1A84

NMR SOLUTION STRUCTURE OF A DNA DODECAMER DUPLEX CONTAINING A CIS-DIAMMINEPLATINUM(II) D(GPG) INTRASTRAND CROSS-LINK, THE MAJOR ADDUCT OF THE ANTICANCER DRUG CISPLATIN, 1 STRUCTURE


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 
  • Conformers Submitted: 
  • Selection Criteria: LEAST RESTRAINT VIOLATION 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

NMR solution structure of a DNA dodecamer duplex containing a cis-diammineplatinum(II) d(GpG) intrastrand cross-link, the major adduct of the anticancer drug cisplatin.

Gelasco, A.Lippard, S.J.

(1998) Biochemistry 37: 9230-9239

  • DOI: 10.1021/bi973176v

  • PubMed Abstract: 
  • The structure of the DNA duplex dodecamer, d(CCTCTGGTCTCC. GGAGACCAGAGG), containing the cisplatin d(GpG) 1,2-intrastrand cross-link at the position denoted by asterisks, was determined in solution by high-resolution 2D NMR spectroscopy and restraine ...

    The structure of the DNA duplex dodecamer, d(CCTCTGGTCTCC. GGAGACCAGAGG), containing the cisplatin d(GpG) 1,2-intrastrand cross-link at the position denoted by asterisks, was determined in solution by high-resolution 2D NMR spectroscopy and restrained molecular dynamics refinement. The cis-[Pt(NH3)2¿d(GpG-N7(1), N7(2))¿] lesion causes the adjacent guanine bases to roll toward one another by 49 degrees, leading to an overall helix bend angle of 78 degrees. These features are more exaggerated than those observed in the X-ray crystal structure determined for the same platinated duplex [Takahara et al. (1995) Nature 377, 649-652]. A common property of the solution and crystal structures is the widening and flattening of the minor groove opposite the platinum adduct, affording geometric parameters resembling those found in A-form DNA. This deformation is especially noteworthy for the solution structure because its sugar puckers are primarily those of B-form DNA. The unwinding of the helix at the site of platination is 25 degrees. The curvature and shape of the platinated duplex are remarkably similar to those observed in DNA duplexes complexed by the HMG-domain proteins SRY and LEF-1. The structure reveals how cisplatin binding alters DNA in such a manner as to facilitate HMG-domain protein recognition.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA D(CCTCTG*G*TCTCC)A12N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA D(GGAGACCAGAGG)B12N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CPT
Query on CPT

Download SDF File 
Download CCD File 
A
Cisplatin
diammine(dichloro)platinum
Cl2 H6 N2 Pt
LXZZYRPGZAFOLE-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 
  • Conformers Submitted: 
  • Selection Criteria: LEAST RESTRAINT VIOLATION 
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-11-25
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance