Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 8-mer - A2BCD Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Hetero 8-mer - A6B2 

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

Macromolecule Content

• Total Structure Weight: 199.58 kDa 
• Atom Count: 12097 
• Residue Count: 1053 
• Unique protein chains: 4
• Unique nucleic acid chains: 2

5CP6

Nucleosome Core Particle with Adducts from the Anticancer Compound, [(eta6-5,8,9,10-tetrahydroanthracene)Ru(ethylenediamine)Cl][PF6]

• DOI: 10.2210/pdb5CP6/pdb
• NDB: 5CP6

• Classification: STRUCTURAL PROTEIN/DNA
• Organism(s): Xenopus laevis, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-07-21 Released: 2016-06-01 
• Deposition Author(s): Ma, Z., Adhireksan, Z., Murray, B.S., Dyson, P.J., Davey, C.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.251 
• R-Value Work: 0.210 
• R-Value Observed: 0.211 

Literature

An Organometallic Compound which Exhibits a DNA Topology-Dependent One-Stranded Intercalation Mode.

Ma, Z., Palermo, G., Adhireksan, Z., Murray, B.S., von Erlach, T., Dyson, P.J., Rothlisberger, U., Davey, C.A.

(2016) Angew Chem Int Ed Engl 55: 7441-7444

• PubMed: 27184539 
• DOI: 10.1002/anie.201602145
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Understanding how small molecules interact with DNA is essential since it underlies a multitude of pathological conditions and therapeutic interventions. Many different intercalator compounds have been studied because of their activity as mutagens or drugs, but little is known regarding their interaction with nucleosomes, the protein-packaged form of DNA in cells. Here, using crystallographic methods and molecular dynamics simulations, we discovered that adducts formed by [(η(6) -THA)Ru(ethylenediamine)Cl][PF6 ] (THA=5,8,9,10-tetrahydroanthracene; RAED-THA-Cl[PF6 ]) in the nucleosome comprise a novel one-stranded intercalation and DNA distortion mode. Conversely, the THA group in fact remains solvent exposed and does not disrupt base stacking in RAED-THA adducts on B-form DNA. This newly observed DNA binding mode and topology dependence may actually be prevalent and should be considered when studying covalently binding intercalating compounds.

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Organizational Affiliation: 

School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore. [e-mail].

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Histone H3.2	A, E	135	Xenopus laevis	Mutation(s): 1
Find proteins for P84233 (Xenopus laevis) Go to UniProtKB:  P84233

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
Histone H2B 1.1	D, H	125	Xenopus laevis	Mutation(s): 1
Find proteins for P02281 (Xenopus laevis) Go to UniProtKB:  P02281

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Histone H4	B, F	102	Xenopus laevis	Mutation(s): 0
Find proteins for P62799 (Xenopus laevis) Go to UniProtKB:  P62799

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
Histone H2A	C, G	128	Xenopus laevis	Mutation(s): 0  Gene Names: hist1h2aj, LOC494591
Find proteins for P06897 (Xenopus laevis) Go to UniProtKB:  P06897

Entity ID: 1
Molecule	Chains	Length	Organism
DNA (145-MER)	I	145	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism
DNA (145-MER)	J	145	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RUH	I, J	(ethane6-5,8,9,10-tetrahydroanthracene)Ru(II)(ethylene-diamine)Cl C16 H22 Cl N2 Ru GYWLGEANONYPCA-UHFFFAOYSA-M
SO4	D, G, H	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	E	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.251 
• R-Value Work: 0.210 
• R-Value Observed: 0.211 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.57	α = 90
b = 109.57	β = 90
c = 182.61	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-07-21 
• Released Date: 2016-06-01 
Deposition Author(s): Ma, Z., Adhireksan, Z., Murray, B.S., Dyson, P.J., Davey, C.A.

Revision History 

• Version 1.0: 2016-06-01
  Type: Initial release
  
• Version 1.1: 2016-06-08
  Changes: Other
• Version 1.2: 2016-06-29
  Changes: Database references
• Version 1.3: 2017-10-04
  Changes: Data collection, Database references, Derived calculations