3O62 image
Deposition Date 2010-07-28
Release Date 2011-01-05
Last Version Date 2024-02-21
Entry Detail
PDB ID:
3O62
Title:
Nucleosome core particle modified with a cisplatin 1,3-cis-{Pt(NH3)2}2+-d(GpTpG) intrastrand cross-link
Biological Source:
Source Organism:
Xenopus laevis (Taxon ID: 8355)
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.22 Å
R-Value Free:
0.30
R-Value Work:
0.24
R-Value Observed:
0.25
Space Group:
P 21 21 21
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H3.2
Chain IDs:A, E
Chain Length:135
Number of Molecules:2
Biological Source:Xenopus laevis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H4
Chain IDs:B, F
Chain Length:102
Number of Molecules:2
Biological Source:Xenopus laevis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2A type 1
Chain IDs:C, G
Chain Length:128
Number of Molecules:2
Biological Source:Xenopus laevis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2B 1.1
Chain IDs:D, H
Chain Length:122
Number of Molecules:2
Biological Source:Xenopus laevis
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (146-MER)
Chain IDs:I
Chain Length:146
Number of Molecules:1
Biological Source:
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (146-MER)
Chain IDs:J
Chain Length:146
Number of Molecules:1
Biological Source:
Ligand Molecules
Primary Citation
Consequences of Cisplatin binding on nucleosome structure and dynamics.
Chem.Biol. 17 1334 1343 (2010)
PMID: 21168769 DOI: 10.1016/j.chembiol.2010.10.018

Abstact

The effects of cisplatin binding to DNA were explored at the nucleosome level to incorporate key features of the eukaryotic nuclear environment. An X-ray crystal structure of a site-specifically platinated nucleosome carrying a 1,3-cis-{Pt(NH₃)₂}²+-d(GpTpG) intrastrand cross-link reveals the details of how this adduct dictates the rotational positioning of DNA in the nucleosome. Results from in vitro nucleosome mobility assays indicate that a single platinum adduct interferes with ATP-independent sliding of DNA around the octamer core. Data from in vitro transcription experiments suggest that RNA polymerases can successfully navigate along cisplatin-damaged DNA templates that contain nucleosomes, but stall when the transcription elongation complex physically contacts a platinum cross-link located on the template strand. These results provide information about the effects of cisplatin binding to nuclear DNA and enhance our understanding of the mechanism of transcription inhibition by platinum anticancer compounds.

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Primary Citation of related structures