2NZD

Nucleosome core particle containing 145 bp of DNA

Summary for 2NZD

• Entry DOI: 10.2210/pdb2nzd/pdb
• Related: 1KX3 1KX4 1KX5
• Descriptor: DNA (145-MER), Histone H3, Histone H4, ... (8 entities in total)
• Functional Keywords: nucleosome, chromatin, histone, dna stretching, dna kinking, double-helix, structural protein-dna complex, structural protein/dna
• Biological source: Xenopus laevis (African clawed frog); More
• Cellular location: Nucleus: P62799 P02281; Nucleus (By similarity): Q6AZJ8
• Total number of polymer chains: 10
• Total formula weight: 196807.34

Authors

Ong, M.S.,Richmond, T.J.,Davey, C.A. (deposition date: 2006-11-23, release date: 2007-04-10, Last modification date: 2023-08-30)

Primary citation

Ong, M.S.,Richmond, T.J.,Davey, C.A.
DNA stretching and extreme kinking in the nucleosome core
J.Mol.Biol., 368:1067-1074, 2007

PubMed Abstract: DNA stretching in chromatin may facilitate its compaction and influence site recognition by nuclear factors. In vivo, stretching has been estimated to occur at the equivalent of one to two base-pairs (bp) per nucleosome. We have determined the crystal structure of a nucleosome core particle containing 145 bp of DNA (NCP145). Compared to the structure with 147 bp, the NCP145 displays two incidences of stretching one to two double-helical turns from the particle dyad axis. The stretching illustrates clearly a mechanism for shifting DNA position by displacement of a single base-pair while maintaining nearly identical histone-DNA interactions. Increased DNA twist localized to a short section between adjacent histone-DNA binding sites advances the rotational setting, while a translational component involves DNA kinking at a flanking region that initiates elongation by unstacking bases. Furthermore, one stretched region of the NCP145 displays an extraordinary 55 degrees kink into the minor groove situated 1.5 double-helical turns from the particle dyad axis, a hot spot for gene insertion by HIV-integrase, which prefers highly distorted substrate. This suggests that nucleosome position and context within chromatin could promote extreme DNA kinking that may influence genomic processes.

PubMed: 17379244
DOI: 10.1016/j.jmb.2007.02.062

Experimental method

X-RAY DIFFRACTION (2.65 Å)