1CKT

CRYSTAL STRUCTURE OF HMG1 DOMAIN A BOUND TO A CISPLATIN-MODIFIED DNA DUPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Basis for recognition of cisplatin-modified DNA by high-mobility-group proteins.

Ohndorf, U.M.Rould, M.A.He, Q.Pabo, C.O.Lippard, S.J.

(1999) Nature 399: 708-712

  • DOI: 10.1038/21460
  • Primary Citation of Related Structures:  
    1CKT

  • PubMed Abstract: 
  • The anticancer activity of cis-diamminedichloroplatinum(II) (cisplatin) arises from its ability to damage DNA, with the major adducts formed being intrastrand d(GpG) and d(ApG) crosslinks. These crosslinks bend and unwind the duplex, and the altered ...

    The anticancer activity of cis-diamminedichloroplatinum(II) (cisplatin) arises from its ability to damage DNA, with the major adducts formed being intrastrand d(GpG) and d(ApG) crosslinks. These crosslinks bend and unwind the duplex, and the altered structure attracts high-mobility-group domain (HMG) and other proteins. This binding of HMG-domain proteins to cisplatin-modified DNA has been postulated to mediate the antitumour properties of the drug. Many HMG-domain proteins recognize altered DNA structures such as four-way junctions and cisplatin-modified DNA, but until now the molecular basis for this recognition was unknown. Here we describe mutagenesis, hydroxyl-radical footprinting and X-ray studies that elucidate the structure of a 1:1 cisplatin-modified DNA/HMG-domain complex. Domain A of the structure-specific HMG-domain protein HMG1 binds to the widened minor groove of a 16-base-pair DNA duplex containing a site-specific cis-[Pt(NH3)2[d(GpG)-N7(1),-N7(2)]] adduct. The DNA is strongly kinked at a hydrophobic notch created at the platinum-DNA crosslink and protein binding extends exclusively to the 3' side of the platinated strand. A phenylalanine residue at position 37 intercalates into a hydrophobic notch created at the platinum crosslinked d(GpG) site and binding of the domain is dramatically reduced in a mutant in which alanine is substituted for phenylalanine at this position.


    Organizational Affiliation

    Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HIGH MOBILITY GROUP 1 PROTEINA71Rattus norvegicusMutation(s): 0 
Gene Names: Hmgb1Hmg-1Hmg1
Find proteins for P63159 (Rattus norvegicus)
Explore P63159 
Go to UniProtKB:  P63159
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*GP*AP*AP*GP*GP*TP*CP*CP*AP*GP*AP*GP*AP*GP*G)-3')C16N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 1
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*CP*CP*(5IU)P*CP*TP*CP*TP*GP*GP*AP*CP*CP*TP*TP*CP*C)-3')B16N/A
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      CPT
      Query on CPT

      Download CCD File 
      B
      Cisplatin
      Cl2 H6 N2 Pt
      LXZZYRPGZAFOLE-UHFFFAOYSA-L
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.50 Å
      • R-Value Free: 0.239 
      • R-Value Work: 0.238 
      • R-Value Observed: 0.238 
      • Space Group: C 1 2 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 105.21α = 90
      b = 50.41β = 99.82
      c = 53.13γ = 90
      Software Package:
      Software NamePurpose
      X-PLORmodel building
      X-PLORrefinement
      SCALEPACKdata scaling
      X-PLORphasing

      Structure Validation

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      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 1999-06-30
        Type: Initial release
      • Version 1.1: 2008-04-26
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Non-polymer description, Version format compliance