5XFR

Ternary complex of MTF2, DNA and histone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Polycomb-like proteins link the PRC2 complex to CpG islands

Li, H.Liefke, R.Jiang, J.Kurland, J.V.Tian, W.Deng, P.Zhang, W.He, Q.Patel, D.J.Bulyk, M.L.Shi, Y.Wang, Z.

(2017) Nature 549: 287-291

  • DOI: 10.1038/nature23881
  • Primary Citation of Related Structures:  
    5XFN, 5XFP, 5XFO, 5XFR, 5XFQ

  • PubMed Abstract: 
  • The Polycomb repressive complex 2 (PRC2) mainly mediates transcriptional repression and has essential roles in various biological processes including the maintenance of cell identity and proper differentiation. Polycomb-like (PCL) proteins, such as P ...

    The Polycomb repressive complex 2 (PRC2) mainly mediates transcriptional repression and has essential roles in various biological processes including the maintenance of cell identity and proper differentiation. Polycomb-like (PCL) proteins, such as PHF1, MTF2 and PHF19, are PRC2-associated factors that form sub-complexes with PRC2 core components, and have been proposed to modulate the enzymatic activity of PRC2 or the recruitment of PRC2 to specific genomic loci. Mammalian PRC2-binding sites are enriched in CG content, which correlates with CpG islands that display a low level of DNA methylation. However, the mechanism of PRC2 recruitment to CpG islands is not fully understood. Here we solve the crystal structures of the N-terminal domains of PHF1 and MTF2 with bound CpG-containing DNAs in the presence of H3K36me3-containing histone peptides. We show that the extended homologous regions of both proteins fold into a winged-helix structure, which specifically binds to the unmethylated CpG motif but in a completely different manner from the canonical winged-helix DNA recognition motif. We also show that the PCL extended homologous domains are required for efficient recruitment of PRC2 to CpG island-containing promoters in mouse embryonic stem cells. Our research provides the first, to our knowledge, direct evidence to demonstrate that PCL proteins are crucial for PRC2 recruitment to CpG islands, and further clarifies the roles of these proteins in transcriptional regulation in vivo.


    Organizational Affiliation

    Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing 100875, China.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Metal-response element-binding transcription factor 2AB317Homo sapiensMutation(s): 0 
Gene Names: MTF2PCL2
Find proteins for Q9Y483 (Homo sapiens)
Explore Q9Y483 
Go to UniProtKB:  Q9Y483
NIH Common Fund Data Resources
PHAROS  Q9Y483
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Peptide from Histone H3.1CD8Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
NIH Common Fund Data Resources
PHAROS  P68431
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*GP*GP*CP*GP*GP*CP*CP*GP*CP*CP*CP*T)-3')E, F13synthetic construct
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

    Download CCD File 
    A, B
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    Modified Residues  1 Unique
    IDChainsTypeFormula2D DiagramParent
    M3L
    Query on M3L
    C,DL-PEPTIDE LINKINGC9 H21 N2 O2LYS
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.25 Å
    • R-Value Free: 0.231 
    • R-Value Work: 0.203 
    • R-Value Observed: 0.204 
    • Space Group: P 31 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 137.743α = 90
    b = 137.743β = 90
    c = 101.226γ = 120
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    HKL-2000data reduction
    HKL-2000data scaling
    PHENIXphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    • Deposited Date: 2017-04-11 
    • Released Date: 2017-09-13 
    • Deposition Author(s): Wang, Z., Li, H.

    Revision History 

    • Version 1.0: 2017-09-13
      Type: Initial release
    • Version 1.1: 2017-09-27
      Changes: Database references