2R5Y

Structure of Scr/Exd complex bound to a consensus Hox-Exd site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.255 

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:  

  • 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: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Homeotic protein Sex combs reduced
A
88Drosophila melanogasterMutation(s): 1 
Gene Names: Scr
Find proteins for P09077 (Drosophila melanogaster)
Go to UniProtKB:  P09077
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Homeobox protein extradenticle
B
63Drosophila melanogasterMutation(s): 0 
Gene Names: exd
Find proteins for P40427 (Drosophila melanogaster)
Go to UniProtKB:  P40427
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*DAP*DCP*DTP*DCP*DTP*DAP*DTP*DGP*DAP*DTP*DTP*DTP*DAP*DTP*DGP*DGP*DGP*DCP*DTP*DG)-3')C20N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*DTP*DCP*DAP*DGP*DCP*DCP*DCP*DAP*DTP*DAP*DAP*DAP*DTP*DCP*DAP*DTP*DAP*DGP*DAP*DG)-3')D20N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.255 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 65.310α = 90.00
b = 65.310β = 90.00
c = 200.300γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
CNSrefinement
HKL-2000data collection
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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