+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6q6g | |||||||||
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タイトル | Cryo-EM structure of the APC/C-Cdc20-Cdk2-cyclinA2-Cks2 complex, the D1 box class | |||||||||
要素 |
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キーワード | CELL CYCLE (細胞周期) / spindle assembly checkpoint (紡錘体チェックポイント) / anaphase-promoting complex (後期促進複合体) / cyclin (サイクリン) / ubiquitination (ユビキチン) | |||||||||
機能・相同性 | 機能・相同性情報 metaphase/anaphase transition of cell cycle / metaphase/anaphase transition of meiosis I / Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components / mitotic checkpoint complex / positive regulation of anaphase-promoting complex-dependent catabolic process / regulation of mitotic cell cycle spindle assembly checkpoint / regulation of meiotic nuclear division / positive regulation of synapse maturation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex ...metaphase/anaphase transition of cell cycle / metaphase/anaphase transition of meiosis I / Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components / mitotic checkpoint complex / positive regulation of anaphase-promoting complex-dependent catabolic process / regulation of mitotic cell cycle spindle assembly checkpoint / regulation of meiotic nuclear division / positive regulation of synapse maturation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Phosphorylation of Emi1 / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / 後期促進複合体 / Aberrant regulation of mitotic exit in cancer due to RB1 defects / cell cycle G1/S phase transition / anaphase-promoting complex-dependent catabolic process / regulation of meiotic cell cycle / positive regulation of mitotic metaphase/anaphase transition / cellular response to luteinizing hormone stimulus / metaphase/anaphase transition of mitotic cell cycle / regulation of exit from mitosis / positive regulation of synaptic plasticity / Phosphorylation of the APC/C / anaphase-promoting complex binding / mitotic cell cycle phase transition / ubiquitin ligase activator activity / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / positive regulation of ubiquitin protein ligase activity / protein K11-linked ubiquitination / cellular response to leptin stimulus / male pronucleus / enzyme-substrate adaptor activity / female pronucleus / regulation of mitotic metaphase/anaphase transition / cellular response to cocaine / response to glucagon / positive regulation of dendrite morphogenesis / ubiquitin-ubiquitin ligase activity / cyclin-dependent protein serine/threonine kinase regulator activity / cellular response to insulin-like growth factor stimulus / mitotic sister chromatid cohesion / positive regulation of DNA biosynthetic process / mitotic metaphase chromosome alignment / cochlea development / mitotic spindle assembly checkpoint signaling / cellular response to platelet-derived growth factor stimulus / cyclin A2-CDK2 complex / G2期 / p53-Dependent G1 DNA Damage Response / cullin family protein binding / regulation of DNA replication / Regulation of APC/C activators between G1/S and early anaphase / Telomere Extension By Telomerase / G0 and Early G1 / Transcriptional Regulation by VENTX / mitotic spindle assembly / cyclin-dependent protein kinase holoenzyme complex / cellular response to nitric oxide / positive regulation of axon extension / animal organ regeneration / ヘテロクロマチン / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Cyclin A/B1/B2 associated events during G2/M transition / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Cyclin A:Cdk2-associated events at S phase entry / Resolution of Sister Chromatid Cohesion / APC/C:Cdc20 mediated degradation of Cyclin B / regulation of mitotic cell cycle / APC-Cdc20 mediated degradation of Nek2A / nuclear periphery / post-translational protein modification / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / SCF-beta-TrCP mediated degradation of Emi1 / cellular response to estradiol stimulus / Assembly of the pre-replicative complex / RHO GTPases Activate Formins / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / brain development / G1/S transition of mitotic cell cycle / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / DNA Damage/Telomere Stress Induced Senescence / 紡錘体 / spindle / 動原体 / CDK-mediated phosphorylation and removal of Cdc6 / SCF(Skp2)-mediated degradation of p27/p21 / 紡錘体 / Orc1 removal from chromatin / ubiquitin-protein transferase activity / Separation of Sister Chromatids / ubiquitin protein ligase activity / microtubule cytoskeleton / G2/M transition of mitotic cell cycle / positive regulation of fibroblast proliferation / Antigen processing: Ubiquitination & Proteasome degradation 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: 3.2 Å | |||||||||
データ登録者 | Zhang, S. / Barford, D. | |||||||||
資金援助 | 英国, 2件
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引用 | ジャーナル: Nat Commun / 年: 2019 タイトル: Cyclin A2 degradation during the spindle assembly checkpoint requires multiple binding modes to the APC/C. 著者: Suyang Zhang / Thomas Tischer / David Barford / 要旨: The anaphase-promoting complex/cyclosome (APC/C) orchestrates cell cycle progression by controlling the temporal degradation of specific cell cycle regulators. Although cyclin A2 and cyclin B1 are ...The anaphase-promoting complex/cyclosome (APC/C) orchestrates cell cycle progression by controlling the temporal degradation of specific cell cycle regulators. Although cyclin A2 and cyclin B1 are both targeted for degradation by the APC/C, during the spindle assembly checkpoint (SAC), the mitotic checkpoint complex (MCC) represses APC/C's activity towards cyclin B1, but not cyclin A2. Through structural, biochemical and in vivo analysis, we identify a non-canonical D box (D2) that is critical for cyclin A2 ubiquitination in vitro and degradation in vivo. During the SAC, cyclin A2 is ubiquitinated by the repressed APC/C-MCC, mediated by the cooperative engagement of its KEN and D2 boxes, ABBA motif, and the cofactor Cks. Once the SAC is satisfied, cyclin A2 binds APC/C-Cdc20 through two mutually exclusive binding modes, resulting in differential ubiquitination efficiency. Our findings reveal that a single substrate can engage an E3 ligase through multiple binding modes, affecting its degradation timing and efficiency. | |||||||||
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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 6q6g.cif.gz | 1.5 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6q6g.ent.gz | 1.2 MB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6q6g.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/q6/6q6g ftp://data.pdbj.org/pub/pdb/validation_reports/q6/6q6g | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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-要素
-Cell division cycle protein ... , 4種, 7分子 RKQJPUV
#1: タンパク質 | 分子量: 54796.508 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CDC20 / 発現宿主: unidentified baculovirus (ウイルス) / 参照: UniProt: Q12834 | ||||
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#9: タンパク質 | 分子量: 71747.516 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: CDC16, ANAPC6 / 発現宿主: unidentified baculovirus (ウイルス) / 参照: UniProt: Q13042 #14: タンパク質 | 分子量: 91973.125 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: CDC27, ANAPC3, D0S1430E, D17S978E / 発現宿主: unidentified baculovirus (ウイルス) / 参照: UniProt: P30260 #16: タンパク質 | 分子量: 68921.031 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: CDC23, ANAPC8 / 発現宿主: unidentified baculovirus (ウイルス) / 参照: UniProt: Q9UJX2 |
-タンパク質 , 1種, 1分子 S
#2: タンパク質 | 分子量: 44944.344 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CCNA2, CCN1, CCNA / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P20248 |
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-Anaphase-promoting complex subunit ... , 11種, 13分子 LDANIOCGWMHYZ
#3: タンパク質 | 分子量: 21282.143 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ANAPC10, APC10 / 発現宿主: unidentified baculovirus (ウイルス) / 参照: UniProt: Q9UM13 | ||||||
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#4: タンパク質 | 分子量: 14286.727 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ANAPC15, C11orf51, HSPC020 / 発現宿主: unidentified baculovirus (ウイルス) / 参照: UniProt: P60006 | ||||||
#5: タンパク質 | 分子量: 207282.328 Da / 分子数: 1 Mutation: deletion of residues 307-395,deletion of residues 307-395 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ANAPC1, TSG24 / 発現宿主: unidentified baculovirus (ウイルス) / 参照: UniProt: Q9H1A4 | ||||||
#6: タンパク質 | 分子量: 93938.977 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ANAPC2, APC2, KIAA1406 / 発現宿主: unidentified baculovirus (ウイルス) / 参照: UniProt: Q9UJX6 | ||||||
#7: タンパク質 | 分子量: 92219.227 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ANAPC4, APC4 / 発現宿主: unidentified baculovirus (ウイルス) / 参照: UniProt: Q9UJX5 | ||||||
#8: タンパク質 | 分子量: 85179.766 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ANAPC5, APC5 / 発現宿主: unidentified baculovirus (ウイルス) / 参照: UniProt: Q9UJX4 | ||||||
#10: タンパク質 | 分子量: 9854.647 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ANAPC11, HSPC214 / 発現宿主: unidentified baculovirus (ウイルス) / 参照: UniProt: Q9NYG5 | ||||||
#11: タンパク質 | 分子量: 9793.999 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: CDC26, ANAPC12, C9orf17 / 発現宿主: unidentified baculovirus (ウイルス) / 参照: UniProt: Q8NHZ8 #12: タンパク質 | | 分子量: 8528.309 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ANAPC13 / 発現宿主: unidentified baculovirus (ウイルス) / 参照: UniProt: Q9BS18 #13: タンパク質 | | 分子量: 11677.995 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ANAPC16, C10orf104, CENP-27 / 発現宿主: unidentified baculovirus (ウイルス) / 参照: UniProt: Q96DE5 #15: タンパク質 | 分子量: 66929.367 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: ANAPC7, APC7 / 発現宿主: unidentified baculovirus (ウイルス) / 参照: UniProt: Q9UJX3 |
-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: 1.3 MDa | ||||||||||||||||||||||||
由来(天然) |
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由来(組換発現) |
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緩衝液 | pH: 8 / 詳細: 20mM Hepes, 150mM NaCl, 0.5mM TCEP | ||||||||||||||||||||||||
試料 | 濃度: 0.15 mg/ml / 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 FIELDBright-field microscopy |
撮影 | 電子線照射量: 28 e/Å2 フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) |
-解析
EMソフトウェア | 名称: RELION / バージョン: 3 / カテゴリ: 3次元再構成 |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION |
対称性 | 点対称性: C1 (非対称) |
3次元再構成 | 解像度: 3.2 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 176826 / 対称性のタイプ: POINT |