7YI3

Cryo-EM structure of Rpd3S in close-state Rpd3S-NCP complex

7YI3 の概要

• エントリーDOI: 10.2210/pdb7yi3/pdb
• 関連するPDBエントリー: 7YI0 7YI1 7YI2
• EMDBエントリー: 33845 33848 33849 33850
• 分子名称: Transcriptional regulatory protein SIN3, Histone deacetylase RPD3, Chromatin modification-related protein EAF3, ... (5 entities in total)
• 機能のキーワード: dynamic histone modifications, gene regulation, histone deacetylase complex
• 由来する生物種: Saccharomyces cerevisiae S288C (baker's yeast); 詳細
• タンパク質・核酸の鎖数: 5
• 化学式量合計: 427505.28

構造登録者

Li, H.T.,Yan, C.Y.,Guan, H.P.,Wang, P. (登録日: 2022-07-14, 公開日: 2023-06-14, 最終更新日: 2023-08-30)

主引用文献

Guan, H.,Wang, P.,Zhang, P.,Ruan, C.,Ou, Y.,Peng, B.,Zheng, X.,Lei, J.,Li, B.,Yan, C.,Li, H.
Diverse modes of H3K36me3-guided nucleosomal deacetylation by Rpd3S.
Nature, 620:669-675, 2023

PubMed Abstract: Context-dependent dynamic histone modifications constitute a key epigenetic mechanism in gene regulation. The Rpd3 small (Rpd3S) complex recognizes histone H3 trimethylation on lysine 36 (H3K36me3) and deacetylates histones H3 and H4 at multiple sites across transcribed regions. Here we solved the cryo-electron microscopy structures of Saccharomyces cerevisiae Rpd3S in its free and H3K36me3 nucleosome-bound states. We demonstrated a unique architecture of Rpd3S, in which two copies of Eaf3-Rco1 heterodimers are asymmetrically assembled with Rpd3 and Sin3 to form a catalytic core complex. Multivalent recognition of two H3K36me3 marks, nucleosomal DNA and linker DNAs by Eaf3, Sin3 and Rco1 positions the catalytic centre of Rpd3 next to the histone H4 N-terminal tail for deacetylation. In an alternative catalytic mode, combinatorial readout of unmethylated histone H3 lysine 4 and H3K36me3 by Rco1 and Eaf3 directs histone H3-specific deacetylation except for the registered histone H3 acetylated lysine 9. Collectively, our work illustrates dynamic and diverse modes of multivalent nucleosomal engagement and methylation-guided deacetylation by Rpd3S, highlighting the exquisite complexity of epigenetic regulation with delicately designed multi-subunit enzymatic machineries in transcription and beyond.

PubMed: 37468628
DOI: 10.1038/s41586-023-06349-1

実験手法

ELECTRON MICROSCOPY (3.3 Å)