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Yorodumi- EMDB-54290: in situ S. pombe hibernating ribosome after 7 days of glucose dep... -
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Open data
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Basic information
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| Title | in situ S. pombe hibernating ribosome after 7 days of glucose depletion | |||||||||
Map data | Filtered sharpened map generated by M from in situ hibernating ribosomes in S. pombe after 7 days of glucose depletion | |||||||||
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Keywords | RIBOSOME / SNOR / pombe / Yeast / Hibernating / Glucose / Cryo-ET / in-situ | |||||||||
| Function / homology | Function and homology informationPeptide chain elongation / Hypusine synthesis from eIF5A-lysine / Synthesis of diphthamide-EEF2 / mTORC1-mediated signalling / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Platelet degranulation / Protein methylation / Protein hydroxylation ...Peptide chain elongation / Hypusine synthesis from eIF5A-lysine / Synthesis of diphthamide-EEF2 / mTORC1-mediated signalling / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Platelet degranulation / Protein methylation / Protein hydroxylation / regulation of cytoplasmic translational initiation in response to stress / RMTs methylate histone arginines / Neutrophil degranulation / Major pathway of rRNA processing in the nucleolus and cytosol / negative regulation of cell integrity MAPK cascade / positive regulation of conjugation with cellular fusion / 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 / ribonuclease MRP complex / translational frameshifting / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / regulation of cytoplasmic translation / cytoplasmic translational elongation / GCN2-mediated signaling / positive regulation of translational termination / translation termination factor activity / translation activator activity / negative regulation of p38MAPK cascade / cytoplasmic translational termination / ribosome hibernation / positive regulation of translational elongation / preribosome / G-quadruplex DNA binding / tRNA processing / cytosolic large ribosomal subunit assembly / signaling receptor activator activity / negative regulation of translational frameshifting / ribosomal small subunit binding / TOR signaling / translational elongation / pre-mRNA intronic binding / ribosomal large subunit export from nucleus / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation elongation factor activity / protein-RNA complex assembly / maturation of LSU-rRNA / negative regulation of cytoplasmic translation / 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) / protein-membrane adaptor activity / positive regulation of autophagy / rescue of stalled cytosolic ribosome / protein kinase C binding / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of actin cytoskeleton organization / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / maintenance of translational fidelity / modification-dependent protein catabolic process / cytoplasmic stress granule / protein tag activity / rRNA processing / ribosomal small subunit assembly / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / 5S rRNA binding / small ribosomal subunit / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / structural constituent of ribosome / protein ubiquitination / ribosome / translation / ribonucleoprotein complex / negative regulation of gene expression / mRNA binding / GTPase activity / ubiquitin protein ligase binding / GTP binding / nucleolus / protein-containing complex / RNA binding / zinc ion binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
| Biological species | ![]() | |||||||||
| Method | subtomogram averaging / cryo EM / Resolution: 3.38 Å | |||||||||
Authors | Rosa H / Gluc M / Jomaa A / Mattei S | |||||||||
| Funding support | United States, Germany, 2 items
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Citation | Journal: Nature / Year: 2026Title: SNOR promotes translation restart after dormancy. Authors: Maciej Gluc / Higor Rosa / Maria Bozko / Lesley A Turner / Cassidy R Prince / Yelena Peskova / Heather A Feaga / Kathleen L Gould / Simone Mattei / Ahmad Jomaa / ![]() Abstract: Cellular dormancy enables survival during prolonged nutrient limitation by reversibly suppressing protein synthesis. How inactive eukaryotic ribosomes are reactivated when nutrients return remains ...Cellular dormancy enables survival during prolonged nutrient limitation by reversibly suppressing protein synthesis. How inactive eukaryotic ribosomes are reactivated when nutrients return remains unclear. Here, using high-resolution in situ cryo-electron tomography in Schizosaccharomyces pombe, we identify SNOR, an SBDS domain-containing ribosome-associated factor that binds at the peptidyl transferase centre and contacts the hypusinated loop of eIF5A during glucose depletion-induced dormancy. Rather than acting as a canonical hibernation factor, SNOR licenses dormant ribosomes for rapid translational restart. Upon glucose repletion, SNOR and eIF5A act together to promote efficient recovery of polysomes and exit from dormancy. These findings define a stress-responsive ribosome restart module that couples carbon-source limitation to surveillance of the ribosomal active site and reactivation of protein synthesis. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_54290.map.gz | 694.3 MB | EMDB map data format | |
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| Header (meta data) | emd-54290-v30.xml emd-54290.xml | 113.7 KB 113.7 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_54290_fsc_1.xml emd_54290_fsc_2.xml | 20.8 KB 12.9 KB | Display Display | FSC data file |
| Images | emd_54290.png | 165.6 KB | ||
| Filedesc metadata | emd-54290.cif.gz | 21 KB | ||
| Others | emd_54290_additional_1.map.gz emd_54290_half_map_1.map.gz emd_54290_half_map_2.map.gz | 395.1 MB 383.5 MB 383.5 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-54290 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-54290 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9rvuMC ![]() 9phcC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_54290.map.gz / Format: CCP4 / Size: 744.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | Filtered sharpened map generated by M from in situ hibernating ribosomes in S. pombe after 7 days of glucose depletion | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.01 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Additional map: Locally filtered sharpened map generated by M from...
| File | emd_54290_additional_1.map | ||||||||||||
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| Annotation | Locally filtered sharpened map generated by M from in situ hibernating ribosomes in S. pombe after 7 days of glucose depletion | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: Half-map 2 generated by M from in situ...
| File | emd_54290_half_map_1.map | ||||||||||||
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| Annotation | Half-map 2 generated by M from in situ hibernating ribosomes in S. pombe after 7 days of glucose depletion | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: Half-map 1 generated by M from in situ...
| File | emd_54290_half_map_2.map | ||||||||||||
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| Annotation | Half-map 1 generated by M from in situ hibernating ribosomes in S. pombe after 7 days of glucose depletion | ||||||||||||
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| Density Histograms |
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Sample components
+Entire : In situ cryo-ET Hibernating Ribosome from S. pombe under 7-day gl...
+Supramolecule #1: In situ cryo-ET Hibernating Ribosome from S. pombe under 7-day gl...
+Macromolecule #1: 18S small subunit ribosomal RNA
+Macromolecule #36: 28S large subunit ribosomal RNA
+Macromolecule #37: 5S large subunit ribosomal RNA
+Macromolecule #38: 5.8S large subunit ribosomal RNA
+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 uS11A
+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 uS13A
+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 eS30A
+Macromolecule #33: Small ribosomal subunit protein RACK1
+Macromolecule #34: Large ribosomal subunit protein eL42
+Macromolecule #35: Large ribosomal subunit protein eL43A
+Macromolecule #39: Large ribosomal subunit protein uL2A
+Macromolecule #40: Large ribosomal subunit protein uL3A
+Macromolecule #41: Large ribosomal subunit protein uL4A
+Macromolecule #42: Large ribosomal subunit protein uL18B
+Macromolecule #43: Large ribosomal subunit protein eL6
+Macromolecule #44: Large ribosomal subunit protein uL30C
+Macromolecule #45: Large ribosomal subunit protein eL8
+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 eL18B
+Macromolecule #53: Large ribosomal subunit protein eL19B
+Macromolecule #54: Large ribosomal subunit protein eL20A
+Macromolecule #55: Large ribosomal subunit protein eL21B
+Macromolecule #56: Large ribosomal subunit protein eL22
+Macromolecule #57: Large ribosomal subunit protein uL14A
+Macromolecule #58: Large ribosomal subunit protein eL24B
+Macromolecule #59: Large ribosomal subunit protein uL23A
+Macromolecule #60: Large ribosomal subunit protein uL24
+Macromolecule #61: Large ribosomal subunit protein eL27A
+Macromolecule #62: Large ribosomal subunit protein uL15B
+Macromolecule #63: Large ribosomal subunit protein eL29
+Macromolecule #64: Large ribosomal subunit protein eL30A
+Macromolecule #65: Large ribosomal subunit protein eL31
+Macromolecule #66: Large ribosomal subunit protein eL32A
+Macromolecule #67: Large ribosomal subunit protein eL33A
+Macromolecule #68: Large ribosomal subunit protein eL34B
+Macromolecule #69: Large ribosomal subunit protein uL29
+Macromolecule #70: Large ribosomal subunit protein eL36B
+Macromolecule #71: Large ribosomal subunit protein eL37B
+Macromolecule #72: Large ribosomal subunit protein eL38A
+Macromolecule #73: Large ribosomal subunit protein eL39
+Macromolecule #74: Large ribosomal subunit protein eL28
+Macromolecule #75: Ribosome-associated protein oga1
+Macromolecule #76: Elongation factor 2
+Macromolecule #77: Large ribosomal subunit protein uL1B
+Macromolecule #78: SDO1-like protein C21C3.19
+Macromolecule #79: Eukaryotic translation initiation factor 5A-1
+Macromolecule #80: Large ribosomal subunit protein eL40A
+Macromolecule #81: Large ribosomal subunit protein uL6B
+Macromolecule #82: Large ribosomal subunit protein uL22A
+Macromolecule #83: Large ribosomal subunit protein uL22A
+Macromolecule #84: ZINC ION
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | subtomogram averaging |
| Aggregation state | cell |
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Sample preparation
| Buffer | pH: 5.5 |
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| Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 300 K / Instrument: LEICA EM GP |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Specialist optics | Energy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV |
| Details | Objective Aperture 70 um |
| Image recording | Film or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 3.4 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 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 |
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About Yorodumi



Keywords
Authors
United States,
Germany, 2 items
Citation














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Processing
FIELD EMISSION GUN

