positive regulation of DNA N-glycosylase activity / negative regulation of DNA repair / response to TNF agonist / oxidized pyrimidine DNA binding / positive regulation of base-excision repair / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / protein tyrosine kinase inhibitor activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage ...positive regulation of DNA N-glycosylase activity / negative regulation of DNA repair / response to TNF agonist / oxidized pyrimidine DNA binding / positive regulation of base-excision repair / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / protein tyrosine kinase inhibitor activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / positive regulation of Golgi to plasma membrane protein transport / NF-kappaB complex / negative regulation of RNA splicing / response to extracellular stimulus / IRE1-RACK1-PP2A complex / ubiquitin ligase inhibitor activity / laminin receptor activity / cytoplasmic side of rough endoplasmic reticulum membrane / positive regulation of endodeoxyribonuclease activity / regulation of cell division / oxidized purine DNA binding / protein kinase A binding / negative regulation of endoplasmic reticulum unfolded protein response / translation regulator activity / supercoiled DNA binding / negative regulation of hydrogen peroxide-induced neuron death / negative regulation of ubiquitin protein ligase activity / positive regulation of ceramide biosynthetic process / erythrocyte homeostasis / negative regulation of phagocytosis / mammalian oogenesis stage / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / pigmentation / signaling adaptor activity / cysteine-type endopeptidase activator activity involved in apoptotic process / negative regulation of Wnt signaling pathway / activation-induced cell death of T cells / positive regulation of T cell receptor signaling pathway / positive regulation of mitochondrial depolarization / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of smoothened signaling pathway / phagocytic cup / ion channel inhibitor activity / positive regulation of activated T cell proliferation / iron-sulfur cluster binding / positive regulation of cellular component movement / fibroblast growth factor binding / rescue of stalled ribosome / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of apoptotic signaling pathway / stress granule assembly / DNA-(apurinic or apyrimidinic site) lyase / monocyte chemotaxis / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / positive regulation of ubiquitin-protein transferase activity / BH3 domain binding / 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) / spindle assembly / erythrocyte development / positive regulation of cyclic-nucleotide phosphodiesterase activity / ribosomal small subunit export from nucleus / negative regulation of protein kinase B signaling / TOR signaling / positive regulation of JUN kinase activity / SRP-dependent cotranslational protein targeting to membrane / regulation of tumor necrosis factor-mediated signaling pathway / maturation of SSU-rRNA / regulation of translational fidelity / negative regulation of ubiquitin-dependent protein catabolic process / T cell proliferation involved in immune response / negative regulation of respiratory burst involved in inflammatory response / small-subunit processome / positive regulation of microtubule polymerization / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / translation initiation factor binding / ribosomal small subunit biogenesis / molecular adaptor activity / gastrulation / positive regulation of DNA repair / Hsp70 protein binding / laminin binding / erythrocyte differentiation / cellular response to interleukin-4 / positive regulation of cell cycle / polysome / tubulin binding / translational initiation / mitotic cell cycle checkpoint / negative regulation of peptidyl-serine phosphorylation / positive regulation of intrinsic apoptotic signaling pathway / innate immune response in mucosa / negative regulation of protein ubiquitination / endodeoxyribonuclease activity / MyD88-independent toll-like receptor signaling pathway / polysomal ribosome / nucleotide-binding oligomerization domain containing signaling pathway / DNA-(apurinic or apyrimidinic site) endonuclease activity / mRNA 3'-UTR binding
Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S27e / Ribosomal protein S7 domain / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein S7e / Ribosomal protein S15P / Ribosomal protein S4/S9 / Ribosomal protein S12e ...Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S27e / Ribosomal protein S7 domain / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein S7e / Ribosomal protein S15P / Ribosomal protein S4/S9 / Ribosomal protein S12e / DPUP/SUD, C-terminal, betacoronavirus / Ribosomal protein S28e / Ubiquitin-like domain / Non-structural protein NSP1, betacoronavirus / Ribosomal protein S19 conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S17/S11 / G-protein beta WD-40 repeat / Ribosomal protein S17, conserved site / Ubiquitin domain / Non-structural protein NSP3, N-terminal, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Ribosomal protein S5/S7 / 50S ribosomal protein L30e-like / Ribosomal protein S4e / Ribosomal protein S8 superfamily / Non-structural protein NSP3, nucleic acid-binding (NAR) domain, betacoronavirus / Non-structural protein NSP4, C-terminal, coronavirus / 40S ribosomal protein S11, N-terminal / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein S4, C-terminal domain / Ubiquitin-like domain superfamily / Ribosomal protein S5 / S-adenosyl-L-methionine-dependent methyltransferase / (+) RNA virus helicase core domain / Ribosomal protein S28e conserved site / Ribosomal protein S17, archaeal/eukaryotic / 40S ribosomal protein SA / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S2, eukaryotic / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein S9 / Ribosomal protein S8 / P-loop containing nucleoside triphosphate hydrolase / Ubiquitin conserved site / WD40 repeat, conserved site / Ribosomal protein S8e / K homology domain superfamily, prokaryotic type / WD40/YVTN repeat-like-containing domain superfamily / Non-structural protein NSP8, coronavirus-like / Non-structural protein NSP7, coronavirus / Non-structural protein NSP9, coronavirus / Ribosomal protein L2, domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S6, eukaryotic / Ribosomal protein S4e, central region / Ribosomal protein S4e, N-terminal / Ribosomal protein S5, N-terminal / WD40-repeat-containing domain / Peptidase C16, coronavirus / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein S13/S15, N-terminal / Nucleic acid-binding, OB-fold / Zinc-binding ribosomal protein / Ribosomal protein S13-like, H2TH / RNA polymerase, N-terminal, coronaviral / Non-structural protein 14, coronavirus / Non-structural protein NSP16, coronavirus-like / K homology domain-like, alpha/beta / Ribosomal protein S4, conserved site / RNA synthesis protein NSP10, coronavirus / Ribosomal protein S14, conserved site / Ribosomal protein S8e, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein S3Ae, conserved site / KOW / Ribosomal protein S3, conserved site / Ribosomal protein S21e, conserved site / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S12/S23 / Ribosomal S24e conserved site / Ribosomal protein S30 / Ribosomal protein L41 / Ribosomal protein S13, conserved site / Peptidase C30, coronavirus / Ribosomal protein S10, conserved site / Peptidase S1, PA clan / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S2, conserved site / Ribosomal S11, conserved site / Ribosomal protein S26e / Ribosomal protein S15 / WD40-repeat-containing domain superfamily / Ribosomal protein S11
40S ribosomal protein S24 / 40S ribosomal protein S29 / 40S ribosomal protein S13 / 40S ribosomal protein S11 / 40S ribosomal protein S4, X isoform / 40S ribosomal protein S6 / 40S ribosomal protein S15 / 60S ribosomal protein L41 / 40S ribosomal protein S25 / 40S ribosomal protein S26 ...40S ribosomal protein S24 / 40S ribosomal protein S29 / 40S ribosomal protein S13 / 40S ribosomal protein S11 / 40S ribosomal protein S4, X isoform / 40S ribosomal protein S6 / 40S ribosomal protein S15 / 60S ribosomal protein L41 / 40S ribosomal protein S25 / 40S ribosomal protein S26 / 40S ribosomal protein S28 / 40S ribosomal protein S30 / 40S ribosomal protein S23 / Ubiquitin-40S ribosomal protein S27a / 40S ribosomal protein S21 / Receptor of activated protein C kinase 1 / 40S ribosomal protein S18 / 40S ribosomal protein S7 / 40S ribosomal protein S14 / 40S ribosomal protein S19 / 40S ribosomal protein S17 / 40S ribosomal protein SA / Replicase polyprotein 1ab / 40S ribosomal protein S2 / 40S ribosomal protein S3 / 40S ribosomal protein S12 / 40S ribosomal protein S27 / 40S ribosomal protein S16 / 40S ribosomal protein S9 / 40S ribosomal protein S5 / 40S ribosomal protein S10 / 40S ribosomal protein S20 / 40S ribosomal protein S3a / 40S ribosomal protein S8 / 40S ribosomal protein S15a / 40S ribosomal protein S27a
Biological species
Homo sapiens (human) / Severe acute respiratory syndrome coronavirus 2 / Human (human)
Method
single particle reconstruction / cryo EM / Resolution: 2.8 Å
Journal: Nat Struct Mol Biol / Year: 2020 Title: SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation. Authors: Katharina Schubert / Evangelos D Karousis / Ahmad Jomaa / Alain Scaiola / Blanca Echeverria / Lukas-Adrian Gurzeler / Marc Leibundgut / Volker Thiel / Oliver Mühlemann / Nenad Ban / Abstract: The SARS-CoV-2 non-structural protein 1 (Nsp1), also referred to as the host shutoff factor, suppresses host innate immune functions. By combining cryo-electron microscopy and biochemistry, we show ...The SARS-CoV-2 non-structural protein 1 (Nsp1), also referred to as the host shutoff factor, suppresses host innate immune functions. By combining cryo-electron microscopy and biochemistry, we show that SARS-CoV-2 Nsp1 binds to the human 40S subunit in ribosomal complexes, including the 43S pre-initiation complex and the non-translating 80S ribosome. The protein inserts its C-terminal domain into the mRNA channel, where it interferes with mRNA binding. We observe translation inhibition in the presence of Nsp1 in an in vitro translation system and in human cells. Based on the high-resolution structure of the 40S-Nsp1 complex, we identify residues of Nsp1 crucial for mediating translation inhibition. We further show that the full-length 5' untranslated region of the genomic viral mRNA stimulates translation in vitro, suggesting that SARS-CoV-2 combines global inhibition of translation by Nsp1 with efficient translation of the viral mRNA to allow expression of viral genes.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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