5N9J

Core Mediator of transcriptional regulation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 

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This is version 1.1 of the entry. See complete history


Literature

Core Mediator structure at 3.4 Angstrom extends model of transcription initiation complex.

Nozawa, K.Schneider, T.R.Cramer, P.

(2017) Nature 545: 248-251

  • DOI: 10.1038/nature22328
  • Primary Citation of Related Structures:  
    5N9J

  • PubMed Abstract: 
  • Mediator is a multiprotein co-activator that binds the transcription pre-initiation complex (PIC) and regulates RNA polymerase (Pol) II. The Mediator head and middle modules form the essential core Mediator (cMed), whereas the tail and kinase modules play regulatory roles ...

    Mediator is a multiprotein co-activator that binds the transcription pre-initiation complex (PIC) and regulates RNA polymerase (Pol) II. The Mediator head and middle modules form the essential core Mediator (cMed), whereas the tail and kinase modules play regulatory roles. The architecture of Mediator and its position on the PIC are known, but atomic details are limited to Mediator subcomplexes. Here we report the crystal structure of the 15-subunit cMed from Schizosaccharomyces pombe at 3.4 Å resolution. The structure shows an unaltered head module, and reveals the intricate middle module, which we show is globally required for transcription. Sites of known Mediator mutations cluster at the interface between the head and middle modules, and in terminal regions of the head subunits Med6 (ref. 16) and Med17 (ref. 17) that tether the middle module. The structure led to a model for Saccharomyces cerevisiae cMed that could be combined with the 3.6 Å cryo-electron microscopy structure of the core PIC (cPIC). The resulting atomic model of the cPIC-cMed complex informs on interactions of the submodules forming the middle module, called beam, knob, plank, connector, and hook. The hook is flexibly linked to Mediator by a conserved hinge and contacts the transcription initiation factor IIH (TFIIH) kinase that phosphorylates the carboxy (C)-terminal domain (CTD) of Pol II and was recently positioned on the PIC. The hook also contains residues that crosslink to the CTD and reside in a previously described cradle. These results provide a framework for understanding Mediator function, including its role in stimulating CTD phosphorylation by TFIIH.


    Organizational Affiliation

    Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 14A591Schizosaccharomyces pombeMutation(s): 0 
Gene Names: med14pmc1SPBC1A4.10cSPBP23A10.01c
UniProt
Find proteins for Q9P7Y4 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 10B144Schizosaccharomyces pombeMutation(s): 0 
Gene Names: med10nut2SPBC31F10.09c
UniProt
Find proteins for P87310 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 19C138Schizosaccharomyces pombeMutation(s): 0 
Gene Names: med19rox3SPCC1450.05c
UniProt
Find proteins for Q9Y7N2 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 21D138Schizosaccharomyces pombeMutation(s): 0 
Gene Names: med21srb7SPBC1604.10
UniProt
Find proteins for O94376 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 7E376Schizosaccharomyces pombeMutation(s): 0 
Gene Names: med7SPBC14F5.08
UniProt
Find proteins for O60104 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator Complex Subunit 9F121Schizosaccharomyces pombeMutation(s): 0 
Gene Names: SPAC24C9.04
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 4G239Schizosaccharomyces pombeMutation(s): 0 
Gene Names: med4pmc4SPBC1105.06
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 31H [auth R]139Schizosaccharomyces pombeMutation(s): 0 
Gene Names: med31sep10SPCP31B10.03c
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 6I [auth S]216Schizosaccharomyces pombeMutation(s): 0 
Gene Names: med6pmc5SPAC1002.15c
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 8J [auth U]200Schizosaccharomyces pombeMutation(s): 0 
Gene Names: med8sep15SPBC21.04
UniProt
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 11K [auth V]112Schizosaccharomyces pombeMutation(s): 0 
Gene Names: med11SPAC644.10
UniProt
Find proteins for Q9P6Q0 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 17L [auth W]545Schizosaccharomyces pombeMutation(s): 0 
Gene Names: med17srb4SPBC31F10.04c
UniProt
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 18M [auth X]210Schizosaccharomyces pombeMutation(s): 0 
Gene Names: med18pmc6sep11SPAC5D6.05
UniProt
Find proteins for O14198 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 20N [auth Y]193Schizosaccharomyces pombeMutation(s): 0 
Gene Names: med20SPAC17G8.05
UniProt
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 22O [auth Z]136Schizosaccharomyces pombeMutation(s): 0 
Gene Names: med22srb6SPAC29A4.07
UniProt
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.864α = 90
b = 211.768β = 90
c = 267.028γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
SOLVEphasing
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB860, SPP1935
European Research Council Advanced Investigator Grant TRANSREGULONGermany693023
Volkswagen Foundation.Germany--
Human Frontier Science ProgramFranceLT000621/2012-L
Japan Society for the Promotion of ScienceJapan--
Uehara Memorial FoundationJapan--

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-17
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Author supporting evidence, Data collection