1XPX

Structural basis of prospero-DNA interaction; implications for transcription regulation in developing cells


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Basis of Prospero-DNA Interaction: Implications for Transcription Regulationin Developing Cells.

Yousef, M.S.Matthews, B.W.

(2005) Structure 13: 601-607

  • DOI: 10.1016/j.str.2005.01.023
  • Primary Citation of Related Structures:  
    1XPX

  • PubMed Abstract: 
  • The crystal structure of a complex between the novel homeodomain of the neural transcription factor Prospero and DNA shows that the invariant residues Lys1290, Asn1294, and Asp1297 make specific contacts with the noncanonical DNA binding site. The overall structure includes the homeodomain and the adjacent Prospero domain and confirms that they act as a single structural unit, a Homeo-Prospero domain ...

    The crystal structure of a complex between the novel homeodomain of the neural transcription factor Prospero and DNA shows that the invariant residues Lys1290, Asn1294, and Asp1297 make specific contacts with the noncanonical DNA binding site. The overall structure includes the homeodomain and the adjacent Prospero domain and confirms that they act as a single structural unit, a Homeo-Prospero domain. The Prospero domain facilitates the proper alignment of the protein on the DNA. Knowledge of the structure reconciles two different DNA sequences that have been proposed as transcriptional targets for Prospero. As in the apo structure, the C terminus of the Prospero domain shields a short helix within the homeodomain that includes a nuclear export signal (NES). The structural results suggest that exposure of the NES is not coupled directly to DNA binding. We propose a DNA recognition mechanism specific to Prospero-type homeodomains in developing cells.


    Related Citations: 
    • Structure of the DNA binding region of prospero reveals a novel homeo-prospero domain.
      Ryter, J.M., Doe, C.Q., Matthews, B.W.
      (2002) Structure 10: 1541

    Organizational Affiliation

    Institute of Molecular Biology, Howard Hughes Medical Institute, Department of Physics, University of Oregon, Eugene, Oregon 97403, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Protein prosperoC [auth A]163Drosophila melanogasterMutation(s): 0 
Gene Names: prosCG17228
UniProt
Find proteins for P29617 (Drosophila melanogaster)
Explore P29617 
Go to UniProtKB:  P29617
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*AP*GP*CP*AP*TP*GP*CP*CP*TP*G)-3'A [auth D]10N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*CP*AP*GP*GP*CP*AP*TP*GP*CP*T)-3'B [auth C]10N/A
      Protein Feature View
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      • Reference Sequence
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.80 Å
      • R-Value Free: 0.282 
      • R-Value Work: 0.217 
      • R-Value Observed: 0.217 
      • Space Group: P 43 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 44.708α = 90
      b = 44.708β = 90
      c = 226.661γ = 90
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      SCALEPACKdata scaling
      CNSrefinement

      Structure Validation

      View Full Validation Report




      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2005-05-03
        Type: Initial release
      • Version 1.1: 2008-04-30
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance