1A2E

CRYSTAL STRUCTURE OF A DOUBLE-STRANDED DNA DECAMER CONTAINING A CISPLATIN INTERSTRAND CROSS-LINK ADDUCT

  • Classification: DNA
  • Mutation(s): No 

  • Deposited: 1998-01-05 Released: 1999-04-12 
  • Deposition Author(s): Coste, F., Zelwer, C.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of a double-stranded DNA containing a cisplatin interstrand cross-link at 1.63 A resolution: hydration at the platinated site.

Coste, F.Malinge, J.M.Serre, L.Shepard, W.Roth, M.Leng, M.Zelwer, C.

(1999) Nucleic Acids Res 27: 1837-1846

  • DOI: 10.1093/nar/27.8.1837
  • Primary Citation of Related Structures:  
    1A2E

  • PubMed Abstract: 
  • cis-diamminedichloroplatinum (II) (cisplatin) is a powerful anti-tumor drug whose target is cellular DNA. In the reaction between DNA and cisplatin, covalent intrastrand and interstrand cross-links (ICL) are formed. Two solution structures of the ICL have been published recently ...

    cis-diamminedichloroplatinum (II) (cisplatin) is a powerful anti-tumor drug whose target is cellular DNA. In the reaction between DNA and cisplatin, covalent intrastrand and interstrand cross-links (ICL) are formed. Two solution structures of the ICL have been published recently. In both models the double-helix is bent and unwound but with significantly different angle values. We solved the crystal structure at 100K of a double-stranded DNA decamer containing a single cisplatin ICL, using the anomalous scattering (MAD) of platinum as a unique source of phase information. We found 47 degrees for double-helix bending and 70 degrees for unwinding in agreement with previous electrophoretic assays. The crystals are stabilized by intermolecular contacts involving two cytosines extruded from the double-helix, one of which makes a triplet with a terminal G.C pair. The platinum coordination is nearly square and the platinum residue is embedded into a cage of nine water molecules linked to the cross-linked guanines, to the two amine groups, and to the phosphodiester backbone through other water molecules. This water molecule organization is discussed in relation with the chemical stability of the ICL.


    Organizational Affiliation

    Centre de Biophysique Moléculaire, Centre de National de la Recherche Scientifique, affiliated to the Université d'Orléans, rue Charles Sadron, 45071 Orleans Cedex, France.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*CP*TP*CP*GP*CP*TP*CP*TP*C)-3')A10N/A
    Protein Feature View
    Expand
    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*GP*AP*GP*AP*GP*CP*GP*AP*GP*G)-3')B10N/A
      Protein Feature View
      Expand
      • Reference Sequence
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      CPT (Subject of Investigation/LOI)
      Query on CPT

      Download Ideal Coordinates CCD File 
      C [auth A]Cisplatin
      Cl2 H6 N2 Pt
      LXZZYRPGZAFOLE-UHFFFAOYSA-L
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.63 Å
      • R-Value Observed: 0.169 
      • Space Group: C 1 2 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 42.89α = 90
      b = 29.98β = 95.98
      c = 46.57γ = 90
      Software Package:
      Software NamePurpose
      SHARPphasing
      SHELXL-96refinement
      MOSFLMdata reduction
      CCP4data scaling

      Structure Validation

      View Full Validation Report




      Entry History 

      Deposition Data

      • Deposited Date: 1998-01-05 
      • Released Date: 1999-04-12 
      • Deposition Author(s): Coste, F., Zelwer, C.

      Revision History  (Full details and data files)

      • Version 1.0: 1999-04-12
        Type: Initial release
      • Version 1.1: 2008-05-22
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Non-polymer description, Version format compliance