National Natural Science Foundation of China (NSFC)
中国
引用
ジャーナル: Nat Struct Mol Biol / 年: 2023 タイトル: Structure of histone deacetylase complex Rpd3S bound to nucleosome. 著者: Wulong Li / Hengjun Cui / Zhimin Lu / Haibo Wang / 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.
全体 : Rpd3S histone deacetylase in complex with nucleosome
全体
名称: Rpd3S histone deacetylase in complex with nucleosome
要素
複合体: Rpd3S histone deacetylase in complex with nucleosome
タンパク質・ペプチド: Histone H3
タンパク質・ペプチド: Histone H4
タンパク質・ペプチド: Histone H2A
タンパク質・ペプチド: Histone H2B
DNA: DNA (352-MER)
DNA: DNA (352-MER)
タンパク質・ペプチド: Transcriptional regulatory protein SIN3
タンパク質・ペプチド: Histone deacetylase RPD3
タンパク質・ペプチド: Chromatin modification-related protein EAF3
タンパク質・ペプチド: RCO1 isoform 1
リガンド: ZINC ION
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超分子 #1: Rpd3S histone deacetylase in complex with nucleosome
超分子
名称: Rpd3S histone deacetylase in complex with nucleosome タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#10
由来(天然)
生物種: Saccharomyces cerevisiae (パン酵母)
分子量
理論値: 800 KDa
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分子 #1: Histone H3
分子
名称: Histone H3 / タイプ: protein_or_peptide / ID: 1 詳細: Author stated that Cys110 residues of chain A/E were mutated to Ala due to the preparation of ML3-modified nucleosome. コピー数: 2 / 光学異性体: LEVO