+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-2924 | |||||||||
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タイトル | Cryo-EM structure of the human APC/C-Cdh1-Emi1 ternary complex at 3.6 angstrom resolution. | |||||||||
マップデータ | Cryo-EM structure of the human APC/C-Cdh1-Emi1 ternary complex at 3.6 angstrom resolution. | |||||||||
試料 |
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キーワード | Ubiquitination / Cell cycle. | |||||||||
機能・相同性 | 機能・相同性情報 negative regulation of DNA endoreduplication / negative regulation of mitotic metaphase/anaphase transition / negative regulation of meiotic nuclear division / positive regulation of biomineral tissue development / positive regulation of anaphase-promoting complex-dependent catabolic process / positive regulation of mesenchymal stem cell migration / Mitotic Metaphase/Anaphase Transition / 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 ...negative regulation of DNA endoreduplication / negative regulation of mitotic metaphase/anaphase transition / negative regulation of meiotic nuclear division / positive regulation of biomineral tissue development / positive regulation of anaphase-promoting complex-dependent catabolic process / positive regulation of mesenchymal stem cell migration / Mitotic Metaphase/Anaphase Transition / 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 / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / vesicle organization / Phosphorylation of Emi1 / 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 / positive regulation of synaptic plasticity / regulation of exit from mitosis / anaphase-promoting complex binding / Phosphorylation of the APC/C / negative regulation of ubiquitin-protein transferase activity / positive regulation of mitotic metaphase/anaphase transition / positive regulation of ubiquitin protein ligase activity / ubiquitin ligase activator activity / spindle assembly involved in female meiosis I / protein K11-linked ubiquitination / enzyme-substrate adaptor activity / meiotic spindle / positive regulation of dendrite morphogenesis / regulation of mitotic metaphase/anaphase transition / oocyte maturation / ubiquitin-ubiquitin ligase activity / negative regulation of ubiquitin protein ligase activity / regulation of mitotic nuclear division / mitotic metaphase chromosome alignment / molecular function inhibitor activity / G1/S-Specific Transcription / regulation of DNA replication / microtubule polymerization / mitotic G2 DNA damage checkpoint signaling / negative regulation of cellular senescence / cullin family protein binding / Regulation of APC/C activators between G1/S and early anaphase / ubiquitin ligase inhibitor activity / Transcriptional Regulation by VENTX / ubiquitin-like ligase-substrate adaptor activity / positive regulation of axon extension / protein K48-linked ubiquitination / positive regulation of osteoblast differentiation / heterochromatin / Cyclin A:Cdk2-associated events at S phase entry / 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 / nuclear periphery / 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 / brain development / CDK-mediated phosphorylation and removal of Cdc6 / mitotic spindle / kinetochore / spindle / Separation of Sister Chromatids / ubiquitin-protein transferase activity / microtubule cytoskeleton / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / mitotic cell cycle / nervous system development / Senescence-Associated Secretory Phenotype (SASP) / ubiquitin-dependent protein catabolic process / protein phosphatase binding / nuclear membrane / molecular adaptor activity / cell differentiation / protein ubiquitination / cell division / negative regulation of gene expression / DNA repair / centrosome / ubiquitin protein ligase binding / DNA damage response / positive regulation of cell population proliferation / nucleolus / protein kinase binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytosol 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: 3.6 Å | |||||||||
データ登録者 | Chang L / Zhang Z / Yang J / McLaughlin SH / Barford D | |||||||||
引用 | ジャーナル: Nature / 年: 2015 タイトル: Atomic structure of the APC/C and its mechanism of protein ubiquitination. 著者: Leifu Chang / Ziguo Zhang / Jing Yang / Stephen H McLaughlin / David Barford / 要旨: The anaphase-promoting complex (APC/C) is a multimeric RING E3 ubiquitin ligase that controls chromosome segregation and mitotic exit. Its regulation by coactivator subunits, phosphorylation, the ...The anaphase-promoting complex (APC/C) is a multimeric RING E3 ubiquitin ligase that controls chromosome segregation and mitotic exit. Its regulation by coactivator subunits, phosphorylation, the mitotic checkpoint complex and interphase early mitotic inhibitor 1 (Emi1) ensures the correct order and timing of distinct cell-cycle transitions. Here we use cryo-electron microscopy to determine atomic structures of APC/C-coactivator complexes with either Emi1 or a UbcH10-ubiquitin conjugate. These structures define the architecture of all APC/C subunits, the position of the catalytic module and explain how Emi1 mediates inhibition of the two E2s UbcH10 and Ube2S. Definition of Cdh1 interactions with the APC/C indicates how they are antagonized by Cdh1 phosphorylation. The structure of the APC/C with UbcH10-ubiquitin reveals insights into the initiating ubiquitination reaction. Our results provide a quantitative framework for the design of future experiments to investigate APC/C functions in vivo. | |||||||||
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: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_2924.map.gz | 8.3 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-2924-v30.xml emd-2924.xml | 17 KB 17 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_2924.jpg | 191.6 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-2924 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2924 | HTTPS FTP |
-関連構造データ
-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_2924.map.gz / 形式: CCP4 / 大きさ: 68.5 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Cryo-EM structure of the human APC/C-Cdh1-Emi1 ternary complex at 3.6 angstrom resolution. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.36 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
-試料の構成要素
+全体 : Recombinant human APC/C-Cdh1-Emi1 ternary complex
+超分子 #1000: Recombinant human APC/C-Cdh1-Emi1 ternary complex
+分子 #1: Apc1
+分子 #2: Apc2
+分子 #3: Apc3
+分子 #4: Apc4
+分子 #5: Apc5
+分子 #6: Apc6
+分子 #7: Apc7
+分子 #8: Apc8
+分子 #9: Apc10
+分子 #10: Apc11
+分子 #11: Apc12
+分子 #12: Apc13
+分子 #13: Apc15
+分子 #14: Apc16
+分子 #15: Cdh1
+分子 #16: Emi1
-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
濃度 | 0.2 mg/mL |
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緩衝液 | pH: 8 / 詳細: 20 mM HEPES, 150 mM NaCl, 1 mM DTT |
グリッド | 詳細: R2/2 Quantifoil grid with thin carbon support. |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / 装置: FEI VITROBOT MARK III / 手法: Blot for 5 seconds before plunging |
-電子顕微鏡法
顕微鏡 | FEI POLARA 300 |
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日付 | 2014年2月9日 |
撮影 | カテゴリ: CCD フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 平均電子線量: 27 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: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.0 mm / 最大 デフォーカス(公称値): 4.0 µm / 最小 デフォーカス(公称値): 2.0 µm / 倍率(公称値): 78000 |
試料ステージ | 試料ホルダーモデル: OTHER |
実験機器 | モデル: Tecnai Polara / 画像提供: FEI Company |
-画像解析
詳細 | The particles were selected using an automatic selection program. |
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CTF補正 | 詳細: Each micrograph |
最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / 解像度のタイプ: BY AUTHOR / 解像度: 3.6 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: RELION / 使用した粒子像数: 202084 |