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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 8ga8 | |||||||||||||||||||||||||||||||||||||||
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タイトル | Structure of the yeast (HDAC) Rpd3L complex | |||||||||||||||||||||||||||||||||||||||
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![]() | TRANSCRIPTION / HDAC / Silencing / chromatin | |||||||||||||||||||||||||||||||||||||||
機能・相同性 | ![]() negative regulation of phosphatidylserine biosynthetic process / negative regulation of inositol biosynthetic process / positive regulation of phosphatidylserine biosynthetic process / negative regulation of phosphatidylcholine biosynthetic process / positive regulation of inositol biosynthetic process / regulation of invasive growth in response to glucose limitation / PI5P Regulates TP53 Acetylation / conjugation with cellular fusion / positive regulation of phosphatidylcholine biosynthetic process / Snt2C complex ...negative regulation of phosphatidylserine biosynthetic process / negative regulation of inositol biosynthetic process / positive regulation of phosphatidylserine biosynthetic process / negative regulation of phosphatidylcholine biosynthetic process / positive regulation of inositol biosynthetic process / regulation of invasive growth in response to glucose limitation / PI5P Regulates TP53 Acetylation / conjugation with cellular fusion / positive regulation of phosphatidylcholine biosynthetic process / Snt2C complex / negative regulation of silent mating-type cassette heterochromatin formation / negative regulation of reciprocal meiotic recombination / positive regulation of invasive growth in response to glucose limitation / Rpd3L complex / protein localization to nucleolar rDNA repeats / invasive growth in response to glucose limitation / negative regulation of rDNA heterochromatin formation / Rpd3L-Expanded complex / Rpd3S complex / rDNA chromatin condensation / SUMOylation of transcription cofactors / nucleophagy / HDACs deacetylate histones / histone deacetylase activity, hydrolytic mechanism / histone deacetylase / histone H3K4me3 reader activity / cell adhesion involved in single-species biofilm formation / SUMOylation of chromatin organization proteins / cellular response to nitrogen starvation / regulation of DNA-templated DNA replication initiation / negative regulation of transcription by RNA polymerase I / histone deacetylase activity / Sin3-type complex / : / Estrogen-dependent gene expression / histone deacetylase complex / positive regulation of macroautophagy / Ub-specific processing proteases / nuclear periphery / meiotic cell cycle / transcription coregulator activity / transcription elongation by RNA polymerase II / G1/S transition of mitotic cell cycle / double-strand break repair via nonhomologous end joining / G2/M transition of mitotic cell cycle / histone deacetylase binding / transcription corepressor activity / heterochromatin formation / nucleosome assembly / cellular response to heat / chromatin organization / response to oxidative stress / transcription coactivator activity / cell division / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm 類似検索 - 分子機能 | |||||||||||||||||||||||||||||||||||||||
生物種 | ![]() ![]() | |||||||||||||||||||||||||||||||||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.5 Å | |||||||||||||||||||||||||||||||||||||||
![]() | Patel, A.B. / Radhakrishnan, I. / He, Y. | |||||||||||||||||||||||||||||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Cryo-EM structure of the Saccharomyces cerevisiae Rpd3L histone deacetylase complex. 著者: Avinash B Patel / Jinkang Qing / Kelly H Tam / Sara Zaman / Maria Luiso / Ishwar Radhakrishnan / Yuan He / ![]() 要旨: The Rpd3L histone deacetylase (HDAC) complex is an ancient 12-subunit complex conserved in a broad range of eukaryotes that performs localized deacetylation at or near sites of recruitment by DNA- ...The Rpd3L histone deacetylase (HDAC) complex is an ancient 12-subunit complex conserved in a broad range of eukaryotes that performs localized deacetylation at or near sites of recruitment by DNA-bound factors. Here we describe the cryo-EM structure of this prototypical HDAC complex that is characterized by as many as seven subunits performing scaffolding roles for the tight integration of the only catalytic subunit, Rpd3. The principal scaffolding protein, Sin3, along with Rpd3 and the histone chaperone, Ume1, are present in two copies, with each copy organized into separate lobes of an asymmetric dimeric molecular assembly. The active site of one Rpd3 is completely occluded by a leucine side chain of Rxt2, while the tips of the two lobes and the more peripherally associated subunits exhibit varying levels of flexibility and positional disorder. The structure reveals unexpected structural homology/analogy between unrelated subunits in the fungal and mammalian complexes and provides a foundation for deeper interrogations of structure, biology, and mechanism of these complexes, as well as for the discovery of HDAC complex-specific inhibitors. | |||||||||||||||||||||||||||||||||||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 546.9 KB | 表示 | ![]() |
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PDB形式 | ![]() | 409.8 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 1.3 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.4 MB | 表示 | |
XML形式データ | ![]() | 77.7 KB | 表示 | |
CIF形式データ | ![]() | 117.6 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 29892MC M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 ( |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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リンク
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集合体
登録構造単位 | ![]()
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要素
-Transcriptional regulatory protein ... , 7種, 8分子 HADJLMGK
#1: タンパク質 | 分子量: 37685.301 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() | ||||||||||
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#2: タンパク質 | 分子量: 175047.266 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() #3: タンパク質 | | 分子量: 23064.215 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() #4: タンパク質 | | 分子量: 37081.430 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() #5: タンパク質 | | 分子量: 48684.082 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() #6: タンパク質 | | 分子量: 47035.723 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() #8: タンパク質 | | 分子量: 33851.535 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() |
-タンパク質 / 非ポリマー , 2種, 4分子 BE

#7: タンパク質 | 分子量: 48961.957 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() #9: 化合物 | |
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-詳細
研究の焦点であるリガンドがあるか | Y |
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Has protein modification | N |
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
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試料調製
構成要素 | 名称: Rpd3L / タイプ: COMPLEX / Entity ID: #1-#8 / 由来: NATURAL |
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由来(天然) | 生物種: ![]() ![]() |
緩衝液 | pH: 7.9 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | グリッドの材料: COPPER / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: Quantifoil R2/1 |
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 277 K |
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電子顕微鏡撮影
顕微鏡 | モデル: FEI TITAN |
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電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 3000 nm / 最小 デフォーカス(公称値): 1000 nm |
撮影 | 電子線照射量: 1 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) |
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解析
ソフトウェア | 名称: PHENIX / バージョン: 1.20.1_4487: / 分類: 精密化 | ||||||||||||||||||||||||
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EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3次元再構成 | 解像度: 3.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 210993 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
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