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Yorodumi- EMDB-11609: SARS-CoV-2-Nsp1 bound to a translationally inactive 80S ribosome -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11609 | ||||||||||||
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Title | SARS-CoV-2-Nsp1 bound to a translationally inactive 80S ribosome | ||||||||||||
Map data | |||||||||||||
Sample |
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Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.5 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_11609.map.gz | 338.2 MB | EMDB map data format | |
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Header (meta data) | emd-11609-v30.xml emd-11609.xml | 19.5 KB 19.5 KB | Display Display | EMDB header |
Images | emd_11609.png | 197.5 KB | ||
Masks | emd_11609_msk_1.map | 669.9 MB | Mask map | |
Others | emd_11609_additional.map.gz emd_11609_additional_1.map.gz emd_11609_half_map_1.map.gz emd_11609_half_map_2.map.gz | 309.6 MB 309.6 MB 622.8 MB 622.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11609 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11609 | HTTPS FTP |
-Validation report
Summary document | emd_11609_validation.pdf.gz | 407.8 KB | Display | EMDB validaton report |
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Full document | emd_11609_full_validation.pdf.gz | 406.9 KB | Display | |
Data in XML | emd_11609_validation.xml.gz | 17.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11609 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11609 | HTTPS FTP |
-Related 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_11609.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_11609_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: This map has been resampled to the map...
File | emd_11609_additional.map | ||||||||||||
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Annotation | This map has been resampled to the map of the 40S-Nsp1 complex (EMD-11320, PDB 6ZOJ) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: This map has been resampled to the map...
File | emd_11609_additional_1.map | ||||||||||||
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Annotation | This map has been resampled to the map of the 40S-Nsp1 complex (EMD-11320, PDB 6ZOJ) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_11609_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_11609_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-2-Nsp1 bound to a translationally inactive 80S ribosome
Entire | Name: SARS-CoV-2-Nsp1 bound to a translationally inactive 80S ribosome |
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Components |
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-Supramolecule #1: SARS-CoV-2-Nsp1 bound to a translationally inactive 80S ribosome
Supramolecule | Name: SARS-CoV-2-Nsp1 bound to a translationally inactive 80S ribosome type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#36 |
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Source (natural) | Organism: Homo sapiens (human) |
-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 / Chamber humidity: 100 % / Chamber temperature: 277.15 K |
-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
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 300147 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |