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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: EMDB / ID: EMD-9844 | ||||||||||||
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| タイトル | cryo-EM structure of DOT1L bound to H2B ubiquitinated nucleosome | ||||||||||||
マップデータ | catalytic domain of DOT1L bound to H2B ubiquitinated nucleosome. | ||||||||||||
試料 |
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キーワード | histone / nucleosome / methylation / GENE REGULATION | ||||||||||||
| 機能・相同性 | 機能・相同性情報[histone H3]-lysine79 N-trimethyltransferase / histone H3K79 methyltransferase activity / histone H3K79 trimethyltransferase activity / regulation of transcription regulatory region DNA binding / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / regulation of receptor signaling pathway via JAK-STAT / fat pad development / mitochondrion transport along microtubule ...[histone H3]-lysine79 N-trimethyltransferase / histone H3K79 methyltransferase activity / histone H3K79 trimethyltransferase activity / regulation of transcription regulatory region DNA binding / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / regulation of receptor signaling pathway via JAK-STAT / fat pad development / mitochondrion transport along microtubule / histone H3 methyltransferase activity / histone methyltransferase activity / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / subtelomeric heterochromatin formation / energy homeostasis / regulation of neuron apoptotic process / neuron projection morphogenesis / regulation of proteasomal protein catabolic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / IRAK2 mediated activation of TAK1 complex / Prevention of phagosomal-lysosomal fusion / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / telomere organization / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / DNA damage checkpoint signaling / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / positive regulation of protein ubiquitination / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / regulation of mitochondrial membrane potential / Autodegradation of Cdh1 by Cdh1:APC/C / TCF dependent signaling in response to WNT / APC/C:Cdc20 mediated degradation of Securin / Regulation of NF-kappa B signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / activated TAK1 mediates p38 MAPK activation / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A 類似検索 - 分子機能 | ||||||||||||
| 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: 6.8 Å | ||||||||||||
データ登録者 | Jang S / Song JJ | ||||||||||||
| 資金援助 | 韓国, 3件
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引用 | ジャーナル: Genes Dev / 年: 2019タイトル: Structural basis of recognition and destabilization of the histone H2B ubiquitinated nucleosome by the DOT1L histone H3 Lys79 methyltransferase. 著者: Seongmin Jang / Chanshin Kang / Han-Sol Yang / Taeyang Jung / Hans Hebert / Ka Young Chung / Seung Joong Kim / Sungchul Hohng / Ji-Joon Song / ![]() 要旨: DOT1L is a histone H3 Lys79 methyltransferase whose activity is stimulated by histone H2B Lys120 ubiquitination, suggesting cross-talk between histone H3 methylation and H2B ubiquitination. Here, we ...DOT1L is a histone H3 Lys79 methyltransferase whose activity is stimulated by histone H2B Lys120 ubiquitination, suggesting cross-talk between histone H3 methylation and H2B ubiquitination. Here, we present cryo-EM structures of DOT1L complexes with unmodified or H2B ubiquitinated nucleosomes, showing that DOT1L recognizes H2B ubiquitin and the H2A/H2B acidic patch through a C-terminal hydrophobic helix and an arginine anchor in DOT1L, respectively. Furthermore, the structures combined with single-molecule FRET experiments show that H2B ubiquitination enhances a noncatalytic function of the DOT1L-destabilizing nucleosome. These results establish the molecular basis of the cross-talk between H2B ubiquitination and H3 Lys79 methylation as well as nucleosome destabilization by DOT1L. | ||||||||||||
| 履歴 |
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構造の表示
| ムービー |
ムービービューア |
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| 構造ビューア | EMマップ: SurfView Molmil Jmol/JSmol |
| 添付画像 |
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ダウンロードとリンク
-EMDBアーカイブ
| マップデータ | emd_9844.map.gz | 37.9 MB | EMDBマップデータ形式 | |
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| ヘッダ (付随情報) | emd-9844-v30.xml emd-9844.xml | 17.6 KB 17.6 KB | 表示 表示 | EMDBヘッダ |
| FSC (解像度算出) | emd_9844_fsc.xml | 8 KB | 表示 | FSCデータファイル |
| 画像 | emd_9844.png | 112.4 KB | ||
| Filedesc metadata | emd-9844.cif.gz | 6.1 KB | ||
| アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-9844 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9844 | HTTPS FTP |
-検証レポート
| 文書・要旨 | emd_9844_validation.pdf.gz | 474.6 KB | 表示 | EMDB検証レポート |
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| 文書・詳細版 | emd_9844_full_validation.pdf.gz | 474.2 KB | 表示 | |
| XML形式データ | emd_9844_validation.xml.gz | 10 KB | 表示 | |
| CIF形式データ | emd_9844_validation.cif.gz | 12.8 KB | 表示 | |
| アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9844 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9844 | HTTPS FTP |
-関連構造データ
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リンク
| EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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| 「今月の分子」の関連する項目 |
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マップ
| ファイル | ダウンロード / ファイル: emd_9844.map.gz / 形式: CCP4 / 大きさ: 40.6 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| 注釈 | catalytic domain of DOT1L bound to H2B ubiquitinated nucleosome. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| ボクセルのサイズ | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 密度 |
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| 対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
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試料の構成要素
-全体 : DOT1L bound to H2B ubiquitinated nucleosome
| 全体 | 名称: DOT1L bound to H2B ubiquitinated nucleosome |
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| 要素 |
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-超分子 #1: DOT1L bound to H2B ubiquitinated nucleosome
| 超分子 | 名称: DOT1L bound to H2B ubiquitinated nucleosome / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#7 |
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| 由来(天然) | 生物種: |
| 分子量 | 理論値: 290 KDa |
-分子 #1: DNA I&J
| 分子 | 名称: DNA I&J / タイプ: dna / ID: 1 / コピー数: 2 / 分類: DNA |
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| 由来(天然) | 生物種: synthetic construct (人工物) |
| 分子量 | 理論値: 35.168547 KDa |
| 配列 | 文字列: (DA)(DG)(DA)(DT)(DT)(DC)(DT)(DA)(DC)(DC) (DA)(DA)(DA)(DA)(DG)(DT)(DG)(DT)(DA)(DT) (DT)(DT)(DG)(DG)(DA)(DA)(DA)(DC)(DT) (DG)(DC)(DT)(DC)(DC)(DA)(DT)(DC)(DA)(DA) (DA) (DA)(DG)(DG)(DC)(DA) ...文字列: (DA)(DG)(DA)(DT)(DT)(DC)(DT)(DA)(DC)(DC) (DA)(DA)(DA)(DA)(DG)(DT)(DG)(DT)(DA)(DT) (DT)(DT)(DG)(DG)(DA)(DA)(DA)(DC)(DT) (DG)(DC)(DT)(DC)(DC)(DA)(DT)(DC)(DA)(DA) (DA) (DA)(DG)(DG)(DC)(DA)(DT)(DG)(DT) (DT)(DC)(DA)(DG)(DC)(DT)(DG)(DA)(DA)(DT) (DT)(DC) (DA)(DG)(DC)(DT)(DG)(DA)(DA) (DC)(DA)(DT)(DG)(DC)(DC)(DT)(DT)(DT)(DT) (DG)(DA)(DT) (DG)(DG)(DA)(DG)(DC)(DA) (DG)(DT)(DT)(DT)(DC)(DC)(DA)(DA)(DA)(DT) (DA)(DC)(DA)(DC) (DT)(DT)(DT)(DT)(DG) (DG)(DT)(DA)(DG)(DA)(DA)(DT)(DC)(DT) |
-分子 #2: Histone H3.2
| 分子 | 名称: Histone H3.2 / タイプ: protein_or_peptide / ID: 2 / コピー数: 2 / 光学異性体: LEVO |
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| 由来(天然) | 生物種: |
| 分子量 | 理論値: 11.48841 KDa |
| 組換発現 | 生物種: ![]() |
| 配列 | 文字列: PHRYRPGTVA LREIRRYQKS TELLIRKLPF QRLVREIAQD FKTDLRFQSS AVMALQEASE AYLVGLFEDT NLCAIHAKRV TIMPKDIQL ARRIRGERA UniProtKB: Histone H3.2 |
-分子 #3: Histone H4
| 分子 | 名称: Histone H4 / タイプ: protein_or_peptide / ID: 3 / コピー数: 2 / 光学異性体: LEVO |
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| 由来(天然) | 生物種: |
| 分子量 | 理論値: 9.99077 KDa |
| 組換発現 | 生物種: ![]() |
| 配列 | 文字列: KRHRKVLRDN IQGITKPAIR RLARRGGVKR ISGLIYEETR GVLKVFLENV IRDAVTYTEH AKRKTVTAMD VVYALKRQGR TLYGFGG UniProtKB: Histone H4 |
-分子 #4: Histone H2A
| 分子 | 名称: Histone H2A / タイプ: protein_or_peptide / ID: 4 / コピー数: 2 / 光学異性体: LEVO |
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| 由来(天然) | 生物種: |
| 分子量 | 理論値: 12.660719 KDa |
| 組換発現 | 生物種: ![]() |
| 配列 | 文字列: AKTRSSRAGL QFPVGRVHRL LRKGNYAERV GAGAPVYLAA VLEYLTAEIL ELAGNAARDN KKTRIIPRHL QLAVRNDEEL NKLLGRVTI AQGGVLPNIQ SVLLPKKTES SKSAKSK UniProtKB: Histone H2A |
-分子 #5: Histone H2B 1.1
| 分子 | 名称: Histone H2B 1.1 / タイプ: protein_or_peptide / ID: 5 / コピー数: 2 / 光学異性体: LEVO |
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| 由来(天然) | 生物種: |
| 分子量 | 理論値: 10.478032 KDa |
| 組換発現 | 生物種: ![]() |
| 配列 | 文字列: TRKESYAIYV YKVLKQVHPD TGISSKAMSI MNSFVNDVFE RIAGEASRLA HYNKRSTITS REIQTAVRLL LPGELAKHAV SEGTKAVTK YTSAK UniProtKB: Histone H2B 1.1 |
-分子 #6: Histone-lysine N-methyltransferase, H3 lysine-79 specific
| 分子 | 名称: Histone-lysine N-methyltransferase, H3 lysine-79 specific タイプ: protein_or_peptide / ID: 6 / コピー数: 1 / 光学異性体: LEVO / EC番号: histone-lysine N-methyltransferase |
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| 由来(天然) | 生物種: Homo sapiens (ヒト) |
| 分子量 | 理論値: 37.930039 KDa |
| 組換発現 | 生物種: ![]() |
| 配列 | 文字列: LELRLKSPVG AEPAVYPWPL PVYDKHHDAA HEIIETIRWV CEEIPDLKLA MENYVLIDYD TKSFESMQRL CDKYNRAIDS IHQLWKGTT QPMKLNTRPS TGLLRHILQQ VYNHSVTDPE KLNNYEPFSP EVYGETSFDL VAQMIDEIKM TDDDLFVDLG S GVGQVVLQ ...文字列: LELRLKSPVG AEPAVYPWPL PVYDKHHDAA HEIIETIRWV CEEIPDLKLA MENYVLIDYD TKSFESMQRL CDKYNRAIDS IHQLWKGTT QPMKLNTRPS TGLLRHILQQ VYNHSVTDPE KLNNYEPFSP EVYGETSFDL VAQMIDEIKM TDDDLFVDLG S GVGQVVLQ VAAATNCKHH YGVEKADIPA KYAETMDREF RKWMKWYGKK HAEYTLERGD FLSEEWRERI ANTSVIFVNN FA FGPEVDH QLKERFANMK EGGRIVSSKP FAPLNFRINS RNLSDIGTIM RVVELSPLKG SVSWTGKPVS YYLHTIDRTI LEN YFSSLK NP UniProtKB: Histone-lysine N-methyltransferase, H3 lysine-79 specific |
-分子 #7: Ubiquitin
| 分子 | 名称: Ubiquitin / タイプ: protein_or_peptide / ID: 7 / コピー数: 1 / 光学異性体: LEVO |
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| 由来(天然) | 生物種: Homo sapiens (ヒト) |
| 分子量 | 理論値: 8.576831 KDa |
| 組換発現 | 生物種: ![]() |
| 配列 | 文字列: MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG UniProtKB: Polyubiquitin-B |
-分子 #8: S-ADENOSYLMETHIONINE
| 分子 | 名称: S-ADENOSYLMETHIONINE / タイプ: ligand / ID: 8 / コピー数: 1 / 式: SAM |
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| 分子量 | 理論値: 398.437 Da |
| Chemical component information | ![]() ChemComp-SAM: |
-実験情報
-構造解析
| 手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
| 試料の集合状態 | particle |
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試料調製
| 緩衝液 | pH: 7.5 |
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| 凍結 | 凍結剤: ETHANE |
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電子顕微鏡法
| 顕微鏡 | FEI TITAN |
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| 撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 平均電子線量: 37.28 e/Å2 |
| 電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
| 電子光学系 | 照射モード: OTHER / 撮影モード: BRIGHT FIELD |
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画像解析
-原子モデル構築 1
| 精密化 | プロトコル: FLEXIBLE FIT |
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| 得られたモデル | ![]() PDB-6jma: |
ムービー
コントローラー
万見について



キーワード
Homo sapiens (ヒト)
データ登録者
韓国, 3件
引用
UCSF Chimera





























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