4H63

Structure of the Schizosaccharomyces pombe Mediator head module


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.233 

wwPDB Validation   3D Report Full Report


This is version 1.2 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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 6A [auth F]183Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: med6pmc5SPAC1002.15c
Find proteins for Q9US45 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 8B [auth H]200Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: med8sep15SPBC21.04
Find proteins for O94646 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 11C [auth K]112Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: med11SPAC644.10
Find proteins for Q9P6Q0 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 17D [auth Q]469Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: med17SPBC31F10.04csrb4
Find proteins for P87306 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 18E [auth R]209Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: med18pmc6sep11SPAC5D6.05
Find proteins for O14198 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 22F [auth V]135Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: med22SPAC29A4.07srb6
Find proteins for O14010 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.233 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.6α = 90
b = 145.6β = 90
c = 241.62γ = 120
Software Package:
Software NamePurpose
RemDAqdata collection
SHARPphasing
BUSTERrefinement
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