2R5Z

Structure of Scr/Exd complex bound to a DNA sequence derived from the fkh gene


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Functional specificity of a Hox protein mediated by the recognition of minor groove structure

Joshi, R.Passner, J.M.Rohs, R.Jain, R.Sosinsky, A.Crickmore, M.A.Jacob, V.Aggarwal, A.K.Honig, B.Mann, R.S.

(2007) Cell 131: 530-543

  • DOI: 10.1016/j.cell.2007.09.024
  • Primary Citation of Related Structures:  
    2R5Z, 2R5Y

  • PubMed Abstract: 
  • The recognition of specific DNA-binding sites by transcription factors is a critical yet poorly understood step in the control of gene expression. Members of the Hox family of transcription factors bind DNA by making nearly identical major groove con ...

    The recognition of specific DNA-binding sites by transcription factors is a critical yet poorly understood step in the control of gene expression. Members of the Hox family of transcription factors bind DNA by making nearly identical major groove contacts via the recognition helices of their homeodomains. In vivo specificity, however, often depends on extended and unstructured regions that link Hox homeodomains to a DNA-bound cofactor, Extradenticle (Exd). Using a combination of structure determination, computational analysis, and in vitro and in vivo assays, we show that Hox proteins recognize specific Hox-Exd binding sites via residues located in these extended regions that insert into the minor groove but only when presented with the correct DNA sequence. Our results suggest that these residues, which are conserved in a paralog-specific manner, confer specificity by recognizing a sequence-dependent DNA structure instead of directly reading a specific DNA sequence.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, HHSC 1104, New York, NY 10032, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Homeotic protein Sex combs reducedA88Drosophila melanogasterMutation(s): 1 
Gene Names: ScrCG1030
Find proteins for P09077 (Drosophila melanogaster)
Explore P09077 
Go to UniProtKB:  P09077
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Homeobox protein extradenticleB63Drosophila melanogasterMutation(s): 0 
Gene Names: exdCG8933
Find proteins for P40427 (Drosophila melanogaster)
Explore P40427 
Go to UniProtKB:  P40427
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*DAP*DCP*DTP*DCP*DTP*DAP*DAP*DGP*DAP*DTP*DTP*DAP*DAP*DTP*DCP*DGP*DGP*DCP*DTP*DG)-3')C20N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*DTP*DCP*DAP*DGP*DCP*DCP*DGP*DAP*DTP*DTP*DAP*DAP*DTP*DCP*DTP*DTP*DAP*DGP*DAP*DG)-3')D20N/A
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.60 Å
      • R-Value Free: 0.303 
      • R-Value Work: 0.233 
      • R-Value Observed: 0.233 
      • Space Group: C 2 2 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 88.84α = 90
      b = 92.6β = 90
      c = 78.84γ = 90
      Software Package:
      Software NamePurpose
      CNSrefinement
      HKL-2000data collection
      HKL-2000data reduction
      HKL-2000data scaling
      AMoREphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2008-02-05
        Type: Initial release
      • Version 1.1: 2011-07-13
        Changes: Version format compliance