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 

wwPDB Validation 3D Report Full Report


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

  • 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 n ...

    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.,School of Biological Sciences & NTU Institute of Structural Biology, Nanyang Technological University (NTU), Singapore, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.1
A, E
98Homo sapiensMutation(s): 0 
Gene Names: H3C1, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3C10, H3C11, H3C12 (H3FA, HIST1H3A, H3FL, HIST1H3B, H3FC HIST1H3C, H3FB, HIST1H3D, H3FD, HIST1H3E, H3FI, HIST1H3F, H3FH, HIST1H3G, H3FK, HIST1H3H, H3FF, HIST1H3I, H3FJ, HIST1H3J)
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B
82Homo sapiensMutation(s): 0 
Gene Names: H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4-16 (H4/A, H4FA, HIST1H4A, H4/I, H4FI, HIST1H4B, H4/G, H4FG, HIST1H4C, H4/B, H4FB, HIST1H4D, H4/J, H4FJ, HIST1H4E, H4/C, H4FC, HIST1H4F, H4/H, H4FH, HIST1H4H, H4/M, H4FM, HIST1H4I, H4/E, H4FE, HIST1H4J, H4/D, H4FD, HIST1H4K, H4/K, H4FK, HIST1H4L, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4/O, H4FO, HIST2H4B, HIST4H4)
Find proteins for P62805 (Homo sapiens)
Go to UniProtKB:  P62805
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1-B/E
C, G
106Homo sapiensMutation(s): 0 
Gene Names: H2AC4, H2AC8 (H2AFM, HIST1H2AB, H2AFA, HIST1H2AE)
Find proteins for P04908 (Homo sapiens)
Go to UniProtKB:  P04908
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B type 1-J
D, H
95Homo sapiensMutation(s): 0 
Gene Names: H2BC11 (H2BFR, HIST1H2BJ)
Find proteins for P06899 (Homo sapiens)
Go to UniProtKB:  P06899
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Histone H4
F
87Homo sapiensMutation(s): 0 
Gene Names: H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4-16 (H4/A, H4FA, HIST1H4A, H4/I, H4FI, HIST1H4B, H4/G, H4FG, HIST1H4C, H4/B, H4FB, HIST1H4D, H4/J, H4FJ, HIST1H4E, H4/C, H4FC, HIST1H4F, H4/H, H4FH, HIST1H4H, H4/M, H4FM, HIST1H4I, H4/E, H4FE, HIST1H4J, H4/D, H4FD, HIST1H4K, H4/K, H4FK, HIST1H4L, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4/O, H4FO, HIST2H4B, HIST4H4)
Find proteins for P62805 (Homo sapiens)
Go to UniProtKB:  P62805
Entity ID: 6
MoleculeChainsLengthOrganism
DNA (145-MER)I145Homo sapiens
Entity ID: 7
MoleculeChainsLengthOrganism
DNA (145-MER)J145Homo sapiens
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XIS
Query on XIS

Download SDF File 
Download CCD File 
A
4-diphenylphosphanylbenzoic acid
C19 H15 O2 P
GXMHDTPYKRTARV-UHFFFAOYSA-N
 Ligand Interaction
AU
Query on AU

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Download CCD File 
A
GOLD ION
Au
ZBKIUFWVEIBQRT-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
D, I, J
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
D0X
Query on D0X

Download SDF File 
Download CCD File 
G
[Ru(eta(6)-p-cymene)Cl-2(pta)
C16 H22 Cl2 N3 P Ru
HCFRVYRXZWDWIV-UHFFFAOYSA-M
 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 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 107.307α = 90.00
b = 109.741β = 90.00
c = 183.254γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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