+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7y5v | |||||||||||||||||||||||||||||||||
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タイトル | Cryo-EM structure of the dimeric human CAF1LC-H3-H4 complex | |||||||||||||||||||||||||||||||||
要素 |
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キーワード | REPLICATION / Histone chaperone / Chromatin assembly factor | |||||||||||||||||||||||||||||||||
機能・相同性 | 機能・相同性情報 CAF-1 complex / NURF complex / NuRD complex / regulation of cell fate specification / chromo shadow domain binding / negative regulation of stem cell population maintenance / DNA replication-dependent chromatin assembly / ESC/E(Z) complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of stem cell differentiation ...CAF-1 complex / NURF complex / NuRD complex / regulation of cell fate specification / chromo shadow domain binding / negative regulation of stem cell population maintenance / DNA replication-dependent chromatin assembly / ESC/E(Z) complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of stem cell differentiation / Transcription of E2F targets under negative control by DREAM complex / Polo-like kinase mediated events / G0 and Early G1 / Cyclin E associated events during G1/S transition / positive regulation of stem cell population maintenance / G1/S-Specific Transcription / ATPase complex / Sin3-type complex / Cyclin A:Cdk2-associated events at S phase entry / Transcriptional Regulation by E2F6 / RNA Polymerase I Transcription Initiation / histone deacetylase complex / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / lipoxygenase pathway / telomere organization / arachidonate metabolic process / Chromatin modifying enzymes / lipid oxidation / Deposition of new CENPA-containing nucleosomes at the centromere / hepoxilin biosynthetic process / linoleic acid metabolic process / Regulation of TP53 Activity through Acetylation / Regulation of PTEN gene transcription / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Interleukin-7 signaling / epigenetic regulation of gene expression / DNA methylation / 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 / PRC2 methylates histones and DNA / negative regulation of transforming growth factor beta receptor signaling pathway / negative regulation of cell migration / Defective pyroptosis / Meiotic recombination / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Transcriptional regulation of granulopoiesis / HDMs demethylate histones / Formation of the beta-catenin:TCF transactivating complex / HCMV Early Events / 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 / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / brain development / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / histone deacetylase binding / structural constituent of chromatin / nucleosome / unfolded protein binding / Factors involved in megakaryocyte development and platelet production / nucleosome assembly / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / gene expression / histone binding / chromosome, telomeric region / DNA replication / Potential therapeutics for SARS / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromatin remodeling / cadherin binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / Amyloid fiber formation / negative regulation of cell population proliferation / DNA repair / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region 類似検索 - 分子機能 | |||||||||||||||||||||||||||||||||
生物種 | 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: 6.1 Å | |||||||||||||||||||||||||||||||||
データ登録者 | Liu, C.P. / Yu, C. / Yu, Z.Y. / Xu, R.M. | |||||||||||||||||||||||||||||||||
資金援助 | 中国, 10件
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引用 | ジャーナル: Science / 年: 2023 タイトル: Structural insights into histone binding and nucleosome assembly by chromatin assembly factor-1. 著者: Chao-Pei Liu / Zhenyu Yu / Jun Xiong / Jie Hu / Aoqun Song / Dongbo Ding / Cong Yu / Na Yang / Mingzhu Wang / Juan Yu / Peini Hou / Kangning Zeng / Zhenyu Li / Zhuqiang Zhang / Xinzheng Zhang ...著者: Chao-Pei Liu / Zhenyu Yu / Jun Xiong / Jie Hu / Aoqun Song / Dongbo Ding / Cong Yu / Na Yang / Mingzhu Wang / Juan Yu / Peini Hou / Kangning Zeng / Zhenyu Li / Zhuqiang Zhang / Xinzheng Zhang / Wei Li / Zhiguo Zhang / Bing Zhu / Guohong Li / Rui-Ming Xu / 要旨: Chromatin inheritance entails de novo nucleosome assembly after DNA replication by chromatin assembly factor-1 (CAF-1). Yet direct knowledge about CAF-1's histone binding mode and nucleosome assembly ...Chromatin inheritance entails de novo nucleosome assembly after DNA replication by chromatin assembly factor-1 (CAF-1). Yet direct knowledge about CAF-1's histone binding mode and nucleosome assembly process is lacking. In this work, we report the crystal structure of human CAF-1 in the absence of histones and the cryo-electron microscopy structure of CAF-1 in complex with histones H3 and H4. One histone H3-H4 heterodimer is bound by one CAF-1 complex mainly through the p60 subunit and the acidic domain of the p150 subunit. We also observed a dimeric CAF-1-H3-H4 supercomplex in which two H3-H4 heterodimers are poised for tetramer assembly and discovered that CAF-1 facilitates right-handed DNA wrapping of H3-H4 tetramers. These findings signify the involvement of DNA in H3-H4 tetramer formation and suggest a right-handed nucleosome precursor in chromatin replication. | |||||||||||||||||||||||||||||||||
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 | 7y5v.cif.gz | 372.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7y5v.ent.gz | 235.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7y5v.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 | 7y5v_validation.pdf.gz | 1.2 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7y5v_full_validation.pdf.gz | 1.2 MB | 表示 | |
XML形式データ | 7y5v_validation.xml.gz | 56.9 KB | 表示 | |
CIF形式データ | 7y5v_validation.cif.gz | 92.9 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/y5/7y5v ftp://data.pdbj.org/pub/pdb/validation_reports/y5/7y5v | HTTPS FTP |
-関連構造データ
関連構造データ | 33626MC 7y5kC 7y5lC 7y5oC 7y5uC 7y5wC 7y60C 7y61C 8iqfC 8iqgC 8j6sC 8j6tC C: 同じ文献を引用 (文献) M: このデータのモデリングに利用したマップデータ |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
-集合体
登録構造単位 |
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-要素
#1: タンパク質 | 分子量: 47228.848 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CHAF1A 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: Q13111 #2: タンパク質 | 分子量: 15437.167 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P68431 #3: タンパク質 | 分子量: 11394.426 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P62805 #4: タンパク質 | 分子量: 47709.527 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RBBP4 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: Q09028 #5: タンパク質 | 分子量: 46714.941 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CHAF1B 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: Q13112 |
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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 |
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分子量 | 値: 0.336 MDa / 実験値: YES | ||||||||||||||||||||||||
由来(天然) |
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由来(組換発現) |
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緩衝液 | pH: 7.5 / 詳細: 20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT | ||||||||||||||||||||||||
試料 | 濃度: 0.4 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK I / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 283 K |
-電子顕微鏡撮影
実験機器 | モデル: Talos Arctica / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TECNAI ARCTICA |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 200 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): 1500 nm / 最小 デフォーカス(公称値): 1000 nm |
撮影 | 電子線照射量: 50 e/Å2 フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) |
-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: NONE | ||||||||||||||||||||||||
対称性 | 点対称性: C2 (2回回転対称) | ||||||||||||||||||||||||
3次元再構成 | 解像度: 6.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 24904 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
原子モデル構築 | B value: 321 / プロトコル: RIGID BODY FIT / 空間: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||
原子モデル構築 | PDB-ID: 7Y5U Accession code: 7Y5U / Source name: PDB / タイプ: experimental model | ||||||||||||||||||||||||
拘束条件 |
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