5N9J

Core Mediator of transcriptional regulation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


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

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 14
A
591Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: med14 (pmc1)
Find proteins for Q9P7Y4 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q9P7Y4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 10
B
144Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: med10 (nut2)
Find proteins for P87310 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  P87310
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 19
C
138Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: med19 (rox3)
Find proteins for Q9Y7N2 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q9Y7N2
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 21
D
138Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: med21 (srb7)
Find proteins for O94376 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O94376
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 7
E
376Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: med7
Find proteins for O60104 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O60104
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Mediator Complex Subunit 9
F
121Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Find proteins for O13964 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O13964
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 4
G
239Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: med4 (pmc4)
Find proteins for Q9Y821 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q9Y821
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 31
R
139Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: med31 (sep10)
Find proteins for Q9USH1 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q9USH1
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 6
S
216Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: med6 (pmc5)
Find proteins for Q9US45 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q9US45
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 8
U
200Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: med8 (sep15)
Find proteins for O94646 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O94646
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 11
V
112Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: med11
Find proteins for Q9P6Q0 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q9P6Q0
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 17
W
545Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: med17 (srb4)
Find proteins for P87306 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  P87306
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 18
X
210Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: med18 (pmc6, sep11)
Find proteins for O14198 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O14198
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 20
Y
193Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: med20
Find proteins for Q10317 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q10317
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 22
Z
136Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: med22 (srb6)
Find proteins for O14010 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O14010
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.233 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 145.864α = 90.00
b = 211.768β = 90.00
c = 267.028γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

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