+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17805 | ||||||||||||||||||||||||||||||||||||||||||
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Title | MERS-CoV Nsp1 bound to the human 43S pre-initiation complex | ||||||||||||||||||||||||||||||||||||||||||
Map data | |||||||||||||||||||||||||||||||||||||||||||
Sample |
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Keywords | Nsp1 / MERS / SARS / SARS-CoV2 / ribosome / 40S ribosomal subunit / translation inhibition / coronavirus / 43S PIC / 43S pre-initiation complex / mRNA channel / initiation factor / eIF2 / eIF3 / eIF1 / eIF1A / VIRAL PROTEIN / TRANSLATION | ||||||||||||||||||||||||||||||||||||||||||
Function / homology | Function and homology information male germ cell proliferation / positive regulation of mRNA binding / regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / glial limiting end-foot / positive regulation of mRNA cis splicing, via spliceosome / HRI-mediated signaling / response to kainic acid / 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 / glial limiting end-foot / positive regulation of mRNA cis splicing, via spliceosome / HRI-mediated signaling / response to kainic acid / 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 / negative regulation of translational initiation in response to stress / eukaryotic translation initiation factor 3 complex, eIF3e / Response of EIF2AK1 (HRI) to heme deficiency / Recycling of eIF2:GDP / cap-dependent translational initiation / eukaryotic translation initiation factor 3 complex, eIF3m / PERK-mediated unfolded protein response / methionyl-initiator methionine tRNA binding / PERK regulates gene expression / IRES-dependent viral translational initiation / translation reinitiation / regulation of translational initiation in response to stress / eukaryotic translation initiation factor 2 complex / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / multi-eIF complex / cytoplasmic translational initiation / translation factor activity, RNA binding / protein-synthesizing GTPase / mRNA cap binding / eukaryotic 43S preinitiation complex / formation of translation preinitiation complex / : / 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 / eukaryotic 48S preinitiation complex / 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 RNA splicing / negative regulation of DNA repair / metal-dependent deubiquitinase activity / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / supercoiled DNA binding / oxidized purine 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 / positive regulation of ubiquitin-protein transferase activity / negative regulation of phagocytosis / 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 / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / laminin receptor activity / pigmentation / 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 / mammalian oogenesis stage / fibroblast growth factor binding / positive regulation of mitochondrial depolarization / activation-induced cell death of T cells / positive regulation of T cell receptor signaling pathway / negative regulation of peptidyl-serine phosphorylation / iron-sulfur cluster binding / negative regulation of Wnt signaling pathway / 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 / ribosomal small subunit binding Similarity search - Function | ||||||||||||||||||||||||||||||||||||||||||
Biological species | Homo sapiens (human) / Middle East respiratory syndrome-related coronavirus | ||||||||||||||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.65 Å | ||||||||||||||||||||||||||||||||||||||||||
Authors | Schubert K / Karousis ED / Ban I / Lapointe CP / Leibundgut M / Baeumlin E / Kummerant E / Scaiola A / Schoenhut T / Ziegelmueller J ...Schubert K / Karousis ED / Ban I / Lapointe CP / Leibundgut M / Baeumlin E / Kummerant E / Scaiola A / Schoenhut T / Ziegelmueller J / Puglisi JD / Muehlemann O / Ban N | ||||||||||||||||||||||||||||||||||||||||||
Funding support | Switzerland, United States, 13 items
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Citation | Journal: Mol Cell / Year: 2023 Title: Universal features of Nsp1-mediated translational shutdown by coronaviruses. Authors: Katharina Schubert / Evangelos D Karousis / Ivo Ban / Christopher P Lapointe / Marc Leibundgut / Emilie Bäumlin / Eric Kummerant / Alain Scaiola / Tanja Schönhut / Jana Ziegelmüller / ...Authors: Katharina Schubert / Evangelos D Karousis / Ivo Ban / Christopher P Lapointe / Marc Leibundgut / Emilie Bäumlin / Eric Kummerant / Alain Scaiola / Tanja Schönhut / Jana Ziegelmüller / Joseph D Puglisi / Oliver Mühlemann / Nenad Ban / Abstract: Nonstructural protein 1 (Nsp1) produced by coronaviruses inhibits host protein synthesis. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Nsp1 C-terminal domain was shown to bind the ...Nonstructural protein 1 (Nsp1) produced by coronaviruses inhibits host protein synthesis. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Nsp1 C-terminal domain was shown to bind the ribosomal mRNA channel to inhibit translation, but it is unclear whether this mechanism is broadly used by coronaviruses, whether the Nsp1 N-terminal domain binds the ribosome, or how Nsp1 allows viral RNAs to be translated. Here, we investigated Nsp1 from SARS-CoV-2, Middle East respiratory syndrome coronavirus (MERS-CoV), and Bat-Hp-CoV coronaviruses using structural, biophysical, and biochemical experiments, revealing a conserved role for the C-terminal domain. Additionally, the N-terminal domain of Bat-Hp-CoV Nsp1 binds to the decoding center of the 40S subunit, where it would prevent mRNA and eIF1A accommodation. Structure-based experiments demonstrated the importance of decoding center interactions in all three coronaviruses and showed that the same regions of Nsp1 are necessary for the selective translation of viral RNAs. Our results provide a mechanistic framework to understand how Nsp1 controls preferential translation of viral RNAs. #1: Journal: Mol.Cell / Year: 2023 Title: Universal features of Nsp1-mediated translational shutdown by coronaviruses Authors: Schubert K / Karousis ED / Ban I / Lapointe CP / Leibundgut M / Baeumlin E / Kummerant E / Scaiola A / Schoenhut T / Ziegelmueller J / Puglisi JD / Muehlemann O / Ban N | ||||||||||||||||||||||||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17805.map.gz | 337.9 MB | EMDB map data format | |
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Header (meta data) | emd-17805-v30.xml emd-17805.xml | 85.7 KB 85.7 KB | Display Display | EMDB header |
Images | emd_17805.png | 149.9 KB | ||
Masks | emd_17805_msk_1.map emd_17805_msk_2.map | 669.9 MB 669.9 MB | Mask map | |
Filedesc metadata | emd-17805.cif.gz | 20.3 KB | ||
Others | emd_17805_half_map_1.map.gz emd_17805_half_map_2.map.gz | 622.4 MB 622.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17805 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17805 | HTTPS FTP |
-Validation report
Summary document | emd_17805_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_17805_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_17805_validation.xml.gz | 20 KB | Display | |
Data in CIF | emd_17805_validation.cif.gz | 23.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17805 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17805 | HTTPS FTP |
-Related structure data
Related structure data | 8pplMC 8ppkC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_17805.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.065 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17805_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Mask #2
File | emd_17805_msk_2.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_17805_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17805_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : MERS-CoV Nsp1 - 43S pre-initiation complex
+Supramolecule #1: MERS-CoV Nsp1 - 43S pre-initiation complex
+Macromolecule #1: Eukaryotic translation initiation factor 3 subunit K
+Macromolecule #2: Eukaryotic translation initiation factor 3 subunit F
+Macromolecule #3: Eukaryotic translation initiation factor 3 subunit L
+Macromolecule #4: Eukaryotic translation initiation factor 3 subunit M
+Macromolecule #5: Eukaryotic translation initiation factor 3 subunit H
+Macromolecule #6: Eukaryotic translation initiation factor 3 subunit G
+Macromolecule #7: Eukaryotic translation initiation factor 1
+Macromolecule #8: Eukaryotic translation initiation factor 1A, X-chromosomal
+Macromolecule #9: Eukaryotic translation initiation factor 2 subunit 1
+Macromolecule #10: Eukaryotic translation initiation factor 2 subunit 2
+Macromolecule #11: Eukaryotic translation initiation factor 2 subunit 3
+Macromolecule #12: Eukaryotic translation initiation factor 3 subunit A
+Macromolecule #13: Eukaryotic translation initiation factor 3 subunit E
+Macromolecule #15: Eukaryotic translation initiation factor 3 subunit D
+Macromolecule #16: Eukaryotic translation initiation factor 3 subunit C
+Macromolecule #18: 40S ribosomal protein SA
+Macromolecule #19: 40S ribosomal protein S3a
+Macromolecule #20: 40S ribosomal protein S2
+Macromolecule #21: 40S ribosomal protein S3
+Macromolecule #22: 40S ribosomal protein S4, X isoform
+Macromolecule #23: 40S ribosomal protein S5
+Macromolecule #24: 40S ribosomal protein S6
+Macromolecule #25: 40S ribosomal protein S7
+Macromolecule #26: 40S ribosomal protein S8
+Macromolecule #27: 40S ribosomal protein S9
+Macromolecule #28: 40S ribosomal protein S10
+Macromolecule #29: 40S ribosomal protein S11
+Macromolecule #30: 40S ribosomal protein S12
+Macromolecule #31: 40S ribosomal protein S13
+Macromolecule #32: 40S ribosomal protein S14
+Macromolecule #33: 40S ribosomal protein S15
+Macromolecule #34: 40S ribosomal protein S16
+Macromolecule #35: 40S ribosomal protein S17
+Macromolecule #36: Small ribosomal subunit protein uS13
+Macromolecule #37: Small ribosomal subunit protein eS19
+Macromolecule #38: 40S ribosomal protein S20
+Macromolecule #39: 40S ribosomal protein S21
+Macromolecule #40: 40S ribosomal protein S15a
+Macromolecule #41: 40S ribosomal protein S23
+Macromolecule #42: 40S ribosomal protein S24
+Macromolecule #43: 40S ribosomal protein S25
+Macromolecule #44: 40S ribosomal protein S26
+Macromolecule #45: 40S ribosomal protein S27
+Macromolecule #46: 40S ribosomal protein S28
+Macromolecule #47: 40S ribosomal protein S29
+Macromolecule #48: Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein
+Macromolecule #49: Ubiquitin-40S ribosomal protein S27a
+Macromolecule #50: Receptor of activated protein C kinase 1
+Macromolecule #51: 60S ribosomal protein L41
+Macromolecule #52: Host translation inhibitor nsp1
+Macromolecule #14: Met-tRNAi(Met)
+Macromolecule #17: 18S rRNA
+Macromolecule #53: ZINC ION
+Macromolecule #54: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #55: MAGNESIUM ION
+Macromolecule #56: METHIONINE
+Macromolecule #57: UNKNOWN ATOM OR ION
+Macromolecule #58: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. Details: 15 sec in easiGlow Discharge cleaning system (PELCO) at 15 mA | ||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV | ||||||||
Details | f.c. 100 nM |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 8932 / 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 / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 218516 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Initial model |
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Details | phenix.real_space_refine | |||||||||
Refinement | Space: REAL / Protocol: OTHER | |||||||||
Output model | PDB-8ppl: |