5XFP

Binary complex of PHF1 and a double stranded DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

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
PHD finger protein 1ABE336Homo sapiensMutation(s): 0 
Gene Names: PHF1PCL1
Find proteins for O43189 (Homo sapiens)
Explore O43189 
Go to UniProtKB:  O43189
NIH Common Fund Data Resources
PHAROS  O43189
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*GP*GP*CP*GP*GP*CP*CP*GP*CP*CP*CP*T)-3')C, D13synthetic construct
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    TRS
    Query on TRS

    Download CCD File 
    A, B
    2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
    C4 H12 N O3
    LENZDBCJOHFCAS-UHFFFAOYSA-O
     Ligand Interaction
    ZN
    Query on ZN

    Download CCD File 
    A, B, E
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.30 Å
    • R-Value Free: 0.244 
    • R-Value Work: 0.209 
    • R-Value Observed: 0.211 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 109.601α = 90
    b = 110.291β = 90
    c = 118.853γ = 90
    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