PDBsum entry 5cp6

Structural protein/DNA

PDB id: 5cp6

Contents

Protein chains

96 a.a.

82 a.a.

106 a.a.

95 a.a.

87 a.a.

DNA/RNA

Ligands

RUH ×3

SO4 ×3

Metals

_MG

Waters ×35

PDB id:

5cp6

Name:

Structural protein/DNA

Title:

Nucleosome core particle with adducts from the anticancer compound, [(eta6-5,8,9,10-tetrahydroanthracene)ru(ethylenediamine)cl][pf6]

Structure:

DNA (145-mer). Chain: i. Engineered: yes. DNA (145-mer). Chain: j. Engineered: yes. Histone h3.2. Chain: a, e. Engineered: yes.

Source:

Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Xenopus laevis. African clawed frog. Organism_taxid: 8355. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: hist1h2aj, loc494591.

Resolution:

2.60Å R-factor: 0.211 R-free: 0.251

Authors:

Z.Ma,Z.Adhireksan,B.S.Murray,P.J.Dyson,C.A.Davey

Key ref:

Z.Ma et al. (2016). An Organometallic Compound which Exhibits a DNA Topology-Dependent One-Stranded Intercalation Mode. Angew Chem Int Ed Engl, 55, 7441-7444. PubMed id: 27184539 DOI: 10.1002/anie.201602145

Date:

21-Jul-15 Release date: 01-Jun-16

Protein chains

P84233  (H32_XENLA) -  Histone H3.2 from Xenopus laevis

Seq: 136 a.a.

Struc: 96 a.a.*

Protein chain

P62799  (H4_XENLA) -  Histone H4 from Xenopus laevis

Seq: 103 a.a.

Struc: 82 a.a.

Protein chains

P06897  (H2A1_XENLA) -  Histone H2A type 1 from Xenopus laevis

Seq: 130 a.a.

Struc: 106 a.a.*

Protein chains

P02281  (H2B11_XENLA) -  Histone H2B 1.1 from Xenopus laevis

Seq: 126 a.a.

Struc: 95 a.a.*

Protein chain

P62799  (H4_XENLA) -  Histone H4 from Xenopus laevis

Seq: 103 a.a.

Struc: 87 a.a.

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

DNA/RNA chains

A-T-C-A-A-T-A-T-C-C-A-C-C-T-G-C-A-G-A-T-A-C-T-A-C-C-A-A-A-A-G-T-G-T-A-T-T-T-G- 145 bases

A-T-C-A-A-T-A-T-C-C-A-C-C-T-G-C-A-G-A-T-A-C-T-A-C-C-A-A-A-A-G-T-G-T-A-T-T-T-G- 145 bases

DOI no: 10.1002/anie.201602145

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

PubMed id: 27184539

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

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

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.