6IQ4

Nucleosome core particle cross-linked with a hetero-binuclear molecule possessing RAPTA and gold(I) 4-(diphenylphosphino)benzoic acid groups.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.233 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crosslinking Allosteric Sites on the Nucleosome.

Batchelor, L.K.De Falco, L.von Erlach, T.Sharma, D.Adhireksan, Z.Roethlisberger, U.Davey, C.A.Dyson, P.J.

(2019) Angew Chem Int Ed Engl 58: 15660-15664

  • DOI: 10.1002/anie.201906423
  • Primary Citation of Related Structures:  
    6IQ4

  • PubMed Abstract: 
  • Targeting defined histone protein sites in chromatin is an emerging therapeutic approach that can potentially be enhanced by allosteric effects within the nucleosome. Here we characterized a novel hetero-bimetallic compound with a design based on a nucleosomal allostery effect observed earlier for two unrelated drugs-the Ru II antimetastasis/antitumor RAPTA-T and the Au I anti-arthritic auranofin ...

    Targeting defined histone protein sites in chromatin is an emerging therapeutic approach that can potentially be enhanced by allosteric effects within the nucleosome. Here we characterized a novel hetero-bimetallic compound with a design based on a nucleosomal allostery effect observed earlier for two unrelated drugs-the Ru II antimetastasis/antitumor RAPTA-T and the Au I anti-arthritic auranofin. The Ru II moiety binds specifically to two H2A glutamate residues on the nucleosome acidic patch, allosterically triggering a cascade of structural changes that promote binding of the Au I moiety to selective histidine residues on H3, resulting in cross-linking sites that are over 35 Å distant. By tethering the H2A-H2B dimers to the H3-H4 tetramer, the hetero-bimetallic compound significantly increases stability of the nucleosome, illustrating its utility as a site-selective cross-linking agent.


    Organizational Affiliation

    Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.1A, E98Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
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PHAROS:  P68431
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UniProt GroupP68431
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B82Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P62805 (Homo sapiens)
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PHAROS:  P62805
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UniProt GroupP62805
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1-B/EC, G106Homo sapiensMutation(s): 0 
Gene Names: HIST1H2ABH2AFMHIST1H2AEH2AFAH2AC4H2AC8
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Find proteins for P04908 (Homo sapiens)
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PHAROS:  P04908
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UniProt GroupP04908
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-JD, H95Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJH2BFRH2BC11
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Find proteins for P06899 (Homo sapiens)
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GTEx:  ENSG00000124635 
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UniProt GroupP06899
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4F87Homo sapiensMutation(s): 0 
Gene Names: 
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (145-MER)I 145Homo sapiens
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Entity ID: 7
MoleculeChainsLengthOrganismImage
DNA (145-MER)J 145Homo sapiens
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D0X (Subject of Investigation/LOI)
Query on D0X

Download Ideal Coordinates CCD File 
N [auth G][Ru(eta(6)-p-cymene)Cl-2(pta)
C16 H22 Cl2 N3 P Ru
HCFRVYRXZWDWIV-UHFFFAOYSA-M
 Ligand Interaction
XIS (Subject of Investigation/LOI)
Query on XIS

Download Ideal Coordinates CCD File 
L [auth A]4-diphenylphosphanylbenzoic acid
C19 H15 O2 P
GXMHDTPYKRTARV-UHFFFAOYSA-N
 Ligand Interaction
AU
Query on AU

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K [auth A]GOLD ION
Au
ZBKIUFWVEIBQRT-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
M [auth D],
O [auth I],
P [auth I],
Q [auth J]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.233 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.307α = 90
b = 109.741β = 90
c = 183.254γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-30
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Database references