3BSE

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

  • Classification: DNA

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.274 

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

  • 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 mela ...

    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 proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*DA*DCP*DAP*DCP*DTP*DAP*DCP*DAP*DAP*DTP*DGP*DTP*DTP*DGP*DCP*DAP*DAP*DT)-3')A18N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*DG*DTP*DAP*DTP*DTP*DGP*DCP*DAP*DAP*DCP*DAP*DTP*DTP*DGP*DTP*DAP*DGP*DT)-3')B18N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.274 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 38.740α = 90.00
b = 38.740β = 90.00
c = 161.327γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data collection
CNSrefinement
HKL-2000data scaling
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

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