3LJA

Using Soft X-Rays for a Detailed Picture of Divalent Metal Binding in the Nucleosome

Summary for 3LJA

• Entry DOI: 10.2210/pdb3lja/pdb
• Related: 1KX5
• Descriptor: Histone H3.2, Histone H4, Histone H2A, ... (8 entities in total)
• Functional Keywords: nucleosome, divalent metal, cation binding, counterion, compaction, chromosomal protein, dna-binding, methylation, nucleosome core, nucleus, structural protein-dna complex, structural protein/dna
• Biological source: Xenopus laevis (African clawed frog); More
• Cellular location: Nucleus: P84233 P62799 P02281; Nucleus (By similarity). Nucleus: Q6AZJ8
• Total number of polymer chains: 10
• Total formula weight: 201627.79

Authors

Wu, B.,Davey, C.A. (deposition date: 2010-01-26, release date: 2010-04-14, Last modification date: 2023-11-01)

Primary citation

Wu, B.,Davey, C.A.
Using soft X-rays for a detailed picture of divalent metal binding in the nucleosome
J.Mol.Biol., 398:633-640, 2010

PubMed Abstract: Divalent metals associate with DNA in a site-selective manner, which can influence nucleosome positioning, mobility, compaction, and recognition by nuclear factors. We previously characterized divalent metal binding in the nucleosome core using hard (short-wavelength) X-rays allowing high-resolution crystallographic determination of the strongest affinity sites, which revealed that Mn(2+) associates with the DNA major groove in a sequence- and conformation-dependent manner. In this study, we obtained diffraction data with soft X-rays at the Mn(2+) absorption edge for a core particle crystal in the presence of 10 mM MnSO(4), mimicking prevailing Mg(2+) concentration in the nucleus. This provides an exceptional view of counterion binding in the nucleosome through identification of 45 divalent metal binding sites. In addition to that at the well-characterized major interparticle interface, only one other histone-divalent metal binding site is found, which corresponds to a symmetry-related counterpart on the 'free' H2B alpha1 helix C-terminus. This emphasizes the importance of the alpha-helix dipole in ion binding and suggests that the H2B motif may serve as a nucleation site in nucleosome compaction. The 43 sites associated with the DNA are characterized by (1) high-affinity direct coordination at the most electrostatically favorable major groove locations, (2) metal hydrate binding to the major groove, (3) direct coordination to phosphate groups at sites of high charge density, (4) metal hydrate binding in the minor groove, or (5) metal hydrate-divalent anion pairing. Metal hydrates are found within the minor groove only at locations displaying a narrow range of high-intermediate width and to which histone N-terminal tails are not associated or proximal. This indicates that divalent metals and histone tails can both collaborate and compete in minor groove association, which sheds light on nucleosome solubility and chromatin compaction behavior.

PubMed: 20350553
DOI: 10.1016/j.jmb.2010.03.038

Experimental method

X-RAY DIFFRACTION (2.75 Å)