1D9R

CRYSTAL STRUCTURE OF DNA SHEARED TANDEM G-A BASE PAIRS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure and recognition of sheared tandem G x A base pairs associated with human centromere DNA sequence at atomic resolution.

Gao, Y.G.Robinson, H.Sanishvili, R.Joachimiak, A.Wang, A.H.

(1999) Biochemistry 38: 16452-16460

  • DOI: 10.1021/bi9914614
  • Primary Citation of Related Structures:  
    1D8X, 1D9R, 1DCR

  • PubMed Abstract: 
  • G x A mismatched base pairs are frequently found in nucleic acids. Human centromere DNA sequences contain unusual repeating motifs, e.g. , (GAATG)n x (CATTC)n found in the human chromosome. The purine-rich strand of this repeating pentamer sequence f ...

    G x A mismatched base pairs are frequently found in nucleic acids. Human centromere DNA sequences contain unusual repeating motifs, e.g. , (GAATG)n x (CATTC)n found in the human chromosome. The purine-rich strand of this repeating pentamer sequence forms duplex and hairpin structures with unusual stability. The high stability of these structures is contributed by the "sheared" G x A base pairs which present a novel recognition surface for ligands and proteins. We have solved the crystal structure, by the multiple-wavelength anomalous diffraction (MAD) method of d(CCGAATGAGG) in which the centromere core sequence motif GAATG is embedded. Three crystal forms were refined to near-atomic resolution. The structures reveal the detailed conformation of tandem G x A base pairs whose unique hydrogen-bonding surface has interesting interactions with bases, hydrated magnesium ions, cobalt(III)hexaammine, spermine, and water molecules. The results are relevant in understanding the structure associated with human centromere sequence in particular and G x A base pairs in nucleic acids (including RNA, like ribozyme) in general.


    Organizational Affiliation

    Department of Cell & Structural Biology, University of Illinois at Urbana-Champaign 61801, USA.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*CP*CP*GP*AP*AP*(BRU)P*GP*AP*GP*G)-3'A, B10N/A
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    NCO
    Query on NCO

    Download CCD File 
    A
    COBALT HEXAMMINE(III)
    Co H18 N6
    DYLMFCCYOUSRTK-FGTKAUEHAT
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.50 Å
    • R-Value Free: 0.278 
    • R-Value Work: 0.234 
    • R-Value Observed: 0.234 
    • Space Group: C 2 2 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 22.711α = 90
    b = 67.216β = 90
    c = 72.504γ = 90
    Software Package:
    Software NamePurpose
    SHELXL-97refinement
    CNSrefinement
    HKL-2000data reduction
    HKL-2000data scaling
    CNSphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 1999-11-05
      Type: Initial release
    • Version 1.1: 2008-04-27
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 1.3: 2019-07-24
      Changes: Data collection, Derived calculations, Refinement description