5DNM

Nucleosome core particle containing adducts of ruthenium(II)-toluene PTA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Allosteric cross-talk in chromatin can mediate drug-drug synergy

Adhireksan, Z.Palermo, G.Riedel, T.Ma, Z.Muhammad, R.Rothlisberger, U.Dyson, P.J.Davey, C.A.

(2017) Nat Commun 8: 14860-14860

  • DOI: 10.1038/ncomms14860
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Exploitation of drug-drug synergism and allostery could yield superior therapies by capitalizing on the immensely diverse, but highly specific, potential associated with the biological macromolecular landscape. Here we describe a drug-drug synergy me ...

    Exploitation of drug-drug synergism and allostery could yield superior therapies by capitalizing on the immensely diverse, but highly specific, potential associated with the biological macromolecular landscape. Here we describe a drug-drug synergy mediated by allosteric cross-talk in chromatin, whereby the binding of one drug alters the activity of the second. We found two unrelated drugs, RAPTA-T and auranofin, that yield a synergistic activity in killing cancer cells, which coincides with a substantially greater number of chromatin adducts formed by one of the compounds when adducts from the other agent are also present. We show that this occurs through an allosteric mechanism within the nucleosome, whereby defined histone adducts of one drug promote reaction of the other drug at a distant, specific histone site. This opens up possibilities for epigenetic targeting and suggests that allosteric modulation in nucleosomes may have biological relevance and potential for therapeutic interventions.


    Organizational Affiliation

    NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921, Singapore.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2
A, E
135Xenopus laevisMutation(s): 1 
Find proteins for P84233 (Xenopus laevis)
Go to UniProtKB:  P84233

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B, F
102Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A
C, G
128Xenopus laevisMutation(s): 0 
Gene Names: hist1h2ajLOC494591
Find proteins for P06897 (Xenopus laevis)
Go to UniProtKB:  P06897

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B 1.1
D, H
125Xenopus laevisMutation(s): 1 
Find proteins for P02281 (Xenopus laevis)
Go to UniProtKB:  P02281

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsLengthOrganism
DNA (145-MER)I145synthetic construct

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 6
MoleculeChainsLengthOrganism
DNA (145-MER)J145synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RAX
Query on RAX

Download CCD File 
G, H
dichloro[(1,2,3,4,5,6-eta)-6-methylbenzene]1,3,5-triaza-7lambda~5~-phosphatricyclo[3.3.1.1~3,7~]dec-7-ylruthenium
C13 H20 Cl2 N3 P Ru
HQZSVEABAKKRLM-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: 2.81 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.68α = 90
b = 109.82β = 90
c = 182.34γ = 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: 2016-09-14
    Type: Initial release
  • Version 1.1: 2017-08-16
    Changes: Database references, Derived calculations