2R5Y

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1016/j.cell.2007.09.024
  • Primary Citation of Related Structures:  
    2R5Y, 2R5Z

  • 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 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

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Homeotic protein Sex combs reducedC [auth A]88Drosophila melanogasterMutation(s): 1 
Gene Names: Scr
UniProt
Find proteins for P09077 (Drosophila melanogaster)
Explore P09077 
Go to UniProtKB:  P09077
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09077
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Homeobox protein extradenticleD [auth B]63Drosophila melanogasterMutation(s): 0 
Gene Names: exd
UniProt
Find proteins for P40427 (Drosophila melanogaster)
Explore P40427 
Go to UniProtKB:  P40427
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40427
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*DAP*DCP*DTP*DCP*DTP*DAP*DTP*DGP*DAP*DTP*DTP*DTP*DAP*DTP*DGP*DGP*DGP*DCP*DTP*DG)-3')A [auth C]20synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*DTP*DCP*DAP*DGP*DCP*DCP*DCP*DAP*DTP*DAP*DAP*DAP*DTP*DCP*DAP*DTP*DAP*DGP*DAP*DG)-3')B [auth D]20synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.31α = 90
b = 65.31β = 90
c = 200.3γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-02-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Source and taxonomy
  • Version 1.3: 2023-08-30
    Changes: Data collection, Refinement description