5CP6
Nucleosome Core Particle with Adducts from the Anticancer Compound, [(eta6-5,8,9,10-tetrahydroanthracene)Ru(ethylenediamine)Cl][PF6]
Summary for 5CP6
| Entry DOI | 10.2210/pdb5cp6/pdb |
| Descriptor | DNA (145-MER), Histone H3.2, Histone H4, ... (10 entities in total) |
| Functional Keywords | nucleosome core particle, antitumour compound, structural protein-dna complex, structural protein/dna |
| Biological source | Xenopus laevis (African clawed frog) More |
| Cellular location | Nucleus: P84233 P62799 P02281 |
| Total number of polymer chains | 10 |
| Total formula weight | 199584.29 |
| Authors | Ma, Z.,Adhireksan, Z.,Murray, B.S.,Dyson, P.J.,Davey, C.A. (deposition date: 2015-07-21, release date: 2016-06-01, Last modification date: 2023-11-08) |
| Primary citation | Ma, Z.,Palermo, G.,Adhireksan, Z.,Murray, B.S.,von Erlach, T.,Dyson, P.J.,Rothlisberger, U.,Davey, C.A. An Organometallic Compound which Exhibits a DNA Topology-Dependent One-Stranded Intercalation Mode. Angew.Chem.Int.Ed.Engl., 55:7441-7444, 2016 Cited by PubMed Abstract: Understanding how small molecules interact with DNA is essential since it underlies a multitude of pathological conditions and therapeutic interventions. Many different intercalator compounds have been studied because of their activity as mutagens or drugs, but little is known regarding their interaction with nucleosomes, the protein-packaged form of DNA in cells. Here, using crystallographic methods and molecular dynamics simulations, we discovered that adducts formed by [(η(6) -THA)Ru(ethylenediamine)Cl][PF6 ] (THA=5,8,9,10-tetrahydroanthracene; RAED-THA-Cl[PF6 ]) in the nucleosome comprise a novel one-stranded intercalation and DNA distortion mode. Conversely, the THA group in fact remains solvent exposed and does not disrupt base stacking in RAED-THA adducts on B-form DNA. This newly observed DNA binding mode and topology dependence may actually be prevalent and should be considered when studying covalently binding intercalating compounds. PubMed: 27184539DOI: 10.1002/anie.201602145 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.6 Å) |
Structure validation
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