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Yorodumi- EMDB-12756: Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slipp... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12756 | |||||||||
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Title | Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a pseudoknot (high resolution) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Frameshift / virus / pseudoknot / RIBOSOME | |||||||||
Function / homology | Function and homology information Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / regulation of G1 to G0 transition / laminin receptor activity / exit from mitosis ...Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / regulation of G1 to G0 transition / laminin receptor activity / exit from mitosis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / optic nerve development / retinal ganglion cell axon guidance / mammalian oogenesis stage / G1 to G0 transition / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / phagocytic cup / ubiquitin ligase inhibitor activity / TOR signaling / 90S preribosome / T cell proliferation involved in immune response / protein-RNA complex assembly / erythrocyte development / negative regulation of ubiquitin-dependent protein catabolic process / translation regulator activity / cellular response to actinomycin D / ribosomal small subunit export from nucleus / cytosolic ribosome / laminin binding / rough endoplasmic reticulum / gastrulation / MDM2/MDM4 family protein binding / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / maturation of LSU-rRNA / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / cellular response to leukemia inhibitory factor / maturation of SSU-rRNA / placenta development / small-subunit processome / positive regulation of translation / protein kinase C binding / positive regulation of protein-containing complex assembly / G1/S transition of mitotic cell cycle / cellular response to gamma radiation / transcription coactivator binding / mRNA 5'-UTR binding / modification-dependent protein catabolic process / spindle / cytoplasmic ribonucleoprotein granule / positive regulation of canonical Wnt signaling pathway / rhythmic process / rRNA processing / protein tag activity / antimicrobial humoral immune response mediated by antimicrobial peptide / glucose homeostasis / virus receptor activity / protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / ribosome biogenesis / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / ribosome binding / Lyases; Phosphorus-oxygen lyases / retina development in camera-type eye / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / regulation of translation / 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 / 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 / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell endosome / cell body / symbiont-mediated suppression of host toll-like receptor signaling pathway / T cell differentiation in thymus / symbiont-mediated degradation of host mRNA / 5S rRNA binding Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Severe acute respiratory syndrome coronavirus 2 / Bos taurus (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.2 Å | |||||||||
Authors | Bhatt PR / Scaiola A | |||||||||
Funding support | Switzerland, Ireland, 2 items
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Citation | Journal: Science / Year: 2021 Title: Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome. Authors: Pramod R Bhatt / Alain Scaiola / Gary Loughran / Marc Leibundgut / Annika Kratzel / Romane Meurs / René Dreos / Kate M O'Connor / Angus McMillan / Jeffrey W Bode / Volker Thiel / David ...Authors: Pramod R Bhatt / Alain Scaiola / Gary Loughran / Marc Leibundgut / Annika Kratzel / Romane Meurs / René Dreos / Kate M O'Connor / Angus McMillan / Jeffrey W Bode / Volker Thiel / David Gatfield / John F Atkins / Nenad Ban / Abstract: Programmed ribosomal frameshifting is a key event during translation of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA genome that allows synthesis of the viral RNA-dependent ...Programmed ribosomal frameshifting is a key event during translation of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA genome that allows synthesis of the viral RNA-dependent RNA polymerase and downstream proteins. Here, we present the cryo-electron microscopy structure of a translating mammalian ribosome primed for frameshifting on the viral RNA. The viral RNA adopts a pseudoknot structure that lodges at the entry to the ribosomal messenger RNA (mRNA) channel to generate tension in the mRNA and promote frameshifting, whereas the nascent viral polyprotein forms distinct interactions with the ribosomal tunnel. Biochemical experiments validate the structural observations and reveal mechanistic and regulatory features that influence frameshifting efficiency. Finally, we compare compounds previously shown to reduce frameshifting with respect to their ability to inhibit SARS-CoV-2 replication, establishing coronavirus frameshifting as a target for antiviral intervention. | |||||||||
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_12756.map.gz | 630.5 MB | EMDB map data format | |
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Header (meta data) | emd-12756-v30.xml emd-12756.xml | 124.7 KB 124.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12756_fsc.xml | 19.6 KB | Display | FSC data file |
Images | emd_12756.png | 131 KB | ||
Masks | emd_12756_msk_1.map emd_12756_msk_2.map | 669.9 MB 669.9 MB | Mask map | |
Filedesc metadata | emd-12756.cif.gz | 24.3 KB | ||
Others | emd_12756_half_map_1.map.gz emd_12756_half_map_2.map.gz | 620.3 MB 620.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12756 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12756 | HTTPS FTP |
-Validation report
Summary document | emd_12756_validation.pdf.gz | 931.4 KB | Display | EMDB validaton report |
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Full document | emd_12756_full_validation.pdf.gz | 931 KB | Display | |
Data in XML | emd_12756_validation.xml.gz | 27.8 KB | Display | |
Data in CIF | emd_12756_validation.cif.gz | 37.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12756 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12756 | HTTPS FTP |
-Related structure data
Related structure data | 7o7yMC 7o7zC 7o80C 7o81C C: citing same article (ref.) M: atomic model generated by this map |
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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_12756.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: 1.06 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_12756_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Mask #2
File | emd_12756_msk_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_12756_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_12756_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slipp...
+Supramolecule #1: Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slipp...
+Supramolecule #2: Rabbit 80S ribosome stalled
+Supramolecule #3: SARS-CoV-2 slippery site by a pseudoknot
+Supramolecule #4: Rabbit 80S ribosome stalled
+Supramolecule #5: Replicase polyprotein 1ab
+Macromolecule #1: 18S rRNA
+Macromolecule #9: mRNA containing SARS-CoV-2 sequence
+Macromolecule #10: E-site tRNA
+Macromolecule #11: P-site Phe-tRNA(Phe)
+Macromolecule #39: 28S rRNA
+Macromolecule #40: 5S rRNA
+Macromolecule #41: 5.8S rRNA
+Macromolecule #2: 40S ribosomal protein S27
+Macromolecule #3: Ribosomal protein S28
+Macromolecule #4: Ribosomal protein S27a
+Macromolecule #5: 40S ribosomal protein S30
+Macromolecule #6: Ribosomal protein eS26
+Macromolecule #7: RACK1
+Macromolecule #8: uS14
+Macromolecule #12: 40S ribosomal protein SA
+Macromolecule #13: 40S ribosomal protein S3a
+Macromolecule #14: Ribosomal protein uS5
+Macromolecule #15: 40S ribosomal protein S3
+Macromolecule #16: Ribosomal protein eS4
+Macromolecule #17: Ribosomal protein S5
+Macromolecule #18: 40S ribosomal protein S6
+Macromolecule #19: 40S ribosomal protein S7
+Macromolecule #20: 40S ribosomal protein S8
+Macromolecule #21: Ribosomal protein S9 (Predicted)
+Macromolecule #22: eS10
+Macromolecule #23: 40S ribosomal protein S11
+Macromolecule #24: 40S ribosomal protein S12
+Macromolecule #25: uS15
+Macromolecule #26: 40S ribosomal protein uS11
+Macromolecule #27: 40S ribosomal protein uS19
+Macromolecule #28: uS9
+Macromolecule #29: 40S ribosomal protein eS17
+Macromolecule #30: 40S ribosomal protein S18
+Macromolecule #31: Ribosomal protein eS19
+Macromolecule #32: 40S ribosomal protein uS10
+Macromolecule #33: Ribosomal protein eS21
+Macromolecule #34: Ribosomal protein S15a
+Macromolecule #35: 40S ribosomal protein S23
+Macromolecule #36: 40S ribosomal protein S24
+Macromolecule #37: 40S ribosomal protein S25
+Macromolecule #38: 60s ribosomal protein l41
+Macromolecule #42: Ribosomal protein uL2
+Macromolecule #43: Ribosomal protein L3
+Macromolecule #44: 60S ribosomal protein L4
+Macromolecule #45: Ribosomal_L18_c domain-containing protein
+Macromolecule #46: 60S ribosomal protein L6
+Macromolecule #47: Ribosomal Protein uL30
+Macromolecule #48: Ribosomal protein eL8
+Macromolecule #49: 60S ribosomal protein L9
+Macromolecule #50: 60S ribosomal protein L10
+Macromolecule #51: Ribosomal protein L11
+Macromolecule #52: Replicase polyprotein 1ab
+Macromolecule #53: Ribosomal protein eL13
+Macromolecule #54: Ribosomal protein L14
+Macromolecule #55: Ribosomal protein L15
+Macromolecule #56: Ribosomal protein uL13
+Macromolecule #57: uL22
+Macromolecule #58: Ribosomal Protein eL18
+Macromolecule #59: 60S ribosomal protein L19
+Macromolecule #60: Ribosomal protein eL20
+Macromolecule #61: eL21
+Macromolecule #62: Ribosomal protein eL22
+Macromolecule #63: Ribosomal protein L23
+Macromolecule #64: eL24
+Macromolecule #65: uL23
+Macromolecule #66: Ribosomal protein L26
+Macromolecule #67: 60S ribosomal protein L27
+Macromolecule #68: 60S ribosomal protein L27a
+Macromolecule #69: 60S ribosomal protein L29
+Macromolecule #70: eL30
+Macromolecule #71: eL31
+Macromolecule #72: eL32
+Macromolecule #73: eL33
+Macromolecule #74: 60S ribosomal protein L34
+Macromolecule #75: uL29
+Macromolecule #76: 60S ribosomal protein L36
+Macromolecule #77: Ribosomal protein L37
+Macromolecule #78: eL38
+Macromolecule #79: eL39
+Macromolecule #80: 60S ribosomal protein L40
+Macromolecule #81: eL42
+Macromolecule #82: eL43
+Macromolecule #83: Ribosomal protein eL28
+Macromolecule #84: 60S acidic ribosomal protein P0
+Macromolecule #85: Ribosomal protein L12
+Macromolecule #86: Ribosomal protein uL1
+Macromolecule #87: SPERMIDINE
+Macromolecule #88: SPERMINE
+Macromolecule #89: MAGNESIUM ION
+Macromolecule #90: UNKNOWN ATOM OR ION
+Macromolecule #91: ZINC ION
+Macromolecule #92: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 1 |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
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 | C2 aperture diameter: 100.0 µm / Calibrated magnification: 56604 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / 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 |