1V3N

Crystal structure of d(GCGAGAGC): the DNA quadruplex structure split from the octaplex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structures of a DNA octaplex with I-motif of G-quartets and its splitting into two quadruplexes suggest a folding mechanism of eight tandem repeats

Kondo, J.Adachi, W.Umeda, S.Sunami, T.Takenaka, A.

(2004) Nucleic Acids Res 32: 2541-2549

  • DOI: 10.1093/nar/gkh575
  • Primary Citation of Related Structures:  
    1V3P, 1V3O, 1V3N

  • PubMed Abstract: 
  • Recent genomic analyses revealed many kinds of tandem repeats of specific sequences. Some of them are related to genetic diseases, but their biological functions and structures are still unknown. Two X-ray structures of a short DNA fragment d(gcGA[G]1Agc) show that four base-intercalated duplexes are assembled to form an octaplex at a low K+ concentration, in which the eight G5 residues form a stacked double G-quartet in the central part ...

    Recent genomic analyses revealed many kinds of tandem repeats of specific sequences. Some of them are related to genetic diseases, but their biological functions and structures are still unknown. Two X-ray structures of a short DNA fragment d(gcGA[G]1Agc) show that four base-intercalated duplexes are assembled to form an octaplex at a low K+ concentration, in which the eight G5 residues form a stacked double G-quartet in the central part. At a higher K+ concentration, however, the octaplex is split into just two halves. These structural features suggest a folding process of eight tandem repeats of d(ccGA[G]4Agg), according to a double Greek-key motif. Such a packaging of the repeats could facilitate slippage of a certain sequence during DNA replication, to induce increase or decrease of the repeats.


    Organizational Affiliation

    Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*(CBR)P*GP*AP*GP*AP*GP*C)-3'A, B8N/A
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    K
    Query on K

    Download Ideal Coordinates CCD File 
    C [auth A]POTASSIUM ION
    K
    NPYPAHLBTDXSSS-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.80 Å
    • R-Value Free: 0.249 
    • R-Value Work: 0.225 
    • Space Group: I 2 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 33.81α = 90
    b = 43.47β = 90
    c = 64.2γ = 90
    Software Package:
    Software NamePurpose
    MOSFLMdata reduction
    SCALAdata scaling
    SOLVEphasing
    CNSrefinement
    CCP4data scaling

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2004-06-08
      Type: Initial release
    • Version 1.1: 2008-04-27
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance