3BSE

Crystal structure analysis of a 16-base-pair B-DNA

  • Classification: DNA
  • Mutation(s): No 

  • Deposited: 2007-12-23 Released: 2008-12-23 
  • Deposition Author(s): Narayana, N.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.274 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystallographic Analysis of a Sex-Specific Enhancer Element: Sequence-Dependent DNA Structure, Hydration, and Dynamics

Narayana, N.Weiss, M.A.

(2009) J Mol Biol 385: 469-490

  • DOI: 10.1016/j.jmb.2008.10.041
  • Primary Citation of Related Structures:  
    3BSE

  • PubMed Abstract: 
  • The crystal structure of a sex-specific enhancer element is described at a resolution of 1.6 A. This 16-bp site, designated Dsx(A), functions in the regulation of a genetic switch between male and female patterns of gene expression in Drosophila melanogaster ...

    The crystal structure of a sex-specific enhancer element is described at a resolution of 1.6 A. This 16-bp site, designated Dsx(A), functions in the regulation of a genetic switch between male and female patterns of gene expression in Drosophila melanogaster. Related sites are broadly conserved in metazoans, including in the human genome. This enhancer element is unusually rich in general regulatory sequences related to DNA recognition by multiple classes of eukaryotic transcription factors, including the DM motifs, homeodomain, and high mobility group box. Whereas free DNA is often crystallized as an A-form double helix, Dsx(A) was crystallized as B-DNA and thus provides a model for the prebound conformation of diverse regulatory DNA complexes. Sequence-dependent conformational properties that extend features of shorter B-DNA fragments with respect to double helical parameters, groove widths, hydration, and binding of divalent metal ions are observed. The structure also exhibits a sequence-dependent pattern of isotropic thermal B-factors, suggesting possible variation in the local flexibility of the DNA backbone. Such fluctuations are in accord with structural variability observed in prior B-DNA structures. We speculate that sites of intrinsic flexibility within a DNA control element provide hinges for its protein-directed reorganization in a transcriptional preinitiation complex.


    Related Citations: 
    • Crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium. Erratum in: J Mol Biol 303, 111 (2000).
      Chiu, T.K., Dickerson, R.E.
      (2000) J Mol Biol 301: 915
    • Atomic-resolution crystal structures of B-DNA reveal specific influences of divalent metal ions on conformation and packing
      Minasov, G., Tereshko, V., Egli, M.
      (1999) J Mol Biol 291: 83
    • Structure of d(CGCGAATTCGCG) in the presence of Ca2+ ions
      Liu, J., Subirana, J.A.
      (1999) J Biol Chem 274: 24749

    Organizational Affiliation

    Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA. narayanan3@uthscsa.edu



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*DA*DCP*DAP*DCP*DTP*DAP*DCP*DAP*DAP*DTP*DGP*DTP*DTP*DGP*DCP*DAP*DAP*DT)-3')A18N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*DG*DTP*DAP*DTP*DTP*DGP*DCP*DAP*DAP*DCP*DAP*DTP*DTP*DGP*DTP*DAP*DGP*DT)-3')B18N/A
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.60 Å
      • R-Value Free: 0.274 
      • R-Value Observed: 0.221 
      • Space Group: H 3
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 38.74α = 90
      b = 38.74β = 90
      c = 161.327γ = 120
      Software Package:
      Software NamePurpose
      HKL-2000data collection
      SOLVEphasing
      CNSrefinement
      HKL-2000data reduction
      HKL-2000data scaling

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      • Deposited Date: 2007-12-23 
      • Released Date: 2008-12-23 
      • Deposition Author(s): Narayana, N.

      Revision History  (Full details and data files)

      • Version 1.0: 2008-12-23
        Type: Initial release
      • Version 1.1: 2011-07-13
        Changes: Version format compliance