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Yorodumi- EMDB-47093: Hypopseudouridylated yeast 80S bound with Taura syndrome virus (T... -
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Open data
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Basic information
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| Title | Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B | |||||||||
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Keywords | rRNA pseudouridylation / IRES initiation / confomation / eEF2 / RIBOSOME / hygromycin B | |||||||||
| Function / homology | Function and homology informationribosomal subunit / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / translational readthrough / positive regulation of translational fidelity / RMTs methylate histone arginines / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / positive regulation of protein kinase activity ...ribosomal subunit / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / translational readthrough / positive regulation of translational fidelity / RMTs methylate histone arginines / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / positive regulation of protein kinase activity / ribosome-associated ubiquitin-dependent protein catabolic process / pre-mRNA 5'-splice site binding / GDP-dissociation inhibitor activity / cytosolic large ribosomal subunit assembly / nonfunctional rRNA decay / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / response to cycloheximide / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA destabilization / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of mRNA splicing, via spliceosome / preribosome, large subunit precursor / 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) / L13a-mediated translational silencing of Ceruloplasmin expression / negative regulation of translational frameshifting / translational elongation / ribosomal large subunit export from nucleus / 90S preribosome / G-protein alpha-subunit binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal subunit export from nucleus / regulation of translational fidelity / translational termination / protein-RNA complex assembly / maturation of LSU-rRNA / translation regulator 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 small subunit export from nucleus / DNA-(apurinic or apyrimidinic site) endonuclease activity / rescue of stalled cytosolic ribosome / cellular response to amino acid starvation / protein kinase C binding / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / macroautophagy / 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 / large ribosomal subunit / 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 / 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 / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
| Biological species | ![]() Taura syndrome virus | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.49 Å | |||||||||
Authors | Zhao Y / Li H | |||||||||
| Funding support | United States, 1 items
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Citation | Journal: Sci Adv / Year: 2025Title: Structural basis for hygromycin B inhibition of yeast pseudouridine-deficient ribosomes. Authors: Yu Zhao / Chong Xu / Xin Chen / Hong Jin / Hong Li / ![]() Abstract: Eukaryotic ribosomes are enriched with pseudouridine, particularly at the functional centers targeted by antibiotics. Here, we investigated the roles of pseudouridine in aminoglycoside-mediated ...Eukaryotic ribosomes are enriched with pseudouridine, particularly at the functional centers targeted by antibiotics. Here, we investigated the roles of pseudouridine in aminoglycoside-mediated translation inhibition by comparing the structural and functional properties of the yeast wild-type and the pseudouridine-free ribosomes. We showed that the pseudouridine-free ribosomes have decreased thermostability and high sensitivity to aminoglycosides. When presented with a model internal ribosomal entry site RNA, elongation factor eEF2, GTP (guanosine triphosphate), and sordarin, hygromycin B preferentially binds to the pseudouridine-free ribosomes during initiation by blocking eEF2 binding, stalling ribosomes in a nonrotated conformation. The structures captured hygromycin B bound at the intersubunit bridge B2a enriched with pseudouridine and a deformed codon-anticodon duplex, revealing a functional link between pseudouridine and aminoglycoside inhibition. Our results suggest that pseudouridine enhances both thermostability and conformational fitness of the ribosomes, thereby influencing their susceptibility to aminoglycosides. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_47093.map.gz | 229.9 MB | EMDB map data format | |
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| Header (meta data) | emd-47093-v30.xml emd-47093.xml | 111.7 KB 111.7 KB | Display Display | EMDB header |
| Images | emd_47093.png | 49.5 KB | ||
| Filedesc metadata | emd-47093.cif.gz | 19.7 KB | ||
| Others | emd_47093_half_map_1.map.gz emd_47093_half_map_2.map.gz | 226.3 MB 226.3 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-47093 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-47093 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9dovMC ![]() 9dp7C 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_47093.map.gz / Format: CCP4 / Size: 244.1 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: 1.058 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Half map: #1
| File | emd_47093_half_map_1.map | ||||||||||||
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| Density Histograms |
-Half map: #2
| File | emd_47093_half_map_2.map | ||||||||||||
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| Density Histograms |
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Sample components
+Entire : Hypopseudouridylated ribosome with TSV IRES, eEF2 and GDP
+Supramolecule #1: Hypopseudouridylated ribosome with TSV IRES, eEF2 and GDP
+Supramolecule #2: ribosome
+Supramolecule #3: TSV IRES
+Macromolecule #1: 40S ribosomal protein S0-A
+Macromolecule #2: Small ribosomal subunit protein eS1A
+Macromolecule #3: Small ribosomal subunit protein uS5
+Macromolecule #4: 40S ribosomal protein S4-A
+Macromolecule #5: 40S ribosomal protein S6-A
+Macromolecule #6: 40S ribosomal protein S7-A
+Macromolecule #7: 40S ribosomal protein S8-A
+Macromolecule #8: 40S ribosomal protein S9-A
+Macromolecule #9: 40S ribosomal protein S11-A
+Macromolecule #10: 40S ribosomal protein S13
+Macromolecule #11: 40S ribosomal protein S14-A
+Macromolecule #12: 40S ribosomal protein S21-A
+Macromolecule #13: Small ribosomal subunit protein uS8A
+Macromolecule #14: 40S ribosomal protein S23-A
+Macromolecule #15: 40S ribosomal protein S24-A
+Macromolecule #16: Small ribosomal subunit protein eS26B
+Macromolecule #17: 40S ribosomal protein S27-A
+Macromolecule #18: 40S ribosomal protein S30-A
+Macromolecule #19: Small ribosomal subunit protein uS3
+Macromolecule #20: Rps5p
+Macromolecule #21: 40S ribosomal protein S10-A
+Macromolecule #22: Small ribosomal subunit protein uS19
+Macromolecule #23: 40S ribosomal protein S16-A
+Macromolecule #24: 40S ribosomal protein S17-A
+Macromolecule #25: 40S ribosomal protein S18-A
+Macromolecule #26: 40S ribosomal protein S19-A
+Macromolecule #27: Small ribosomal subunit protein uS10
+Macromolecule #28: Small ribosomal subunit protein eS25A
+Macromolecule #29: Small ribosomal subunit protein eS28A
+Macromolecule #30: Small ribosomal subunit protein uS14A
+Macromolecule #31: Guanine nucleotide-binding protein subunit beta-like protein
+Macromolecule #32: RPS31 isoform 1
+Macromolecule #33: Small ribosomal subunit protein eS12
+Macromolecule #35: 60S ribosomal protein L2-A
+Macromolecule #36: 60S ribosomal protein L3
+Macromolecule #37: Large ribosomal subunit protein uL4A
+Macromolecule #41: Large ribosomal subunit protein uL18
+Macromolecule #42: 60S ribosomal protein L6-A
+Macromolecule #43: 60S ribosomal protein L7-A
+Macromolecule #44: 60S ribosomal protein L8-A
+Macromolecule #45: 60S ribosomal protein L9-A
+Macromolecule #46: Large ribosomal subunit protein uL16
+Macromolecule #47: Large ribosomal subunit protein uL5A
+Macromolecule #48: 60S ribosomal protein L13-A
+Macromolecule #49: 60S ribosomal protein L14-A
+Macromolecule #50: 60S ribosomal protein L15-A
+Macromolecule #51: 60S ribosomal protein L16-A
+Macromolecule #52: 60S ribosomal protein L17-A
+Macromolecule #53: 60S ribosomal protein L18-A
+Macromolecule #54: 60S ribosomal protein L19-A
+Macromolecule #55: 60S ribosomal protein L20
+Macromolecule #56: 60S ribosomal protein L21-A
+Macromolecule #57: 60S ribosomal protein L22-A
+Macromolecule #58: 60S ribosomal protein L23-A
+Macromolecule #59: Large ribosomal subunit protein eL24A
+Macromolecule #60: 60S ribosomal protein L25
+Macromolecule #61: 60S ribosomal protein L26-A
+Macromolecule #62: 60S ribosomal protein L27-A
+Macromolecule #63: 60S ribosomal protein L28
+Macromolecule #64: Large ribosomal subunit protein eL29
+Macromolecule #65: 60S ribosomal protein L30
+Macromolecule #66: 60S ribosomal protein L31-A
+Macromolecule #67: Large ribosomal subunit protein eL32
+Macromolecule #68: 60S ribosomal protein L33-A
+Macromolecule #69: 60S ribosomal protein L34-A
+Macromolecule #70: 60S ribosomal protein L35-A
+Macromolecule #71: 60S ribosomal protein L36-A
+Macromolecule #72: 60S ribosomal protein L37-A
+Macromolecule #73: Large ribosomal subunit protein eL38
+Macromolecule #74: 60S ribosomal protein L39
+Macromolecule #75: Ubiquitin-60S ribosomal protein L40
+Macromolecule #76: 60S ribosomal protein L41-A
+Macromolecule #77: 60S ribosomal protein L42-A
+Macromolecule #78: 60S ribosomal protein L43-A
+Macromolecule #79: Large ribosomal subunit protein uL1A
+Macromolecule #34: 18S rRNA
+Macromolecule #38: 25S rRNA
+Macromolecule #39: 5S rRNA
+Macromolecule #40: 5.8S rRNA
+Macromolecule #80: TSV IRES RNA
+Macromolecule #81: MAGNESIUM ION
+Macromolecule #82: HYGROMYCIN B
+Macromolecule #83: 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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| Sugar embedding | Material: carbon |
| 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: 60.0 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: 2.5 µm / Nominal defocus min: 1.0 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Taura syndrome virus
Authors
United States, 1 items
Citation












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Processing
FIELD EMISSION GUN

