4F2J

Crystal structure of ZNF217 bound to DNA, P6522 crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.253 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

New insights into DNA recognition by zinc fingers revealed by structural analysis of the oncoprotein ZNF217

Vandevenne, M.S.Jacques, D.A.Artuz, C.Nguyen, C.D.Kwan, A.H.Segal, D.J.Matthews, J.M.Crossley, M.Guss, J.M.Mackay, J.P.

(2013) J Biol Chem 288: 10616-10627

  • DOI: 10.1074/jbc.M112.441451
  • Primary Citation of Related Structures:  
    4F2J, 4IS1

  • PubMed Abstract: 
  • Classical zinc fingers (ZFs) are one of the most abundant and best characterized DNA-binding domains. Typically, tandem arrays of three or more ZFs bind DNA target sequences with high affinity and specificity, and the mode of DNA recognition is sufficiently well understood that tailor-made ZF-based DNA-binding proteins can be engineered ...

    Classical zinc fingers (ZFs) are one of the most abundant and best characterized DNA-binding domains. Typically, tandem arrays of three or more ZFs bind DNA target sequences with high affinity and specificity, and the mode of DNA recognition is sufficiently well understood that tailor-made ZF-based DNA-binding proteins can be engineered. We have shown previously that a two-zinc finger unit found in the transcriptional coregulator ZNF217 recognizes DNA but with an affinity and specificity that is lower than other ZF arrays. To investigate the basis for these differences, we determined the structure of a ZNF217-DNA complex. We show that although the overall position of the ZFs on the DNA closely resembles that observed for other ZFs, the side-chain interaction pattern differs substantially from the canonical model. The structure also reveals the presence of two methyl-π interactions, each featuring a tyrosine contacting a thymine methyl group. To our knowledge, interactions of this type have not previously been described in classical ZF-DNA complexes. Finally, we investigated the sequence specificity of this two-ZF unit and discuss how ZNF217 might discriminate its target DNA sites in the cell.


    Organizational Affiliation

    School of Molecular Bioscience, University of Sydney, New South Wales, 2006 Australia.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Zinc finger protein 217B [auth C]57Homo sapiensMutation(s): 0 
Gene Names: ZNF217ZABC1
UniProt & NIH Common Fund Data Resources
Find proteins for O75362 (Homo sapiens)
Explore O75362 
Go to UniProtKB:  O75362
PHAROS:  O75362
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*TP*TP*TP*GP*CP*AP*GP*AP*AP*TP*CP*GP*AP*TP*TP*CP*TP*GP*CP*A)-3'A20N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    C, D [auth C]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.64 Å
    • R-Value Free: 0.264 
    • R-Value Work: 0.252 
    • R-Value Observed: 0.253 
    • Space Group: P 65 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 56.928α = 90
    b = 56.928β = 90
    c = 242.542γ = 120
    Software Package:
    Software NamePurpose
    DENZOdata reduction
    SCALEPACKdata scaling
    SOLVEphasing
    RESOLVEphasing
    REFMACrefinement
    PDB_EXTRACTdata extraction
    MAR345dtbdata collection

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2013-02-27
      Type: Initial release
    • Version 1.1: 2013-09-04
      Changes: Database references