4UUV

Structure of the DNA binding ETS domain of human ETV4 in complex with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures of the Ets Domains of Transcription Factors Etv1, Etv4, Etv5 and Fev: Determinants of DNA Binding and Redox Regulation by Disulfide Bond Formation.

Cooper, C.D.O.Newman, J.A.Aitkenhead, H.Allerston, C.K.Gileadi, O.

(2015) J Biol Chem 290: 13692

  • DOI: 10.1074/jbc.M115.646737
  • Primary Citation of Related Structures:  
    2YPR, 4BNC, 4CO8, 3ZP5, 4UNO, 4UUV, 4AVP

  • PubMed Abstract: 
  • Ets transcription factors, which share the conserved Ets DNA-binding domain, number nearly 30 members in humans and are particularly involved in developmental processes. Their deregulation following changes in expression, transcriptional activity, or by chromosomal translocation plays a critical role in carcinogenesis ...

    Ets transcription factors, which share the conserved Ets DNA-binding domain, number nearly 30 members in humans and are particularly involved in developmental processes. Their deregulation following changes in expression, transcriptional activity, or by chromosomal translocation plays a critical role in carcinogenesis. Ets DNA binding, selectivity, and regulation have been extensively studied; however, questions still arise regarding binding specificity outside the core GGA recognition sequence and the mode of action of Ets post-translational modifications. Here, we report the crystal structures of Etv1, Etv4, Etv5, and Fev, alone and in complex with DNA. We identify previously unrecognized features of the protein-DNA interface. Interactions with the DNA backbone account for most of the binding affinity. We describe a highly coordinated network of water molecules acting in base selection upstream of the GGAA core and the structural features that may account for discrimination against methylated cytidine residues. Unexpectedly, all proteins crystallized as disulfide-linked dimers, exhibiting a novel interface (distant to the DNA recognition helix). Homodimers of Etv1, Etv4, and Etv5 could be reduced to monomers, leading to a 40-200-fold increase in DNA binding affinity. Hence, we present the first indication of a redox-dependent regulatory mechanism that may control the activity of this subset of oncogenic Ets transcription factors.


    Organizational Affiliation

    From the Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom opher.gileadi@sgc.ox.ac.uk.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ETS TRANSLOCATION VARIANT 4 ADGJMPSV100Homo sapiensMutation(s): 0 
Gene Names: ETV4E1AFPEA3
Find proteins for P43268 (Homo sapiens)
Explore P43268 
Go to UniProtKB:  P43268
NIH Common Fund Data Resources
PHAROS:  P43268
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'B, E, H, K, N, Q, T, W10synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP)-3'C, F, I, L, O, R, U10synthetic construct
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        5'-D(*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP)-3'X10synthetic construct
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 2.80 Å
        • R-Value Free: 0.248 
        • R-Value Work: 0.203 
        • R-Value Observed: 0.205 
        • Space Group: C 1 2 1
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 176.651α = 90
        b = 46.133β = 96.69
        c = 171.15γ = 90
        Software Package:
        Software NamePurpose
        PHENIXrefinement
        XDSdata reduction
        XDSdata scaling
        PHASERphasing

        Structure Validation

        View Full Validation Report



        Entry History 

        Deposition Data

        Revision History  (Full details and data files)

        • Version 1.0: 2014-08-13
          Type: Initial release
        • Version 1.1: 2015-04-29
          Changes: Database references
        • Version 1.2: 2015-06-10
          Changes: Database references