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Yorodumi- EMDB-72802: Eukaryotic 80S ribosome with P/P tRNA from uL16 P-site loop mutan... -
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Open data
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Basic information
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| Title | Eukaryotic 80S ribosome with P/P tRNA from uL16 P-site loop mutants in bypass condition | |||||||||
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Keywords | 80S ribosome / Rpl10 loop deletion / RIBOSOME | |||||||||
| Function / homology | Function and homology informationmaturation 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 / RMTs methylate histone arginines / Protein methylation / response to cycloheximide / translational readthrough / mTORC1-mediated signalling / Protein hydroxylation ...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 / RMTs methylate histone arginines / Protein methylation / response to cycloheximide / translational readthrough / mTORC1-mediated signalling / Protein hydroxylation / pre-mRNA 5'-splice site binding / GDP-dissociation inhibitor activity / Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / ascospore wall assembly / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / cytosolic large ribosomal subunit assembly / Ribosomal scanning and start codon recognition / nonfunctional rRNA decay / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / preribosome, small subunit precursor / mRNA destabilization / Major pathway of rRNA processing in the nucleolus and cytosol / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / protein-RNA complex assembly / 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) / preribosome, large subunit precursor / positive regulation of protein kinase activity / L13a-mediated translational silencing of Ceruloplasmin expression / negative regulation of mRNA splicing, via spliceosome / negative regulation of translational frameshifting / ribosomal large subunit export from nucleus / translational elongation / G-protein alpha-subunit binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / ribosomal subunit export from nucleus / translational termination / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity / ribosome-associated ubiquitin-dependent protein catabolic process / maturation of LSU-rRNA / 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 / DNA-(apurinic or apyrimidinic site) endonuclease activity / ribosomal small subunit export from nucleus / cellular response to amino acid starvation / protein kinase C binding / macroautophagy / rescue of stalled cytosolic ribosome / ribosome assembly / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / translational initiation / maintenance of translational fidelity / modification-dependent protein catabolic process / cytoplasmic stress granule / protein tag activity / rRNA processing / cytosolic ribosome / ribosomal small subunit assembly / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / protein ubiquitination / ribosome / translation / structural constituent of ribosome / response to antibiotic / G protein-coupled receptor signaling pathway / negative regulation of gene expression / mRNA binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
| Biological species | ![]() | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.82 Å | |||||||||
Authors | Guan K / Taylor DW | |||||||||
| Funding support | United States, 1 items
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Citation | Journal: To Be PublishedTitle: Cryo-EM structure of 80S ribosomal subunit with Rpl10 loop deletion produced in bypass mutant. P/E, A/P tRNA Authors: Guan K / Taylor DW | |||||||||
| History |
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_72802.map.gz | 413.6 MB | EMDB map data format | |
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| Header (meta data) | emd-72802-v30.xml emd-72802.xml | 98.1 KB 98.1 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_72802_fsc.xml | 19.8 KB | Display | FSC data file |
| Images | emd_72802.png | 84.8 KB | ||
| Filedesc metadata | emd-72802.cif.gz | 18.3 KB | ||
| Others | emd_72802_half_map_1.map.gz emd_72802_half_map_2.map.gz | 763.3 MB 763.2 MB | ||
| Archive directory | https://data.pdbj.org/pub/emdb/structures/EMD-72802 ftp://data.pdbj.org/pub/emdb/structures/EMD-72802 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9ydeMC ![]() 9ydcC ![]() 9yddC 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_72802.map.gz / Format: CCP4 / Size: 824 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: 0.83 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Half map: #2
| File | emd_72802_half_map_1.map | ||||||||||||
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| Density Histograms |
-Half map: #1
| File | emd_72802_half_map_2.map | ||||||||||||
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| Density Histograms |
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Sample components
+Entire : 60S ribosomal subunit with Rpl10 loop deletion produced in bypass...
+Supramolecule #1: 60S ribosomal subunit with Rpl10 loop deletion produced in bypass...
+Macromolecule #1: 25S RNA
+Macromolecule #2: 5S RNA
+Macromolecule #3: 8S RNA
+Macromolecule #4: messenger RNA
+Macromolecule #5: 18S rRNA
+Macromolecule #80: P site tRNA
+Macromolecule #6: 60S ribosomal protein L2-A
+Macromolecule #7: 60S ribosomal protein L3
+Macromolecule #8: 60S ribosomal protein L4-A
+Macromolecule #9: 60S ribosomal protein L5
+Macromolecule #10: Large ribosomal subunit protein eL6B
+Macromolecule #11: 60S ribosomal protein L7-A
+Macromolecule #12: 60S ribosomal protein L8-A
+Macromolecule #13: 60S ribosomal protein L9-A
+Macromolecule #14: Large ribosomal subunit protein uL16
+Macromolecule #15: Large ribosomal subunit protein uL5B
+Macromolecule #16: 60S ribosomal protein L13-A
+Macromolecule #17: 60S ribosomal protein L14-A
+Macromolecule #18: 60S ribosomal protein L15-A
+Macromolecule #19: 60S ribosomal protein L16-A
+Macromolecule #20: 60S ribosomal protein L17-A
+Macromolecule #21: 60S ribosomal protein L18-A
+Macromolecule #22: 60S ribosomal protein L19-A
+Macromolecule #23: 60S ribosomal protein L20-A
+Macromolecule #24: 60S ribosomal protein L21-A
+Macromolecule #25: 60S ribosomal protein L22-A
+Macromolecule #26: 60S ribosomal protein L23-A
+Macromolecule #27: 60S ribosomal protein L24-A
+Macromolecule #28: 60S ribosomal protein L25
+Macromolecule #29: 60S ribosomal protein L26-A
+Macromolecule #30: 60S ribosomal protein L27-A
+Macromolecule #31: 60S ribosomal protein L28
+Macromolecule #32: 60S ribosomal protein L29
+Macromolecule #33: 60S ribosomal protein L30
+Macromolecule #34: 60S ribosomal protein L31-A
+Macromolecule #35: 60S ribosomal protein L32
+Macromolecule #36: 60S ribosomal protein L33-A
+Macromolecule #37: 60S ribosomal protein L34-A
+Macromolecule #38: 60S ribosomal protein L35-A
+Macromolecule #39: 60S ribosomal protein L36-A
+Macromolecule #40: 60S ribosomal protein L37-A
+Macromolecule #41: 60S ribosomal protein L38
+Macromolecule #42: 60S ribosomal protein L39
+Macromolecule #43: Ubiquitin-60S ribosomal protein L40
+Macromolecule #44: 60S ribosomal protein L41-A
+Macromolecule #45: 60S ribosomal protein L42-A
+Macromolecule #46: 60S ribosomal protein L43-A
+Macromolecule #47: 40S ribosomal protein S3
+Macromolecule #48: 40S ribosomal protein S5
+Macromolecule #49: 40S ribosomal protein S10-A
+Macromolecule #50: 40S ribosomal protein S12
+Macromolecule #51: 40S ribosomal protein S15
+Macromolecule #52: 40S ribosomal protein S16-A
+Macromolecule #53: 40S ribosomal protein S17-B
+Macromolecule #54: 40S ribosomal protein S18-A
+Macromolecule #55: 40S ribosomal protein S19-A
+Macromolecule #56: 40S ribosomal protein S20
+Macromolecule #57: 40S ribosomal protein S25-A
+Macromolecule #58: 40S ribosomal protein S28-A
+Macromolecule #59: 40S ribosomal protein S29-A
+Macromolecule #60: Ubiquitin-40S ribosomal protein S31
+Macromolecule #61: Guanine nucleotide-binding protein subunit beta-like protein
+Macromolecule #62: 40S ribosomal protein S0-A
+Macromolecule #63: Small ribosomal subunit protein eS1A
+Macromolecule #64: 40S ribosomal protein S2
+Macromolecule #65: 40S ribosomal protein S4-A
+Macromolecule #66: 40S ribosomal protein S6-A
+Macromolecule #67: 40S ribosomal protein S7-A
+Macromolecule #68: 40S ribosomal protein S8-A
+Macromolecule #69: 40S ribosomal protein S9-A
+Macromolecule #70: 40S ribosomal protein S11-A
+Macromolecule #71: 40S ribosomal protein S13
+Macromolecule #72: 40S ribosomal protein S14-B
+Macromolecule #73: 40S ribosomal protein S21-A
+Macromolecule #74: 40S ribosomal protein S22-A
+Macromolecule #75: 40S ribosomal protein S23-A
+Macromolecule #76: 40S ribosomal protein S24-A
+Macromolecule #77: Small ribosomal subunit protein eS26B
+Macromolecule #78: 40S ribosomal protein S27-A
+Macromolecule #79: 40S ribosomal protein S30-A
+Macromolecule #81: 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethy...
-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 | TFS KRIOS |
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| Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 80.0 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: 2.0 µm / Nominal defocus min: 1.0 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Authors
United States, 1 items
Citation














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Processing
FIELD EMISSION GUN


