3B6F

Nucleosome core particle treated with cisplatin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.402 
  • R-Value Work: 0.330 
  • R-Value Observed: 0.331 

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
  • Structures With Same Primary Citation

  • 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 specific histone methionine residues, which could serve as a nuclear platinum reservoir influencing adduct transfer to DNA ...

    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

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2A, E135Xenopus laevisMutation(s): 0 
Find proteins for P84233 (Xenopus laevis)
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Go to UniProtKB:  P84233
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H4B, F102Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
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Go to UniProtKB:  P62799
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  • Reference Sequence

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Histone H2AC, G128Xenopus laevisMutation(s): 0 
Gene Names: LOC494591
Find proteins for P06897 (Xenopus laevis)
Explore P06897 
Go to UniProtKB:  P06897
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  • Reference Sequence

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Histone H2B 1.1D, H125Xenopus laevisMutation(s): 0 
Find proteins for P02281 (Xenopus laevis)
Explore P02281 
Go to UniProtKB:  P02281
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganism
147-MER DNAI147Homo sapiens

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Entity ID: 2
MoleculeChainsLengthOrganism
147-MER DNAJ147Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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: 0.402 
  • R-Value Work: 0.330 
  • R-Value Observed: 0.331 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.327α = 90
b = 109.38β = 90
c = 180.585γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



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
    Changes: Version format compliance