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 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1002/anie.201602145
  • Structures With Same Primary Citation

  • 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 ...

    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. davey@ntu.edu.sg.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2
A, E
135Xenopus laevisMutation(s): 1 
Find proteins for P84233 (Xenopus laevis)
Go to UniProtKB:  P84233
Protein Feature View
  • Reference Sequence

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Histone H2B 1.1
D, H
125Xenopus laevisMutation(s): 1 
Find proteins for P02281 (Xenopus laevis)
Go to UniProtKB:  P02281
Protein Feature View
  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
102Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Protein Feature View
  • Reference Sequence

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Histone H2A
C, G
128Xenopus laevisMutation(s): 0 
Gene Names: hist1h2ajLOC494591
Find proteins for P06897 (Xenopus laevis)
Go to UniProtKB:  P06897
Protein Feature View
  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganism
DNA (145-MER)I145synthetic construct

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsLengthOrganism
DNA (145-MER)J145synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RUH
Query on RUH

Download CCD File 
I, J
(ethane6-5,8,9,10-tetrahydroanthracene)Ru(II)(ethylene-diamine)Cl
C16 H22 Cl N2 Ru
GYWLGEANONYPCA-UHFFFAOYSA-M
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
D, G, H
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download CCD File 
E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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