EMDB/PDB/SASBDBから引用されている文献のデータベース

キーワード
構造解析手法	All X線回折 NMR 電子顕微鏡小角散乱中性子線回折線維回折粉末回折赤外分光 EPR FRET 理論モデルハイブリッド
著者・登録者
ジャーナル
IF	>30 >20 >10 >5 all

タイトル	Structure of histone deacetylase complex Rpd3S bound to nucleosome.
ジャーナル・号・ページ	Nat Struct Mol Biol, Vol. 30, Issue 12, Page 1893-1901, Year 2023
掲載日	2023年10月5日
著者	Wulong Li / Hengjun Cui / Zhimin Lu / Haibo Wang /
PubMed 要旨	Crosstalk between histone modifications represents a fundamental epigenetic mechanism in gene regulation. During the transcription elongation process, the histone deacetylase complex Rpd3S is ...Crosstalk between histone modifications represents a fundamental epigenetic mechanism in gene regulation. During the transcription elongation process, the histone deacetylase complex Rpd3S is recruited to H3K36-methylated nucleosomes to suppress cryptic transcription initiation. However, how subunits of Rpd3S are assembled and coordinated to recognize nucleosomal substrates and exert their deacetylation function remains unclear. Here we report the structure of Saccharomyces cerevisiae Rpd3S deacetylase bound to H3K36me3-modified nucleosome at 3.1 Å resolution. It shows that Sin3 and Rco1 subunits orchestrate the assembly of the complex and mediate its contact with nucleosome at multiple sites, with the Sin3-DNA interface as a pivotal anchor. The PHD1 domain of Rco1 recognizes the unmodified H3K4 and places the following H3 tail toward the active site of Rpd3, while the chromodomain of Eaf3 subunit recognizes the H3K36me3 mark and contacts both nucleosomal and linker DNA. The second copy of Eaf3-Rco1 is involved in neighboring nucleosome binding. Our work unravels the structural basis of chromatin targeting and deacetylation by the Rpd3S complex.
リンク	Nat Struct Mol Biol / PubMed:37798513
手法	EM (単粒子)
解像度	3.0 - 7.6 Å
構造データ	35081 8hxx EMDB-35081, PDB-8hxx: Cryo-EM structure of the histone deacetylase complex Rpd3S 手法: EM (単粒子) / 解像度: 3.0 Å 35082 8hxy EMDB-35082, PDB-8hxy: Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome 手法: EM (単粒子) / 解像度: 3.1 Å 35083 8hxz EMDB-35083, PDB-8hxz: Cryo-EM structure of Eaf3 CHD in complex with nucleosome 手法: EM (単粒子) / 解像度: 3.4 Å 35084 8hy0 EMDB-35084, PDB-8hy0: Composite cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome 手法: EM (単粒子) / 解像度: 3.1 Å EMDB-35217: Concensus map of the Rpd3S-nucleosome complex 手法: EM (単粒子) / 解像度: 3.7 Å EMDB-35218: Focused refinement map of nucleosome in the Rpd3S-nucleosome complex 手法: EM (単粒子) / 解像度: 3.2 Å EMDB-35219: Focused refinement map of Rpd3S in the Rpd3S-nucleosome complex 手法: EM (単粒子) / 解像度: 3.1 Å EMDB-35220: Focused refinement map of the tail of Rpd3S 手法: EM (単粒子) / 解像度: 3.4 Å EMDB-35221: Focused refinement map of the CHD of Eaf3 in the Rpd3S-nucleosome complex 手法: EM (単粒子) / 解像度: 3.9 Å 36283 8jho EMDB-36283, PDB-8jho: Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with di-nucleosome 手法: EM (単粒子) / 解像度: 7.6 Å
化合物	ChemComp-ZN: Unknown entry
由来	saccharomyces cerevisiae (パン酵母) xenopus laevis (アフリカツメガエル) synthetic construct (人工物) Saccharomyces (菌類)
キーワード	GENE REGULATION / Histone deacetylase complex / Rpd3S-nucleosome complex / Histone deacetylation / Histone modification binding domain / nucleosome / HDAC / di-nucleosome