+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5y3r | |||||||||||||||
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タイトル | Cryo-EM structure of Human DNA-PK Holoenzyme | |||||||||||||||
要素 |
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キーワード | DNA BINDING PROTEIN (DNA結合タンパク質) / Cryo-EM structure / DNA-PK / DNAPKcs / activation (活性化) / NHEJ (非相同末端結合) | |||||||||||||||
機能・相同性 | 機能・相同性情報 Ku70:Ku80 complex / negative regulation of t-circle formation / positive regulation of platelet formation / DNA end binding / 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 ...Ku70:Ku80 complex / negative regulation of t-circle formation / positive regulation of platelet formation / DNA end binding / 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 / immature B cell differentiation / DNA-dependent protein kinase-DNA ligase 4 complex / cellular response to X-ray / immunoglobulin V(D)J recombination / nonhomologous end joining complex / DNA ligation / nuclear telomere cap complex / regulation of smooth muscle cell proliferation / double-strand break repair via alternative nonhomologous end joining / 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 / U3 snoRNA binding / regulation of hematopoietic stem cell differentiation / 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 / T cell lineage commitment / negative regulation of cGAS/STING signaling pathway / telomeric DNA binding / positive regulation of catalytic activity / B cell lineage commitment / 2-LTR circle formation / positive regulation of double-strand break repair via nonhomologous end joining / 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 / enzyme activator activity / 5'-deoxyribose-5-phosphate lyase activity / hematopoietic stem cell differentiation / positive regulation of protein kinase activity / ectopic germ cell programmed cell death / ATP-dependent activity, acting on DNA / somitogenesis / 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 / small-subunit processome / cyclin binding / positive regulation of translation / negative regulation of protein phosphorylation / positive regulation of erythrocyte differentiation / 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 / brain development / peptidyl-threonine phosphorylation / protein destabilization / protein modification process / cellular response to gamma radiation / regulation of circadian rhythm / double-strand break repair via nonhomologous end joining / cellular response to insulin stimulus / rhythmic process / double-strand break repair / intrinsic apoptotic signaling pathway in response to DNA damage / E3 ubiquitin ligases ubiquitinate target proteins / T cell differentiation in thymus / heart development / double-stranded DNA binding / scaffold protein binding / peptidyl-serine phosphorylation / secretory granule lumen / DNA recombination / ficolin-1-rich granule lumen / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / damaged DNA binding / chromosome, telomeric region / transcription cis-regulatory region binding / non-specific serine/threonine protein kinase / protein kinase activity / response to xenobiotic stimulus / ribonucleoprotein complex / positive regulation of apoptotic process / protein domain specific binding / protein phosphorylation 類似検索 - 分子機能 | |||||||||||||||
生物種 | Homo sapiens (ヒト) | |||||||||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 6.6 Å | |||||||||||||||
データ登録者 | Yin, X. / Liu, M. / Tian, Y. / Wang, J. / Xu, Y. | |||||||||||||||
資金援助 | 中国, 4件
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引用 | ジャーナル: Cell Res / 年: 2017 タイトル: Cryo-EM structure of human DNA-PK holoenzyme. 著者: Xiaotong Yin / Mengjie Liu / Yuan Tian / Jiawei Wang / Yanhui Xu / 要旨: DNA-dependent protein kinase (DNA-PK) is a serine/threonine protein kinase complex composed of a catalytic subunit (DNA-PKcs) and KU70/80 heterodimer bound to DNA. DNA-PK holoenzyme plays a critical ...DNA-dependent protein kinase (DNA-PK) is a serine/threonine protein kinase complex composed of a catalytic subunit (DNA-PKcs) and KU70/80 heterodimer bound to DNA. DNA-PK holoenzyme plays a critical role in non-homologous end joining (NHEJ), the major DNA repair pathway. Here, we determined cryo-electron microscopy structure of human DNA-PK holoenzyme at 6.6 Å resolution. In the complex structure, DNA-PKcs, KU70, KU80 and DNA duplex form a 650-kDa heterotetramer with 1:1:1:1 stoichiometry. The N-terminal α-solenoid (∼2 800 residues) of DNA-PKcs adopts a double-ring fold and connects the catalytic core domain of DNA-PKcs and KU70/80-DNA. DNA-PKcs and KU70/80 together form a DNA-binding tunnel, which cradles ∼30-bp DNA and prevents sliding inward of DNA-PKcs along with DNA duplex, suggesting a mechanism by which the broken DNA end is protected from unnecessary processing. Structural and biochemical analyses indicate that KU70/80 and DNA coordinately induce conformational changes of DNA-PKcs and allosterically stimulate its kinase activity. We propose a model for activation of DNA-PKcs in which allosteric signals are generated upon DNA-PK holoenzyme formation and transmitted to the kinase domain through N-terminal HEAT repeats and FAT domain of DNA-PKcs. Our studies suggest a mechanism for recognition and protection of broken DNA ends and provide a structural basis for understanding the activation of DNA-PKcs and DNA-PK-mediated NHEJ pathway. | |||||||||||||||
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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 5y3r.cif.gz | 903 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5y3r.ent.gz | 715.1 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5y3r.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/y3/5y3r ftp://data.pdbj.org/pub/pdb/validation_reports/y3/5y3r | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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-要素
-X-ray repair cross-complementing protein ... , 2種, 2分子 AB
#1: タンパク質 | 分子量: 57619.352 Da / 分子数: 1 / 断片: UNP residues 34-534 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: XRCC6, G22P1 / 発現宿主: Homo sapiens (ヒト) 参照: UniProt: P12956, 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, 付加脱離酵素(リアーゼ); 炭素- ...参照: UniProt: P12956, 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, 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 |
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#2: タンパク質 | 分子量: 60972.969 Da / 分子数: 1 / 断片: UNP residues 6-541 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: XRCC5, G22P2 / 発現宿主: Homo sapiens (ヒト) 参照: UniProt: P13010, 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 |
-DNA鎖 , 2種, 2分子 DE
#4: DNA鎖 | 分子量: 10502.785 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト) |
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#5: DNA鎖 | 分子量: 11042.164 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト) |
-タンパク質・ペプチド / タンパク質 , 2種, 2分子 KC
#3: タンパク質・ペプチド | 分子量: 1084.182 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト) |
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#6: タンパク質 | 分子量: 468885.344 Da / 分子数: 1 / 断片: UNP residues 10-4128 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PRKDC, HYRC, HYRC1 / 細胞株 (発現宿主): HEK293F / 器官 (発現宿主): KIDNEY / 発現宿主: Homo sapiens (ヒト) 参照: UniProt: P78527, non-specific serine/threonine protein kinase |
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: PRKDC-Helix / タイプ: COMPLEX / Entity ID: all / 由来: RECOMBINANT |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
由来(組換発現) | 生物種: Homo sapiens (ヒト) |
緩衝液 | pH: 7.4 |
試料 | 濃度: 0.6 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | グリッドの材料: GOLD / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: Quantifoil R1.2/1.3 |
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 283 K |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: OTHER |
電子レンズ | モード: BRIGHT FIELDBright-field microscopy / 倍率(公称値): 18000 X / 最大 デフォーカス(公称値): 4700 nm / 最小 デフォーカス(公称値): 1700 nm / Cs: 2.7 mm |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 平均露光時間: 8 sec. / 電子線照射量: 50 e/Å2 / 検出モード: SUPER-RESOLUTION フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 実像数: 3496 |
画像スキャン | 動画フレーム数/画像: 32 / 利用したフレーム数/画像: 1-32 |
-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.10.1_2155 / 分類: 精密化 | ||||||||||||||||||||||||
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EMソフトウェア |
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CTF補正 | タイプ: NONE | ||||||||||||||||||||||||
3次元再構成 | 解像度: 6.6 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 53451 / クラス平均像の数: 1 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
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