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Yorodumi- EMDB-28642: Hypopseudouridylated yeast 80S bound with Taura syndrome virus (T... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28642 | |||||||||
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Title | Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure III | |||||||||
Map data | ||||||||||
Sample |
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Keywords | rRNA pseudouridylation / IRES initiation / confomation / eEF2. / RIBOSOME | |||||||||
Function / homology | Function and homology information ribosomal subunit / Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process ...ribosomal subunit / Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / nonfunctional rRNA decay / 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 / L13a-mediated translational silencing of Ceruloplasmin expression / regulation of cellular amino acid metabolic process / preribosome, large subunit precursor / translational elongation / ribosomal large subunit export from nucleus / 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 / positive regulation of protein kinase activity / protein-RNA complex assembly / regulation of translational fidelity / translation elongation factor activity / ribosomal subunit export from nucleus / 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) / Neutrophil degranulation / maturation of LSU-rRNA / cellular response to amino acid starvation / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / translational initiation / macroautophagy / protein kinase C binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / maintenance of translational fidelity / modification-dependent protein catabolic process / cytoplasmic stress granule / rRNA processing / protein tag activity / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / protein-folding chaperone binding / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / ribonucleoprotein complex / G protein-coupled receptor signaling pathway / negative regulation of gene expression / response to antibiotic / GTPase activity / mRNA binding / ubiquitin protein ligase binding / nucleolus / GTP binding / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Taura syndrome virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.87 Å | |||||||||
Authors | Zhao Y / Rai J / Li H | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Sci Adv / Year: 2023 Title: Regulation of translation by ribosomal RNA pseudouridylation. Authors: Yu Zhao / Jay Rai / Hong Li / Abstract: Pseudouridine is enriched in ribosomal, spliceosomal, transfer, and messenger RNA and thus integral to the central dogma. The chemical basis for how pseudouridine affects the molecular apparatus such ...Pseudouridine is enriched in ribosomal, spliceosomal, transfer, and messenger RNA and thus integral to the central dogma. The chemical basis for how pseudouridine affects the molecular apparatus such as ribosome, however, remains elusive owing to the lack of structures without this natural modification. Here, we studied the translation of a hypopseudouridylated ribosome initiated by the internal ribosome entry site (IRES) elements. We analyzed eight cryo-electron microscopy structures of the ribosome bound with the Taura syndrome virus IRES in multiple functional states. We found widespread loss of pseudouridine-mediated interactions through water and long-range base pairings. In the presence of the translocase, eukaryotic elongation factor 2, and guanosine 5'-triphosphate hydrolysis, the hypopseudouridylated ribosome favors a rare unconducive conformation for decoding that is partially recouped in the ribosome population that remains modified at the P-site uridine. The structural principles learned establish the link between functional defects and modification loss and are likely applicable to other pseudouridine-associated processes. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28642.map.gz | 229.9 MB | EMDB map data format | |
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Header (meta data) | emd-28642-v30.xml emd-28642.xml | 103.5 KB 103.5 KB | Display Display | EMDB header |
Images | emd_28642.png | 121.1 KB | ||
Others | emd_28642_half_map_1.map.gz emd_28642_half_map_2.map.gz | 226.3 MB 226.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28642 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28642 | HTTPS FTP |
-Validation report
Summary document | emd_28642_validation.pdf.gz | 1.3 MB | Display | EMDB validaton report |
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Full document | emd_28642_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | emd_28642_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | emd_28642_validation.cif.gz | 19.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28642 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28642 | HTTPS FTP |
-Related structure data
Related structure data | 8ewbMC 8eubC 8evpC 8evqC 8evrC 8evsC 8evtC 8ewcC 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_28642.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_28642_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_28642_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Hypopseudouridylated ribosome with TSV IRES, eEF2 and GDP
+Supramolecule #1: Hypopseudouridylated ribosome with TSV IRES, eEF2 and GDP
+Macromolecule #1: 40S ribosomal protein S0-A
+Macromolecule #2: RPS1A isoform 1
+Macromolecule #3: RPS2 isoform 1
+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: RPS22A isoform 1
+Macromolecule #14: 40S ribosomal protein S23-A
+Macromolecule #15: 40S ribosomal protein S24-A
+Macromolecule #16: RPS26B isoform 1
+Macromolecule #17: 40S ribosomal protein S27-A
+Macromolecule #18: 40S ribosomal protein S30-A
+Macromolecule #19: RPS3 isoform 1
+Macromolecule #20: Rps5p
+Macromolecule #21: 40S ribosomal protein S10-A
+Macromolecule #22: RPS15 isoform 1
+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: RPS20 isoform 1
+Macromolecule #28: RPS25A isoform 1
+Macromolecule #29: RPS28A isoform 1
+Macromolecule #30: RPS29A isoform 1
+Macromolecule #31: Guanine nucleotide-binding protein subunit beta-like protein
+Macromolecule #32: Ubiquitin-40S ribosomal protein S31
+Macromolecule #33: 40S ribosomal protein S12
+Macromolecule #35: 60S ribosomal protein L2-A
+Macromolecule #36: 60S ribosomal protein L3
+Macromolecule #37: RPL4A isoform 1
+Macromolecule #41: RPL5 isoform 1
+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: RPL10 isoform 1
+Macromolecule #47: RPL11A isoform 1
+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: RPL24A isoform 1
+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: RPL29 isoform 1
+Macromolecule #65: 60S ribosomal protein L30
+Macromolecule #66: 60S ribosomal protein L31-A
+Macromolecule #67: RPL32 isoform 1
+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: RPL38 isoform 1
+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: RPL1A isoform 1
+Macromolecule #80: Elongation factor 2
+Macromolecule #81: 60S acidic ribosomal protein P0
+Macromolecule #34: 18S rRNA
+Macromolecule #38: 25S rRNA
+Macromolecule #39: 5s rRNA
+Macromolecule #40: 5.8 S rRNA
+Macromolecule #82: Taura syndrome virus (TSV) internal ribosome entry site (IRES) RNA
+Macromolecule #83: MAGNESIUM ION
+Macromolecule #84: ZINC ION
+Macromolecule #85: GUANOSINE-5'-DIPHOSPHATE
-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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Sugar embedding | Material: carbon |
Vitrification | Cryogen name: ETHANE |
-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 |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 20205 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |