4BNC

Crystal structure of the DNA-binding domain of human ETV1 complexed with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.206 

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:  

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HUMAN ETV1
A
106Homo sapiensMutation(s): 0 
Gene Names: ETV1 (ER81)
Find proteins for P50549 (Homo sapiens)
Go to Gene View: ETV1
Go to UniProtKB:  P50549
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP)-3'B10Homo sapiens
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP)-3'C10Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.206 
  • Space Group: P 43 2 2
Unit Cell:
Length (Å)Angle (°)
a = 64.883α = 90.00
b = 64.883β = 90.00
c = 129.587γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
SHARPphasing
XDSdata reduction
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-03
    Type: Initial release
  • Version 1.1: 2015-04-29
    Type: Database references
  • Version 1.2: 2015-06-10
    Type: Database references