4H62

Structure of the Saccharomyces cerevisiae Mediator subcomplex Med17C/Med11C/Med22C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the Mediator head module.

Lariviere, L.Plaschka, C.Seizl, M.Wenzeck, L.Kurth, F.Cramer, P.

(2012) Nature 492: 448-451

  • DOI: 10.1038/nature11670
  • Primary Citation of Related Structures:  
    4H62, 4H63, 4H61

  • PubMed Abstract: 
  • Gene transcription by RNA polymerase (Pol) II requires the coactivator complex Mediator. Mediator connects transcriptional regulators and Pol II, and is linked to human disease. Mediator from the yeast Saccharomyces cerevisiae has a molecular mass of 1.4 megadaltons and comprises 25 subunits that form the head, middle, tail and kinase modules ...

    Gene transcription by RNA polymerase (Pol) II requires the coactivator complex Mediator. Mediator connects transcriptional regulators and Pol II, and is linked to human disease. Mediator from the yeast Saccharomyces cerevisiae has a molecular mass of 1.4 megadaltons and comprises 25 subunits that form the head, middle, tail and kinase modules. The head module constitutes one-half of the essential Mediator core, and comprises the conserved subunits Med6, Med8, Med11, Med17, Med18, Med20 and Med22. Recent X-ray analysis of the S. cerevisiae head module at 4.3 Å resolution led to a partial architectural model with three submodules called neck, fixed jaw and moveable jaw. Here we determine de novo the crystal structure of the head module from the fission yeast Schizosaccharomyces pombe at 3.4 Å resolution. Structure solution was enabled by new structures of Med6 and the fixed jaw, and previous structures of the moveable jaw and part of the neck, and required deletion of Med20. The S. pombe head module resembles the head of a crocodile with eight distinct elements, of which at least four are mobile. The fixed jaw comprises tooth and nose domains, whereas the neck submodule contains a helical spine and one limb, with shoulder, arm and finger elements. The arm and the essential shoulder contact other parts of Mediator. The jaws and a central joint are implicated in interactions with Pol II and its carboxy-terminal domain, and the joint is required for transcription in vitro. The S. pombe head module structure leads to a revised model of the S. cerevisiae module, reveals a high conservation and flexibility, explains known mutations, and provides the basis for unravelling a central mechanism of gene regulation.


    Organizational Affiliation

    Gene Center and Department of Biochemistry, Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, 81377 Munich, Germany. larivier@genzentrum.lmu.de



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 11A [auth K]40Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MED11YM9718.11CYMR112C
Find proteins for Q99278 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q99278 
Go to UniProtKB:  Q99278
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 22B [auth V]31Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MED22SRB6YBR1721YBR253W
Find proteins for P32570 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32570 
Go to UniProtKB:  P32570
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 17C [auth Q]312Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MED17SRB4YER022W
Find proteins for P32569 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32569 
Go to UniProtKB:  P32569
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES

Download Ideal Coordinates CCD File 
D [auth Q]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A [auth K]L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 261.23α = 90
b = 261.23β = 90
c = 47.74γ = 120
Software Package:
Software NamePurpose
RemDAqdata collection
SHELXCDphasing
SHELXEmodel building
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-31
    Type: Initial release
  • Version 1.1: 2012-12-05
    Changes: Database references
  • Version 1.2: 2013-01-02
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description