+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-8752 | |||||||||
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タイトル | Cryo-EM structure of DNAPK | |||||||||
マップデータ | Cryo-EM structure of DNAPK | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 positive regulation of platelet formation / immature B cell differentiation / T cell receptor V(D)J recombination / pro-B cell differentiation / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex ...positive regulation of platelet formation / immature B cell differentiation / T cell receptor V(D)J recombination / pro-B cell differentiation / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination / nonhomologous end joining complex / regulation of smooth muscle cell proliferation / Cytosolic sensors of pathogen-associated DNA / IRF3-mediated induction of type I IFN / regulation of epithelial cell proliferation / telomere capping / regulation of hematopoietic stem cell differentiation / U3 snoRNA binding / double-strand break repair via alternative nonhomologous end joining / T cell lineage commitment / negative regulation of cGAS/STING signaling pathway / positive regulation of double-strand break repair via nonhomologous end joining / maturation of 5.8S rRNA / B cell lineage commitment / ectopic germ cell programmed cell death / somitogenesis / mitotic G1 DNA damage checkpoint signaling / activation of innate immune response / telomere maintenance / positive regulation of erythrocyte differentiation / negative regulation of protein phosphorylation / protein-DNA complex / small-subunit processome / positive regulation of translation / response to gamma radiation / Nonhomologous End-Joining (NHEJ) / peptidyl-threonine phosphorylation / protein destabilization / protein modification process / brain development / regulation of circadian rhythm / double-strand break repair via nonhomologous end joining / cellular response to insulin stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / double-strand break repair / rhythmic process / E3 ubiquitin ligases ubiquitinate target proteins / heart development / T cell differentiation in thymus / double-stranded DNA binding / peptidyl-serine phosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / chromosome, telomeric region / non-specific serine/threonine protein kinase / protein kinase activity / positive regulation of apoptotic process / protein domain specific binding / protein phosphorylation / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / chromatin / nucleolus / negative regulation of apoptotic process / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / nucleoplasm / ATP binding / membrane / nucleus / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) / human (ヒト) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 5.8 Å | |||||||||
データ登録者 | Sharif H / Li Y / Wu H | |||||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Proc Natl Acad Sci U S A / 年: 2017 タイトル: Cryo-EM structure of the DNA-PK holoenzyme. 著者: Humayun Sharif / Yang Li / Yuanchen Dong / Liyi Dong / Wei Li Wang / Youdong Mao / Hao Wu / 要旨: DNA-dependent protein kinase (DNA-PK) is a large protein complex central to the nonhomologous end joining (NHEJ) DNA-repair pathway. It comprises the DNA-PK catalytic subunit (DNA-PKcs) and the ...DNA-dependent protein kinase (DNA-PK) is a large protein complex central to the nonhomologous end joining (NHEJ) DNA-repair pathway. It comprises the DNA-PK catalytic subunit (DNA-PKcs) and the heterodimer of DNA-binding proteins Ku70 and Ku80. Here, we report the cryo-electron microscopy (cryo-EM) structures of human DNA-PKcs at 4.4-Å resolution and the DNA-PK holoenzyme at 5.8-Å resolution. The DNA-PKcs structure contains three distinct segments: the N-terminal region with an arm and a bridge, the circular cradle, and the head that includes the kinase domain. Two perpendicular apertures exist in the structure, which are sufficiently large for the passage of dsDNA. The DNA-PK holoenzyme cryo-EM map reveals density for the C-terminal globular domain of Ku80 that interacts with the arm of DNA-PKcs. The Ku80-binding site is adjacent to the previously identified density for the DNA-binding region of the Ku70/Ku80 complex, suggesting concerted DNA interaction by DNA-PKcs and the Ku complex. | |||||||||
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_8752.map.gz | 14.4 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-8752-v30.xml emd-8752.xml | 13.8 KB 13.8 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_8752.png | 182.9 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-8752 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8752 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_8752_validation.pdf.gz | 78.5 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_8752_full_validation.pdf.gz | 77.6 KB | 表示 | |
XML形式データ | emd_8752_validation.xml.gz | 494 B | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8752 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8752 | 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_8752.map.gz / 形式: CCP4 / 大きさ: 15.6 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Cryo-EM structure of DNAPK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.51 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 : DNA-PK holoenzyme complex
全体 | 名称: DNA-PK holoenzyme complex |
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要素 |
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-超分子 #1: DNA-PK holoenzyme complex
超分子 | 名称: DNA-PK holoenzyme complex / タイプ: organelle_or_cellular_component / ID: 1 / 親要素: 0 / 含まれる分子: all / 詳細: DNA-PK (DNA-PKcs in complex with Ku80-CTR) |
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由来(天然) | 生物種: Homo sapiens (ヒト) / 器官: Cervical / 細胞中の位置: Nucleus |
-分子 #1: DNA-PK
分子 | 名称: DNA-PK / タイプ: protein_or_peptide / ID: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: human (ヒト) / 器官: CERVICAL |
配列 | 文字列: MAGSGAGVR CSLLRLQETL SAADRCGAAL AGHQLIRGLG QECVLSSSPA VLALQTSLVF S RDFGLLVF VRKSLNSIEF RECREEILKF LCIFLEKMGQ KIAPYSVEIK NTCTSVYTKD RA AKCKIPA LDLLIKLLQT FRSSRLMDEF KIGELFSKFY GELALKKKIP ...文字列: MAGSGAGVR CSLLRLQETL SAADRCGAAL AGHQLIRGLG QECVLSSSPA VLALQTSLVF S RDFGLLVF VRKSLNSIEF RECREEILKF LCIFLEKMGQ KIAPYSVEIK NTCTSVYTKD RA AKCKIPA LDLLIKLLQT FRSSRLMDEF KIGELFSKFY GELALKKKIP DTVLEKVYEL LGL LGEVHP SEMINNAENL FRAFLGELKT QMTSAVREPK LPVLAGCLKG LSSLLCNFTK SMEE DPQTS REIFNFVLKA IRPQIDLKRY AVPSAGLRLF ALHASQFSTC LLDNYVSLFE VLLKW CAHT NVELKKAALS ALESFLKQVS NMVAKNAEMH KNKLQYFMEQ FYGIIRNVDS NNKELS IAI RGYGLFAGPC KVINAKDVDF MYVELIQRCK QMFLTQTDTG DDRVYQMPSF LQSVASV LL YLDTVPEVYT PVLEHLVVMQ IDSFPQYSPK MQLVCCRAIV KVFLALAAKG PVLRNCIS T VVHQGLIRIC SKPVVLPKGP ESESEDHRAS GEVRTGKWKV PTYKDYVDLF RHLLSSDQM MDSILADEAF FSVNSSSESL NHLLYDEFVK SVLKIVEKLD LTLEIQTVGE QENGDEAPGV WMIPTSDPA ANLHPAKPKD FSAFINLVEF CREILPEKQA EFFEPWVYSF SYELILQSTR L PLISGFYK LLSITVRNAK KIKYFEGVSP KSLKHSPEDP EKYSCFALFV KFGKEVAVKM KQ YKDELLA SCLTFLLSLP HNIIELDVRA YVPALQMAFK LGLSYTPLAE VGLNALEEWS IYI DRHVMQ PYYKDILPCL DGYLKTSALS DETKNNWEVS ALSRAAQKGF NKVVLKHLKK TKNL SSNEA ISLEEIRIRV VQMLGSLGGQ INKNLLTVTS SDEMMKSYVA WDREKRLSFA VPFRE MKPV IFLDVFLPRV TELALTASDR QTKVAACELL HSMVMFMLGK ATQMPEGGQG APPMYQ LYK RTFPVLLRLA CDVDQVTRQL YEPLVMQLIH WFTNNKKFES QDTVALLEAI LDGIVDP VD STLRDFCGRC IREFLKWSIK QITPQQQEKS PVNTKSLFKR LYSLALHPNA FKRLGASL A FNNIYREFRE EESLVEQFVF EALVIYMESL ALAHADEKSL GTIQQCCDAI DHLCRIIEK KHVSLNKAKK RRLPRGFPPS ASLCLLDLVK WLLAHCGRPQ TECRHKSIEL FYKFVPLLPG NRSPNLWLK DVLKEEGVSF LINTFEGGGC GQPSGILAQP TLLYLRGPFS LQATLCWLDL L LAALECYN TFIGERTVGA LQVLGTEAQS SLLKAVAFFL ESIAMHDIIA AEKCFGTGAA GN RTSPQEG ERYNYSKCTV VVRIMEFTTT LLNTSPEGWK LLKKDLCNTH LMRVLVQTLC EPA SIGFNI GDVQVMAHLP DVCVNLMKAL KMSPYKDILE THLREKITAQ SIEELCAVNL YGPD AQVDR SRLAAVVSAC KQLHRAGLLH NILPSQSTDL HHSVGTELLS LVYKGIAPGD ERQCL PSLD LSCKQLASGL LELAFAFGGL CERLVSLLLN PAVLSTASLG SSQGSVIHFS HGEYFY SLF SETINTELLK NLDLAVLELM QSSVDNTKMV SAVLNGMLDQ SFRERANQKH QGLKLAT TI LQHWKKCDSW WAKDSPLETK MAVLALLAKI LQIDSSVSFN TSHGSFPEVF TTYISLLA D TKLDLHLKGQ AVTLLPFFTS LTGGSLEELR RVLEQLIVAH FPMQSREFPP GTPRFNNYV DCMKKFLDAL ELSQSPMLLE LMTEVLCREQ QHVMEELFQS SFRRIARRGS CVTQVGLLES VYEMFRKDD PRLSFTRQSF VDRSLLTLLW HCSLDALREF FSTIVVDAID VLKSRFTKLN E STFDTQIT KKMGYYKILD VMYSRLPKDD VHAKESKINQ VFHGSCITEG NELTKTLIKL CY DAFTENM AGENQLLERR RLYHCAAYNC AISVICCVFN ELKFYQGFLF SEKPEKNLLI FEN LIDLKR RYNFPVEVEV PMERKKKYIE IRKEAREAAN GDSDGPSYMS SLSYLADSTL SEEM SQFDF STGVQSYSYS SQDPRPATGR FRRREQRDPT VHDDVLELEM DELNRHECMA PLTAL VKHM HRSLGPPQGE EDSVPRDLPS WMKFLHGKLG NPIVPLNIRL FLAKLVINTE EVFRPY AKH WLSPLLQLAA SENNGGEGIH YMVVEIVATI LSWTGLATPT GVPKDEVLAN RLLNFLM KH VFHPKRAVFR HNLEIIKTLV ECWKDCLSIP YRLIFEKFSG KDPNSKDNSV GIQLLGIV M ANDLPPYDPQ CGIQSSEYFQ ALVNNMSFVR YKEVYAAAAE VLGLILRYVM ERKNILEES LCELVAKQLK QHQNTMEDKF IVCLNKVTKS FPPLADRFMN AVFFLLPKFH GVLKTLCLEV VLCRVEGMT ELYFQLKSKD FVQVMRHRDD ERQKVCLDII YKMMPKLKPV ELRELLNPVV E FVSHPSTT CREQMYNILM WIHDNYRDPE SETDNDSQEI FKLAKDVLIQ GLIDENPGLQ LI IRNFWSH ETRLPSNTLD RLLALNSLYS PKIEVHFLSL ATNFLLEMTS MSPDYPNPMF EHP LSECEF QEYTIDSDWR FRSTVLTPMF VETQASQGTL QTRTQEGSLS ARWPVAGQIR ATQQ QHDFT LTQTADGRSS FDWLTGSSTD PLVDHTSPSS DSLLFAHKRS ERLQRAPLKS VGPDF GKKR LGLPGDEVDN KVKGAAGRTD LLRLRRRFMR DQEKLSLMYA RKGVAEQKRE KEIKSE LKM KQDAQVVLYR SYRHGDLPDI QIKHSSLITP LQAVAQRDPI IAKQLFSSLF SGILKEM DK FKTLSEKNNI TQKLLQDFNR FLNTTFSFFP PFVSCIQDIS CQHAALLSLD PAAVSAGC L ASLQQPVGIR LLEEALLRLL PAELPAKRVR GKARLPPDVL RWVELAKLYR SIGEYDVLR GIFTSEIGTK QITQSALLAE ARSDYSEAAK QYDEALNKQD WVDGEPTEAE KDFWELASLD CYNHLAEWK SLEYCSTASI DSENPPDLNK IWSEPFYQET YLPYMIRSKL KLLLQGEADQ S LLTFIDKA MHGELQKAIL ELHYSQELSL LYLLQDDVDR AKYYIQNGIQ SFMQNYSSID VL LHQSRLT KLQSVQALTE IQEFISFISK QGNLSSQVPL KRLLNTWTNR YPDAKMDPMN IWD DIITNR CFFLSKIEEK LTPLPEDNSM NVDQDGDPSD RMEVQEQEED ISSLIRSCKF SMKM KMIDS ARKQNNFSLA MKLLKELHKE SKTRDDWLVS WVQSYCRLSH CRSRSQGCSE QVLTV LKTV SLLDENNVSS YLSKNILAFR DQNILLGTTY RIIANALSSE PACLAEIEED KARRIL ELS GSSSEDSEKV IAGLYQRAFQ HLSEAVQAAE EEAQPPSWSC GPAAGVIDAY MTLADFC DQ QLRKEEENAS VIDSAELQAY PALVVEKMLK ALKLNSNEAR LKFPRLLQII ERYPEETL S LMTKEISSVP CWQFISWISH MVALLDKDQA VAVQHSVEEI TDNYPQAIVY PFIISSESY SFKDTSTGHK NKEFVARIKS KLDQGGVIQD FINALDQLSN PELLFKDWSN DVRAELAKTP VNKKNIEKM YERMYAALGD PKAPGLGAFR RKFIQTFGKE FDKHFGKGGS KLLRMKLSDF N DITNMLLL KMNKDSKPPG NLKECSPWMS DFKVEFLRNE LEIPGQYDGR GKPLPEYHVR IA GFDERVT VMASLRRPKR IIIRGHDERE HPFLVKGGED LRQDQRVEQL FQVMNGILAQ DSA CSQRAL QLRTYSVVPM TSRLGLIEWL ENTVTLKDLL LNTMSQEEKA AYLSDPRAPP CEYK DWLTK MSGKHDVGAY MLMYKGANRT ETVTSFRKRE SKVPADLLKR AFVRMSTSPE AFLAL RSHF ASSHALICIS HWILGIGDRH LNNFMVAMET GGVIGIDFGH AFGSATQFLP VPELMP FRL TRQFINLMLP MKETGLMYSI MVHALRAFRS DPGLLTNTMD VFVKEPSFDW KNFEQKM LK KGGSWIQEIN VAEKNWYPRQ KICYAKRKLA GANPAVITCD ELLLGHEKAP AFRDYVAV A RGSKDHNIRA QEPESGLSEE TQVKCLMDQA TDPNILGRTW EGWEPWM |
-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 | 0.6 mg/mL |
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緩衝液 | pH: 7.4 / 詳細: 20mM Hepes pH 7.4, 150mM NaCl, 0.5mM EDTA, 1mM DTT |
糖包埋 | 材質: ice |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV |
詳細 | DNA-PK holoenzyme containing DNA-PKcs and Ku70/80 proteins purified from Hela cell nuclear extracts. |
-電子顕微鏡法
顕微鏡 | FEI TECNAI ARCTICA |
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撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: SUPER-RESOLUTION / 平均電子線量: 40.0 e/Å2 |
電子線 | 加速電圧: 200 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 |
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: Talos Arctica / 画像提供: FEI Company |
-画像解析
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 5.8 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 46415 |
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初期 角度割当 | タイプ: PROJECTION MATCHING |
最終 角度割当 | タイプ: PROJECTION MATCHING |