4UNO | pdb_00004uno

Crystal structure of the ETS domain of human ETV5 in complex with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.203 (Depositor), 0.205 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 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 Biological Chem 290: 13692

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

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 17.97 kDa 
  • Atom Count: 1,314 
  • Modeled Residue Count: 115 
  • Deposited Residue Count: 120 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ETS TRANSLOCATION VARIANT 5100Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P41161 (Homo sapiens)
Explore P41161 
Go to UniProtKB:  P41161
PHAROS:  P41161
GTEx:  ENSG00000244405 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41161
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'10synthetic construct
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 3
MoleculeChains LengthOrganismImage
5'-D(*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP)-3'10synthetic construct
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.203 (Depositor), 0.205 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: P 32 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.022α = 90
b = 58.022β = 90
c = 84.711γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-11
    Type: Initial release
  • Version 1.1: 2015-04-29
    Changes: Database references
  • Version 1.2: 2015-06-10
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary