3TVB

A Highly Symmetric DNA G-4 Quadruplex/drug Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The high-resolution crystal structure of a parallel intermolecular DNA G-4 quadruplex/drug complex employing syn glycosyl linkages.

Clark, G.R.Pytel, P.D.Squire, C.J.

(2012) Nucleic Acids Res 40: 5731-5738

  • DOI: 10.1093/nar/gks193
  • Primary Citation of Related Structures:  
    3TVB

  • PubMed Abstract: 
  • We have determined the X-ray structure of the complex between the DNA quadruplex d(5'-GGGG-3')(4) and daunomycin, as a potential model for studying drug-telomere interactions. The structure was solved at 1.08 Å by direct methods in space group I4. Th ...

    We have determined the X-ray structure of the complex between the DNA quadruplex d(5'-GGGG-3')(4) and daunomycin, as a potential model for studying drug-telomere interactions. The structure was solved at 1.08 Å by direct methods in space group I4. The asymmetric unit comprises a linear arrangement of one d(GGGG) strand, four daunomycin molecules, a second d(GGGG) strand facing in the opposite direction to the first, and Na and Mg cations. The crystallographic 4-fold axis generates the biological unit, which is a 12-layered structure comprising two sets of four guanine layers, with four layers each of four daunomycins stacked between the 5' faces of the two quadruplexes. The daunomycin layers fall into two groups which are novel in their mode of self assembly. The only contacts between daunomycin molecules within any one of these layers are van der Waals interactions, however there is substantial π-π stacking between successive daunomycin layers and also with adjacent guanine layers. The structure differs significantly from all other parallel d(TGGGGT)(4) quadruplexes in that the 5' guanine adopts the unusual syn glycosyl linkage, refuting the widespread belief that such conformations should all be anti. In contrast to the related d(TGGGGT)/daunomycin complex, there are no ligand-quadruplex groove insertion interactions.


    Organizational Affiliation

    Chemistry Department and School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1044, New Zealand. g.clark@auckland.ac.nz



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*GP*GP*G)-3')A, B4N/A
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    DM1
    Query on DM1

    Download CCD File 
    A, B
    DAUNOMYCIN
    C27 H29 N O10
    STQGQHZAVUOBTE-VGBVRHCVSA-N
     Ligand Interaction
    MG
    Query on MG

    Download CCD File 
    B
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    NA
    Query on NA

    Download CCD File 
    A, B
    SODIUM ION
    Na
    FKNQFGJONOIPTF-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.08 Å
    • R-Value Free: 0.202 
    • R-Value Work: 0.159 
    • R-Value Observed: 0.162 
    • Space Group: I 4
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 40.209α = 90
    b = 40.209β = 90
    c = 49.831γ = 90
    Software Package:
    Software NamePurpose
    SHELXmodel building
    SHELXL-97refinement
    DENZOdata reduction
    SCALEPACKdata scaling
    SHELXphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2012-03-14
      Type: Initial release
    • Version 1.1: 2012-07-11
      Changes: Database references
    • Version 1.2: 2020-01-29
      Changes: Advisory, Data collection, Derived calculations