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- EMDB-41002: Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) in... -
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Open data
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Basic information
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Title | Hypomethylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2, GDP, and sordarin, Structure V | |||||||||
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![]() | RNA modification / 2'-O-methylation / IRES initiation / eEF2 / Ribosome | |||||||||
Function / homology | ![]() Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / ribosomal subunit / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process ...Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / ribosomal subunit / Protein methylation / 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 / nonfunctional rRNA decay / response to cycloheximide / 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 translational frameshifting / 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 / Formation of a pool of free 40S subunits / preribosome, large subunit precursor / 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 / positive regulation of protein kinase activity / translation elongation factor activity / ribosomal subunit export from nucleus / regulation of translational fidelity / protein-RNA complex assembly / 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) / maturation of LSU-rRNA / translation regulator activity / rescue of stalled ribosome / Neutrophil degranulation / cellular response to amino acid starvation / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / protein kinase C binding / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / translational initiation / small-subunit processome / macroautophagy / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / cytoplasmic stress granule / rRNA processing / ribosome biogenesis / protein-folding chaperone binding / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small ribosomal subunit rRNA binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / protein ubiquitination / ribosome / structural constituent of ribosome / G protein-coupled receptor signaling pathway / translation / ribonucleoprotein complex / negative regulation of gene expression / response to antibiotic / GTPase activity / mRNA binding / ubiquitin protein ligase binding / GTP binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / metal ion binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.09 Å | |||||||||
![]() | Zhao Y / Li H | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Regulation of Translation by Ribosome RNA 2'-O-Methylation Authors: Zhao Y / Li H | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 230.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 99.5 KB 99.5 KB | Display Display | ![]() |
Images | ![]() | 66.5 KB | ||
Filedesc metadata | ![]() | 20 KB | ||
Others | ![]() ![]() | 226.5 MB 226.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8t3fMC ![]() 8t2yC ![]() 8t30C ![]() 8t3aC ![]() 8t3bC ![]() 8t3cC ![]() 8t3dC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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_41002_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41002_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
+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: 60S ribosomal protein L10
+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 #34: 18S rRNA
+Macromolecule #38: 25S rRNA
+Macromolecule #39: 5s rRNA
+Macromolecule #40: 5.8 S rRNA
+Macromolecule #81: TSV IRES
+Macromolecule #82: ZINC ION
+Macromolecule #83: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #84: MAGNESIUM ION
+Macromolecule #85: [1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA...
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | 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: ![]() |
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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Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49671 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |