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Yorodumi- EMDB-12757: Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slipp... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12757 | |||||||||
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Title | Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a pseudoknot (classified for pseudoknot) | |||||||||
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) / ribosomal subunit / DNA-(apurinic or apyrimidinic site) lyase / cytosolic ribosome ...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) / ribosomal subunit / DNA-(apurinic or apyrimidinic site) lyase / cytosolic ribosome / protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / TRAF3-dependent IRF activation pathway / snRNP Assembly / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / 5S rRNA binding / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / SARS coronavirus main proteinase / cytosolic large ribosomal subunit / host cell endosome / 3'-5'-RNA exonuclease activity / : / host cell endoplasmic reticulum-Golgi intermediate compartment / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / SARS-CoV-2 modulates host translation machinery / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / DNA helicase / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / RNA helicase / ribosome / structural constituent of ribosome / induction by virus of host autophagy / ribonucleoprotein complex / translation / RNA-directed RNA polymerase / copper ion binding / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / nucleolus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Severe acute respiratory syndrome coronavirus 2 / Bos taurus (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.4 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_12757.map.gz | 179.4 MB | EMDB map data format | |
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Header (meta data) | emd-12757-v30.xml emd-12757.xml | 124.8 KB 124.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12757_fsc.xml | 19.6 KB | Display | FSC data file |
Images | emd_12757.png | 113.9 KB | ||
Masks | emd_12757_msk_1.map emd_12757_msk_2.map | 669.9 MB 669.9 MB | Mask map | |
Filedesc metadata | emd-12757.cif.gz | 24.3 KB | ||
Others | emd_12757_half_map_1.map.gz emd_12757_half_map_2.map.gz | 622.7 MB 622.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12757 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12757 | HTTPS FTP |
-Related structure data
Related structure data | 7o7zMC 7o7yC 7o80C 7o81C 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_12757.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_12757_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Mask #2
File | emd_12757_msk_2.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_12757_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_12757_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
+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 / Pretreatment - Type: GLOW DISCHARGE |
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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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 FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 81000 |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |