+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-11301 | ||||||||||||
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タイトル | SARS-CoV-2 Nsp1 bound to a pre-40S-like ribosome complex | ||||||||||||
マップデータ | SARS-CoV-2 Nsp1 bound to a pre-40S-like ribosome complex | ||||||||||||
試料 |
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キーワード | Translational Inhibition / SARS-CoV-2 / Immune Evasion / Human Ribosome / VIRAL PROTEIN | ||||||||||||
機能・相同性 | 機能・相同性情報 endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / : / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein tyrosine kinase inhibitor activity / positive regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation ...endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / : / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein tyrosine kinase inhibitor activity / positive regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / nucleolus organization / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / IRE1-RACK1-PP2A complex / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of DNA repair / negative regulation of RNA splicing / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / U3 snoRNA binding / supercoiled DNA binding / oxidized purine DNA binding / neural crest cell differentiation / NF-kappaB complex / ubiquitin-like protein conjugating enzyme binding / negative regulation of phagocytosis / regulation of establishment of cell polarity / positive regulation of ubiquitin-protein transferase activity / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / Formation of the ternary complex, and subsequently, the 43S complex / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / pigmentation / protein kinase A binding / preribosome, small subunit precursor / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / Translation initiation complex formation / fibroblast growth factor binding / mammalian oogenesis stage / positive regulation of mitochondrial depolarization / activation-induced cell death of T cells / positive regulation of T cell receptor signaling pathway / negative regulation of Wnt signaling pathway / negative regulation of peptidyl-serine phosphorylation / iron-sulfur cluster binding / positive regulation of activated T cell proliferation / monocyte chemotaxis / Protein hydroxylation / regulation of cell division / BH3 domain binding / cysteine-type endopeptidase activator activity involved in apoptotic process / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / phagocytic cup / negative regulation of respiratory burst involved in inflammatory response / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / T cell proliferation involved in immune response / positive regulation of cell cycle / regulation of translational fidelity / spindle assembly / Major pathway of rRNA processing in the nucleolus and cytosol / erythrocyte development / Protein methylation / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of ubiquitin-dependent protein catabolic process / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / positive regulation of intrinsic apoptotic signaling pathway / Nuclear events stimulated by ALK signaling in cancer / ribosomal small subunit export from nucleus / translation regulator activity / signaling adaptor activity / stress granule assembly / negative regulation of smoothened signaling pathway / laminin binding / rough endoplasmic reticulum / Mitotic Prometaphase / antiviral innate immune response / positive regulation of JUN kinase activity / EML4 and NUDC in mitotic spindle formation / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / gastrulation / MDM2/MDM4 family protein binding 類似検索 - 分子機能 | ||||||||||||
生物種 | Homo sapiens (ヒト) / Severe acute respiratory syndrome coronavirus 2 (ウイルス) | ||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.0 Å | ||||||||||||
データ登録者 | Thoms M / Buschauer R | ||||||||||||
資金援助 | ドイツ, 3件
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引用 | ジャーナル: Science / 年: 2020 タイトル: Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2. 著者: Matthias Thoms / Robert Buschauer / Michael Ameismeier / Lennart Koepke / Timo Denk / Maximilian Hirschenberger / Hanna Kratzat / Manuel Hayn / Timur Mackens-Kiani / Jingdong Cheng / Jan H ...著者: Matthias Thoms / Robert Buschauer / Michael Ameismeier / Lennart Koepke / Timo Denk / Maximilian Hirschenberger / Hanna Kratzat / Manuel Hayn / Timur Mackens-Kiani / Jingdong Cheng / Jan H Straub / Christina M Stürzel / Thomas Fröhlich / Otto Berninghausen / Thomas Becker / Frank Kirchhoff / Konstantin M J Sparrer / Roland Beckmann / 要旨: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the current coronavirus disease 2019 (COVID-19) pandemic. A major virulence factor of SARS-CoVs is the ...Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the current coronavirus disease 2019 (COVID-19) pandemic. A major virulence factor of SARS-CoVs is the nonstructural protein 1 (Nsp1), which suppresses host gene expression by ribosome association. Here, we show that Nsp1 from SARS-CoV-2 binds to the 40 ribosomal subunit, resulting in shutdown of messenger RNA (mRNA) translation both in vitro and in cells. Structural analysis by cryo-electron microscopy of in vitro-reconstituted Nsp1-40 and various native Nsp1-40 and -80 complexes revealed that the Nsp1 C terminus binds to and obstructs the mRNA entry tunnel. Thereby, Nsp1 effectively blocks retinoic acid-inducible gene I-dependent innate immune responses that would otherwise facilitate clearance of the infection. Thus, the structural characterization of the inhibitory mechanism of Nsp1 may aid structure-based drug design against SARS-CoV-2. | ||||||||||||
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_11301.map.gz | 97.1 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-11301-v30.xml emd-11301.xml | 52.3 KB 52.3 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_11301_fsc.xml | 12.8 KB | 表示 | FSCデータファイル |
画像 | emd_11301.png | 33.7 KB | ||
Filedesc metadata | emd-11301.cif.gz | 11.4 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-11301 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11301 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_11301_validation.pdf.gz | 468.3 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_11301_full_validation.pdf.gz | 467.8 KB | 表示 | |
XML形式データ | emd_11301_validation.xml.gz | 13.2 KB | 表示 | |
CIF形式データ | emd_11301_validation.cif.gz | 17.8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11301 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11301 | 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_11301.map.gz / 形式: CCP4 / 大きさ: 178 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | SARS-CoV-2 Nsp1 bound to a pre-40S-like ribosome complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.059 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
-試料の構成要素
+全体 : SARS-CoV-2 Nsp1 bound to a pre-40S-like ribosome complex
+超分子 #1: SARS-CoV-2 Nsp1 bound to a pre-40S-like ribosome complex
+超分子 #2: Pre-40S-like ribosome complex
+超分子 #3: SARS-CoV-2 Nsp1
+分子 #1: 40S ribosomal protein SA
+分子 #2: 40S ribosomal protein S3a
+分子 #3: 40S ribosomal protein S2
+分子 #4: 40S ribosomal protein S4, X isoform
+分子 #5: 40S ribosomal protein S3
+分子 #6: 40S ribosomal protein S6
+分子 #7: 40S ribosomal protein S7
+分子 #8: 40S ribosomal protein S8
+分子 #9: 40S ribosomal protein S9
+分子 #10: 40S ribosomal protein S5
+分子 #11: 40S ribosomal protein S11
+分子 #12: 40S ribosomal protein S10
+分子 #13: 40S ribosomal protein S13
+分子 #14: 40S ribosomal protein S12
+分子 #15: 40S ribosomal protein S14
+分子 #16: 40S ribosomal protein S15
+分子 #17: 40S ribosomal protein S16
+分子 #18: 40S ribosomal protein S17
+分子 #19: 40S ribosomal protein S18
+分子 #20: 40S ribosomal protein S19
+分子 #21: 40S ribosomal protein S20
+分子 #22: 40S ribosomal protein S15a
+分子 #23: 40S ribosomal protein S23
+分子 #24: 40S ribosomal protein S24
+分子 #25: 40S ribosomal protein S21
+分子 #26: 40S ribosomal protein S25
+分子 #27: 40S ribosomal protein S27
+分子 #28: 40S ribosomal protein S28
+分子 #29: 40S ribosomal protein S30
+分子 #30: 40S ribosomal protein S29
+分子 #31: Ubiquitin-40S ribosomal protein S27a
+分子 #32: Receptor of activated protein C kinase 1
+分子 #34: Non-structural protein 1
+分子 #35: Pre-rRNA-processing protein TSR1 homolog
+分子 #33: 18S ribosomal RNA
+分子 #36: ZINC ION
-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
緩衝液 | pH: 7.5 |
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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 K2 SUMMIT (4k x 4k) 平均電子線量: 44.8 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
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 |