9D3O

167-bp 5S rDNA nucleosome - closed

9D3O の概要

• エントリーDOI: 10.2210/pdb9d3o/pdb
• 関連するPDBエントリー: 9D3K 9D3L 9D3M 9D3N 9D3P 9D3Q 9D3R 9D3S 9D3T
• EMDBエントリー: 46539 46541 46542
• 分子名称: Histone H3.2, Histone H4, Histone H2B type 1-M, ... (6 entities in total)
• 機能のキーワード: 5s rdna nucleosome, natural nucleosome positioning sequence, dna sequence-dependent breathing, gene regulation, gene regulation-dna complex, gene regulation/dna
• 由来する生物種: Homo sapiens (human); 詳細
• タンパク質・核酸の鎖数: 10
• 化学式量合計: 176611.55

構造登録者

Alegrio Louro, J.,Cruz-Becerra, G.,Kadonaga, J.T.,Leschziner, A.E. (登録日: 2024-08-11, 公開日: 2025-08-13, 最終更新日: 2025-10-15)

主引用文献

Alegrio-Louro, J.,Cruz-Becerra, G.,Kassavetis, G.A.,Kadonaga, J.T.,Leschziner, A.E.
Structural basis of nucleosome recognition by the conserved Dsup and HMGN nucleosome-binding motif.
Genes Dev., 39:1155-1161, 2025

PubMed Abstract: The tardigrade damage suppressor (Dsup) and vertebrate high-mobility group N (HMGN) proteins bind specifically to nucleosomes via a conserved motif whose structure has not been experimentally determined. Here we used cryo-EM to show that both proteins bind to the nucleosome acidic patch via analogous arginine anchors with one molecule bound to each face of the nucleosome. We additionally used the natural promoter-containing 5S rDNA sequence for structural analysis of the nucleosome. These structures of an ancient nucleosome-binding motif suggest that there is an untapped realm of proteins with a related mode of binding to chromatin.

PubMed: 40721296
DOI: 10.1101/gad.352720.125

実験手法

ELECTRON MICROSCOPY (3 Å)