PDBsum entry 3mgr

Structural protein/DNA

PDB id: 3mgr

Contents

Protein chains

99 a.a. *

79 a.a. *

104 a.a. *

99 a.a. *

87 a.a. *

DNA/RNA

Metals

_CL ×4

_RB ×5

_MN ×14

* Residue conservation analysis

PDB id:

3mgr

Name:

Structural protein/DNA

Title:

Binding of rubidium ions to the nucleosome core particle

Structure:

Histone h3.2. Chain: a, e. Engineered: yes. Histone h4. Chain: b, f. Engineered: yes. Histone h2a. Chain: c, g. Fragment: unp residues 2-120.

Source:

Xenopus laevis. African clawed frog. Organism_taxid: 8355. Gene: histone 3 or h3. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: histone 4 or h4. Gene: histone 2a or h2a, loc494591. Gene: histone 2b or h2b.

Resolution:

2.30Å R-factor: 0.242 R-free: 0.267

Authors:

K.Mohideen,R.Muhammad,C.A.Davey

Key ref:

K.Mohideen et al. (2010). Perturbations in nucleosome structure from heavy metal association. Nucleic Acids Res, 38, 6301-6311. PubMed id: 20494975

Date:

07-Apr-10 Release date: 16-Jun-10

Protein chains

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

Seq: 136 a.a.

Struc: 99 a.a.*

Protein chain

P62799  (H4_XENLA) -  Histone H4 from Xenopus laevis

Seq: 103 a.a.

Struc: 79 a.a.

Protein chains

Q6AZJ8  (Q6AZJ8_XENLA) -  Histone H2A from Xenopus laevis

Seq: 130 a.a.

Struc: 104 a.a.

Protein chains

P02281  (H2B11_XENLA) -  Histone H2B 1.1 from Xenopus laevis

Seq: 126 a.a.

Struc: 99 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 2 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- 147 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- 147 bases

Nucleic Acids Res 38:6301-6311 (2010)

PubMed id: 20494975

Perturbations in nucleosome structure from heavy metal association.

K.Mohideen, R.Muhammad, C.A.Davey.

ABSTRACT

Heavy metals have the potential to engage in strong bonding interactions and can thus function in essential as well as toxic or therapeutic capacities. We conducted crystallographic analyses of heavy cation binding to the nucleosome core particle and found that Co(2+) and Ni(2+) preferentially associate with the DNA major groove, in a sequence- and conformation-dependent manner. Conversely, Rb(+) and Cs(+) are found to bind only opportunistically to minor groove elements of the DNA, in particular at narrow AT dinucleotide sites. Furthermore, relative to Mn(2+) the aggressive coordination of Co(2+) and Ni(2+) to guanine bases is observed to induce a shift in histone-DNA register around the nucleosome center by stabilizing DNA stretching over one region accompanied by expulsion of two bases at an opposing location. These 'softer' transition metals also associate with multiple histone protein sites, including inter-nucleosomal cross-linking, and display a proclivity for coordination to histidine. Sustained binding and the ability to induce structural perturbations at specific locations in the nucleosome may contribute to genetic and epigenetic mechanisms of carcinogenesis mediated by Co(2+) and Ni(2+).