登録情報 データベース : EMDB / ID : EMD-16449 ダウンロードとリンクタイトル Cryo-EM structure of the human SIN3B full-length complex at 3.4 Angstrom resolution マップデータSIN3B full-length complex 詳細 試料複合体 : Human SIN3B complexタンパク質・ペプチド : Isoform 2 of Paired amphipathic helix protein Sin3bタンパク質・ペプチド : Histone deacetylase 2タンパク質・ペプチド : PHD finger protein 12タンパク質・ペプチド : Mortality factor 4-like protein 1リガンド : ZINC IONリガンド : CALCIUM ION 詳細 キーワード Chromatin / Histone deacetylase / HDAC / HYDROLASE機能・相同性 機能・相同性情報分子機能 ドメイン・相同性 構成要素
autosome / positive regulation of male mating behavior / protein de-2-hydroxyisobutyrylase activity / protein lysine delactylase activity / negative regulation of dendritic spine development / p75NTR negatively regulates cell cycle via SC1 / epidermal cell differentiation / histone decrotonylase activity / fungiform papilla formation / positive regulation of interleukin-1 production ... autosome / positive regulation of male mating behavior / protein de-2-hydroxyisobutyrylase activity / protein lysine delactylase activity / negative regulation of dendritic spine development / p75NTR negatively regulates cell cycle via SC1 / epidermal cell differentiation / histone decrotonylase activity / fungiform papilla formation / positive regulation of interleukin-1 production / behavioral response to ethanol / NuRD complex / regulation of cell fate specification / negative regulation of transcription by competitive promoter binding / EGR2 and SOX10-mediated initiation of Schwann cell myelination / negative regulation of stem cell population maintenance / histone deacetylase activity, hydrolytic mechanism / ESC/E(Z) complex / XY body / histone deacetylase / regulation of stem cell differentiation / cardiac muscle hypertrophy / cellular response to dopamine / regulation of double-strand break repair / STAT3 nuclear events downstream of ALK signaling / protein lysine deacetylase activity / response to caffeine / 加水分解酵素; ペプチド以外のCN結合加水分解酵素; 鎖状アミドに作用 / embryonic digit morphogenesis / histone deacetylase activity / positive regulation of intracellular estrogen receptor signaling pathway / Notch-HLH transcription pathway / Y chromosome / X chromosome / NuA4 histone acetyltransferase complex / Sin3-type complex / positive regulation of stem cell population maintenance / eyelid development in camera-type eye / odontogenesis of dentin-containing tooth / dendrite development / response to amyloid-beta / positive regulation of proteolysis / RNA Polymerase I Transcription Initiation / positive regulation of oligodendrocyte differentiation / histone deacetylase complex / Regulation of MECP2 expression and activity / progesterone receptor signaling pathway / hair follicle placode formation / response to hyperoxia / NF-kappaB binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of epithelial to mesenchymal transition / cellular response to transforming growth factor beta stimulus / positive regulation of double-strand break repair via homologous recombination / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / MECP2 regulates neuronal receptors and channels / Regulation of TP53 Activity through Acetylation / cellular response to retinoic acid / heat shock protein binding / Regulation of lipid metabolism by PPARalpha / transcription repressor complex / phosphatidylinositol binding / SUMOylation of chromatin organization proteins / negative regulation of cell migration / response to amphetamine / Regulation of PTEN gene transcription / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / transcription coregulator binding / transcription corepressor binding / Regulation of endogenous retroelements by KRAB-ZFP proteins / double-strand break repair via homologous recombination / response to nicotine / response to cocaine / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / negative regulation of transforming growth factor beta receptor signaling pathway / NOTCH1 Intracellular Domain Regulates Transcription / promoter-specific chromatin binding / circadian regulation of gene expression / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Cytoprotection by HMOX1 / NoRC negatively regulates rRNA expression / protein modification process / histone deacetylase binding / cellular response to hydrogen peroxide / positive regulation of tumor necrosis factor production / transcription corepressor activity / nucleosome / heterochromatin formation / negative regulation of neuron projection development / HATs acetylate histones / cellular response to heat / Factors involved in megakaryocyte development and platelet production / chromatin organization / fibroblast proliferation / histone binding / response to lipopolysaccharide / regulation of apoptotic process 類似検索 - 分子機能 PHD finger protein 12, MRG binding domain / PHD finger protein 12, MRG binding domain superfamily / PHD finger protein 12 / PHD finger protein 12 MRG binding domain / Histone deacetylase interacting domain / Sin3, C-terminal / Transcriptional regulatory protein Sin3-like / Sin3 family co-repressor / C-terminal domain of Sin3a protein / Histone deacetylase (HDAC) interacting ... PHD finger protein 12, MRG binding domain / PHD finger protein 12, MRG binding domain superfamily / PHD finger protein 12 / PHD finger protein 12 MRG binding domain / Histone deacetylase interacting domain / Sin3, C-terminal / Transcriptional regulatory protein Sin3-like / Sin3 family co-repressor / C-terminal domain of Sin3a protein / Histone deacetylase (HDAC) interacting / Paired amphipathic helix / Paired amphipathic helix superfamily / Paired amphipathic helix repeat / PAH domain profile. / MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Histone deacetylase / Forkhead-associated (FHA) domain profile. / Forkhead-associated (FHA) domain / Chromo-like domain superfamily / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / SMAD/FHA domain superfamily / Ureohydrolase domain superfamily / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type 類似検索 - ドメイン・相同性 Paired amphipathic helix protein Sin3b / Histone deacetylase 2 / PHD finger protein 12 / Mortality factor 4-like protein 1 類似検索 - 構成要素生物種 Homo sapiens (ヒト)手法 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度 : 3.4 Å 詳細 データ登録者Alfieri C / Wan SM / Muhammad R 資金援助 英国, 1件 詳細 詳細を隠すOrganization Grant number 国 Wellcome Trust 215458/Z/19/Z 英国
引用ジャーナル : Nat Commun / 年 : 2023タイトル : Mechanism of assembly, activation and lysine selection by the SIN3B histone deacetylase complex.著者 : Mandy S M Wan / Reyhan Muhammad / Marios G Koliopoulos / Theodoros I Roumeliotis / Jyoti S Choudhary / Claudio Alfieri / 要旨 : Lysine acetylation in histone tails is a key post-translational modification that controls transcription activation. Histone deacetylase complexes remove histone acetylation, thereby repressing ... Lysine acetylation in histone tails is a key post-translational modification that controls transcription activation. Histone deacetylase complexes remove histone acetylation, thereby repressing transcription and regulating the transcriptional output of each gene. Although these complexes are drug targets and crucial regulators of organismal physiology, their structure and mechanisms of action are largely unclear. Here, we present the structure of a complete human SIN3B histone deacetylase holo-complex with and without a substrate mimic. Remarkably, SIN3B encircles the deacetylase and contacts its allosteric basic patch thereby stimulating catalysis. A SIN3B loop inserts into the catalytic tunnel, rearranges to accommodate the acetyl-lysine moiety, and stabilises the substrate for specific deacetylation, which is guided by a substrate receptor subunit. Our findings provide a model of specificity for a main transcriptional regulator conserved from yeast to human and a resource of protein-protein interactions for future drug designs. 履歴 登録 2023年1月10日 - ヘッダ(付随情報) 公開 2023年5月10日 - マップ公開 2023年5月10日 - 更新 2025年7月2日 - 現状 2025年7月2日 処理サイト : PDBe / 状態 : 公開
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