3B6G

Nucleosome core particle treated with oxaliplatin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.435 
  • R-Value Work: 0.339 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Site selectivity of platinum anticancer therapeutics

Wu, B.Droge, P.Davey, C.A.

(2008) Nat.Chem.Biol. 4: 110-112

  • DOI: 10.1038/nchembio.2007.58
  • Primary Citation of Related Structures:  3B6F

  • PubMed Abstract: 
  • X-ray crystallographic and biochemical investigation of the reaction of cisplatin and oxaliplatin with nucleosome core particle and naked DNA reveals that histone octamer association can modulate DNA platination. Adduct formation also occurs at speci ...

    X-ray crystallographic and biochemical investigation of the reaction of cisplatin and oxaliplatin with nucleosome core particle and naked DNA reveals that histone octamer association can modulate DNA platination. Adduct formation also occurs at specific histone methionine residues, which could serve as a nuclear platinum reservoir influencing adduct transfer to DNA. Our findings suggest that the nucleosome center may provide a favorable target for the design of improved platinum anticancer drugs.


    Related Citations: 
    • Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution
      Davey, C.A.,Sargent, D.F.,Luger, K.,Maeder, A.W.,Richmond, T.J.
      (2002) J.Mol.Biol. 319: 1097


    Organizational Affiliation

    Division of Structural and Computational Biology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2
A, E
135Xenopus laevisN/A
Find proteins for P84233 (Xenopus laevis)
Go to UniProtKB:  P84233
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
102Xenopus laevisN/A
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Histone H2A
C, G
128Xenopus laevisN/A
Find proteins for P06897 (Xenopus laevis)
Go to UniProtKB:  P06897
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Histone H2B 1.1
D, H
125Xenopus laevisN/A
Find proteins for P02281 (Xenopus laevis)
Go to UniProtKB:  P02281
Entity ID: 1
MoleculeChainsLengthOrganism
147-MER DNAI147Homo sapiens
Entity ID: 2
MoleculeChainsLengthOrganism
147-MER DNAJ147Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
E
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.435 
  • R-Value Work: 0.339 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 106.298α = 90.00
b = 109.655β = 90.00
c = 181.807γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-10-29 
  • Released Date: 2007-12-25 
  • Deposition Author(s): Wu, B., Davey, C.A.

Revision History 

  • Version 1.0: 2007-12-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance