+
データを開く
-
基本情報
| 登録情報 | データベース: PDB / ID: 7thm | |||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| タイトル | SARS-CoV-2 nsp12/7/8 complex with a native N-terminus nsp9 | |||||||||||||||||||||
要素 |
| |||||||||||||||||||||
キーワード | VIRAL PROTEIN / polymerase / NiRAN / capping / nsp9 | |||||||||||||||||||||
| 機能・相同性 | 機能・相同性情報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) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity ...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) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity / 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 / host cell endoplasmic reticulum-Golgi intermediate compartment / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease 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 / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase 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 | |||||||||||||||||||||
データ登録者 | Osinski, A. / Tagliabracci, V.S. / Chen, Z. / Li, Y. | |||||||||||||||||||||
| 資金援助 | 米国, 4件
| |||||||||||||||||||||
引用 | ジャーナル: Nature / 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 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 |
|
-
構造の表示
| ムービー |
ムービービューア |
|---|---|
| 構造ビューア | 分子: Molmil Jmol/JSmol |
-
ダウンロードとリンク
-
ダウンロード
| PDBx/mmCIF形式 | 7thm.cif.gz | 391.1 KB | 表示 | PDBx/mmCIF形式 |
|---|---|---|---|---|
| PDB形式 | pdb7thm.ent.gz | 317.1 KB | 表示 | PDB形式 |
| PDBx/mmJSON形式 | 7thm.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
| 文書・要旨 | 7thm_validation.pdf.gz | 891 KB | 表示 | wwPDB検証レポート |
|---|---|---|---|---|
| 文書・詳細版 | 7thm_full_validation.pdf.gz | 896.4 KB | 表示 | |
| XML形式データ | 7thm_validation.xml.gz | 34.2 KB | 表示 | |
| CIF形式データ | 7thm_validation.cif.gz | 52.2 KB | 表示 | |
| アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/th/7thm ftp://data.pdbj.org/pub/pdb/validation_reports/th/7thm | HTTPS FTP |
-関連構造データ
-
リンク
-
集合体
| 登録構造単位 | ![]()
|
|---|---|
| 1 |
|
-
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: ![]() |
|---|
-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: ![]() |
|---|
-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 / | |
|---|
-詳細
| 研究の焦点であるリガンドがあるか | Y |
|---|---|
| Has protein modification | N |
-実験情報
-実験
| 実験 | 手法: 電子顕微鏡法 |
|---|---|
| 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: 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 | |||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 |
| |||||||||||||||||||||||||
| 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 |
-
電子顕微鏡撮影
| 実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
|---|---|
| 顕微鏡 | モデル: TFS KRIOS |
| 電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
| 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) |
-
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 | ||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 |
|
ムービー
コントローラー
万見について






米国, 4件
引用

UCSF Chimera









PDBj















