8KE0

Structure of H1.2 bound to the nucleosome

8KE0 の概要

• エントリーDOI: 10.2210/pdb8ke0/pdb
• EMDBエントリー: 37149
• 分子名称: Histone H3.1, Histone H4, Histone H2A type 1-B/E, ... (7 entities in total)
• 機能のキーワード: nucleosome, chromatin, dna, h1.2, complex, dna binding protein
• 由来する生物種: Homo sapiens (human); 詳細
• タンパク質・核酸の鎖数: 11
• 化学式量合計: 253450.77

構造登録者

Kujirai, T.,Echigoya, K.,Takizawa, Y.,Kurumizaka, H. (登録日: 2023-08-11, 公開日: 2025-03-12, 最終更新日: 2025-07-30)

主引用文献

Kujirai, T.,Echigoya, K.,Kishi, Y.,Saeki, M.,Ito, T.,Kato, J.,Negishi, L.,Kimura, H.,Masumoto, H.,Takizawa, Y.,Gotoh, Y.,Kurumizaka, H.
Structural insights into how DEK nucleosome binding facilitates H3K27 trimethylation in chromatin.
Nat.Struct.Mol.Biol., 32:1183-1192, 2025

PubMed Abstract: Structural diversity of the nucleosome affects chromatin conformations and regulates eukaryotic genome functions. Here we identify DEK, whose function is unknown, as a nucleosome-binding protein. In embryonic neural progenitor cells, DEK colocalizes with H3 K27 trimethylation (H3K27me3), the facultative heterochromatin mark. DEK stimulates the methyltransferase activity of Polycomb repressive complex 2 (PRC2), which is responsible for H3K27me3 deposition in vitro. Cryo-electron microscopy structures of the DEK-nucleosome complexes reveal that DEK binds the nucleosome by its tripartite DNA-binding mode on the dyad and linker DNAs and interacts with the nucleosomal acidic patch by its newly identified histone-binding region. The DEK-nucleosome interaction mediates linker DNA reorientation and induces chromatin compaction, which may facilitate PRC2 activation. These findings provide mechanistic insights into chromatin structure-mediated gene regulation by DEK.

PubMed: 39984731
DOI: 10.1038/s41594-025-01493-w

実験手法

ELECTRON MICROSCOPY (4 Å)