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基本情報
登録情報 | データベース: PDB / ID: 7thm | |||||||||||||||||||||
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タイトル | SARS-CoV-2 nsp12/7/8 complex with a native N-terminus nsp9 | |||||||||||||||||||||
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![]() | VIRAL PROTEIN / polymerase / NiRAN / capping / nsp9 | |||||||||||||||||||||
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 / 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 / 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: 3.18 Å | |||||||||||||||||||||
![]() | Osinski, A. / Tagliabracci, V.S. / Chen, Z. / Li, Y. | |||||||||||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: The mechanism of RNA capping by SARS-CoV-2. 著者: Gina J Park / Adam Osinski / Genaro Hernandez / Jennifer L Eitson / Abir Majumdar / Marco Tonelli / Katie Henzler-Wildman / Krzysztof Pawłowski / Zhe Chen / Yang Li / John W Schoggins / ...著者: Gina J Park / Adam Osinski / Genaro Hernandez / Jennifer L Eitson / Abir Majumdar / Marco Tonelli / Katie Henzler-Wildman / Krzysztof Pawłowski / Zhe Chen / Yang Li / John W Schoggins / Vincent S Tagliabracci / ![]() ![]() ![]() 要旨: The RNA genome of SARS-CoV-2 contains a 5' cap that facilitates the translation of viral proteins, protection from exonucleases and evasion of the host immune response. How this cap is made in SARS- ...The RNA genome of SARS-CoV-2 contains a 5' cap that facilitates the translation of viral proteins, protection from exonucleases and evasion of the host immune response. How this cap is made in SARS-CoV-2 is not completely understood. Here we reconstitute the N7- and 2'-O-methylated SARS-CoV-2 RNA cap (GpppA) using virally encoded non-structural proteins (nsps). We show that the kinase-like nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain of nsp12 transfers the RNA to the amino terminus of nsp9, forming a covalent RNA-protein intermediate (a process termed RNAylation). Subsequently, the NiRAN domain transfers the RNA to GDP, forming the core cap structure GpppA-RNA. The nsp14 and nsp16 methyltransferases then add methyl groups to form functional cap structures. Structural analyses of the replication-transcription complex bound to nsp9 identified key interactions that mediate the capping reaction. Furthermore, we demonstrate in a reverse genetics system that the N terminus of nsp9 and the kinase-like active-site residues in the NiRAN domain are required for successful SARS-CoV-2 replication. Collectively, our results reveal an unconventional mechanism by which SARS-CoV-2 caps its RNA genome, thus exposing a new target in the development of antivirals to treat COVID-19. #1: ジャーナル: Res Sq / 年: 2022 タイトル: The mechanism of RNA capping by SARS-CoV-2. 著者: Gina J Park / Adam Osinski / Genaro Hernandez / Jennifer L Eitson / Abir Majumdar / Marco Tonelli / Katie Henzler-Wildman / Krzysztof Pawłowski / Zhe Chen / Yang Li / John W Schoggins / ...著者: Gina J Park / Adam Osinski / Genaro Hernandez / Jennifer L Eitson / Abir Majumdar / Marco Tonelli / Katie Henzler-Wildman / Krzysztof Pawłowski / Zhe Chen / Yang Li / John W Schoggins / Vincent S Tagliabracci / ![]() ![]() 要旨: The SARS-CoV-2 RNA genome contains a 5'-cap that facilitates translation of viral proteins, protection from exonucleases and evasion of the host immune response1-4. How this cap is made is not ...The SARS-CoV-2 RNA genome contains a 5'-cap that facilitates translation of viral proteins, protection from exonucleases and evasion of the host immune response1-4. How this cap is made is not completely understood. Here, we reconstitute the SARS-CoV-2 7MeGpppA2'-O-Me-RNA cap using virally encoded non-structural proteins (nsps). We show that the kinase-like NiRAN domain5 of nsp12 transfers RNA to the amino terminus of nsp9, forming a covalent RNA-protein intermediate (a process termed RNAylation). Subsequently, the NiRAN domain transfers RNA to GDP, forming the cap core structure GpppA-RNA. The nsp146 and nsp167 methyltransferases then add methyl groups to form functional cap structures. Structural analyses of the replication-transcription complex bound to nsp9 identified key interactions that mediate the capping reaction. Furthermore, we demonstrate in a reverse genetics system8 that the N-terminus of nsp9 and the kinase-like active site residues in the NiRAN domain are required for successful SARS-CoV-2 replication. Collectively, our results reveal an unconventional mechanism by which SARS-CoV-2 caps its RNA genome, thus exposing a new target in the development of antivirals to treat COVID-19. | |||||||||||||||||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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PDBx/mmCIF形式 | ![]() | 391.1 KB | 表示 | ![]() |
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PDB形式 | ![]() | 317.1 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-関連構造データ
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リンク
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集合体
登録構造単位 | ![]()
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要素
-タンパク質 , 1種, 1分子 A
#1: タンパク質 | 分子量: 106780.977 Da / 分子数: 1 / 断片: UNP residues 4393-5324 / 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: ![]() ![]() |
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-Non-structural protein ... , 3種, 4分子 BDCG
#2: タンパク質 | 分子量: 21903.047 Da / 分子数: 2 / 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: ![]() ![]() #3: タンパク質 | | 分子量: 9248.804 Da / 分子数: 1 / 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: ![]() ![]() #4: タンパク質 | | 分子量: 12391.171 Da / 分子数: 1 / 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: ![]() ![]() |
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-非ポリマー , 3種, 4分子 




#5: 化合物 | #6: 化合物 | ChemComp-MN / | #7: 化合物 | ChemComp-POP / | |
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-詳細
研究の焦点であるリガンドがあるか | Y |
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Has protein modification | N |
-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: SARS-CoV-2 replication-transcription complex with a native N-terminus nsp9 bound to NiRAN domain of nsp12. タイプ: COMPLEX / Entity ID: #1-#4 / 由来: RECOMBINANT | |||||||||||||||||||||||||
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分子量 | 値: 0.17203949 MDa / 実験値: NO | |||||||||||||||||||||||||
由来(天然) | 生物種: ![]() ![]() | |||||||||||||||||||||||||
由来(組換発現) | 生物種: ![]() ![]() | |||||||||||||||||||||||||
緩衝液 | pH: 7.5 | |||||||||||||||||||||||||
緩衝液成分 |
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試料 | 濃度: 2 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | |||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 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: TFS KRIOS |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2500 nm / 最小 デフォーカス(公称値): 1000 nm |
撮影 | 電子線照射量: 54 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: 1.19.2_4158: / 分類: 精密化 | ||||||||||||||||||||||||
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EMソフトウェア | 名称: PHENIX / カテゴリ: モデル精密化 | ||||||||||||||||||||||||
CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3次元再構成 | 解像度: 3.18 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 39985 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
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