+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8w9d | ||||||
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タイトル | Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 1 | ||||||
要素 |
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キーワード | DNA BINDING PROTEIN/DNA / Rpd3S / HDAC / Sin3 / Rpd3 / DNA BINDING PROTEIN-DNA COMPLEX | ||||||
機能・相同性 | 機能・相同性情報 nucleosome disassembly/reassembly complex / negative regulation of antisense RNA transcription / Snt2C complex / negative regulation of reciprocal meiotic recombination / negative regulation of silent mating-type cassette heterochromatin formation / Rpd3L complex / protein localization to nucleolar rDNA repeats / Rpd3L-Expanded complex / negative regulation of rDNA heterochromatin formation / Rpd3S complex ...nucleosome disassembly/reassembly complex / negative regulation of antisense RNA transcription / Snt2C complex / negative regulation of reciprocal meiotic recombination / negative regulation of silent mating-type cassette heterochromatin formation / Rpd3L complex / protein localization to nucleolar rDNA repeats / Rpd3L-Expanded complex / negative regulation of rDNA heterochromatin formation / Rpd3S complex / regulation of RNA stability / rDNA chromatin condensation / nucleophagy / HDACs deacetylate histones / DNA replication-dependent chromatin assembly / histone deacetylase / SUMOylation of chromatin organization proteins / nucleosome disassembly / cellular response to nitrogen starvation / negative regulation of transcription by RNA polymerase I / regulation of DNA-templated DNA replication initiation / histone deacetylase activity / NuA4 histone acetyltransferase complex / Sin3-type complex / Estrogen-dependent gene expression / histone deacetylase complex / positive regulation of macroautophagy / histone acetyltransferase complex / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / nucleosomal DNA binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / telomere organization / Meiotic synapsis / methylated histone binding / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Regulation of endogenous retroelements by KRAB-ZFP proteins / nuclear periphery / Condensation of Prophase Chromosomes / HCMV Late Events / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / innate immune response in mucosa / PRC2 methylates histones and DNA / meiotic cell cycle / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / positive regulation of transcription elongation by RNA polymerase II / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / transcription elongation by RNA polymerase II / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / heterochromatin formation / PKMTs methylate histone lysines / Metalloprotease DUBs / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / double-strand break repair via nonhomologous end joining / HCMV Early Events / Transcriptional regulation of granulopoiesis / G1/S transition of mitotic cell cycle / structural constituent of chromatin / transcription corepressor activity / G2/M transition of mitotic cell cycle / UCH proteinases / antimicrobial humoral immune response mediated by antimicrobial peptide / nucleosome / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / antibacterial humoral response / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs 類似検索 - 分子機能 | ||||||
生物種 | Saccharomyces cerevisiae (パン酵母) Homo sapiens (ヒト) | ||||||
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: 3.9 Å | ||||||
データ登録者 | Wang, C. / Zhan, X. | ||||||
資金援助 | 中国, 1件
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引用 | ジャーナル: Sci Adv / 年: 2024 タイトル: Structures and dynamics of Rpd3S complex bound to nucleosome. 著者: Chengcheng Wang / Chen Chu / Zhouyan Guo / Xiechao Zhan / 要旨: The Rpd3S complex plays a pivotal role in facilitating local histone deacetylation in the transcribed regions to suppress intragenic transcription initiation. Here, we present the cryo-electron ...The Rpd3S complex plays a pivotal role in facilitating local histone deacetylation in the transcribed regions to suppress intragenic transcription initiation. Here, we present the cryo-electron microscopy structures of the budding yeast Rpd3S complex in both its apo and three nucleosome-bound states at atomic resolutions, revealing the exquisite architecture of Rpd3S to well accommodate a mononucleosome without linker DNA. The Rpd3S core, containing a Sin3 Lobe and two NB modules, is a rigid complex and provides three positive-charged anchors (Sin3_HCR and two Rco1_NIDs) to connect nucleosomal DNA. In three nucleosome-bound states, the Rpd3S core exhibits three distinct orientations relative to the nucleosome, assisting the sector-shaped deacetylase Rpd3 to locate above the SHL5-6, SHL0-1, or SHL2-3, respectively. Our work provides a structural framework that reveals a dynamic working model for the Rpd3S complex to engage diverse deacetylation sites. | ||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 8w9d.cif.gz | 685.1 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8w9d.ent.gz | 513.1 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8w9d.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 8w9d_validation.pdf.gz | 1.4 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 8w9d_full_validation.pdf.gz | 1.5 MB | 表示 | |
XML形式データ | 8w9d_validation.xml.gz | 89.5 KB | 表示 | |
CIF形式データ | 8w9d_validation.cif.gz | 138 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/w9/8w9d ftp://data.pdbj.org/pub/pdb/validation_reports/w9/8w9d | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
-Transcriptional regulatory protein ... , 2種, 3分子 AEF
#1: タンパク質 | 分子量: 175047.266 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P22579 |
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#2: タンパク質 | 分子量: 78951.305 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: Q04779 |
-タンパク質 , 6種, 12分子 BCDGaebfcgdh
#3: タンパク質 | 分子量: 48961.957 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P32561 | ||||||||
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#4: タンパク質 | 分子量: 45266.406 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: Q12432 #5: タンパク質 | 分子量: 15437.167 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P68431 #6: タンパク質 | 分子量: 11394.426 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P62805 #7: タンパク質 | 分子量: 14165.551 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P04908 #8: タンパク質 | 分子量: 13921.213 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: O60814 |
-DNA鎖 , 2種, 2分子 ij
#9: DNA鎖 | 分子量: 45368.051 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) |
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#10: DNA鎖 | 分子量: 45359.035 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) |
-タンパク質・ペプチド , 1種, 1分子 H
#11: タンパク質・ペプチド | 分子量: 487.614 Da / 分子数: 1 / 由来タイプ: 天然 詳細: Authors could not experimentally confirm this sequence, but the sequence should be a part of some chain. Therefore the residue numbers and chain ID are meaningless for molecule 11' 由来: (天然) Saccharomyces cerevisiae (パン酵母) |
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-非ポリマー , 2種, 9分子
#12: 化合物 | ChemComp-ZN / #13: 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 | N |
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-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 |
-試料調製
構成要素 | 名称: The Rpd3S complex / タイプ: COMPLEX / Entity ID: #1-#4 / 由来: NATURAL |
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由来(天然) | 生物種: Saccharomyces cerevisiae (パン酵母) |
緩衝液 | pH: 7.6 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 凍結剤: ETHANE |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2300 nm / 最小 デフォーカス(公称値): 1800 nm |
撮影 | 電子線照射量: 50 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) |
-解析
CTF補正 | タイプ: NONE | ||||||||||||||||||||||||
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3次元再構成 | 解像度: 3.9 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 422198 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
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