2CV5

Crystal structure of human nucleosome core particle

2CV5 の概要

• エントリーDOI: 10.2210/pdb2cv5/pdb
• 分子名称: DNA (146-MER), Histone H3.1, Histone H4, ... (8 entities in total)
• 機能のキーワード: human nucleosome structure, supercoiled dna path, metal binding site, structural protein-dna complex, structural protein/dna
• 由来する生物種: Homo sapiens (human); 詳細
• 細胞内の位置: Nucleus: P68431 P62805 O60814
• タンパク質・核酸の鎖数: 10
• 化学式量合計: 200580.68

構造登録者

Tsunaka, Y.,Kajimura, N.,Tate, S.,Morikawa, K. (登録日: 2005-05-31, 公開日: 2005-06-28, 最終更新日: 2024-03-13)

主引用文献

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

実験手法

X-RAY DIFFRACTION (2.5 Å)