+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-16070 | |||||||||
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タイトル | DNA-PK XLF mediated dimer bound to PAXX | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | DNA-PK / DNA-PKcs (DNA依存性プロテインキナーゼ触媒サブユニット) / Ku70 (Ku70) / Ku80 (Ku80) / PAXX / NHEJ (非相同末端結合) / DNA BINDING PROTEIN (DNA結合タンパク質) | |||||||||
機能・相同性 | 機能・相同性情報 DNA ligation involved in DNA recombination / FHA domain binding / positive regulation of chromosome organization / positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / DNA ligase activity / Ku70:Ku80 complex / DN2 thymocyte differentiation / negative regulation of t-circle formation ...DNA ligation involved in DNA recombination / FHA domain binding / positive regulation of chromosome organization / positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / DNA ligase activity / Ku70:Ku80 complex / DN2 thymocyte differentiation / negative regulation of t-circle formation / positive regulation of platelet formation / DNA end binding / DNAリガーゼ / T cell receptor V(D)J recombination / pro-B cell differentiation / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA ligase (ATP) activity / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / DNA-dependent protein kinase complex / immature B cell differentiation / nucleotide-excision repair, DNA gap filling / DNA-dependent protein kinase-DNA ligase 4 complex / single strand break repair / cellular response to X-ray / immunoglobulin V(D)J recombination / nonhomologous end joining complex / protein localization to site of double-strand break / nuclear telomere cap complex / DNA ligation / regulation of smooth muscle cell proliferation / V(D)J遺伝子再構成 / double-strand break repair via alternative nonhomologous end joining / クラススイッチ / Cytosolic sensors of pathogen-associated DNA / double-strand break repair via classical nonhomologous end joining / regulation of epithelial cell proliferation / IRF3-mediated induction of type I IFN / telomere capping / 相同組換え / regulation of telomere maintenance / regulation of hematopoietic stem cell differentiation / U3 snoRNA binding / positive regulation of neurogenesis / protein localization to chromosome, telomeric region / cellular response to fatty acid / hematopoietic stem cell proliferation / cellular hyperosmotic salinity response / maturation of 5.8S rRNA / response to ionizing radiation / T cell lineage commitment / telomeric DNA binding / negative regulation of cGAS/STING signaling pathway / DNA biosynthetic process / positive regulation of catalytic activity / B cell lineage commitment / cellular response to lithium ion / 2-LTR circle formation / positive regulation of double-strand break repair via nonhomologous end joining / site of DNA damage / somatic stem cell population maintenance / ligase activity / 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 / T cell differentiation / enzyme activator activity / response to X-ray / 5'-deoxyribose-5-phosphate lyase activity / chromosome organization / hematopoietic stem cell differentiation / positive regulation of protein kinase activity / ectopic germ cell programmed cell death / ATP-dependent activity, acting on DNA / somitogenesis / SUMOylation of DNA damage response and repair proteins / DNA polymerase binding / condensed chromosome / positive regulation of telomerase activity / mitotic G1 DNA damage checkpoint signaling / positive regulation of telomere maintenance via telomerase / DNA helicase activity / activation of innate immune response / telomere maintenance / cellular response to leukemia inhibitory factor / 神経発生 / cyclin binding / small-subunit processome / B cell differentiation / positive regulation of translation / positive regulation of erythrocyte differentiation / negative regulation of protein phosphorylation / central nervous system development / stem cell proliferation / cellular response to ionizing radiation / デオキシリボ核酸 / response to gamma radiation / 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 / peptidyl-threonine phosphorylation / brain development 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: 4.51 Å | |||||||||
データ登録者 | Hardwick SW / Chaplin AK | |||||||||
資金援助 | 英国, 1件
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引用 | ジャーナル: Sci Adv / 年: 2023 タイトル: PAXX binding to the NHEJ machinery explains functional redundancy with XLF. 著者: Murielle Seif-El-Dahan / Antonia Kefala-Stavridi / Philippe Frit / Steven W Hardwick / Dima Y Chirgadze / Taiana Maia De Oliviera / Jessica Andreani / Sébastien Britton / Nadia Barboule / ...著者: Murielle Seif-El-Dahan / Antonia Kefala-Stavridi / Philippe Frit / Steven W Hardwick / Dima Y Chirgadze / Taiana Maia De Oliviera / Jessica Andreani / Sébastien Britton / Nadia Barboule / Madeleine Bossaert / Arun Prasad Pandurangan / Katheryn Meek / Tom L Blundell / Virginie Ropars / Patrick Calsou / Jean-Baptiste Charbonnier / Amanda K Chaplin / 要旨: Nonhomologous end joining is a critical mechanism that repairs DNA double-strand breaks in human cells. In this work, we address the structural and functional role of the accessory protein PAXX ...Nonhomologous end joining is a critical mechanism that repairs DNA double-strand breaks in human cells. In this work, we address the structural and functional role of the accessory protein PAXX [paralog of x-ray repair cross-complementing protein 4 (XRCC4) and XRCC4-like factor (XLF)] in this mechanism. Here, we report high-resolution cryo-electron microscopy (cryo-EM) and x-ray crystallography structures of the PAXX C-terminal Ku-binding motif bound to Ku70/80 and cryo-EM structures of PAXX bound to two alternate DNA-dependent protein kinase (DNA-PK) end-bridging dimers, mediated by either Ku80 or XLF. We identify residues critical for the Ku70/PAXX interaction in vitro and in cells. We demonstrate that PAXX and XLF can bind simultaneously to the Ku heterodimer and act as structural bridges in alternate forms of DNA-PK dimers. Last, we show that engagement of both proteins provides a complementary advantage for DNA end synapsis and end joining in cells. | |||||||||
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_16070.map.gz | 267 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-16070-v30.xml emd-16070.xml | 33.7 KB 33.7 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_16070_fsc.xml | 17.3 KB | 表示 | FSCデータファイル |
画像 | emd_16070.png | 57 KB | ||
その他 | emd_16070_additional_1.map.gz emd_16070_half_map_1.map.gz emd_16070_half_map_2.map.gz | 255.8 MB 498.4 MB 498.4 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-16070 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16070 | 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_16070.map.gz / 形式: CCP4 / 大きさ: 536.4 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 1.304 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
-追加マップ: Locally refined composite map for presentation purposes
ファイル | emd_16070_additional_1.map | ||||||||||||
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注釈 | Locally refined composite map for presentation purposes | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_16070_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_16070_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 : DNA-PK XLF mediated dimer bound to PAXX
+超分子 #1: DNA-PK XLF mediated dimer bound to PAXX
+分子 #1: DNA-dependent protein kinase catalytic subunit
+分子 #2: DNA repair protein XRCC4
+分子 #3: DNA ligase 4
+分子 #4: Non-homologous end-joining factor 1
+分子 #5: X-ray repair cross-complementing protein 6
+分子 #6: X-ray repair cross-complementing protein 5
+分子 #7: Protein PAXX
+分子 #8: DNA (26-MER)
+分子 #9: DNA (27-MER)
+分子 #10: DNA (28-MER)
+分子 #11: DNA (24-MER)
-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 | 3 mg/mL |
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緩衝液 | pH: 8 |
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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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 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / 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): 0.8 µm / 倍率(公称値): 130000 |
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 |
撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 平均電子線量: 48.03 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |