+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-14955 | |||||||||
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タイトル | Cryo-EM structure of Ku 70/80 bound to inositol hexakisphosphate | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | DNA repair / NHEJ / Ku 70/80 / DNA-PK / cancer / double-strand break / DNA binding protein | |||||||||
機能・相同性 | 機能・相同性情報 Ku70:Ku80 complex / negative regulation of t-circle formation / DNA end binding / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / cellular response to X-ray / nonhomologous end joining complex / DNA ligation ...Ku70:Ku80 complex / negative regulation of t-circle formation / DNA end binding / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / cellular response to X-ray / nonhomologous end joining complex / DNA ligation / regulation of smooth muscle cell proliferation / nuclear telomere cap complex / Cytosolic sensors of pathogen-associated DNA / double-strand break repair via classical nonhomologous end joining / IRF3-mediated induction of type I IFN / recombinational repair / regulation of telomere maintenance / U3 snoRNA binding / positive regulation of neurogenesis / cellular response to fatty acid / hematopoietic stem cell proliferation / protein localization to chromosome, telomeric region / cellular hyperosmotic salinity response / telomeric DNA binding / positive regulation of catalytic activity / 2-LTR circle formation / site of DNA damage / 付加脱離酵素(リアーゼ); 炭素-酸素リアーゼ類; その他の炭素-酸素リアーゼ / 5'-deoxyribose-5-phosphate lyase activity / hematopoietic stem cell differentiation / positive regulation of protein kinase activity / ATP-dependent activity, acting on DNA / DNA helicase activity / : / enzyme activator activity / positive regulation of telomere maintenance via telomerase / activation of innate immune response / telomere maintenance / cyclin binding / neurogenesis / cellular response to leukemia inhibitory factor / protein-DNA complex / small-subunit processome / Nonhomologous End-Joining (NHEJ) / 加水分解酵素; 酸無水物に作用; 酸無水物に作用・細胞または細胞小器官の運動に関与 / cellular response to gamma radiation / double-strand break repair via nonhomologous end joining / double-strand break repair / scaffold protein binding / double-stranded DNA binding / secretory granule lumen / DNA recombination / ficolin-1-rich granule lumen / transcription regulator complex / chromosome, telomeric region / damaged DNA binding / transcription cis-regulatory region binding / ribonucleoprotein complex / response to xenobiotic stimulus / innate immune response / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / DNA damage response / Neutrophil degranulation / protein-containing complex binding / nucleolus / positive regulation of DNA-templated transcription / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular region / nucleoplasm / ATP binding / membrane / nucleus / plasma membrane / 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: 3.5 Å | |||||||||
データ登録者 | Kefala Stavridi A / Chaplin AK / Blundell TL | |||||||||
資金援助 | 英国, 1件
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引用 | ジャーナル: Nucleic Acids Res / 年: 2023 タイトル: Structural and functional basis of inositol hexaphosphate stimulation of NHEJ through stabilization of Ku-XLF interaction. 著者: Antonia Kefala Stavridi / Amandine Gontier / Vincent Morin / Philippe Frit / Virginie Ropars / Nadia Barboule / Carine Racca / Sagun Jonchhe / Michael J Morten / Jessica Andreani / Alexey Rak ...著者: Antonia Kefala Stavridi / Amandine Gontier / Vincent Morin / Philippe Frit / Virginie Ropars / Nadia Barboule / Carine Racca / Sagun Jonchhe / Michael J Morten / Jessica Andreani / Alexey Rak / Pierre Legrand / Alexa Bourand-Plantefol / Steven W Hardwick / Dimitri Y Chirgadze / Paul Davey / Taiana Maia De Oliveira / Eli Rothenberg / Sebastien Britton / Patrick Calsou / Tom L Blundell / Paloma F Varela / Amanda K Chaplin / Jean-Baptiste Charbonnier / 要旨: The classical Non-Homologous End Joining (c-NHEJ) pathway is the predominant process in mammals for repairing endogenous, accidental or programmed DNA Double-Strand Breaks. c-NHEJ is regulated by ...The classical Non-Homologous End Joining (c-NHEJ) pathway is the predominant process in mammals for repairing endogenous, accidental or programmed DNA Double-Strand Breaks. c-NHEJ is regulated by several accessory factors, post-translational modifications, endogenous chemical agents and metabolites. The metabolite inositol-hexaphosphate (IP6) stimulates c-NHEJ by interacting with the Ku70-Ku80 heterodimer (Ku). We report cryo-EM structures of apo- and DNA-bound Ku in complex with IP6, at 3.5 Å and 2.74 Å resolutions respectively, and an X-ray crystallography structure of a Ku in complex with DNA and IP6 at 3.7 Å. The Ku-IP6 interaction is mediated predominantly via salt bridges at the interface of the Ku70 and Ku80 subunits. This interaction is distant from the DNA, DNA-PKcs, APLF and PAXX binding sites and in close proximity to XLF binding site. Biophysical experiments show that IP6 binding increases the thermal stability of Ku by 2°C in a DNA-dependent manner, stabilizes Ku on DNA and enhances XLF affinity for Ku. In cells, selected mutagenesis of the IP6 binding pocket reduces both Ku accrual at damaged sites and XLF enrolment in the NHEJ complex, which translate into a lower end-joining efficiency. Thus, this study defines the molecular bases of the IP6 metabolite stimulatory effect on the c-NHEJ repair activity. | |||||||||
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_14955.map.gz | 51 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-14955-v30.xml emd-14955.xml | 17 KB 17 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_14955_fsc.xml | 13.8 KB | 表示 | FSCデータファイル |
画像 | emd_14955.png | 56.9 KB | ||
Filedesc metadata | emd-14955.cif.gz | 6.5 KB | ||
その他 | emd_14955_half_map_1.map.gz emd_14955_half_map_2.map.gz | 95.5 MB 95.5 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-14955 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14955 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_14955_validation.pdf.gz | 949.4 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_14955_full_validation.pdf.gz | 949 KB | 表示 | |
XML形式データ | emd_14955_validation.xml.gz | 17.9 KB | 表示 | |
CIF形式データ | emd_14955_validation.cif.gz | 23.7 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14955 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14955 | 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_14955.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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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: 0.652 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
-ハーフマップ: #2
ファイル | emd_14955_half_map_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: #1
ファイル | emd_14955_half_map_2.map | ||||||||||||
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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 : Cryo-EM structure of Ku 70/80 bound to inositol hexakisphosphate
全体 | 名称: Cryo-EM structure of Ku 70/80 bound to inositol hexakisphosphate |
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要素 |
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-超分子 #1: Cryo-EM structure of Ku 70/80 bound to inositol hexakisphosphate
超分子 | 名称: Cryo-EM structure of Ku 70/80 bound to inositol hexakisphosphate タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#2 |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
-分子 #1: X-ray repair cross-complementing protein 6
分子 | 名称: X-ray repair cross-complementing protein 6 / タイプ: protein_or_peptide / ID: 1 / コピー数: 1 / 光学異性体: LEVO EC番号: 加水分解酵素; 酸無水物に作用; 酸無水物に作用・細胞または細胞小器官の運動に関与 |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 73.890336 KDa |
組換発現 | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) |
配列 | 文字列: MNTIHHHHHH NTSGSGGGGG RLVPRGSMSE NLYFQGSMSG WESYYKTEGD EEAEEEQEEN LEASGDYKYS GRDSLIFLVD ASKAMFESQ SEDELTPFDM SIQCIQSVYI SKIISSDRDL LAVVFYGTEK DKNSVNFKNI YVLQELDNPG AKRILELDQF K GQQGQKRF ...文字列: MNTIHHHHHH NTSGSGGGGG RLVPRGSMSE NLYFQGSMSG WESYYKTEGD EEAEEEQEEN LEASGDYKYS GRDSLIFLVD ASKAMFESQ SEDELTPFDM SIQCIQSVYI SKIISSDRDL LAVVFYGTEK DKNSVNFKNI YVLQELDNPG AKRILELDQF K GQQGQKRF QDMMGHGSDY SLSEVLWVCA NLFSDVQFKM SHKRIMLFTN EDNPHGNDSA KASRARTKAG DLRDTGIFLD LM HLKKPGG FDISLFYRDI ISIAEDEDLR VHFEESSKLE DLLRKVRAKE TRKRALSRLK LKLNKDIVIS VGIYNLVQKA LKP PPIKLY RETNEPVKTK TRTFNTSTGG LLLPSDTKRS QIYGSRQIIL EKEETEELKR FDDPGLMLMG FKPLVLLKKH HYLR PSLFV YPEESLVIGS STLFSALLIK CLEKEVAALC RYTPRRNIPP YFVALVPQEE ELDDQKIQVT PPGFQLVFLP FADDK RKMP FTEKIMATPE QVGKMKAIVE KLRFTYRSDS FENPVLQQHF RNLEALALDL MEPEQAVDLT LPKVEAMNKR LGSLVD EFK ELVYPPDYNP EGKVTKRKHD NEGSGSKRPK VEYSEEELKT HISKGTLGKF TVPMLKEACR AYGLKSGLKK QELLEAL TK HFQD UniProtKB: X-ray repair cross-complementing protein 6 |
-分子 #2: X-ray repair cross-complementing protein 5
分子 | 名称: X-ray repair cross-complementing protein 5 / タイプ: protein_or_peptide / ID: 2 / コピー数: 1 / 光学異性体: LEVO EC番号: 加水分解酵素; 酸無水物に作用; 酸無水物に作用・細胞または細胞小器官の運動に関与 |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 82.812438 KDa |
組換発現 | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) |
配列 | 文字列: MVRSGNKAAV VLCMDVGFTM SNSIPGIESP FEQAKKVITM FVQRQVFAEN KDEIALVLFG TDGTDNPLSG GDQYQNITVH RHLMLPDFD LLEDIESKIQ PGSQQADFLD ALIVSMDVIQ HETIGKKFEK RHIEIFTDLS SRFSKSQLDI IIHSLKKCDI S LQFFLPFS ...文字列: MVRSGNKAAV VLCMDVGFTM SNSIPGIESP FEQAKKVITM FVQRQVFAEN KDEIALVLFG TDGTDNPLSG GDQYQNITVH RHLMLPDFD LLEDIESKIQ PGSQQADFLD ALIVSMDVIQ HETIGKKFEK RHIEIFTDLS SRFSKSQLDI IIHSLKKCDI S LQFFLPFS LGKEDGSGDR GDGPFRLGGH GPSFPLKGIT EQQKEGLEIV KMVMISLEGE DGLDEIYSFS ESLRKLCVFK KI ERHSIHW PCRLTIGSNL SIRIAAYKSI LQERVKKTWT VVDAKTLKKE DIQKETVYCL NDDDETEVLK EDIIQGFRYG SDI VPFSKV DEEQMKYKSE GKCFSVLGFC KSSQVQRRFF MGNQVLKVFA ARDDEAAAVA LSSLIHALDD LDMVAIVRYA YDKR ANPQV GVAFPHIKHN YECLVYVQLP FMEDLRQYMF SSLKNSKKYA PTEAQLNAVD ALIDSMSLAK KDEKTDTLED LFPTT KIPN PRFQRLFQCL LHRALHPREP LPPIQQHIWN MLNPPAEVTT KSQIPLSKIK TLFPLIEAKK KDQVTAQEIF QDNHED GPT AKKLKTEQGG AHFSVSSLAE GSVTSVGSVN PAENFRVLVK QKKASFEEAS NQLINHIEQF LDTNETPYFM KSIDCIR AF REEAIKFSEE QRFNNFLKAL QEKVEIKQLN HFWEIVVQDG ITLITKEEAS GSSVTAEEAK KFLAPKDKPS GDTAAVFE E GGDVDDLLDM I UniProtKB: X-ray repair cross-complementing protein 5 |
-分子 #3: INOSITOL HEXAKISPHOSPHATE
分子 | 名称: INOSITOL HEXAKISPHOSPHATE / タイプ: ligand / ID: 3 / コピー数: 1 / 式: IHP |
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分子量 | 理論値: 660.035 Da |
Chemical component information | ChemComp-IHP: |
-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
緩衝液 | pH: 8 |
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凍結 | 凍結剤: ETHANE |
-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 (6k x 4k) / 平均電子線量: 49.43 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 / 最大 デフォーカス(公称値): 2.7 µm / 最小 デフォーカス(公称値): 0.9 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |