4MHG

Crystal structure of ETV6 bound to a specific DNA sequence


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.199 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Steric Mechanism of Auto-Inhibitory Regulation of Specific and Non-Specific DNA Binding by the ETS Transcriptional Repressor ETV6.

De, S.Chan, A.C.Coyne, H.J.Bhachech, N.Hermsdorf, U.Okon, M.Murphy, M.E.Graves, B.J.McIntosh, L.P.

(2014) J.Mol.Biol. 426: 1390-1406

  • DOI: 10.1016/j.jmb.2013.11.031
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • DNA binding by the ETS transcriptional repressor ETV6 (or TEL) is auto-inhibited ~50-fold due to an α-helix that sterically blocks its ETS domain binding interface. Using NMR spectroscopy, we demonstrate that this marginally stable helix is unfolded, ...

    DNA binding by the ETS transcriptional repressor ETV6 (or TEL) is auto-inhibited ~50-fold due to an α-helix that sterically blocks its ETS domain binding interface. Using NMR spectroscopy, we demonstrate that this marginally stable helix is unfolded, and not displaced to a non-inhibitory position, when ETV6 is bound to DNA containing a consensus (5')GGAA(3') recognition site. Although significantly lower in affinity, binding to non-specific DNA is auto-inhibited ~5-fold and is also accompanied by helix unfolding. Based on NMR chemical shift perturbations, both specific and non-specific DNA are bound via the same canonical ETS domain interface. However, spectral perturbations are smaller for the non-specific complex, suggesting weaker and less well-defined interactions than in the specific complex. In parallel, the crystal structure of ETV6 bound to a specific DNA duplex was determined. The structure of this complex reveals that a non-conserved histidine residue in the ETS domain recognition helix helps establish the specificity of ETV6 for DNA-binding sites containing (5')GGAA(3')versus(5')GGAT(3'). These studies provide a unified steric mechanism for attenuating ETV6 binding to both specific and non-specific DNA and expand the repertoire of characterized auto-inhibitory strategies utilized to regulate ETS factors.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z3.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Transcription factor ETV6
A
102Mus musculusMutation(s): 1 
Gene Names: Etv6 (Tel, Tel1)
Find proteins for P97360 (Mus musculus)
Go to UniProtKB:  P97360
Entity ID: 1
MoleculeChainsLengthOrganism
Specific 14 bp DNAB14synthetic construct
Entity ID: 2
MoleculeChainsLengthOrganism
Complementary Specific 14 bp DNAC14synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.199 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.175 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 57.582α = 90.00
b = 57.582β = 90.00
c = 130.481γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
PDB_EXTRACTdata extraction
Blu-Icedata collection
MOLREPphasing
SCALEPACKdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-08
    Type: Initial release
  • Version 1.1: 2014-03-26
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description
  • Version 1.3: 2019-01-30
    Type: Data collection, Source and taxonomy, Structure summary