+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11321 | ||||||||||||
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Title | SARS-CoV-2-Nsp1-40S complex, focused on body | ||||||||||||
Map data | |||||||||||||
Sample |
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Function / homology | Function and homology information negative regulation of RNA splicing / neural crest cell differentiation / 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 / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition ...negative regulation of RNA splicing / neural crest cell differentiation / 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 / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / Translation initiation complex formation / mammalian oogenesis stage / activation-induced cell death of T cells / fibroblast growth factor binding / Protein hydroxylation / 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 / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / ubiquitin ligase inhibitor activity / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / L13a-mediated translational silencing of Ceruloplasmin expression / T cell proliferation involved in immune response / Major pathway of rRNA processing in the nucleolus and cytosol / erythrocyte development / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of ubiquitin-dependent protein catabolic process / Protein methylation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / translation regulator activity / Nuclear events stimulated by ALK signaling in cancer / positive regulation of cell cycle / stress granule assembly / Mitotic Prometaphase / cytosolic ribosome / laminin binding / 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) / rough endoplasmic reticulum / antiviral innate immune response / gastrulation / translation initiation factor binding / Resolution of Sister Chromatid Cohesion / erythrocyte differentiation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / innate immune response in mucosa / maturation of SSU-rRNA / neural tube closure / placenta development / small-subunit processome / mRNA 3'-UTR binding / positive regulation of translation / translational initiation / RHO GTPases Activate Formins / maintenance of translational fidelity / response to virus / G1/S transition of mitotic cell cycle / RMTs methylate histone arginines / mRNA 5'-UTR binding / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / rRNA processing / Separation of Sister Chromatids / antimicrobial humoral immune response mediated by antimicrobial peptide / glucose homeostasis / virus receptor activity / protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / ribosome binding / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / ribosomal small subunit biogenesis / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / TRAF3-dependent IRF activation pathway / ribosomal small subunit assembly / Replication of the SARS-CoV-2 genome / snRNP Assembly / antibacterial humoral response / small ribosomal subunit / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / small ribosomal subunit rRNA binding / 5'-3' DNA helicase activity / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) / Severe acute respiratory syndrome coronavirus 2 / Human (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||||||||
Authors | Schubert K / Karousis ED / Jomaa A / Scaiola A / Echeverria B / Gurzeler L-A / Leibundgut M / Thiel V / Muehlemann O / Ban N | ||||||||||||
Funding support | Switzerland, 3 items
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Citation | 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. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11321.map.gz | 632.7 MB | EMDB map data format | |
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Header (meta data) | emd-11321-v30.xml emd-11321.xml | 39.1 KB 39.1 KB | Display Display | EMDB header |
Images | emd_11321.png | 109.3 KB | ||
Masks | emd_11321_msk_1.map | 669.9 MB | Mask map | |
Others | emd_11321_half_map_1.map.gz emd_11321_half_map_2.map.gz | 621.6 MB 621.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11321 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11321 | HTTPS FTP |
-Validation report
Summary document | emd_11321_validation.pdf.gz | 343.5 KB | Display | EMDB validaton report |
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Full document | emd_11321_full_validation.pdf.gz | 342.6 KB | Display | |
Data in XML | emd_11321_validation.xml.gz | 17.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11321 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11321 | HTTPS FTP |
-Related structure data
Related structure data | 6zokMC 6zojC 6zolC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11321.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_11321_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_11321_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_11321_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : SARS-CoV-2-Nsp1-40S, focused on body
+Supramolecule #1: SARS-CoV-2-Nsp1-40S, focused on body
+Supramolecule #2: Ribosomal proteins
+Supramolecule #3: SARS-CoV-2-Nsp1-40S
+Macromolecule #1: 18S ribosomal RNA
+Macromolecule #2: 40S ribosomal protein SA
+Macromolecule #3: 40S ribosomal protein S3a
+Macromolecule #4: 40S ribosomal protein S2
+Macromolecule #5: 40S ribosomal protein S4, X isoform
+Macromolecule #6: 40S ribosomal protein S6
+Macromolecule #7: 40S ribosomal protein S7
+Macromolecule #8: 40S ribosomal protein S8
+Macromolecule #9: 40S ribosomal protein S9
+Macromolecule #10: 40S ribosomal protein S11
+Macromolecule #11: 40S ribosomal protein S13
+Macromolecule #12: 40S ribosomal protein S14
+Macromolecule #13: 40S ribosomal protein S17
+Macromolecule #14: 40S ribosomal protein S21
+Macromolecule #15: 40S ribosomal protein S15a
+Macromolecule #16: 40S ribosomal protein S23
+Macromolecule #17: 40S ribosomal protein S24
+Macromolecule #18: 40S ribosomal protein S26
+Macromolecule #19: 40S ribosomal protein S27
+Macromolecule #20: 40S ribosomal protein S30
+Macromolecule #21: Non-structural protein 1
+Macromolecule #22: 60S ribosomal protein L41
+Macromolecule #23: MAGNESIUM ION
+Macromolecule #24: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 118765 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |