3U2B

Structure of the Sox4 HMG domain bound to DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.238 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The crystal structure of the Sox4 HMG domain-DNA complex suggests a mechanism for positional interdependence in DNA recognition

Jauch, R.Ng, C.K.L.Narasimhan, K.Kolatkar, P.R.

(2012) Biochem J 443: 39-47

  • DOI: 10.1042/BJ20111768
  • Primary Citation of Related Structures:  
    3U2B

  • PubMed Abstract: 
  • It has recently been proposed that the sequence preferences of DNA-binding TFs (transcription factors) can be well described by models that include the positional interdependence of the nucleotides of the target sites. Such binding models allow for m ...

    It has recently been proposed that the sequence preferences of DNA-binding TFs (transcription factors) can be well described by models that include the positional interdependence of the nucleotides of the target sites. Such binding models allow for multiple motifs to be invoked, such as principal and secondary motifs differing at two or more nucleotide positions. However, the structural mechanisms underlying the accommodation of such variant motifs by TFs remain elusive. In the present study we examine the crystal structure of the HMG (high-mobility group) domain of Sox4 [Sry (sex-determining region on the Y chromosome)-related HMG box 4] bound to DNA. By comparing this structure with previously solved structures of Sox17 and Sox2, we observed subtle conformational differences at the DNA-binding interface. Furthermore, using quantitative electrophoretic mobility-shift assays we validated the positional interdependence of two nucleotides and the presence of a secondary Sox motif in the affinity landscape of Sox4. These results suggest that a concerted rearrangement of two interface amino acids enables Sox4 to accommodate primary and secondary motifs. The structural adaptations lead to altered dinucleotide preferences that mutually reinforce each other. These analyses underline the complexity of the DNA recognition by TFs and provide an experimental validation for the conceptual framework of positional interdependence and secondary binding motifs.


    Organizational Affiliation

    Laboratory for Structural Biochemistry, Genome Institute of Singapore, 60 Biopolis St, Singapore 138672. jauchr@gis.a-star.edu.sg



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription factor SOX-4C79Mus musculusMutation(s): 0 
Gene Names: Sox4Sox-4
Find proteins for Q06831 (Mus musculus)
Explore Q06831 
Go to UniProtKB:  Q06831
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*TP*CP*TP*CP*TP*AP*TP*TP*GP*TP*CP*CP*TP*GP*G)-3')A16N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*CP*CP*AP*GP*GP*AP*CP*AP*AP*TP*AP*GP*AP*GP*AP*C)-3')B16N/A
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.40 Å
      • R-Value Free: 0.280 
      • R-Value Work: 0.235 
      • R-Value Observed: 0.238 
      • Space Group: P 32 2 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 69.941α = 90
      b = 69.941β = 90
      c = 63.205γ = 120
      Software Package:
      Software NamePurpose
      HKL-2000data collection
      PHASESphasing
      PHENIXrefinement
      HKL-2000data reduction
      HKL-2000data scaling

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2011-12-28
        Type: Initial release
      • Version 1.1: 2014-03-12
        Changes: Database references