+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-12301 | |||||||||
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タイトル | Cryo-EM structure of NHEJ super-complex (monomer) | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | NHEJ / DNA-PKcs / Ku70/80 / XLF / XRCC4 / DNA-LigaseIV / DNA BINDING PROTEIN | |||||||||
機能・相同性 | 機能・相同性情報 DNA ligation involved in DNA recombination / T cell receptor V(D)J recombination / FHA domain binding / positive regulation of chromosome organization / positive regulation of ligase activity / pro-B cell differentiation / DNA ligase IV complex / DNA ligation involved in DNA repair / positive regulation of lymphocyte differentiation / small-subunit processome assembly ...DNA ligation involved in DNA recombination / T cell receptor V(D)J recombination / FHA domain binding / positive regulation of chromosome organization / positive regulation of ligase activity / pro-B cell differentiation / DNA ligase IV complex / DNA ligation involved in DNA repair / positive regulation of lymphocyte differentiation / small-subunit processome assembly / DNA ligase activity / Ku70:Ku80 complex / DN2 thymocyte differentiation / DNA-dependent protein kinase complex / immunoglobulin V(D)J recombination / negative regulation of t-circle formation / DNA end binding / DNA ligase (ATP) / DNA-dependent protein kinase-DNA ligase 4 complex / MHC class II antigen presentation / nonhomologous end joining complex / DNA ligase (ATP) activity / cellular response to X-ray / regulation of smooth muscle cell proliferation / single strand break repair / Cytosolic sensors of pathogen-associated DNA / Neutrophil degranulation / DNA ligation / V(D)J recombination / IRF3-mediated induction of type I IFN / nuclear telomere cap complex / nucleotide-excision repair, DNA gap filling / isotype switching / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / entry into host cell by a symbiont-containing vacuole / positive regulation of catalytic activity / U3 snoRNA binding / recombinational repair / regulation of telomere maintenance / protein localization to chromosome, telomeric region / positive regulation of neurogenesis / cellular response to fatty acid / cellular hyperosmotic salinity response / hematopoietic stem cell proliferation / response to ionizing radiation / cellular response to lithium ion / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; アスパラギン酸プロテアーゼ / DNA biosynthetic process / telomeric DNA binding / 2-LTR circle formation / ligase activity / : / somatic stem cell population maintenance / site of DNA damage / protein autoprocessing / T cell differentiation / 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 / response to X-ray / 5'-deoxyribose-5-phosphate lyase activity / hematopoietic stem cell differentiation / positive regulation of protein kinase activity / chromosome organization / ATP-dependent activity, acting on DNA / SUMOylation of DNA damage response and repair proteins / DNA polymerase binding / activation of innate immune response / condensed chromosome / enzyme activator activity / transport vesicle / positive regulation of telomere maintenance via telomerase / telomere maintenance / DNA helicase activity / neurogenesis / B cell differentiation / cyclin binding / protein-DNA complex / stem cell proliferation / response to gamma radiation / cellular response to leukemia inhibitory factor / central nervous system development / small-subunit processome / cellular response to ionizing 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 / cellular response to gamma radiation / fibrillar center / protein processing / double-strand break repair via nonhomologous end joining / establishment of integrated proviral latency / positive regulation of fibroblast proliferation / double-strand break repair / site of double-strand break / T cell differentiation in thymus / double-stranded DNA binding / scaffold protein binding / fibroblast proliferation / secretory granule lumen / in utero embryonic development / DNA recombination 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: 4.29 Å | |||||||||
データ登録者 | Chaplin AK / Hardwick SW | |||||||||
資金援助 | 英国, 1件
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引用 | ジャーナル: Mol Cell / 年: 2021 タイトル: Cryo-EM of NHEJ supercomplexes provides insights into DNA repair. 著者: Amanda K Chaplin / Steven W Hardwick / Antonia Kefala Stavridi / Christopher J Buehl / Noah J Goff / Virginie Ropars / Shikang Liang / Taiana Maia De Oliveira / Dimitri Y Chirgadze / Katheryn ...著者: Amanda K Chaplin / Steven W Hardwick / Antonia Kefala Stavridi / Christopher J Buehl / Noah J Goff / Virginie Ropars / Shikang Liang / Taiana Maia De Oliveira / Dimitri Y Chirgadze / Katheryn Meek / Jean-Baptiste Charbonnier / Tom L Blundell / 要旨: Non-homologous end joining (NHEJ) is one of two critical mechanisms utilized in humans to repair DNA double-strand breaks (DSBs). Unrepaired or incorrect repair of DSBs can lead to apoptosis or ...Non-homologous end joining (NHEJ) is one of two critical mechanisms utilized in humans to repair DNA double-strand breaks (DSBs). Unrepaired or incorrect repair of DSBs can lead to apoptosis or cancer. NHEJ involves several proteins, including the Ku70/80 heterodimer, DNA-dependent protein kinase catalytic subunit (DNA-PKcs), X-ray cross-complementing protein 4 (XRCC4), XRCC4-like factor (XLF), and ligase IV. These core proteins bind DSBs and ligate the damaged DNA ends. However, details of the structural assembly of these proteins remain unclear. Here, we present cryo-EM structures of NHEJ supercomplexes that are composed of these core proteins and DNA, revealing the detailed structural architecture of this assembly. We describe monomeric and dimeric forms of this supercomplex and also propose the existence of alternate dimeric forms of long-range synaptic complexes. Finally, we show that mutational disruption of several structural features within these NHEJ complexes negatively affects DNA repair. | |||||||||
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_12301.map.gz | 557.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-12301-v30.xml emd-12301.xml | 31.4 KB 31.4 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_12301_fsc.xml | 18.8 KB | 表示 | FSCデータファイル |
画像 | emd_12301.png | 57.1 KB | ||
Filedesc metadata | emd-12301.cif.gz | 10.9 KB | ||
その他 | emd_12301_half_map_1.map.gz emd_12301_half_map_2.map.gz | 556.7 MB 556.7 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-12301 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12301 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_12301_validation.pdf.gz | 1.2 MB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_12301_full_validation.pdf.gz | 1.2 MB | 表示 | |
XML形式データ | emd_12301_validation.xml.gz | 27.2 KB | 表示 | |
CIF形式データ | emd_12301_validation.cif.gz | 36 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12301 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12301 | 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_12301.map.gz / 形式: CCP4 / 大きさ: 600.7 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: 1.304 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
-ハーフマップ: #2
ファイル | emd_12301_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_12301_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 : NHEJ super-complex (monomer)
+超分子 #1: NHEJ super-complex (monomer)
+超分子 #2: DNA-dependent protein kinase catalytic subunit
+超分子 #3: X-ray repair cross-complementing protein 6 and 5
+超分子 #4: Non-homologous end-joining factor 1,DNA repair protein XRCC4, DNA...
+超分子 #5: DNA
+分子 #1: DNA-dependent protein kinase catalytic subunit,DNA-dependent prot...
+分子 #2: X-ray repair cross-complementing protein 6
+分子 #3: X-ray repair cross-complementing protein 5
+分子 #4: Non-homologous end-joining factor 1
+分子 #5: DNA repair protein XRCC4
+分子 #6: DNA ligase 4
+分子 #7: DNA (5'-D(P*AP*AP*TP*AP*AP*AP*CP*TP*AP*AP*AP*AP*AP*CP*TP*AP*TP*TP...
+分子 #8: DNA (5'-D(P*TP*AP*AP*TP*AP*AP*TP*AP*GP*TP*TP*TP*TP*TP*AP*GP*TP*TP...
-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: 7.4 |
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 BIOQUANTUM (6k x 4k) 平均露光時間: 1.3 sec. / 平均電子線量: 46.8 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: 50.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 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 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |