+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-16325 | |||||||||
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タイトル | Cryo-EM structure of SKP1-SKP2-CKS1-CDK2-CyclinA-p27KIP1 Complex | |||||||||
マップデータ | Full map | |||||||||
試料 |
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キーワード | cell cycle / cyclin-dependent kinase / signalling / ubiquitination | |||||||||
機能・相同性 | 機能・相同性情報 positive regulation of protein polyubiquitination / F-box domain binding / G2 Phase / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / cyclin A2-CDK2 complex / PcG protein complex / cell cycle G1/S phase transition / Aberrant regulation of mitotic exit in cancer due to RB1 defects / cellular response to luteinizing hormone stimulus ...positive regulation of protein polyubiquitination / F-box domain binding / G2 Phase / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / cyclin A2-CDK2 complex / PcG protein complex / cell cycle G1/S phase transition / Aberrant regulation of mitotic exit in cancer due to RB1 defects / cellular response to luteinizing hormone stimulus / p53-Dependent G1 DNA Damage Response / mitotic cell cycle phase transition / Cul7-RING ubiquitin ligase complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / positive regulation of ubiquitin protein ligase activity / Regulation of APC/C activators between G1/S and early anaphase / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / maintenance of protein location in nucleus / cyclin-dependent protein serine/threonine kinase inhibitor activity / cellular response to leptin stimulus / male pronucleus / Telomere Extension By Telomerase / G0 and Early G1 / female pronucleus / cyclin-dependent protein serine/threonine kinase activator activity / response to glucagon / cellular response to cocaine / negative regulation of mitotic cell cycle / cellular response to nitric oxide / positive regulation of intracellular estrogen receptor signaling pathway / cyclin-dependent protein serine/threonine kinase regulator activity / SCF ubiquitin ligase complex / cellular response to insulin-like growth factor stimulus / ubiquitin ligase complex scaffold activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / positive regulation of DNA biosynthetic process / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / cochlea development / cellular response to platelet-derived growth factor stimulus / Cyclin A/B1/B2 associated events during G2/M transition / Prolactin receptor signaling / Cyclin A:Cdk2-associated events at S phase entry / cyclin-dependent protein kinase holoenzyme complex / protein monoubiquitination / regulation of DNA replication / regulation of mitotic cell cycle / cullin family protein binding / protein K63-linked ubiquitination / positive regulation of double-strand break repair via homologous recombination / ubiquitin-like ligase-substrate adaptor activity / animal organ regeneration / protein K48-linked ubiquitination / post-translational protein modification / Nuclear events stimulated by ALK signaling in cancer / cellular response to estradiol stimulus / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / DNA Damage/Telomere Stress Induced Senescence / ubiquitin binding / molecular function activator activity / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Vpu mediated degradation of CD4 / CDK-mediated phosphorylation and removal of Cdc6 / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Negative regulation of NOTCH4 signaling / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Orc1 removal from chromatin / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Degradation of beta-catenin by the destruction complex / Cyclin D associated events in G1 / G1/S transition of mitotic cell cycle / NOTCH1 Intracellular Domain Regulates Transcription / CLEC7A (Dectin-1) signaling / G2/M transition of mitotic cell cycle / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / FCERI mediated NF-kB activation / beta-catenin binding / positive regulation of fibroblast proliferation / Interleukin-1 signaling / Regulation of TP53 Degradation / protein polyubiquitination / Regulation of RUNX2 expression and activity / Regulation of PLK1 Activity at G2/M Transition / Circadian Clock / Processing of DNA double-strand break ends / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / Senescence-Associated Secretory Phenotype (SASP) / cellular response to hypoxia / Neddylation 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: 3.38 Å | |||||||||
データ登録者 | Rowland RJ / Salamina M / Endicott JA / Noble ME | |||||||||
資金援助 | 英国, 1件
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引用 | ジャーナル: Sci Rep / 年: 2023 タイトル: Cryo-EM structure of SKP1-SKP2-CKS1 in complex with CDK2-cyclin A-p27KIP1. 著者: Rhianna J Rowland / Richard Heath / Daniel Maskell / Rebecca F Thompson / Neil A Ranson / James N Blaza / Jane A Endicott / Martin E M Noble / Marco Salamina / 要旨: p27KIP1 (cyclin-dependent kinase inhibitor 1B, p27) is a member of the CIP/KIP family of CDK (cyclin dependent kinase) regulators that inhibit cell cycle CDKs. p27 phosphorylation by CDK1/2, signals ...p27KIP1 (cyclin-dependent kinase inhibitor 1B, p27) is a member of the CIP/KIP family of CDK (cyclin dependent kinase) regulators that inhibit cell cycle CDKs. p27 phosphorylation by CDK1/2, signals its recruitment to the SCF (S-phase kinase associated protein 1 (SKP1)-cullin-SKP2) E3 ubiquitin ligase complex for proteasomal degradation. The nature of p27 binding to SKP2 and CKS1 was revealed by the SKP1-SKP2-CKS1-p27 phosphopeptide crystal structure. Subsequently, a model for the hexameric CDK2-cyclin A-CKS1-p27-SKP1-SKP2 complex was proposed by overlaying an independently determined CDK2-cyclin A-p27 structure. Here we describe the experimentally determined structure of the isolated CDK2-cyclin A-CKS1-p27-SKP1-SKP2 complex at 3.4 Å global resolution using cryogenic electron microscopy. This structure supports previous analysis in which p27 was found to be structurally dynamic, transitioning from disordered to nascent secondary structure on target binding. We employed 3D variability analysis to further explore the conformational space of the hexameric complex and uncovered a previously unidentified hinge motion centred on CKS1. This flexibility gives rise to open and closed conformations of the hexameric complex that we propose may contribute to p27 regulation by facilitating recognition with SCF. This 3D variability analysis further informed particle subtraction and local refinement approaches to enhance the local resolution of the complex. | |||||||||
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_16325.map.gz | 97.3 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-16325-v30.xml emd-16325.xml | 24.6 KB 24.6 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_16325_fsc.xml | 9.9 KB | 表示 | FSCデータファイル |
画像 | emd_16325.png | 96.2 KB | ||
マスクデータ | emd_16325_msk_1.map | 103 MB | マスクマップ | |
その他 | emd_16325_half_map_1.map.gz emd_16325_half_map_2.map.gz | 95.7 MB 95.7 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-16325 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16325 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_16325_validation.pdf.gz | 899.2 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_16325_full_validation.pdf.gz | 898.7 KB | 表示 | |
XML形式データ | emd_16325_validation.xml.gz | 18.2 KB | 表示 | |
CIF形式データ | emd_16325_validation.cif.gz | 23.5 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16325 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16325 | 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_16325.map.gz / 形式: CCP4 / 大きさ: 103 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | Full map | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.07 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
-マスク #1
ファイル | emd_16325_msk_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: Half map A
ファイル | emd_16325_half_map_1.map | ||||||||||||
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注釈 | Half map A | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half map B
ファイル | emd_16325_half_map_2.map | ||||||||||||
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注釈 | Half map B | ||||||||||||
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 : Hexameric complex of SKP1-SKP2-CKS1 with CDK2-CyclinA-p27(kip1)
全体 | 名称: Hexameric complex of SKP1-SKP2-CKS1 with CDK2-CyclinA-p27(kip1) |
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要素 |
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-超分子 #1: Hexameric complex of SKP1-SKP2-CKS1 with CDK2-CyclinA-p27(kip1)
超分子 | 名称: Hexameric complex of SKP1-SKP2-CKS1 with CDK2-CyclinA-p27(kip1) タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 175 KDa |
-分子 #1: Cyclin-dependent kinase 2
分子 | 名称: Cyclin-dependent kinase 2 / タイプ: protein_or_peptide / ID: 1 / 詳細: Thr160 phosphorylated CDK2 / 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: 33.994398 KDa |
組換発現 | 生物種: Escherichia coli BL21(DE3) (大腸菌) |
配列 | 文字列: MENFQKVEKI GEGTYGVVYK ARNKLTGEVV ALKKIRLDTE TEGVPSTAIR EISLLKELNH PNIVKLLDVI HTENKLYLVF EFLHQDLKK FMDASALTGI PLPLIKSYLF QLLQGLAFCH SHRVLHRDLK PQNLLINTEG AIKLADFGLA RAFGVPVRT (TPO) ...文字列: MENFQKVEKI GEGTYGVVYK ARNKLTGEVV ALKKIRLDTE TEGVPSTAIR EISLLKELNH PNIVKLLDVI HTENKLYLVF EFLHQDLKK FMDASALTGI PLPLIKSYLF QLLQGLAFCH SHRVLHRDLK PQNLLINTEG AIKLADFGLA RAFGVPVRT (TPO)THEVVTLWY RAPEILLGCK YYSTAVDIWS LGCIFAEMVT RRALFPGDSE IDQLFRIFRT LGTPDEVVWP GVTSMP DYK PSFPKWARQD FSKVVPPLDE DGRSLLSQML HYDPNKRISA KAALAHPFFQ DVTKPVPHLR L UniProtKB: Uncharacterized protein |
-分子 #2: Cyclin-A2
分子 | 名称: Cyclin-A2 / タイプ: protein_or_peptide / ID: 2 / 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: 48.609574 KDa |
組換発現 | 生物種: Escherichia coli BL21(DE3) (大腸菌) |
配列 | 文字列: MLGNSAPGPA TREAGSALLA LQQTALQEDQ ENINPEKAAP VQQPRTRAAL AVLKSGNPRG LAQQQRPKTR RVAPLKDLPV NDEHVTVPP WKANSKQPAF TIHVDEAEKE AQKKPAESQK IEREDALAFN SAISLPGPRK PLVPLDYPMD GSFESPHTMD M SIILEDEK ...文字列: MLGNSAPGPA TREAGSALLA LQQTALQEDQ ENINPEKAAP VQQPRTRAAL AVLKSGNPRG LAQQQRPKTR RVAPLKDLPV NDEHVTVPP WKANSKQPAF TIHVDEAEKE AQKKPAESQK IEREDALAFN SAISLPGPRK PLVPLDYPMD GSFESPHTMD M SIILEDEK PVSVNEVPDY HEDIHTYLRE MEVKCKPKVG YMKKQPDITN SMRAILVDWL VEVGEEYKLQ NETLHLAVNY ID RFLSSMS VLRGKLQLVG TAAMLLASKF EEIYPPEVAE FVYITDDTYT KKQVLRMEHL VLKVLTFDLA APTVNQFLTQ YFL HQQPAN CKVESLAMFL GELSLIDADP YLKYLPSVIA GAAFHLALYT VTGQSWPESL IRKTGYTLES LKPCLMDLHQ TYLK APQHA QQSIREKYKN SKYHGVSLLN PPETLNL UniProtKB: Cyclin-A2 |
-分子 #3: Cyclin-dependent kinase inhibitor 1B
分子 | 名称: Cyclin-dependent kinase inhibitor 1B / 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: 17.678531 KDa |
組換発現 | 生物種: Escherichia coli BL21(DE3) (大腸菌) |
配列 | 文字列: MSNVRVSNGS PSLERMDARQ AEHPKPSACR NLFGPVDHEE LTRDLEKHCR DMEEASQRKW NFDFQNHKPL EGKYEWQEVE KGSLPEFYY RPPRPPKGAC KVPAQESQDG SGSRPAAPLI GAPANSEDTH LVDPKTDPSD SQTGLAEQCA GIRKRPATD UniProtKB: Cyclin-dependent kinase inhibitor 1B |
-分子 #4: S-phase kinase-associated protein 1
分子 | 名称: S-phase kinase-associated protein 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: 18.679965 KDa |
組換発現 | 生物種: Escherichia coli BL21(DE3) (大腸菌) |
配列 | 文字列: MPSIKLQSSD GEIFEVDVEI AKQSVTIKTM LEDLGMDDEG DDDPVPLPNV NAAILKKVIQ WCTHHKDDPP PPEDDENKEK RTDDIPVWD QEFLKVDQGT LFELILAANY LDIKGLLDVT CKTVANMIKG KTPEEIRKTF NIKNDFTEEE EAQVRKENQW C EEK UniProtKB: S-phase kinase-associated protein 1 |
-分子 #5: S-phase kinase-associated protein 2
分子 | 名称: S-phase kinase-associated protein 2 / タイプ: protein_or_peptide / ID: 5 / 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: 47.817785 KDa |
組換発現 | 生物種: Escherichia coli BL21(DE3) (大腸菌) |
配列 | 文字列: MHRKHLQEIP DLSSNVATSF TWGWDSSKTS ELLSGMGVSA LEKEEPDSEN IPQELLSNLG HPESPPRKRL KSKGSDKDFV IVRRPKLNR ENFPGVSWDS LPDELLLGIF SCLCLPELLK VSGVCKRWYR LASDESLWQT LDLTGKNLHP DVTGRLLSQG V IAFRCPRS ...文字列: MHRKHLQEIP DLSSNVATSF TWGWDSSKTS ELLSGMGVSA LEKEEPDSEN IPQELLSNLG HPESPPRKRL KSKGSDKDFV IVRRPKLNR ENFPGVSWDS LPDELLLGIF SCLCLPELLK VSGVCKRWYR LASDESLWQT LDLTGKNLHP DVTGRLLSQG V IAFRCPRS FMDQPLAEHF SPFRVQHMDL SNSVIEVSTL HGILSQCSKL QNLSLEGLRL SDPIVNTLAK NSNLVRLNLS GC SGFSEFA LQTLLSSCSR LDELNLSWCF DFTEKHVQVA VAHVSETITQ LNLSGYRKNL QKSDLSTLVR RCPNLVHLDL SDS VMLKND CFQEFFQLNY LQHLSLSRCY DIIPETLLEL GEIPTLKTLQ VFGIVPDGTL QLLKEALPHL QINCSHFTTI ARPT IGNKK NQEIWGIKCR LTLQKPSCL UniProtKB: S-phase kinase-associated protein 2 |
-分子 #6: Cyclin-dependent kinases regulatory subunit 1
分子 | 名称: Cyclin-dependent kinases regulatory subunit 1 / タイプ: protein_or_peptide / ID: 6 / 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: Escherichia coli BL21(DE3) (大腸菌) |
配列 | 文字列: MSHKQIYYSD KYDDEEFEYR HVMLPKDIAK LVPKTHLMSE SEWRNLGVQQ SQGWVHYMIH EPEPHILLFR RPLPKKPKK UniProtKB: Cyclin-dependent kinases regulatory subunit 1 |
-分子 #7: p27 KIP1 C-terminus
分子 | 名称: p27 KIP1 C-terminus / タイプ: protein_or_peptide / ID: 7 / 詳細: C-terminus of p27 KIP1 / 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: 1.126154 KDa |
組換発現 | 生物種: Escherichia coli BL21(DE3) (大腸菌) |
配列 | 文字列: AGSVEQ(TPO)PKK |
-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: 7.8 |
グリッド | モデル: Quantifoil R1.2/1.3 / 材質: COPPER / メッシュ: 400 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 60 sec. / 前処理 - 雰囲気: OTHER |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 95 % / チャンバー内温度: 278.15 K / 装置: FEI VITROBOT MARK IV |
-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 SUMMIT (4k x 4k) 平均露光時間: 9.0 sec. / 平均電子線量: 65.0 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: 70.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): 3.0 µm / 最小 デフォーカス(公称値): 1.0 µm / 倍率(公称値): 130000 |
試料ステージ | 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
-原子モデル構築 1
詳細 | Initial fitting was performed in chimera followed by real space refinement in Phenix |
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精密化 | 空間: REAL / プロトコル: RIGID BODY FIT / 温度因子: 121 |
得られたモデル | PDB-8bya: |