+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-12368 | |||||||||
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タイトル | CryoEM structure of the human Separase-Cdk1-cyclin B1-Cks1 complex | |||||||||
マップデータ | Separase-Cdk1-cyclin B1-Cks1 complex (postprocessed). | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 negative regulation of mitotic sister chromatid separation / negative regulation of sister chromatid cohesion / separase / regulation of Schwann cell differentiation / cyclin A1-CDK1 complex / cyclin-dependent protein kinase activity / regulation of attachment of mitotic spindle microtubules to kinetochore / pronuclear fusion / cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport ...negative regulation of mitotic sister chromatid separation / negative regulation of sister chromatid cohesion / separase / regulation of Schwann cell differentiation / cyclin A1-CDK1 complex / cyclin-dependent protein kinase activity / regulation of attachment of mitotic spindle microtubules to kinetochore / pronuclear fusion / cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase / positive regulation of mitotic sister chromatid segregation / meiotic chromosome separation / histone kinase activity / Golgi disassembly / microtubule cytoskeleton organization involved in mitosis / G2/M DNA replication checkpoint / E2F-enabled inhibition of pre-replication complex formation / ventricular cardiac muscle cell development / Depolymerization of the Nuclear Lamina / positive regulation of attachment of spindle microtubules to kinetochore / MASTL Facilitates Mitotic Progression / regulation of mitotic cell cycle spindle assembly checkpoint / establishment of mitotic spindle localization / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / mitotic nuclear membrane disassembly / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / Phosphorylation of Emi1 / cyclin A2-CDK1 complex / patched binding / meiotic spindle organization / Nuclear Pore Complex (NPC) Disassembly / Transcriptional regulation by RUNX2 / outer kinetochore / Phosphorylation of the APC/C / mitotic cell cycle phase transition / positive regulation of mitotic metaphase/anaphase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Initiation of Nuclear Envelope (NE) Reformation / Regulation of APC/C activators between G1/S and early anaphase / protein localization to kinetochore / Polo-like kinase mediated events / Golgi Cisternae Pericentriolar Stack Reorganization / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / cyclin-dependent protein serine/threonine kinase activator activity / cyclin-dependent kinase / Condensation of Prometaphase Chromosomes / response to copper ion / cyclin-dependent protein serine/threonine kinase activity / chromosome condensation / centrosome cycle / [RNA-polymerase]-subunit kinase / cyclin-dependent protein serine/threonine kinase regulator activity / SCF ubiquitin ligase complex / cysteine-type endopeptidase inhibitor activity / mitotic metaphase chromosome alignment / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of DNA replication / G1/S-Specific Transcription / Cyclin A/B1/B2 associated events during G2/M transition / MAPK3 (ERK1) activation / cyclin-dependent protein kinase holoenzyme complex / response to amine / ubiquitin-like protein ligase binding / regulation of mitotic cell cycle / RNA polymerase II CTD heptapeptide repeat kinase activity / mitotic sister chromatid segregation / mitotic G2 DNA damage checkpoint signaling / regulation of embryonic development / cellular response to organic cyclic compound / mitotic cytokinesis / cyclin binding / epithelial cell differentiation / response to axon injury / chromosome organization / animal organ regeneration / catalytic activity / Nuclear events stimulated by ALK signaling in cancer / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / response to cadmium ion / cysteine-type peptidase activity / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / positive regulation of cardiac muscle cell proliferation / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Resolution of Sister Chromatid Cohesion / Hsp70 protein binding / APC/C:Cdc20 mediated degradation of Cyclin B / ERK1 and ERK2 cascade / AURKA Activation by TPX2 / positive regulation of mitotic cell cycle / Condensation of Prophase Chromosomes / mitotic spindle organization / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / response to activity / ubiquitin binding / APC/C:Cdc20 mediated degradation of Securin 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 | Yu J / Raia P / Ghent CM / Raisch T / Sadian Y / Barford D / Raunser S / Morgan DO / Boland A | |||||||||
資金援助 | スイス, 米国, 2件
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引用 | ジャーナル: Nature / 年: 2021 タイトル: Structural basis of human separase regulation by securin and CDK1-cyclin B1. 著者: Jun Yu / Pierre Raia / Chloe M Ghent / Tobias Raisch / Yashar Sadian / Simone Cavadini / Pramod M Sabale / David Barford / Stefan Raunser / David O Morgan / Andreas Boland / 要旨: In early mitosis, the duplicated chromosomes are held together by the ring-shaped cohesin complex. Separation of chromosomes during anaphase is triggered by separase-a large cysteine endopeptidase ...In early mitosis, the duplicated chromosomes are held together by the ring-shaped cohesin complex. Separation of chromosomes during anaphase is triggered by separase-a large cysteine endopeptidase that cleaves the cohesin subunit SCC1 (also known as RAD21). Separase is activated by degradation of its inhibitors, securin and cyclin B, but the molecular mechanisms of separase regulation are not clear. Here we used cryogenic electron microscopy to determine the structures of human separase in complex with either securin or CDK1-cyclin B1-CKS1. In both complexes, separase is inhibited by pseudosubstrate motifs that block substrate binding at the catalytic site and at nearby docking sites. As in Caenorhabditis elegans and yeast, human securin contains its own pseudosubstrate motifs. By contrast, CDK1-cyclin B1 inhibits separase by deploying pseudosubstrate motifs from intrinsically disordered loops in separase itself. One autoinhibitory loop is oriented by CDK1-cyclin B1 to block the catalytic sites of both separase and CDK1. Another autoinhibitory loop blocks substrate docking in a cleft adjacent to the separase catalytic site. A third separase loop contains a phosphoserine that promotes complex assembly by binding to a conserved phosphate-binding pocket in cyclin B1. Our study reveals the diverse array of mechanisms by which securin and CDK1-cyclin B1 bind and inhibit separase, providing the molecular basis for the robust control of chromosome segregation. | |||||||||
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_12368.map.gz | 12.1 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-12368-v30.xml emd-12368.xml | 21.4 KB 21.4 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_12368.png | 166.1 KB | ||
その他 | emd_12368_additional_1.map.gz | 140.5 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-12368 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12368 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_12368_validation.pdf.gz | 212.3 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_12368_full_validation.pdf.gz | 211.4 KB | 表示 | |
XML形式データ | emd_12368_validation.xml.gz | 6.9 KB | 表示 | |
CIF形式データ | emd_12368_validation.cif.gz | 7.9 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12368 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12368 | 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_12368.map.gz / 形式: CCP4 / 大きさ: 178 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Separase-Cdk1-cyclin B1-Cks1 complex (postprocessed). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.88 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
-追加マップ: Separase-Cdk1-cyclin B1-Cks1 complex (unsharpened).
ファイル | emd_12368_additional_1.map | ||||||||||||
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注釈 | Separase-Cdk1-cyclin B1-Cks1 complex (unsharpened). | ||||||||||||
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 : Mutual inhibitory complex of human separase-Cdk1-cyclin B1-Cks1 (...
全体 | 名称: Mutual inhibitory complex of human separase-Cdk1-cyclin B1-Cks1 (CCC) complex. |
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要素 |
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-超分子 #1: Mutual inhibitory complex of human separase-Cdk1-cyclin B1-Cks1 (...
超分子 | 名称: Mutual inhibitory complex of human separase-Cdk1-cyclin B1-Cks1 (CCC) complex. タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#4 |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
組換発現 | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) |
-分子 #1: Securin,Separin
分子 | 名称: Securin,Separin / タイプ: protein_or_peptide / ID: 1 / コピー数: 1 / 光学異性体: LEVO / EC番号: separase |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 244.677328 KDa |
組換発現 | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) |
配列 | 文字列: MQLGPPSPVK MPSPPWESNL LQSPSSILST LDVELPPVCC DIDIGGSGGS GGGSGGGSGE NLYFQGGGSG GSGMRSFKRV NFGTLLSSQ KEAEELLPDL KEFLSNPPAG FPSSRSDAER RQACDAILRA CNQQLTAKLA CPRHLGSLLE LAELACDGYL V STPQRPPL ...文字列: MQLGPPSPVK MPSPPWESNL LQSPSSILST LDVELPPVCC DIDIGGSGGS GGGSGGGSGE NLYFQGGGSG GSGMRSFKRV NFGTLLSSQ KEAEELLPDL KEFLSNPPAG FPSSRSDAER RQACDAILRA CNQQLTAKLA CPRHLGSLLE LAELACDGYL V STPQRPPL YLERILFVLL RNAAAQGSPE VTLRLAQPLH ACLVQCSREA APQDYEAVAR GSFSLLWKGA EALLERRAAF AA RLKALSF LVLLEDESTP CEVPHFASPT ACRAVAAHQL FDASGHGLNE ADADFLDDLL SRHVIRALVG ERGSSSGLLS PQR ALCLLE LTLEHCRRFC WSRHHDKAIS AVEKAHSYLR NTNLAPSLQL CQLGVKLLQV GEEGPQAVAK LLIKASAVLS KSME APSPP LRALYESCQF FLSGLERGTK RRYRLDAILS LFAFLGGYCS LLQQLRDDGV YGGSSKQQQS FLQMYFQGLH LYTVV VYDF AQGCQIVDLA DLTQLVDSCK STVVWMLEAL EGLSGQELTD HMGMTASYTS NLAYSFYSHK LYAEACAISE PLCQHL GLV KPGTYPEVPP EKLHRCFRLQ VESLKKLGKQ AQGCKMVILW LAALQPCSPE HMAEPVTFWV RVKMDAARAG DKELQLK TL RDSLSGWDPE TLALLLREEL QAYKAVRADT GQERFNIICD LLELSPEETP AGAWARATHL VELAQVLCYH DFTQQTNC S ALDAIREALQ LLDSVRPEAQ ARDQLLDDKA QALLWLYICT LEAKIQEGIE RDRRAQAPGN LEEFEVNDLN YEDKLQEDR FLYSNIAFNL AADAAQSKCL DQALALWKEL LTKGQAPAVR CLQQTAASLQ ILAALYQLVA KPMQALEVLL LLRIVSERLK DHSKAAGSS CHITQLLLTL GCPSYAQLHL EEAASSLKHL DQTTDTYLLL SLTCDLLRSQ LYWTHQKVTK GVSLLLSVLR D PALQKSSK AWYLLRVQVL QLVAAYLSLP SNNLSHSLWE QLCAQGWQTP EIALIDSHKL LRSIILLLMG SDILSTQKAA VE TSFLDYG ENLVQKWQVL SEVLSCSEKL VCHLGRLGSV SEAKAFCLEA LKLTTKLQIP RQCALFLVLK GELELARNDI DLC QSDLQQ VLFLLESCTE FGGVTQHLDS VKKVHLQKGK QQAQVPCPPQ LPEEELFLRG PALELVATVA KEPGPIAPST NS (SEP)PVLKTK PQPIPNFLSH SPTCDCSLCA SPVLTAVCLR WVLVTAGVRL AMGHQAQGLD LLQVVLKGCP EAAERLTQA LQASLNHKTP PSLVPSLLDE ILAQAYTLLA LEGLNQPSNE SLQKVLQSGL KFVAARIPHL EPWRASLLLI WALTKLGGLS CCTTQLFAS SWGWQPPLIK SVPGSEPSKT QGQKRSGRGR QKLASAPLSL NNTSQKGLEG RGLPCTPKPP DRIRQAGPHV P FTVFEEVC PTESKPEVPQ APRVQQRVQT RLKVNFSDDS DLEDPVSAEA WLAEEPKRRG TASRGRGRAR KGLSLKTDAV VA PGSAPGN PGLNGRSRRA KKVASRHCEE RRPQRASDQA RPGPEIMRTI PEEELTDNWR KMSFEILRGS DGEDSASGGK TPA PGPEAA SGEWELLRLD SSKKKLPSPC PDKESDKDLG PRLQLPSAPV ATGLSTLDSI CDSLSVAFRG ISHCPPSGLY AHLC RFLAL CLGHRDPYAT AFLVTESVSI TCRHQLLTHL HRQLSKAQKH RGSLEIADQL QGLSLQEMPG DVPLARIQRL FSFRA LESG HFPQPEKESF QERLALIPSG VTVCVLALAT LQPGTVGNTL LLTRLEKDSP PVSVQIPTGQ NKLHLRSVLN EFDAIQ KAQ KENSSCTDKR EWWTGRLALD HRMEVLIASL EKSVLGCWKG LLLPSSEEPG PAQEASRLQE LLQDCGWKYP DRTLLKI ML SGAGALTPQD IQALAYGLCP TQPERAQELL NEAVGRLQGL TVPSNSHLVL VLDKDLQKLP WESMPSLQAL PVTRLPSF R FLLSYSIIKE YGASPVLSQG VDPRSTFYVL NPHNNLSSTE EQFRANFSSE AGWRGVVGEV PRPEQVQEAL TKHDLYIYA GHGAGARFLD GQAVLRLSCR AVALLFGSSS AALAVHGNLE GAGIVLKYIM AGCPLFLGNL WDVTDRDIDR YTEALLQGWL GAGPGAPLL YYVNQARQAP RLKYLIGAAP IAYGLPVSLR SSLAEENLYF QSWSHPQFEK GGGSGGGSGG GSWSHPQFEK |
-分子 #2: Cyclin-dependent kinase 1
分子 | 名称: Cyclin-dependent kinase 1 / タイプ: protein_or_peptide / ID: 2 / コピー数: 1 / 光学異性体: LEVO / EC番号: cyclin-dependent kinase |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 36.667098 KDa |
組換発現 | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) |
配列 | 文字列: MEDYTKIEKI GEGTYGVVYK GRHKTTGQVV AMKKIRLESE EEGVPSTAIR EISLLKELRH PNIVSLQDVL MQDSRLYLIF EFLSMDLKK YLDSIPPGQY MDSSLVKSYL YQILQGIVFC HSRRVLHRDL KPQNLLIDDK GTIKLADFGL ARAFGIPIRV Y (TPO) ...文字列: MEDYTKIEKI GEGTYGVVYK GRHKTTGQVV AMKKIRLESE EEGVPSTAIR EISLLKELRH PNIVSLQDVL MQDSRLYLIF EFLSMDLKK YLDSIPPGQY MDSSLVKSYL YQILQGIVFC HSRRVLHRDL KPQNLLIDDK GTIKLADFGL ARAFGIPIRV Y (TPO)HEVVTLW YRSPEVLLGS ARYSTPVDIW SIGTIFAELA TKKPLFHGDS EIDQLFRIFR ALGTPNNEVW PEVESLQD Y KNTFPKWKPG SLASHVKNLD ENGLDLLSKM LIYDPAKRIS GKMALNHPYF NDLDNQIKKM IAAEALEVLF QGPHHHHHH HH |
-分子 #3: G2/mitotic-specific cyclin-B1,G2/mitotic-specific cyclin-B1
分子 | 名称: G2/mitotic-specific cyclin-B1,G2/mitotic-specific cyclin-B1 タイプ: protein_or_peptide / ID: 3 / 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: 52.625723 KDa |
組換発現 | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) |
配列 | 文字列: MALRVTRNSK INAENKAKIN MAGAKRVPTA PAATSKPGLR PRTALGDIGN KVSEQLQAKM PMKKEAKPSA TGKVIDKKLP KPLEKVPML VPVPVSEPVP EPEPEPEPEP VKEEKLSPEP ILVDTASPSP METSGCAPAE EDLCQAFSDV ILAVNDVDAE D GADPNLCS ...文字列: MALRVTRNSK INAENKAKIN MAGAKRVPTA PAATSKPGLR PRTALGDIGN KVSEQLQAKM PMKKEAKPSA TGKVIDKKLP KPLEKVPML VPVPVSEPVP EPEPEPEPEP VKEEKLSPEP ILVDTASPSP METSGCAPAE EDLCQAFSDV ILAVNDVDAE D GADPNLCS EYVKDIYAYL RQLEEEQAVR PKYLLGREVT GNMRAILIDW LVQVQMKFRL LQETMYMTVS IIDRFMQNNC VP KKMLQLV GVTAMFIASK YEEMYPPEIG DFAFVTDNTY TKHQIRQMEM KILRALNFGL GRPLPLHFLR RASKIGEVDV EQH TLAKYL MELTMLDYDM VHFPPSQIAA GAFCLALKIL DNGEWTPTLQ HYLSYTEESL LPVMQHLAKN VVMVNQGLTK HMTV KNKYA TSKHAKISTL PQLNSALVQD LAKAVAKVSS LAEENLYFQS WSHPQFEKGG GSGGGSGGGS WSHPQFEK |
-分子 #4: Cyclin-dependent kinases regulatory subunit 1
分子 | 名称: Cyclin-dependent kinases regulatory subunit 1 / タイプ: protein_or_peptide / ID: 4 / 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: 9.679211 KDa |
組換発現 | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) |
配列 | 文字列: MSHKQIYYSD KYDDEEFEYR HVMLPKDIAK LVPKTHLMSE SEWRNLGVQQ SQGWVHYMIH EPEPHILLFR RPLPKKPKK |
-分子 #5: PHOSPHATE ION
分子 | 名称: PHOSPHATE ION / タイプ: ligand / ID: 5 / コピー数: 1 / 式: PO4 |
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分子量 | 理論値: 94.971 Da |
Chemical component information | ChemComp-PO4: |
-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 | 0.050 mg/mL |
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緩衝液 | pH: 7.8 |
グリッド | モデル: Quantifoil R1.2/1.3 / 材質: GOLD / 支持フィルム - 材質: GRAPHENE OXIDE / 支持フィルム - トポロジー: CONTINUOUS / 前処理 - タイプ: GLOW DISCHARGE |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 90 % / チャンバー内温度: 293 K / 装置: LEICA EM GP |
詳細 | The sample was monodisperse. We use graphene oxide-coated EM grids. |
-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 K3 BIOQUANTUM (6k x 4k) 撮影したグリッド数: 5 / 実像数: 13640 / 平均露光時間: 3.0 sec. / 平均電子線量: 78.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 50.0 µm / 最大 デフォーカス(補正後): 2.5 µm / 最小 デフォーカス(補正後): 1.3 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2.5 µm / 最小 デフォーカス(公称値): 1.3 µm / 倍率(公称値): 105000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
CTF補正 | ソフトウェア: (名称: Gctf, cryoSPARC) |
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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: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION / 使用した粒子像数: 312836 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |