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基本情報
登録情報 | データベース: EMDB / ID: EMD-24391 | |||||||||
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タイトル | Cryo-EM structure of SARS-CoV-2 NSP15 NendoU at pH 7.5 | |||||||||
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![]() | nsp15 / sars-cov-2 / nendoU / coronavirus / covid-19 / VIRAL PROTEIN | |||||||||
機能・相同性 | ![]() protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / 付加脱離酵素(リアーゼ); P-Oリアーゼ類; - / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs ...protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / 付加脱離酵素(リアーゼ); P-Oリアーゼ類; - / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / TRAF3-dependent IRF activation pathway / Replication of the SARS-CoV-2 genome / snRNP Assembly / double membrane vesicle viral factory outer membrane / 加水分解酵素; エステル加水分解酵素; 5'-リン酸モノエステル産生エキソリボヌクレアーゼ / 5'-3' DNA helicase activity / SARS coronavirus main proteinase / host cell endosome / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host toll-like receptor signaling pathway / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / SARS-CoV-2 modulates host translation machinery / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / DNA helicase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; システインプロテアーゼ / single-stranded RNA binding / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / copper ion binding / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.98 Å | |||||||||
![]() | Godoy AS / Song Y | |||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease. 著者: Andre Schutzer Godoy / Aline Minalli Nakamura / Alice Douangamath / Yun Song / Gabriela Dias Noske / Victor Oliveira Gawriljuk / Rafaela Sachetto Fernandes / Humberto D Muniz Pereira / ...著者: Andre Schutzer Godoy / Aline Minalli Nakamura / Alice Douangamath / Yun Song / Gabriela Dias Noske / Victor Oliveira Gawriljuk / Rafaela Sachetto Fernandes / Humberto D Muniz Pereira / Ketllyn Irene Zagato Oliveira / Daren Fearon / Alexandre Dias / Tobias Krojer / Michael Fairhead / Alisa Powell / Louise Dunnet / Jose Brandao-Neto / Rachael Skyner / Rod Chalk / Dávid Bajusz / Miklós Bege / Anikó Borbás / György Miklós Keserű / Frank von Delft / Glaucius Oliva / ![]() ![]() ![]() ![]() ![]() 要旨: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). The NSP15 endoribonuclease enzyme, known as NendoU, is highly conserved and ...Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). The NSP15 endoribonuclease enzyme, known as NendoU, is highly conserved and plays a critical role in the ability of the virus to evade the immune system. NendoU is a promising target for the development of new antiviral drugs. However, the complexity of the enzyme's structure and kinetics, along with the broad range of recognition sequences and lack of structural complexes, hampers the development of inhibitors. Here, we performed enzymatic characterization of NendoU in its monomeric and hexameric form, showing that hexamers are allosteric enzymes with a positive cooperative index, and with no influence of manganese on enzymatic activity. Through combining cryo-electron microscopy at different pHs, X-ray crystallography and biochemical and structural analysis, we showed that NendoU can shift between open and closed forms, which probably correspond to active and inactive states, respectively. We also explored the possibility of NendoU assembling into larger supramolecular structures and proposed a mechanism for allosteric regulation. In addition, we conducted a large fragment screening campaign against NendoU and identified several new allosteric sites that could be targeted for the development of new inhibitors. Overall, our findings provide insights into the complex structure and function of NendoU and offer new opportunities for the development of inhibitors. | |||||||||
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構造の表示
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構造ビューア | EMマップ: ![]() ![]() ![]() |
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マップデータ | ![]() | 58.3 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 17.8 KB 17.8 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 8.9 KB | 表示 | ![]() |
画像 | ![]() | 28.2 KB | ||
Filedesc metadata | ![]() | 5.6 KB | ||
その他 | ![]() ![]() ![]() | 59.2 MB 31.1 MB 59.2 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 549.7 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 549.3 KB | 表示 | |
XML形式データ | ![]() | 11.2 KB | 表示 | |
CIF形式データ | ![]() | 14.5 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 7rb0MC ![]() 5s6xC ![]() 5s6yC ![]() 5s6zC ![]() 5s70C ![]() 5s71C ![]() 5s72C ![]() 5sa4C ![]() 5sa5C ![]() 5sa6C ![]() 5sa7C ![]() 5sa8C ![]() 5sa9C ![]() 5saaC ![]() 5sabC ![]() 5sacC ![]() 5sadC ![]() 5saeC ![]() 5safC ![]() 5sagC ![]() 5sahC ![]() 5saiC ![]() 5sbfC ![]() 7kegC ![]() 7kehC ![]() 7kf4C ![]() 7me0C ![]() 7n7rC ![]() 7n7uC ![]() 7n7wC ![]() 7n7yC ![]() 7n83C ![]() 7rb2C M: このマップから作成された原子モデル C: 同じ文献を引用 ( |
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類似構造データ |
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 0.831 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
-追加マップ: #1
ファイル | emd_24391_additional_1.map | ||||||||||||
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密度ヒストグラム |
-追加マップ: #2
ファイル | emd_24391_additional_2.map | ||||||||||||
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密度ヒストグラム |
-追加マップ: #3
ファイル | emd_24391_additional_3.map | ||||||||||||
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試料の構成要素
-全体 : Structure of SARS-CoV-2 NSP15
全体 | 名称: Structure of SARS-CoV-2 NSP15 |
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要素 |
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-超分子 #1: Structure of SARS-CoV-2 NSP15
超分子 | 名称: Structure of SARS-CoV-2 NSP15 / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all |
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由来(天然) | 生物種: ![]() ![]() |
-分子 #1: Uridylate-specific endoribonuclease
分子 | 名称: Uridylate-specific endoribonuclease / タイプ: protein_or_peptide / ID: 1 / コピー数: 6 / 光学異性体: LEVO EC番号: 加水分解酵素; エステル加水分解酵素 |
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由来(天然) | 生物種: ![]() ![]() |
分子量 | 理論値: 39.112535 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: GAMSLENVAF NVVNKGHFDG QQGEVPVSII NNTVYTKVDG VDVELFENKT TLPVNVAFEL WAKRNIKPVP EVKILNNLGV DIAANTVIW DYKRDAPAHI STIGVCSMTD IAKKPTETIC APLTVFFDGR VDGQVDLFRN ARNGVLITEG SVKGLQPSVG P KQASLNGV ...文字列: GAMSLENVAF NVVNKGHFDG QQGEVPVSII NNTVYTKVDG VDVELFENKT TLPVNVAFEL WAKRNIKPVP EVKILNNLGV DIAANTVIW DYKRDAPAHI STIGVCSMTD IAKKPTETIC APLTVFFDGR VDGQVDLFRN ARNGVLITEG SVKGLQPSVG P KQASLNGV TLIGEAVKTQ FNYYKKVDGV VQQLPETYFT QSRNLQEFKP RSQMEIDFLE LAMDEFIERY KLEGYAFEHI VY GDFSHSQ LGGLHLLIGL AKRFKESPFE LEDFIPMDST VKNYFITDAQ TGSSKCVCSV IDLLLDDFVE IIKSQDLSVV SKV VKVTID YTEISFMLWC KDGHVETFYP KLQ UniProtKB: Replicase polyprotein 1ab |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
濃度 | 0.5 mg/mL |
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緩衝液 | pH: 7.5 / 詳細: Hepes pH 7.5, 200 mM NaCl |
凍結 | 凍結剤: ETHANE |
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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) 平均電子線量: 42.414791 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |