]121Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator complex subunit 19O [auth S]139Schizosaccharomyces pombeMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator complex subunit 10P [auth J]132Schizosaccharomyces pombeMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit Rpb1Q [auth a]1,752Schizosaccharomyces pombeMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P36594 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit Rpb2R [auth b]1,210Schizosaccharomyces pombeMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q02061 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit Rpb3S [auth c]297Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P37382 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit Rpb4T [auth d]135Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O74825 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit Rpb5U [auth e]210Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q09191 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit Rpb6V [auth f]142Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P36595 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit Rpb7W [auth g]172Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O14459 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit Rpb8X [auth h]125Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q92399 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit Rpb9Y [auth i]113Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O74635 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit Rpb10Z [auth j]71Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O13877 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit Rpb11AA [auth k]123Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit Rpb12BA [auth l]63Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P48011 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4

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 StatesGM67167
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM41628

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-08
    Type: Initial release
  • Version 1.1: 2017-03-15
    Changes: Database references
  • Version 1.2: 2017-04-19
    Changes: Database references
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2018-07-18
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2020-01-01
    Changes: Author supporting evidence