5XF6

Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having an ethylenediamine linker


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Nucleosome acidic patch-targeting binuclear ruthenium compounds induce aberrant chromatin condensation

Davey, G.E.Adhireksan, Z.Ma, Z.Riedel, T.Sharma, D.Padavattan, S.Rhodes, D.Ludwig, A.Sandin, S.Murray, B.S.Dyson, P.J.Davey, C.A.

(2017) Nat Commun 8: 1575-1575

  • DOI: 10.1038/s41467-017-01680-4
  • Primary Citation of Related Structures:  
    5XF4, 5XF3, 5XF6, 5XF5

  • PubMed Abstract: 
  • The 'acidic patch' is a highly electronegative cleft on the histone H2A-H2B dimer in the nucleosome. It is a fundamental motif for protein binding and chromatin dynamics, but the cellular impact of targeting this potentially therapeutic site with exo ...

    The 'acidic patch' is a highly electronegative cleft on the histone H2A-H2B dimer in the nucleosome. It is a fundamental motif for protein binding and chromatin dynamics, but the cellular impact of targeting this potentially therapeutic site with exogenous molecules remains unclear. Here, we characterize a family of binuclear ruthenium compounds that selectively target the nucleosome acidic patch, generating intra-nucleosomal H2A-H2B cross-links as well as inter-nucleosomal cross-links. In contrast to cisplatin or the progenitor RAPTA-C anticancer drugs, the binuclear agents neither arrest specific cell cycle phases nor elicit DNA damage response, but rather induce an irreversible, anomalous state of condensed chromatin that ultimately results in apoptosis. In vitro, the compounds induce misfolding of chromatin fibre and block the binding of the regulator of chromatin condensation 1 (RCC1) acidic patch-binding protein. This family of chromatin-modifying molecules has potential for applications in drug development and as tools for chromatin research.


    Organizational Affiliation

    NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore, 636921, Singapore. davey@ntu.edu.sg.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2AE135Xenopus laevisMutation(s): 1 
Find proteins for P84233 (Xenopus laevis)
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Go to UniProtKB:  P84233
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4BF102Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
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Go to UniProtKB:  P62799
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2ACG128Xenopus laevisMutation(s): 0 
Gene Names: hist1h2ajLOC494591
Find proteins for P06897 (Xenopus laevis)
Explore P06897 
Go to UniProtKB:  P06897
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B 1.1DH125Xenopus laevisMutation(s): 1 
Find proteins for P02281 (Xenopus laevis)
Explore P02281 
Go to UniProtKB:  P02281
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (145-MER)I145Homo sapiens
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (145-MER)J145Homo sapiens
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RUD
Query on RUD

Download CCD File 
G, H
[ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2
C16 H24 Cl2 N3 O2 P Ru
UZIJOIXYBLAWLW-UHFFFAOYSA-M
 Ligand Interaction
SO4
Query on SO4

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C, G, H
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDN
Query on EDN

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G
ETHANE-1,2-DIAMINE
C2 H8 N2
PIICEJLVQHRZGT-UHFFFAOYSA-N
 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: 2.63 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.84α = 90
b = 109.729β = 90
c = 182.527γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-10-11
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Database references