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 1.3 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: https://doi.org/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 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.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein prosperoC [auth A]163Drosophila melanogasterMutation(s): 0 
Gene Names: pros
UniProt
Find proteins for P29617 (Drosophila melanogaster)
Explore P29617 
Go to UniProtKB:  P29617
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29617
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*AP*GP*CP*AP*TP*GP*CP*CP*TP*G)-3'A [auth D]10N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*CP*AP*GP*GP*CP*AP*TP*GP*CP*T)-3'B [auth C]10N/A
Sequence Annotations
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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

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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
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references