Biological Assembly 1  

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 8-mer - A2B2C2D2 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 8-mer -A8 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: native gel electrophoresis, cross-linking

Macromolecule Content

• Total Structure Weight: 177347.31 
• Atom Count: 12085 
• Residue Count: 1057 
• Unique protein chains: 5
• Unique nucleic acid chains: 2

6IQ4

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

• DOI: 10.2210/pdb6IQ4/pdb
• NDB: 6IQ4

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2018-11-06 Released: 2019-10-30 
• Deposition Author(s): DeFalco, L., Batchelor, L.K., Adhireksan, Z., Dyson, P.J., Davey, C.A.

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Experimental Data Snapshot

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

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

• PubMed: 31478581 
• 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 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
Histone H3.1	A, E	98	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
Histone H4	B	82	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
Histone H2A type 1-B/E	C, G	106	Homo sapiens	Mutation(s): 0  Gene Names: H2AC4, H2AC8 (H2AFM, HIST1H2AB, H2AFA, HIST1H2AE)
Find proteins for P04908 (Homo sapiens) Go to UniProtKB:  P04908

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Histone H2B type 1-J	D, H	95	Homo sapiens	Mutation(s): 0  Gene Names: H2BC11 (H2BFR, HIST1H2BJ)
Find proteins for P06899 (Homo sapiens) Go to UniProtKB:  P06899

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
Histone H4	F	87	Homo sapiens	Mutation(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
Molecule	Chains	Length	Organism
DNA (145-MER)	I	145	Homo sapiens

Entity ID: 7
Molecule	Chains	Length	Organism
DNA (145-MER)	J	145	Homo sapiens

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
XIS	A	4-diphenylphosphanylbenzoic acid C19 H15 O2 P GXMHDTPYKRTARV-UHFFFAOYSA-N
AU	A	GOLD ION Au ZBKIUFWVEIBQRT-UHFFFAOYSA-N
MG	D, I, J	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
D0X	G	[Ru(eta(6)-p-cymene)Cl-2(pta) C16 H22 Cl2 N3 P Ru HCFRVYRXZWDWIV-UHFFFAOYSA-M

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 = 107.307	α = 90.00
b = 109.741	β = 90.00
c = 183.254	γ = 90.00

Software Package:

Software Name	Purpose
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-11-06 
• Released Date: 2019-10-30 
• Deposition Author(s): DeFalco, L., Batchelor, L.K., Adhireksan, Z., Dyson, P.J., Davey, C.A.

Revision History 

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