+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-41142 | |||||||||||||||
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タイトル | APC/C-CDH1-UBE2C-UBE2S-Ubiquitin-CyclinB | |||||||||||||||
マップデータ | ||||||||||||||||
試料 |
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キーワード | E3 RING Ligase / Ubiquitin Ligase / APC/C / Anaphase-Promoting Complex-Cyclosome / Cell Cycle / Cullin-RING ligase / LIGASE | |||||||||||||||
機能・相同性 | 機能・相同性情報 cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase / positive regulation of anaphase-promoting complex-dependent catabolic process / G2/M DNA replication checkpoint / E2F-enabled inhibition of pre-replication complex formation / protein K29-linked ubiquitination / Depolymerization of the Nuclear Lamina / positive regulation of exit from mitosis / positive regulation of attachment of spindle microtubules to kinetochore ...cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase / positive regulation of anaphase-promoting complex-dependent catabolic process / G2/M DNA replication checkpoint / E2F-enabled inhibition of pre-replication complex formation / protein K29-linked ubiquitination / Depolymerization of the Nuclear Lamina / positive regulation of exit from mitosis / positive regulation of attachment of spindle microtubules to kinetochore / protein K27-linked ubiquitination / MASTL Facilitates Mitotic Progression / free ubiquitin chain polymerization / regulation of meiotic nuclear division / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / regulation of mitotic cell cycle spindle assembly checkpoint / positive regulation of synapse maturation / Activation of NIMA Kinases NEK9, NEK6, NEK7 / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Phosphorylation of Emi1 / patched binding / anaphase-promoting complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / regulation of meiotic cell cycle / metaphase/anaphase transition of mitotic cell cycle / anaphase-promoting complex-dependent catabolic process / lens fiber cell differentiation / (E3-independent) E2 ubiquitin-conjugating enzyme / positive regulation of synaptic plasticity / regulation of exit from mitosis / Nuclear Pore Complex (NPC) Disassembly / Transcriptional regulation by RUNX2 / anaphase-promoting complex binding / Phosphorylation of the APC/C / outer kinetochore / mitotic cell cycle phase transition / protein K6-linked ubiquitination / ubiquitin ligase activator activity / positive regulation of mitotic metaphase/anaphase transition / positive regulation of ubiquitin protein ligase activity / Initiation of Nuclear Envelope (NE) Reformation / protein K11-linked ubiquitination / Polo-like kinase mediated events / Golgi Cisternae Pericentriolar Stack Reorganization / enzyme-substrate adaptor activity / cyclin-dependent protein serine/threonine kinase activator activity / Condensation of Prometaphase Chromosomes / regulation of mitotic metaphase/anaphase transition / positive regulation of dendrite morphogenesis / ubiquitin-ubiquitin ligase activity / cyclin-dependent protein serine/threonine kinase regulator activity / exit from mitosis / mitotic metaphase chromosome alignment / E2 ubiquitin-conjugating enzyme / ubiquitin-like protein ligase binding / mitotic G2 DNA damage checkpoint signaling / negative regulation of cellular senescence / ubiquitin conjugating enzyme activity / cullin family protein binding / Regulation of APC/C activators between G1/S and early anaphase / protein K63-linked ubiquitination / ubiquitin-like ligase-substrate adaptor activity / Transcriptional Regulation by VENTX / positive regulation of axon extension / heterochromatin / Nuclear events stimulated by ALK signaling in cancer / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / protein K48-linked ubiquitination / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / ubiquitin ligase complex / Resolution of Sister Chromatid Cohesion / regulation of mitotic cell cycle / positive regulation of G2/M transition of mitotic cell cycle / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / positive regulation of mitotic cell cycle / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / nuclear periphery / Condensation of Prophase Chromosomes / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / mitotic spindle organization / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / SCF-beta-TrCP mediated degradation of Emi1 / Assembly of the pre-replicative complex / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / protein modification process / brain development / CDK-mediated phosphorylation and removal of Cdc6 / mitotic spindle / kinetochore / spindle pole / spindle / protein polyubiquitination / Separation of Sister Chromatids / ubiquitin-protein transferase activity / G2/M transition of mitotic cell cycle 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: 3.5 Å | |||||||||||||||
データ登録者 | Bodrug T / Welsh KA / Bolhuis DL / Paulakonis E / Martinez-Chacin RC / Liu B / Pinkin N / Bonacci T / Cui L / Xu P ...Bodrug T / Welsh KA / Bolhuis DL / Paulakonis E / Martinez-Chacin RC / Liu B / Pinkin N / Bonacci T / Cui L / Xu P / Roscow O / Amann SJ / Grishkovskaya I / Emanuele MJ / Harrison JS / Steimel JP / Hahn KM / Zhang W / Zhong E / Haselbach D / Brown NG | |||||||||||||||
資金援助 | 米国, オーストリア, 4件
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引用 | ジャーナル: Nat Struct Mol Biol / 年: 2023 タイトル: Time-resolved cryo-EM (TR-EM) analysis of substrate polyubiquitination by the RING E3 anaphase-promoting complex/cyclosome (APC/C). 著者: Tatyana Bodrug / Kaeli A Welsh / Derek L Bolhuis / Ethan Paulаkonis / Raquel C Martinez-Chacin / Bei Liu / Nicholas Pinkin / Thomas Bonacci / Liying Cui / Pengning Xu / Olivia Roscow / ...著者: Tatyana Bodrug / Kaeli A Welsh / Derek L Bolhuis / Ethan Paulаkonis / Raquel C Martinez-Chacin / Bei Liu / Nicholas Pinkin / Thomas Bonacci / Liying Cui / Pengning Xu / Olivia Roscow / Sascha Josef Amann / Irina Grishkovskaya / Michael J Emanuele / Joseph S Harrison / Joshua P Steimel / Klaus M Hahn / Wei Zhang / Ellen D Zhong / David Haselbach / Nicholas G Brown / 要旨: Substrate polyubiquitination drives a myriad of cellular processes, including the cell cycle, apoptosis and immune responses. Polyubiquitination is highly dynamic, and obtaining mechanistic insight ...Substrate polyubiquitination drives a myriad of cellular processes, including the cell cycle, apoptosis and immune responses. Polyubiquitination is highly dynamic, and obtaining mechanistic insight has thus far required artificially trapped structures to stabilize specific steps along the enzymatic process. So far, how any ubiquitin ligase builds a proteasomal degradation signal, which is canonically regarded as four or more ubiquitins, remains unclear. Here we present time-resolved cryogenic electron microscopy studies of the 1.2 MDa E3 ubiquitin ligase, known as the anaphase-promoting complex/cyclosome (APC/C), and its E2 co-enzymes (UBE2C/UBCH10 and UBE2S) during substrate polyubiquitination. Using cryoDRGN (Deep Reconstructing Generative Networks), a neural network-based approach, we reconstruct the conformational changes undergone by the human APC/C during polyubiquitination, directly visualize an active E3-E2 pair modifying its substrate, and identify unexpected interactions between multiple ubiquitins with parts of the APC/C machinery, including its coactivator CDH1. Together, we demonstrate how modification of substrates with nascent ubiquitin chains helps to potentiate processive substrate polyubiquitination, allowing us to model how a ubiquitin ligase builds a proteasomal degradation signal. | |||||||||||||||
履歴 |
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-構造の表示
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_41142.map.gz | 222.7 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-41142-v30.xml emd-41142.xml | 41.4 KB 41.4 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_41142.png | 71.7 KB | ||
Filedesc metadata | emd-41142.cif.gz | 12.3 KB | ||
その他 | emd_41142_half_map_1.map.gz emd_41142_half_map_2.map.gz | 226.3 MB 226.3 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-41142 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41142 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_41142_validation.pdf.gz | 784.5 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_41142_full_validation.pdf.gz | 784.1 KB | 表示 | |
XML形式データ | emd_41142_validation.xml.gz | 15.6 KB | 表示 | |
CIF形式データ | emd_41142_validation.cif.gz | 18.4 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41142 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41142 | HTTPS FTP |
-関連構造データ
関連構造データ | 8tauMC 8tarC M: このマップから作成された原子モデル C: 同じ文献を引用 (文献) |
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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
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 |
-マップ
ファイル | ダウンロード / ファイル: emd_41142.map.gz / 形式: CCP4 / 大きさ: 244.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 1.1 Å | ||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-ハーフマップ: #2
ファイル | emd_41142_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_41142_half_map_2.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
+全体 : Anaphase-Promoting Complex/Cyclosome in complex with CDH1, UBE2C,...
+超分子 #1: Anaphase-Promoting Complex/Cyclosome in complex with CDH1, UBE2C,...
+分子 #1: Anaphase-promoting complex subunit 1
+分子 #2: G2/mitotic-specific cyclin-B1
+分子 #3: Anaphase-promoting complex subunit 11
+分子 #4: Anaphase-promoting complex subunit 15
+分子 #5: Ubiquitin-conjugating enzyme E2 S
+分子 #6: Anaphase-promoting complex subunit CDC26
+分子 #7: Anaphase-promoting complex subunit 16
+分子 #8: Anaphase-promoting complex subunit 4
+分子 #9: Cell division cycle protein 27 homolog
+分子 #10: Cell division cycle protein 16 homolog
+分子 #11: Anaphase-promoting complex subunit 10
+分子 #12: Anaphase-promoting complex subunit 13
+分子 #13: Anaphase-promoting complex subunit 2
+分子 #14: Anaphase-promoting complex subunit 5
+分子 #15: Ubiquitin-conjugating enzyme E2 C
+分子 #16: Fizzy-related protein homolog
+分子 #17: Cell division cycle protein 23 homolog
+分子 #18: Anaphase-promoting complex subunit 7
+分子 #19: ZINC ION
-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 |
-試料調製
緩衝液 | pH: 8 |
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凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K2 BASE (4k x 4k) 平均電子線量: 42.0 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: SPOT SCAN / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2.0 µm / 最小 デフォーカス(公称値): 0.5 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: INSILICO MODEL |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 774933 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |