+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16127 | |||||||||
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Title | Yeast 80S, ES7s delta, eIF5A, Stm1 containing | |||||||||
Map data | ||||||||||
Sample |
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Keywords | eIF5A / Stm1 / Rpl41A / delta ES7s / RIBOSOME | |||||||||
Function / homology | Function and homology information positive regulation of translational termination / positive regulation of translational elongation / ribosomal subunit / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / pre-mRNA 5'-splice site binding ...positive regulation of translational termination / positive regulation of translational elongation / ribosomal subunit / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / pre-mRNA 5'-splice site binding / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to cycloheximide / mRNA destabilization / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / 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) / negative regulation of mRNA splicing, via spliceosome / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / regulation of translational fidelity / positive regulation of protein kinase activity / 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) / ribosomal subunit export from nucleus / translation regulator activity / translation elongation factor activity / 90S preribosome / cytosolic ribosome / rescue of stalled ribosome / cellular response to amino acid starvation / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / positive regulation of apoptotic signaling pathway / small-subunit processome / protein kinase C binding / maintenance of translational fidelity / macroautophagy / ribosomal large subunit assembly / modification-dependent protein catabolic process / cytoplasmic stress granule / rRNA processing / protein tag activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosome binding / 5S rRNA binding / large ribosomal subunit rRNA binding / small ribosomal subunit / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / nucleic acid binding / negative regulation of translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.4 Å | |||||||||
Authors | Dimitrova-Paternoga L / Paternoga H / Wilson DN | |||||||||
Funding support | Germany, Switzerland, 2 items
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Citation | Journal: Nucleic Acids Res / Year: 2024 Title: Evolving precision: rRNA expansion segment 7S modulates translation velocity and accuracy in eukaryal ribosomes. Authors: Robert Rauscher / Cristian Eggers / Lyudmila Dimitrova-Paternoga / Vaishnavi Shankar / Alessia Rosina / Marina Cristodero / Helge Paternoga / Daniel N Wilson / Sebastian A Leidel / Norbert Polacek / Abstract: Ribosome-enhanced translational miscoding of the genetic code causes protein dysfunction and loss of cellular fitness. During evolution, open reading frame length increased, necessitating mechanisms ...Ribosome-enhanced translational miscoding of the genetic code causes protein dysfunction and loss of cellular fitness. During evolution, open reading frame length increased, necessitating mechanisms for enhanced translation fidelity. Indeed, eukaryal ribosomes are more accurate than bacterial counterparts, despite their virtually identical, conserved active centers. During the evolution of eukaryotic organisms ribosome expansions at the rRNA and protein level occurred, which potentially increases the options for translation regulation and cotranslational events. Here we tested the hypothesis that ribosomal RNA expansions can modulate the core function of the ribosome, faithful protein synthesis. We demonstrate that a short expansion segment present in all eukaryotes' small subunit, ES7S, is crucial for accurate protein synthesis as its presence adjusts codon-specific velocities and guarantees high levels of cognate tRNA selection. Deletion of ES7S in yeast enhances mistranslation and causes protein destabilization and aggregation, dramatically reducing cellular fitness. Removal of ES7S did not alter ribosome architecture but altered the structural dynamics of inter-subunit bridges thus affecting A-tRNA selection. Exchanging the yeast ES7S sequence with the human ES7S increases accuracy whereas shortening causes the opposite effect. Our study demonstrates that ES7S provided eukaryal ribosomes with higher accuracy without perturbing the structurally conserved decoding center. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16127.map.gz | 337.5 MB | EMDB map data format | |
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Header (meta data) | emd-16127-v30.xml emd-16127.xml | 100.2 KB 100.2 KB | Display Display | EMDB header |
Images | emd_16127.png | 139 KB | ||
Filedesc metadata | emd-16127.cif.gz | 19.2 KB | ||
Others | emd_16127_half_map_1.map.gz emd_16127_half_map_2.map.gz | 338.7 MB 338.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16127 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16127 | HTTPS FTP |
-Related structure data
Related structure data | 8bn3MC 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_16127.map.gz / Format: CCP4 / Size: 421.9 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: 0.783 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_16127_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16127_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Dormant yeast 80S ribosome
+Supramolecule #1: Dormant yeast 80S ribosome
+Macromolecule #1: 60S ribosomal protein L1-A
+Macromolecule #2: Rps5p
+Macromolecule #3: Small ribosomal subunit protein eS10A
+Macromolecule #4: 40S ribosomal protein S14-B
+Macromolecule #5: RPS15 isoform 1
+Macromolecule #6: 40S ribosomal protein S18-A
+Macromolecule #7: RPS20 isoform 1
+Macromolecule #8: 40S ribosomal protein S25
+Macromolecule #9: RPS28A isoform 1
+Macromolecule #10: 60S ribosomal protein L41-A
+Macromolecule #15: Small ribosomal subunit protein uS2A
+Macromolecule #16: Small ribosomal subunit protein eS1
+Macromolecule #17: RPS2 isoform 1
+Macromolecule #18: 40S ribosomal protein S3
+Macromolecule #19: Small ribosomal subunit protein eS6A
+Macromolecule #20: 40S ribosomal protein S7-A
+Macromolecule #21: 40S ribosomal protein S8
+Macromolecule #22: Small ribosomal subunit protein uS4A
+Macromolecule #23: Small ribosomal subunit protein uS17A
+Macromolecule #24: 40S ribosomal protein S13
+Macromolecule #25: 40S ribosomal protein S16-A
+Macromolecule #26: ES17
+Macromolecule #27: 40S ribosomal protein S19-A
+Macromolecule #28: Small ribosomal subunit protein eS21A
+Macromolecule #29: RPS22A isoform 1
+Macromolecule #30: 40S ribosomal protein S23-A
+Macromolecule #31: 40S ribosomal protein S24-A
+Macromolecule #32: RPS26B isoform 1
+Macromolecule #33: 40S ribosomal protein S27-A
+Macromolecule #34: RPS29A isoform 1
+Macromolecule #35: 40S ribosomal protein S30-A
+Macromolecule #36: Small ribosomal subunit protein RACK1
+Macromolecule #37: 60S ribosomal protein L2-A
+Macromolecule #38: 60S ribosomal protein L3
+Macromolecule #39: RPL4A isoform 1
+Macromolecule #40: RPL5 isoform 1
+Macromolecule #41: 60S ribosomal protein L6-A
+Macromolecule #42: 60S ribosomal protein L7-A
+Macromolecule #43: 60S ribosomal protein L8-A
+Macromolecule #44: RPL9A isoform 1
+Macromolecule #45: RPL10 isoform 1
+Macromolecule #46: RPL11B isoform 1
+Macromolecule #47: 60S ribosomal protein L13-A
+Macromolecule #48: 60S ribosomal protein L14-A
+Macromolecule #49: Ribosomal protein L15
+Macromolecule #50: 60S ribosomal protein L16-A
+Macromolecule #51: 60S ribosomal protein L17-A
+Macromolecule #52: 60S ribosomal protein L18-A
+Macromolecule #53: 60S ribosomal protein L19-A
+Macromolecule #54: 60S ribosomal protein L20-A
+Macromolecule #55: 60S ribosomal protein L21-A
+Macromolecule #56: 60S ribosomal protein L22-A
+Macromolecule #57: 60S ribosomal protein L23-A
+Macromolecule #58: RPL24A isoform 1
+Macromolecule #59: 60S ribosomal protein L25
+Macromolecule #60: Large ribosomal subunit protein uL24A
+Macromolecule #61: 60S ribosomal protein L27-A
+Macromolecule #62: 60S ribosomal protein L28
+Macromolecule #63: 60S ribosomal protein L29
+Macromolecule #64: 60S ribosomal protein L30
+Macromolecule #65: 60S ribosomal protein L31-A
+Macromolecule #66: RPL32 isoform 1
+Macromolecule #67: 60S ribosomal protein L33-A
+Macromolecule #68: Large ribosomal subunit protein eL34A
+Macromolecule #69: 60S ribosomal protein L35-A
+Macromolecule #70: 60S ribosomal protein L36-A
+Macromolecule #71: Large ribosomal subunit protein eL37A
+Macromolecule #72: RPL38 isoform 1
+Macromolecule #73: 60S ribosomal protein L39
+Macromolecule #74: 60S ribosomal protein L40-A
+Macromolecule #75: Large ribosomal subunit protein eL41B
+Macromolecule #76: 60S ribosomal protein L42-A
+Macromolecule #77: 60S ribosomal protein L43-A
+Macromolecule #78: STM1 isoform 1
+Macromolecule #79: Eukaryotic translation initiation factor 5A
+Macromolecule #80: Small ribosomal subunit protein eS4A
+Macromolecule #81: RPS31 isoform 1
+Macromolecule #11: 5S ribosomal RNA
+Macromolecule #12: 5.8S ribosomal RNA
+Macromolecule #13: 25S ribosomal RNA
+Macromolecule #14: 18S ribosomal RNA
+Macromolecule #82: MAGNESIUM ION
+Macromolecule #83: POTASSIUM ION
+Macromolecule #84: 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethy...
+Macromolecule #85: SPERMIDINE
+Macromolecule #86: ZINC ION
+Macromolecule #87: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 300 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE-PROPANE |
Details | 80S peak from Sucrose gradient |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 32.0 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 254202 |
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Startup model | Type of model: PDB ENTRY PDB model - PDB ID: Details: Crystal structure of Verrucarin bound to the yeast 80S ribosome |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final 3D classification | Number classes: 5 / Software - Name: RELION (ver. 4.1) |
Final angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 4.1) |
Final reconstruction | Number classes used: 2 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.1) / Number images used: 127945 |
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient |
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Output model | PDB-8bn3: |