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Yorodumi- EMDB-24235: Cycloheximide bound vacant 80S structure isolated from cbf5-D95A -
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Open data
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Basic information
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| Title | Cycloheximide bound vacant 80S structure isolated from cbf5-D95A | |||||||||
Map data | Composite maps | |||||||||
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Keywords | yeast / 80S complex / chemical modification / RIBOSOME | |||||||||
| Function / homology | Function and homology informationtriplex DNA binding / ribosome hibernation / translation elongation factor binding / Platelet degranulation / regulation of translational initiation in response to stress / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / Negative regulators of DDX58/IFIH1 signaling ...triplex DNA binding / ribosome hibernation / translation elongation factor binding / Platelet degranulation / regulation of translational initiation in response to stress / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / Negative regulators of DDX58/IFIH1 signaling / RMTs methylate histone arginines / Protein methylation / 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 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nonfunctional rRNA decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / response to cycloheximide / 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) / preribosome, small subunit precursor / telomeric DNA binding / mRNA destabilization / Major pathway of rRNA processing in the nucleolus and cytosol / negative regulation of translational frameshifting / SRP-dependent cotranslational protein targeting to membrane / TOR signaling / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of mRNA splicing, via spliceosome / positive regulation of protein kinase activity / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / preribosome, large subunit precursor / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translational elongation / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / 90S preribosome / Ub-specific processing proteases / regulation of translational fidelity / protein-RNA complex assembly / translational termination / ribosomal subunit export from nucleus / maturation of LSU-rRNA / ribosomal small subunit export from nucleus / 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) / translation regulator activity / translation repressor activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / rescue of stalled ribosome / telomere maintenance / protein kinase C binding / cellular response to amino acid starvation / ribosomal large subunit biogenesis / 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) / ribosome assembly / maturation of SSU-rRNA / macroautophagy / small-subunit processome / translational initiation / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / cytoplasmic stress granule / rRNA processing / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / protein ubiquitination / structural constituent of ribosome / ribosome / translation / G protein-coupled receptor signaling pathway / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / negative regulation of apoptotic process / nucleolus / perinuclear region of cytoplasm / mitochondrion / DNA binding Similarity search - Function | |||||||||
| Biological species | ![]() | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.05 Å | |||||||||
Authors | Rai J / Zhao Y | |||||||||
| Funding support | United States, 1 items
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Citation | Journal: Structure / Year: 2022Title: CryoEM structures of pseudouridine-free ribosome suggest impacts of chemical modifications on ribosome conformations. Authors: Yu Zhao / Jay Rai / Hongguo Yu / Hong Li / ![]() Abstract: Pseudouridine, the most abundant form of RNA modification, is known to play important roles in ribosome function. Mutations in human DKC1, the pseudouridine synthase responsible for catalyzing the ...Pseudouridine, the most abundant form of RNA modification, is known to play important roles in ribosome function. Mutations in human DKC1, the pseudouridine synthase responsible for catalyzing the ribosome RNA modification, cause translation deficiencies and are associated with a complex cancer predisposition. The structural basis for how pseudouridine impacts ribosome function remains uncharacterized. Here, we characterized structures and conformations of a fully modified and a pseudouridine-free ribosome from Saccharomyces cerevisiae in the absence of ligands or when bound with translocation inhibitor cycloheximide by electron cryomicroscopy. In the modified ribosome, the rearranged N1 atom of pseudouridine is observed to stabilize key functional motifs by establishing predominately water-mediated close contacts with the phosphate backbone. The pseudouridine-free ribosome, however, is devoid of such interactions and displays conformations reflective of abnormal inter-subunit movements. The erroneous motions of the pseudouridine-free ribosome may explain its observed deficiencies in translation. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_24235.map.gz | 276.5 MB | EMDB map data format | |
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| Header (meta data) | emd-24235-v30.xml emd-24235.xml | 122.5 KB 122.5 KB | Display Display | EMDB header |
| Images | emd_24235.png | 103.5 KB | ||
| Filedesc metadata | emd-24235.cif.gz | 19.1 KB | ||
| Others | emd_24235_additional_1.map.gz emd_24235_additional_2.map.gz emd_24235_additional_3.map.gz | 272.3 MB 273.6 MB 280.6 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24235 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24235 | HTTPS FTP |
-Validation report
| Summary document | emd_24235_validation.pdf.gz | 632.5 KB | Display | EMDB validaton report |
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| Full document | emd_24235_full_validation.pdf.gz | 632.1 KB | Display | |
| Data in XML | emd_24235_validation.xml.gz | 7.4 KB | Display | |
| Data in CIF | emd_24235_validation.cif.gz | 8.5 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24235 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24235 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 7n8bMC ![]() 7mpiC ![]() 7mpjC 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_24235.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | Composite maps | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.055 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Additional map: 40S-head map from 178,990 particles
| File | emd_24235_additional_1.map | ||||||||||||
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| Annotation | 40S-head map from 178,990 particles | ||||||||||||
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| Density Histograms |
-Additional map: 40S-body map from 178,990 particles
| File | emd_24235_additional_2.map | ||||||||||||
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| Annotation | 40S-body map from 178,990 particles | ||||||||||||
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| Density Histograms |
-Additional map: 60S subunits map from 181,871 particles
| File | emd_24235_additional_3.map | ||||||||||||
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| Annotation | 60S subunits map from 181,871 particles | ||||||||||||
| Projections & Slices |
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| Density Histograms |
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Sample components
+Entire : composite map of Cyclohimide bound vacant 80S structure isolated ...
+Supramolecule #1: composite map of Cyclohimide bound vacant 80S structure isolated ...
+Supramolecule #2: 60S subunit
+Supramolecule #3: 40S subunit
+Supramolecule #4: 80S subunit
+Macromolecule #1: 25S
+Macromolecule #2: 5S
+Macromolecule #3: 5.8S
+Macromolecule #79: 18S RIBOSOMAL RNA
+Macromolecule #4: 60S ribosomal protein L2-A
+Macromolecule #5: 60S ribosomal protein L3
+Macromolecule #6: 60S ribosomal protein L4-A
+Macromolecule #7: 60S ribosomal protein L5
+Macromolecule #8: 60S ribosomal protein L6-A
+Macromolecule #9: 60S ribosomal protein L7-A
+Macromolecule #10: 60S ribosomal protein L8-A
+Macromolecule #11: 60S ribosomal protein L9-A
+Macromolecule #12: 60S ribosomal protein L10
+Macromolecule #13: 60S ribosomal protein L11-A
+Macromolecule #14: 60S ribosomal protein L13-A
+Macromolecule #15: 60S ribosomal protein L14-A
+Macromolecule #16: 60S ribosomal protein L15-A
+Macromolecule #17: 60S ribosomal protein L16-A
+Macromolecule #18: 60S ribosomal protein L17-A
+Macromolecule #19: 60S ribosomal protein L18-A
+Macromolecule #20: 60S ribosomal protein L19-A
+Macromolecule #21: 60S ribosomal protein L20-A
+Macromolecule #22: 60S ribosomal protein L21-A
+Macromolecule #23: 60S ribosomal protein L22-A
+Macromolecule #24: 60S ribosomal protein L23-A
+Macromolecule #25: 60S ribosomal protein L24-A
+Macromolecule #26: 60S ribosomal protein L25
+Macromolecule #27: 60S ribosomal protein L26-A
+Macromolecule #28: 60S ribosomal protein L27-A
+Macromolecule #29: 60S ribosomal protein L28
+Macromolecule #30: 60S ribosomal protein L29
+Macromolecule #31: 60S ribosomal protein L30
+Macromolecule #32: 60S ribosomal protein L31-A
+Macromolecule #33: 60S ribosomal protein L32
+Macromolecule #34: 60S ribosomal protein L33-A
+Macromolecule #35: 60S ribosomal protein L34-A
+Macromolecule #36: 60S ribosomal protein L35-A
+Macromolecule #37: 60S ribosomal protein L36-A
+Macromolecule #38: 60S ribosomal protein L37-A
+Macromolecule #39: 60S ribosomal protein L38
+Macromolecule #40: 60S ribosomal protein L39
+Macromolecule #41: 60S ribosomal protein L40-A
+Macromolecule #42: 60S ribosomal protein L41-A
+Macromolecule #43: 60S ribosomal protein L42-A
+Macromolecule #44: 60S ribosomal protein L43-A
+Macromolecule #45: 40S ribosomal protein S0-A
+Macromolecule #46: 40S ribosomal protein S1-A
+Macromolecule #47: 40S ribosomal protein S2
+Macromolecule #48: 40S ribosomal protein S3
+Macromolecule #49: 40S ribosomal protein S4-A
+Macromolecule #50: 40S ribosomal protein S5
+Macromolecule #51: 40S ribosomal protein S6-A
+Macromolecule #52: 40S ribosomal protein S7-A
+Macromolecule #53: 40S ribosomal protein S8-A
+Macromolecule #54: 40S ribosomal protein S9-A
+Macromolecule #55: 40S ribosomal protein S10-A
+Macromolecule #56: 40S ribosomal protein S11-A
+Macromolecule #57: 40S ribosomal protein S12
+Macromolecule #58: 40S ribosomal protein S13
+Macromolecule #59: 40S ribosomal protein S14-A
+Macromolecule #60: 40S ribosomal protein S15
+Macromolecule #61: 40S ribosomal protein S16-A
+Macromolecule #62: 40S ribosomal protein S17-A
+Macromolecule #63: 40S ribosomal protein S18-A
+Macromolecule #64: 40S ribosomal protein S19-A
+Macromolecule #65: 40S ribosomal protein S20
+Macromolecule #66: 40S ribosomal protein S21-A
+Macromolecule #67: 40S ribosomal protein S22-A
+Macromolecule #68: 40S ribosomal protein S23-A
+Macromolecule #69: 40S ribosomal protein S24-A
+Macromolecule #70: 40S ribosomal protein S25-A
+Macromolecule #71: 40S ribosomal protein S26-B
+Macromolecule #72: 40S ribosomal protein S27-A
+Macromolecule #73: 40S ribosomal protein S28-A
+Macromolecule #74: 40S ribosomal protein S29-A
+Macromolecule #75: 40S ribosomal protein S30-A
+Macromolecule #76: 40S ribosomal protein S31
+Macromolecule #77: Guanine nucleotide-binding protein subunit beta-like protein
+Macromolecule #78: Suppressor protein STM1
+Macromolecule #80: 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethy...
+Macromolecule #81: MAGNESIUM ION
+Macromolecule #82: ZINC ION
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.5 |
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| Vitrification | Cryogen name: ETHANE |
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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: 61.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Authors
United States, 1 items
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Processing
FIELD EMISSION GUN
