4R2E

Wilms Tumor Protein (WT1) zinc fingers in complex with methylated DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence.

Hashimoto, H.Olanrewaju, Y.O.Zheng, Y.Wilson, G.G.Zhang, X.Cheng, X.

(2014) Genes Dev 28: 2304-2313

  • DOI: 10.1101/gad.250746.114
  • Primary Citation of Related Structures:  
    4R2P, 4R2Q, 4R2R, 4R2S, 4R2D, 4R2E, 4R2A, 4R2C

  • PubMed Abstract: 
  • In mammalian DNA, cytosine occurs in several chemical forms, including unmodified cytosine (C), 5-methylcytosine (5 mC), 5-hydroxymethylcytosine (5 hmC), 5-formylcytosine (5 fC), and 5-carboxylcytosine (5 caC). 5 mC is a major epigenetic signal that acts to regulate gene expression ...

    In mammalian DNA, cytosine occurs in several chemical forms, including unmodified cytosine (C), 5-methylcytosine (5 mC), 5-hydroxymethylcytosine (5 hmC), 5-formylcytosine (5 fC), and 5-carboxylcytosine (5 caC). 5 mC is a major epigenetic signal that acts to regulate gene expression. 5 hmC, 5 fC, and 5 caC are oxidized derivatives that might also act as distinct epigenetic signals. We investigated the response of the zinc finger DNA-binding domains of transcription factors early growth response protein 1 (Egr1) and Wilms tumor protein 1 (WT1) to different forms of modified cytosine within their recognition sequence, 5'-GCG(T/G)GGGCG-3'. Both displayed high affinity for the sequence when C or 5 mC was present and much reduced affinity when 5 hmC or 5 fC was present, indicating that they differentiate primarily oxidized C from unoxidized C, rather than methylated C from unmethylated C. 5 caC affected the two proteins differently, abolishing binding by Egr1 but not by WT1. We ascribe this difference to electrostatic interactions in the binding sites. In Egr1, a negatively charged glutamate conflicts with the negatively charged carboxylate of 5 caC, whereas the corresponding glutamine of WT1 interacts with this group favorably. Our analyses shows that zinc finger proteins (and their splice variants) can respond in modulated ways to alternative modifications within their binding sequence.


    Organizational Affiliation

    Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA; xcheng@emory.edu.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Wilms tumor protein, isoform 4/CRA_aA93Homo sapiensMutation(s): 0 
Gene Names: WT1
UniProt & NIH Common Fund Data Resources
Find proteins for P19544 (Homo sapiens)
Explore P19544 
Go to UniProtKB:  P19544
PHAROS:  P19544
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*(5CM)P*GP*T)-3')B11synthetic construct
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*TP*AP*(5CM)P*GP*CP*CP*CP*AP*CP*GP*C)-3')C11synthetic construct
      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 
      D [auth A], E [auth A], F [auth A]ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.84 Å
      • R-Value Free: 0.208 
      • R-Value Work: 0.162 
      • R-Value Observed: 0.164 
      • Space Group: P 21 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 67.06α = 90
      b = 78.301β = 90
      c = 35.59γ = 90
      Software Package:
      Software NamePurpose
      HKL-2000data collection
      PHENIXmodel building
      PHENIXrefinement
      HKL-2000data reduction
      HKL-2000data scaling
      PHENIXphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2014-10-08
        Type: Initial release
      • Version 1.1: 2014-11-19
        Changes: Database references