2CV5

Crystal structure of human nucleosome core particle

Summary for 2CV5

• Entry DOI: 10.2210/pdb2cv5/pdb
• Descriptor: DNA (146-MER), Histone H3.1, Histone H4, ... (8 entities in total)
• Functional Keywords: human nucleosome structure, supercoiled dna path, metal binding site, structural protein-dna complex, structural protein/dna
• Biological source: Homo sapiens (human); More
• Cellular location: Nucleus: P68431 P62805 O60814
• Total number of polymer chains: 10
• Total formula weight: 200580.68

Authors

Tsunaka, Y.,Kajimura, N.,Tate, S.,Morikawa, K. (deposition date: 2005-05-31, release date: 2005-06-28, Last modification date: 2024-03-13)

Primary citation

Tsunaka, Y.,Kajimura, N.,Tate, S.,Morikawa, K.
Alteration of the nucleosomal DNA path in the crystal structure of a human nucleosome core particle
Nucleic Acids Res., 33:3424-3434, 2005

PubMed Abstract: Gene expression in eukaryotes depends upon positioning, mobility and packaging of nucleosomes; thus, we need the detailed information of the human nucleosome core particle (NCP) structure, which could clarify chromatin properties. Here, we report the 2.5 A crystal structure of a human NCP. The overall structure is similar to those of other NCPs reported previously. However, the DNA path of human NCP is remarkably different from that taken within other NCPs with an identical DNA sequence. A comparison of the structural parameters between human and Xenopus laevis DNA reveals that the DNA path of human NCP consecutively shifts by 1 bp in the regions of superhelix axis location -5.0 to -2.0 and 5.0 to 7.0. This alteration of the human DNA path is caused predominantly by tight DNA-DNA contacts within the crystal. It is also likely that the conformational change in the human H2B tail induces the local alteration of the DNA path. In human NCP, the region with the altered DNA path lacks Mn2+ ions and the B-factors of the DNA phosphate groups are substantially high. Therefore, in contrast to the histone octamer, the nucleosomal DNA is sufficiently flexible and mobile and can undergo drastic conformational changes, depending upon the environment.

PubMed: 15951514
DOI: 10.1093/nar/gki663

Experimental method

X-RAY DIFFRACTION (2.5 Å)