6H02

Crystal structure of human Mediator subunit MED23


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


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Literature

Crystal structure of human Mediator subunit MED23.

Monte, D.Clantin, B.Dewitte, F.Lens, Z.Rucktooa, P.Pardon, E.Steyaert, J.Verger, A.Villeret, V.

(2018) Nat Commun 9: 3389-3389

  • DOI: 10.1038/s41467-018-05967-y
  • Primary Citation of Related Structures:  
    6H02

  • PubMed Abstract: 
  • The Mediator complex transduces regulatory information from enhancers to promoters and performs essential roles in the initiation of transcription in eukaryotes. Human Mediator comprises 26 subunits forming three modules termed Head, Middle and Tail. Here we present the 2 ...

    The Mediator complex transduces regulatory information from enhancers to promoters and performs essential roles in the initiation of transcription in eukaryotes. Human Mediator comprises 26 subunits forming three modules termed Head, Middle and Tail. Here we present the 2.8 Å crystal structure of MED23, the largest subunit from the human Tail module. The structure identifies 25 HEAT repeats-like motifs organized into 5 α-solenoids. MED23 adopts an arch-shaped conformation, with an N-terminal domain (Nter) protruding from a large core region. In the core four solenoids, motifs wrap on themselves, creating triangular-shaped structural motifs on both faces of the arch, with extended grooves propagating through the interfaces between the solenoid motifs. MED23 is known to interact with several specific transcription activators and is involved in splicing, elongation, and post-transcriptional events. The structure rationalizes previous biochemical observations and paves the way for improved understanding of the cross-talk between Mediator and transcriptional activators.


    Related Citations: 
    • Transcription control by E1A and MAP kinase pathway via Sur2 mediator subunit.
      Stevens, J.L., Cantin, G.T., Wang, G., Shevchenko, A., Shevchenko, A., Berk, A.J.
      (2002) Science 296: 755
    • Mediator requirement for both recruitment and postrecruitment steps in transcription initiation.
      Wang, G., Balamotis, M.A., Stevens, J.L., Yamaguchi, Y., Handa, H., Berk, A.J.
      (2005) Mol Cell 17: 683
    • Mediator complex regulates alternative mRNA processing via the MED23 subunit.
      Huang, Y., Li, W., Yao, X., Lin, Q.J., Yin, J.W., Liang, Y., Heiner, M., Tian, B., Hui, J., Wang, G.
      (2012) Mol Cell 45: 459

    Organizational Affiliation

    CNRS, UMR 8576-UGSF- Unité de Glycobiologie Structurale et Fonctionnelle, Univ. Lille, 59000, Lille, France. vincent.villeret@univ-lille.fr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 23A1,382Homo sapiensMutation(s): 0 
Gene Names: MED23ARC130CRSP3DRIP130KIAA1216SUR2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULK4 (Homo sapiens)
Explore Q9ULK4 
Go to UniProtKB:  Q9ULK4
PHAROS:  Q9ULK4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ULK4
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
LAMA nanobody NB106B134Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.65α = 90
b = 137.18β = 110.98
c = 90.11γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceDS0401
European UnionFranceINSTRUCT PID1235

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2018-09-05
    Changes: Data collection, Database references, Source and taxonomy