+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-11335 | ||||||||||||
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タイトル | SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 2 | ||||||||||||
マップデータ | SARS-CoV-2 Nsp1 bound to a human 43S preinitiation 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 male germ cell proliferation / positive regulation of mRNA binding / regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / positive regulation of mRNA cis splicing, via spliceosome / glial limiting end-foot / response to kainic acid / HRI-mediated signaling / Cellular response to mitochondrial stress / viral translational termination-reinitiation ...male germ cell proliferation / positive regulation of mRNA binding / regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / positive regulation of mRNA cis splicing, via spliceosome / glial limiting end-foot / response to kainic acid / HRI-mediated signaling / Cellular response to mitochondrial stress / viral translational termination-reinitiation / response to manganese-induced endoplasmic reticulum stress / positive regulation of type B pancreatic cell apoptotic process / methionyl-initiator methionine tRNA binding / eukaryotic translation initiation factor 3 complex, eIF3e / negative regulation of translational initiation in response to stress / Response of EIF2AK1 (HRI) to heme deficiency / cap-dependent translational initiation / eukaryotic translation initiation factor 3 complex, eIF3m / Recycling of eIF2:GDP / PERK-mediated unfolded protein response / translation reinitiation / PERK regulates gene expression / eukaryotic translation initiation factor 2 complex / IRES-dependent viral translational initiation / regulation of translational initiation in response to stress / multi-eIF complex / formation of cytoplasmic translation initiation complex / eukaryotic translation initiation factor 3 complex / protein-synthesizing GTPase / eukaryotic 43S preinitiation complex / cytoplasmic translational initiation / translation factor activity, RNA binding / mRNA cap binding / formation of translation preinitiation complex / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / eukaryotic 48S preinitiation complex / protein tyrosine kinase inhibitor activity / positive regulation of respiratory burst involved in inflammatory response / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / nucleolus organization / 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 / metal-dependent deubiquitinase activity / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / oxidized purine DNA binding / supercoiled DNA binding / neural crest cell differentiation / NF-kappaB complex / ubiquitin-like protein conjugating enzyme binding / regulation of translational initiation / regulation of establishment of cell polarity / negative regulation of phagocytosis / positive regulation of ubiquitin-protein transferase activity / rRNA modification in the nucleus and cytosol / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / protein kinase A binding / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / Translation initiation complex formation / pigmentation / positive regulation of mitochondrial depolarization / mammalian oogenesis stage / activation-induced cell death of T cells / negative regulation of Wnt signaling pathway / positive regulation of T cell receptor signaling pathway / fibroblast growth factor binding / positive regulation of activated T cell proliferation / iron-sulfur cluster binding / regulation of cell division / Protein hydroxylation / monocyte chemotaxis / negative regulation of peptidyl-serine phosphorylation / BH3 domain binding / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / cysteine-type endopeptidase activator activity involved in apoptotic process / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / phagocytic cup / ubiquitin ligase inhibitor activity / Response of EIF2AK4 (GCN2) to amino acid deficiency 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: 2.9 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_11335.map.gz | 96.1 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-11335-v30.xml emd-11335.xml | 78.8 KB 78.8 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_11335_fsc.xml | 12.7 KB | 表示 | FSCデータファイル |
画像 | emd_11335.png | 40 KB | ||
Filedesc metadata | emd-11335.cif.gz | 16.9 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-11335 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11335 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_11335_validation.pdf.gz | 494 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_11335_full_validation.pdf.gz | 493.6 KB | 表示 | |
XML形式データ | emd_11335_validation.xml.gz | 13.2 KB | 表示 | |
CIF形式データ | emd_11335_validation.cif.gz | 17.9 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11335 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11335 | 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_11335.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 human 43S preinitiation ribosome complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 human 43S preinitiation ribosome compl...
+超分子 #1: SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome compl...
+超分子 #2: human 43S preinitiation ribosome complex - state 2
+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 S26
+分子 #5: 40S ribosomal protein S4, X isoform
+分子 #6: 60S ribosomal protein L41
+分子 #7: 40S ribosomal protein S6
+分子 #8: 40S ribosomal protein S7
+分子 #9: 40S ribosomal protein S8
+分子 #10: 40S ribosomal protein S9
+分子 #11: 40S ribosomal protein S11
+分子 #12: 40S ribosomal protein S13
+分子 #13: 40S ribosomal protein S21
+分子 #14: 40S ribosomal protein S15a
+分子 #15: 40S ribosomal protein S24
+分子 #16: 40S ribosomal protein S27
+分子 #17: 40S ribosomal protein S30
+分子 #19: 40S ribosomal protein S17
+分子 #20: 40S ribosomal protein S3
+分子 #21: 40S ribosomal protein S5
+分子 #22: 40S ribosomal protein S10
+分子 #23: 40S ribosomal protein S12
+分子 #24: 40S ribosomal protein S15
+分子 #25: 40S ribosomal protein S16
+分子 #26: 40S ribosomal protein S18
+分子 #27: 40S ribosomal protein S19
+分子 #28: 40S ribosomal protein S20
+分子 #29: 40S ribosomal protein S25
+分子 #30: 40S ribosomal protein S28
+分子 #31: 40S ribosomal protein S29
+分子 #32: Ubiquitin-40S ribosomal protein S27a
+分子 #33: Receptor of activated protein C kinase 1
+分子 #34: 40S ribosomal protein S14
+分子 #35: 40S ribosomal protein S23
+分子 #36: Eukaryotic translation initiation factor 1A, X-chromosomal
+分子 #37: Eukaryotic translation initiation factor 3 subunit I
+分子 #38: Eukaryotic translation initiation factor 3 subunit B
+分子 #39: Eukaryotic translation initiation factor 3 subunit A
+分子 #40: Eukaryotic translation initiation factor 3 subunit C
+分子 #41: Eukaryotic translation initiation factor 3 subunit E
+分子 #42: Eukaryotic translation initiation factor 3 subunit F
+分子 #43: Eukaryotic translation initiation factor 3 subunit H
+分子 #44: Eukaryotic translation initiation factor 3 subunit K
+分子 #45: Eukaryotic translation initiation factor 3 subunit L
+分子 #46: Eukaryotic translation initiation factor 3 subunit M
+分子 #47: Eukaryotic translation initiation factor 3 subunit D
+分子 #48: Unknown factor
+分子 #50: Eukaryotic translation initiation factor 2 subunit 2
+分子 #51: Eukaryotic translation initiation factor 2 subunit 1
+分子 #52: Eukaryotic translation initiation factor 2 subunit 3
+分子 #53: Eukaryotic translation initiation factor 1
+分子 #54: Non-structural protein 1
+分子 #18: 18S ribosomal RNA
+分子 #49: tRNA
+分子 #55: ZINC ION
+分子 #56: GUANOSINE-5'-TRIPHOSPHATE
+分子 #57: MAGNESIUM 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 |