3R84

Structure of the Mediator head subcomplex Med11/22


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Mediator head subcomplex Med11/22 contains a common helix bundle building block with a specific function in transcription initiation complex stabilization.

Seizl, M.Lariviere, L.Pfaffeneder, T.Wenzeck, L.Cramer, P.

(2011) Nucleic Acids Res 39: 6291-6304

  • DOI: https://doi.org/10.1093/nar/gkr229
  • Primary Citation of Related Structures:  
    3R84

  • PubMed Abstract: 

    Mediator is a multiprotein co-activator of RNA polymerase (Pol) II transcription. Mediator contains a conserved core that comprises the 'head' and 'middle' modules. We present here a structure-function analysis of the essential Med11/22 heterodimer, a part of the head module. Med11/22 forms a conserved four-helix bundle domain with C-terminal extensions, which bind the central head subunit Med17. A highly conserved patch on the bundle surface is required for stable transcription pre-initiation complex formation on a Pol II promoter in vitro and in vivo and may recruit the general transcription factor TFIIH. The bundle domain fold is also present in the Mediator middle module subcomplex Med7/21 and is predicted in the Mediator heterodimers Med2/3, Med4/9, Med10/14 and Med28/30. The bundle domain thus represents a common building block that has been multiplied and functionally diversified during Mediator evolution in eukaryotes.


  • 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 11
A, C, E, G, I
A, C, E, G, I, K, M, O, Q, S, U, W
86Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MED11YM9718.11CYMR112C
UniProt
Find proteins for Q99278 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q99278 
Go to UniProtKB:  Q99278
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99278
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 22
B, D, F, H, J
B, D, F, H, J, L, N, P, R, T, V, X
92Saccharomyces cerevisiaeMutation(s): 1 
Gene Names: MED22SRB6YBR1721YBR253W
UniProt
Find proteins for P32570 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32570 
Go to UniProtKB:  P32570
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32570
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, C, E, G, I
A, C, E, G, I, K, M, O, Q, S, U, W
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.49α = 90
b = 173.79β = 90
c = 101.61γ = 90
Software Package:
Software NamePurpose
SOLVEphasing
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: 2011-04-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-08-24
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Refinement description