1YKH

Structure of the mediator MED7/MED21 (Med7/Srb7) subcomplex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.257 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A conserved mediator hinge revealed in the structure of the MED7.MED21 (Med7.Srb7) heterodimer.

Baumli, S.Hoeppner, S.Cramer, P.

(2005) J Biol Chem 280: 18171-18178

  • DOI: 10.1074/jbc.M413466200
  • Primary Citation of Related Structures:  
    1YKE, 1YKH

  • PubMed Abstract: 
  • The Mediator of transcriptional regulation is the central coactivator that enables a response of RNA polymerase II (Pol II) to activators and repressors. We present the 3.0-A crystal structure of a highly conserved part of the Mediator, the MED7.MED21 (Med7 ...

    The Mediator of transcriptional regulation is the central coactivator that enables a response of RNA polymerase II (Pol II) to activators and repressors. We present the 3.0-A crystal structure of a highly conserved part of the Mediator, the MED7.MED21 (Med7.Srb7) heterodimer. The structure is very extended, spanning one-third of the Mediator length and almost the diameter of Pol II. It shows a four-helix bundle domain and a coiled-coil protrusion connected by a flexible hinge. Four putative protein binding sites on the surface allow for assembly of the Mediator middle module and for binding of the conserved subunit MED6, which is shown to bridge to the Mediator head module. A flexible MED6 bridge and the MED7.MED21 hinge could account for changes in overall Mediator structure upon binding to Pol II or activators. Our results support the idea that transcription regulation involves conformational changes within the general machinery.


    Organizational Affiliation

    Gene Center, University of Munich (Ludwig-Maximilians-Universität), Department of Chemistry and Biochemistry, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase II mediator complex protein MED7A108Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q08278 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08278 
Go to UniProtKB:  Q08278
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase II holoenzyme component SRB7B132Saccharomyces cerevisiaeMutation(s): 3 
UniProt
Find proteins for P47822 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P47822 
Go to UniProtKB:  P47822
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.257 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.69α = 90
b = 85.69β = 90
c = 182.95γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-02-22
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-10
    Changes: Database references