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基本情報
登録情報 | データベース: PDB / ID: 7rb2 | ||||||
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タイトル | Cryo-EM structure of SARS-CoV-2 NSP15 NendoU in BIS-Tris pH 6.0 | ||||||
![]() | Uridylate-specific endoribonuclease | ||||||
![]() | VIRAL PROTEIN / nsp15 / sars-cov-2 / nendoU / coronavirus / covid-19 | ||||||
機能・相同性 | ![]() protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / 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; - / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway ...protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / 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; - / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / snRNP Assembly / Replication of the SARS-CoV-2 genome / 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 / double membrane vesicle viral factory outer membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / symbiont-mediated suppression of host NF-kappaB cascade / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase 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 / regulation of autophagy / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / copper ion binding / viral translational frameshifting / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / 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 | 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: 3.27 Å | ||||||
![]() | Godoy, A.S. / Song, Y. / Nakamura, A.M. / Noske, G.D. / Gawriljuk, V.O. / Fernandes, R.S. / Oliva, G. | ||||||
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 | 分子: ![]() ![]() |
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-関連構造データ
関連構造データ | ![]() 24392MC ![]() 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 ![]() 7rb0C M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 ( |
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集合体
登録構造単位 | ![]()
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要素
#1: タンパク質 | 分子量: 39112.535 Da / 分子数: 6 / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 遺伝子: rep, 1a-1b / 発現宿主: ![]() ![]() 参照: UniProt: P0DTD1, 加水分解酵素; エステル加水分解酵素 |
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-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 |
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試料調製
構成要素 | 名称: Structure of SARS-CoV-2 NSP15 / タイプ: COMPLEX / Entity ID: all / 由来: RECOMBINANT |
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由来(天然) | 生物種: ![]() ![]() |
由来(組換発現) | 生物種: ![]() ![]() |
緩衝液 | pH: 6 / 詳細: 100 mM BIS-Tris 6.0, 200 mM NaCl |
試料 | 濃度: 0.5 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 凍結剤: ETHANE |
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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: ![]() |
電子レンズ | モード: BRIGHT FIELD |
撮影 | 電子線照射量: 43.254543 e/Å2 フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) |
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解析
ソフトウェア | 名称: PHENIX / バージョン: 1.18.2_3874: / 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: 3.27 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 263322 / 対称性のタイプ: POINT | |||||||||||||||||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT / 空間: REAL | |||||||||||||||||||||||||||
原子モデル構築 | PDB-ID: 7KEG Accession code: 7KEG / Source name: PDB / タイプ: experimental model | |||||||||||||||||||||||||||
拘束条件 |
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