+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43976 | |||||||||
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Title | Translating S. pombe ribosome | |||||||||
Map data | S. pombe translating 80S ribosome composite map | |||||||||
Sample |
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Keywords | Ribosome / Schizosaccharomyces pombe / protein synthesis / S. pombe / tRNA / mRNA / TRANSLATION | |||||||||
Function / homology | Function and homology information mTORC1-mediated signalling / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Protein methylation / Protein hydroxylation / positive regulation of SREBP signaling pathway / RMTs methylate histone arginines / negative regulation of cell integrity MAPK cascade / positive regulation of conjugation with cellular fusion ...mTORC1-mediated signalling / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Protein methylation / Protein hydroxylation / positive regulation of SREBP signaling pathway / RMTs methylate histone arginines / negative regulation of cell integrity MAPK cascade / positive regulation of conjugation with cellular fusion / cytoplasmic translational elongation / Major pathway of rRNA processing in the nucleolus and cytosol / : / cytosolic large ribosomal subunit assembly / ribonuclease MRP complex / L13a-mediated translational silencing of Ceruloplasmin expression / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / SRP-dependent cotranslational protein targeting to membrane / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / GCN2-mediated signaling / regulation of cytoplasmic translation / translation activator activity / negative regulation of p38MAPK cascade / tRNA processing / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / negative regulation of cytoplasmic translation / positive regulation of autophagy / pre-mRNA intronic binding / 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) / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / protein kinase C binding / maintenance of translational fidelity / cytoplasmic stress granule / rRNA processing / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosome binding / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / 5S rRNA binding / small ribosomal subunit / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / positive regulation of protein phosphorylation / negative regulation of gene expression / mRNA binding / nucleolus / RNA binding / zinc ion binding / membrane / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Schizosaccharomyces pombe 972h- (yeast) / Schizosaccharomyces pombe (fission yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.4 Å | |||||||||
Authors | Gluc M / Gemin O / Purdy M / Mattei S / Jomaa A | |||||||||
Funding support | United States, Germany, 2 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Ribosomes hibernate on mitochondria during cellular stress. Authors: Olivier Gemin / Maciej Gluc / Higor Rosa / Michael Purdy / Moritz Niemann / Yelena Peskova / Simone Mattei / Ahmad Jomaa / Abstract: Cell survival under nutrient-deprived conditions relies on cells' ability to adapt their organelles and rewire their metabolic pathways. In yeast, glucose depletion induces a stress response mediated ...Cell survival under nutrient-deprived conditions relies on cells' ability to adapt their organelles and rewire their metabolic pathways. In yeast, glucose depletion induces a stress response mediated by mitochondrial fragmentation and sequestration of cytosolic ribosomes on mitochondria. This cellular adaptation promotes survival under harsh environmental conditions; however, the underlying mechanism of this response remains unknown. Here, we demonstrate that upon glucose depletion protein synthesis is halted. Cryo-electron microscopy structure of the ribosomes show that they are devoid of both tRNA and mRNA, and a subset of the particles depicted a conformational change in rRNA H69 that could prevent tRNA binding. Our in situ structural analyses reveal that the hibernating ribosomes tether to fragmented mitochondria and establish eukaryotic-specific, higher-order storage structures by assembling into oligomeric arrays on the mitochondrial surface. Notably, we show that hibernating ribosomes exclusively bind to the outer mitochondrial membrane via the small ribosomal subunit during cellular stress. We identify the ribosomal protein Cpc2/RACK1 as the molecule mediating ribosomal tethering to mitochondria. This study unveils the molecular mechanism connecting mitochondrial stress with the shutdown of protein synthesis and broadens our understanding of cellular responses to nutrient scarcity and cell quiescence. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_43976.map.gz | 483.6 MB | EMDB map data format | |
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Header (meta data) | emd-43976-v30.xml emd-43976.xml | 101.6 KB 101.6 KB | Display Display | EMDB header |
Images | emd_43976.png | 105 KB | ||
Masks | emd_43976_msk_1.map | 512 MB | Mask map | |
Filedesc metadata | emd-43976.cif.gz | 18.6 KB | ||
Others | emd_43976_additional_1.map.gz emd_43976_half_map_1.map.gz emd_43976_half_map_2.map.gz | 483.8 MB 474.7 MB 474.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43976 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43976 | HTTPS FTP |
-Validation report
Summary document | emd_43976_validation.pdf.gz | 1.3 MB | Display | EMDB validaton report |
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Full document | emd_43976_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | emd_43976_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | emd_43976_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43976 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43976 | HTTPS FTP |
-Related structure data
Related structure data | 9axvMC 9axtC 9axuC C: citing same article (ref.) M: atomic model generated by this map |
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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_43976.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | S. pombe translating 80S ribosome composite map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_43976_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: S. pombe translating 80S ribosome raw map
File | emd_43976_additional_1.map | ||||||||||||
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Annotation | S. pombe translating 80S ribosome raw map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: S. pombe translating 80S ribosome raw map, half map B
File | emd_43976_half_map_1.map | ||||||||||||
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Annotation | S. pombe translating 80S ribosome raw map, half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: S. pombe translating 80S ribosome raw map, half map A
File | emd_43976_half_map_2.map | ||||||||||||
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Annotation | S. pombe translating 80S ribosome raw map, half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Translating S. pombe ribosome
+Supramolecule #1: Translating S. pombe ribosome
+Macromolecule #1: 18S ribosomal RNA
+Macromolecule #35: 28S ribosomal RNA
+Macromolecule #36: 5S ribosomal RNA
+Macromolecule #37: 5.8S ribosomal RNA
+Macromolecule #77: tRNA
+Macromolecule #78: A/P tRNA
+Macromolecule #79: mRNA
+Macromolecule #2: Small ribosomal subunit protein uS2A
+Macromolecule #3: Small ribosomal subunit protein eS1B
+Macromolecule #4: Small ribosomal subunit protein uS5
+Macromolecule #5: Small ribosomal subunit protein uS3
+Macromolecule #6: Small ribosomal subunit protein eS4C
+Macromolecule #7: Small ribosomal subunit protein uS7A
+Macromolecule #8: Small ribosomal subunit protein eS6B
+Macromolecule #9: Small ribosomal subunit protein eS7
+Macromolecule #10: Small ribosomal subunit protein eS8B
+Macromolecule #11: Small ribosomal subunit protein uS4B
+Macromolecule #12: Small ribosomal subunit protein eS10B
+Macromolecule #13: Small ribosomal subunit protein uS17A
+Macromolecule #14: Small ribosomal subunit protein eS12A
+Macromolecule #15: Small ribosomal subunit protein uS15
+Macromolecule #16: Small ribosomal subunit protein uS11B
+Macromolecule #17: Small ribosomal subunit protein uS19B
+Macromolecule #18: Small ribosomal subunit protein uS9A
+Macromolecule #19: Small ribosomal subunit protein eS17A
+Macromolecule #20: Small ribosomal subunit protein uS13B
+Macromolecule #21: Small ribosomal subunit protein eS19A
+Macromolecule #22: Small ribosomal subunit protein uS10
+Macromolecule #23: Small ribosomal subunit protein eS21
+Macromolecule #24: Small ribosomal subunit protein uS8A
+Macromolecule #25: Small ribosomal subunit protein uS12A
+Macromolecule #26: Small ribosomal subunit protein eS24A
+Macromolecule #27: Small ribosomal subunit protein eS25A
+Macromolecule #28: Small ribosomal subunit protein eS26B
+Macromolecule #29: Small ribosomal subunit protein eS27
+Macromolecule #30: Small ribosomal subunit protein eS28A
+Macromolecule #31: Small ribosomal subunit protein uS14
+Macromolecule #32: Small ribosomal subunit protein eS30B
+Macromolecule #33: Large ribosomal subunit protein eL42
+Macromolecule #34: Large ribosomal subunit protein eL43A
+Macromolecule #38: Large ribosomal subunit protein uL2C
+Macromolecule #39: Large ribosomal subunit protein uL3A
+Macromolecule #40: Large ribosomal subunit protein uL4A
+Macromolecule #41: Large ribosomal subunit protein uL18B
+Macromolecule #42: Large ribosomal subunit protein eL6
+Macromolecule #43: Large ribosomal subunit protein uL30C
+Macromolecule #44: Large ribosomal subunit protein eL8
+Macromolecule #45: Large ribosomal subunit protein uL6B
+Macromolecule #46: Large ribosomal subunit protein uL16A
+Macromolecule #47: Large ribosomal subunit protein uL5A
+Macromolecule #48: Large ribosomal subunit protein eL13
+Macromolecule #49: Large ribosomal subunit protein eL14
+Macromolecule #50: Large ribosomal subunit protein eL15B
+Macromolecule #51: Large ribosomal subunit protein uL13A
+Macromolecule #52: Large ribosomal subunit protein uL22A
+Macromolecule #53: Large ribosomal subunit protein eL18B
+Macromolecule #54: Large ribosomal subunit protein eL19B
+Macromolecule #55: Large ribosomal subunit protein eL20A
+Macromolecule #56: Large ribosomal subunit protein eL21B
+Macromolecule #57: Large ribosomal subunit protein eL22
+Macromolecule #58: Large ribosomal subunit protein uL14B
+Macromolecule #59: Large ribosomal subunit protein eL24B
+Macromolecule #60: Large ribosomal subunit protein uL23A
+Macromolecule #61: Large ribosomal subunit protein uL24
+Macromolecule #62: Large ribosomal subunit protein eL27A
+Macromolecule #63: Large ribosomal subunit protein uL15B
+Macromolecule #64: Large ribosomal subunit protein eL29
+Macromolecule #65: Large ribosomal subunit protein eL30A
+Macromolecule #66: Large ribosomal subunit protein eL31
+Macromolecule #67: Large ribosomal subunit protein eL32A
+Macromolecule #68: Large ribosomal subunit protein eL33A
+Macromolecule #69: Large ribosomal subunit protein eL34B
+Macromolecule #70: Large ribosomal subunit protein uL29
+Macromolecule #71: Large ribosomal subunit protein eL36B
+Macromolecule #72: Large ribosomal subunit protein eL37B
+Macromolecule #73: Large ribosomal subunit protein eL38A
+Macromolecule #74: Large ribosomal subunit protein eL39
+Macromolecule #75: Large ribosomal subunit protein eL28
+Macromolecule #76: Small ribosomal subunit protein RACK1
+Macromolecule #80: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.25 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 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: 1.6 µm / Nominal defocus min: 0.6 µm |
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: OTHER / Details: Ab initio |
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Final reconstruction | Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 58736 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-9axv: |