5CP6

Nucleosome Core Particle with Adducts from the Anticancer Compound, [(eta6-5,8,9,10-tetrahydroanthracene)Ru(ethylenediamine)Cl][PF6]


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

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This is version 1.4 of the entry. See complete history


Literature

An Organometallic Compound which Exhibits a DNA Topology-Dependent One-Stranded Intercalation Mode.

Ma, Z.Palermo, G.Adhireksan, Z.Murray, B.S.von Erlach, T.Dyson, P.J.Rothlisberger, U.Davey, C.A.

(2016) Angew Chem Int Ed Engl 55: 7441-7444

  • DOI: https://doi.org/10.1002/anie.201602145
  • Primary Citation of Related Structures:  
    5CP6

  • 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.


  • Organizational Affiliation

    School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2C [auth A],
G [auth E]
135Xenopus laevisMutation(s): 1 
UniProt
Find proteins for P84233 (Xenopus laevis)
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UniProt GroupP84233
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4D [auth B],
H [auth F]
102Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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UniProt GroupP62799
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2AE [auth C],
I [auth G]
128Xenopus laevisMutation(s): 0 
Gene Names: hist1h2ajLOC494591
UniProt
Find proteins for P06897 (Xenopus laevis)
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UniProt GroupP06897
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B 1.1F [auth D],
J [auth H]
125Xenopus laevisMutation(s): 1 
UniProt
Find proteins for P02281 (Xenopus laevis)
Explore P02281 
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UniProt GroupP02281
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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (145-MER)A [auth I]145synthetic construct
Sequence Annotations
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (145-MER)B [auth J]145synthetic construct
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.57α = 90
b = 109.57β = 90
c = 182.61γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-01
    Type: Initial release
  • Version 1.1: 2016-06-08
    Changes: Other
  • Version 1.2: 2016-06-29
    Changes: Database references
  • Version 1.3: 2017-10-04
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description