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Yorodumi- EMDB-16702: Translocation intermediate 1 (TI-1*) of 80S S. cerevisiae ribosom... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16702 | |||||||||
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Title | Translocation intermediate 1 (TI-1*) of 80S S. cerevisiae ribosome with ligands and eEF2 in the absence of sordarin | |||||||||
Map data | Locally filtered map | |||||||||
Sample |
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Keywords | Eukaryote / ribosome / translocation / elongation | |||||||||
Function / homology | Function and homology information ribosomal subunit / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Negative regulators of DDX58/IFIH1 signaling / Protein methylation / positive regulation of translational fidelity / RMTs methylate histone arginines / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process ...ribosomal subunit / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Negative regulators of DDX58/IFIH1 signaling / Protein methylation / positive regulation of translational fidelity / RMTs methylate histone arginines / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent 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 / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / protein-RNA complex assembly / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / Ub-specific processing proteases / regulation of translational fidelity / positive regulation of protein kinase 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 subunit export from nucleus / translation regulator activity / translational termination / 90S preribosome / rescue of stalled ribosome / cellular response to amino acid starvation / 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) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / positive regulation of apoptotic signaling pathway / small-subunit processome / protein kinase C binding / maintenance of translational fidelity / macroautophagy / ribosomal large subunit assembly / modification-dependent protein catabolic process / cytoplasmic stress granule / rRNA processing / protein tag activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosome binding / 5S rRNA binding / large ribosomal subunit rRNA binding / small ribosomal subunit / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / 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 / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.11 Å | |||||||||
Authors | Milicevic N / Jenner L / Myasnikov A / Yusupov M / Yusupova G | |||||||||
Funding support | France, 1 items
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Citation | Journal: Nature / Year: 2024 Title: mRNA reading frame maintenance during eukaryotic ribosome translocation. Authors: Nemanja Milicevic / Lasse Jenner / Alexander Myasnikov / Marat Yusupov / Gulnara Yusupova / Abstract: One of the most critical steps of protein synthesis is coupled translocation of messenger RNA (mRNA) and transfer RNAs (tRNAs) required to advance the mRNA reading frame by one codon. In ...One of the most critical steps of protein synthesis is coupled translocation of messenger RNA (mRNA) and transfer RNAs (tRNAs) required to advance the mRNA reading frame by one codon. In eukaryotes, translocation is accelerated and its fidelity is maintained by elongation factor 2 (eEF2). At present, only a few snapshots of eukaryotic ribosome translocation have been reported. Here we report ten high-resolution cryogenic-electron microscopy (cryo-EM) structures of the elongating eukaryotic ribosome bound to the full translocation module consisting of mRNA, peptidyl-tRNA and deacylated tRNA, seven of which also contained ribosome-bound, naturally modified eEF2. This study recapitulates mRNA-tRNA-growing peptide module progression through the ribosome, from the earliest states of eEF2 translocase accommodation until the very late stages of the process, and shows an intricate network of interactions preventing the slippage of the translational reading frame. We demonstrate how the accuracy of eukaryotic translocation relies on eukaryote-specific elements of the 80S ribosome, eEF2 and tRNAs. Our findings shed light on the mechanism of translation arrest by the anti-fungal eEF2-binding inhibitor, sordarin. We also propose that the sterically constrained environment imposed by diphthamide, a conserved eukaryotic posttranslational modification in eEF2, not only stabilizes correct Watson-Crick codon-anticodon interactions but may also uncover erroneous peptidyl-tRNA, and therefore contribute to higher accuracy of protein synthesis in eukaryotes. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16702.map.gz | 12 MB | EMDB map data format | |
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Header (meta data) | emd-16702-v30.xml emd-16702.xml | 104.8 KB 104.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16702_fsc.xml | 14.4 KB | Display | FSC data file |
Images | emd_16702.png | 36.5 KB | ||
Filedesc metadata | emd-16702.cif.gz | 21.1 KB | ||
Others | emd_16702_half_map_1.map.gz emd_16702_half_map_2.map.gz | 302 MB 302 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16702 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16702 | HTTPS FTP |
-Related structure data
Related structure data | 8ckuMC 8ccsC 8cdlC 8cdrC 8cehC 8cf5C 8cg8C 8cgnC 8civC 8cmjC C: citing same article (ref.) M: atomic model generated by this map |
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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_16702.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Locally filtered map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.452 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_16702_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16702_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 80S Saccharomyces cerevisiae ribosome in complex with eEF2 and ligands
+Supramolecule #1: 80S Saccharomyces cerevisiae ribosome in complex with eEF2 and ligands
+Macromolecule #1: 40S ribosomal protein S24-A
+Macromolecule #2: 40S ribosomal protein S25-A
+Macromolecule #3: 40S ribosomal protein S26
+Macromolecule #4: 40S ribosomal protein S27-A
+Macromolecule #5: 40S ribosomal protein S28-A
+Macromolecule #6: HLJ1_G0030400.mRNA.1.CDS.1
+Macromolecule #7: 40S ribosomal protein S30-A
+Macromolecule #8: Guanine nucleotide-binding protein subunit beta-like protein
+Macromolecule #9: Ubiquitin-40S ribosomal protein S31
+Macromolecule #10: 60S ribosomal protein L16-A
+Macromolecule #12: Elongation factor 2
+Macromolecule #13: 60S ribosomal protein L17-A
+Macromolecule #16: 60S ribosomal protein L18-A
+Macromolecule #19: 60S ribosomal protein L19-A
+Macromolecule #20: 60S acidic ribosomal protein P0
+Macromolecule #22: 60S ribosomal protein L20-A
+Macromolecule #23: 60S ribosomal protein L2-A
+Macromolecule #24: 60S ribosomal protein L12-A
+Macromolecule #25: 60S ribosomal protein L21-A
+Macromolecule #26: 60S ribosomal protein L3
+Macromolecule #27: 60S ribosomal protein L22-A
+Macromolecule #28: 60S ribosomal protein L4-A
+Macromolecule #29: 60S ribosomal protein L23-A
+Macromolecule #30: 60S ribosomal protein L5
+Macromolecule #31: 60S ribosomal protein L24-A
+Macromolecule #32: 60S ribosomal protein L6-A
+Macromolecule #33: 60S ribosomal protein L25
+Macromolecule #34: 60S ribosomal protein L7-A
+Macromolecule #35: 60S ribosomal protein L26-A
+Macromolecule #36: 60S ribosomal protein L8-A
+Macromolecule #37: 60S ribosomal protein L27-A
+Macromolecule #38: 60S ribosomal protein L9-A
+Macromolecule #39: 60S ribosomal protein L28
+Macromolecule #40: 60S ribosomal protein L10
+Macromolecule #41: 60S ribosomal protein L29
+Macromolecule #42: 60S ribosomal protein L11-A
+Macromolecule #43: 60S ribosomal protein L30
+Macromolecule #44: 60S ribosomal protein L13-A
+Macromolecule #45: 60S ribosomal protein L31-A
+Macromolecule #46: 60S ribosomal protein L14-A
+Macromolecule #47: 60S ribosomal protein L32
+Macromolecule #48: 60S ribosomal protein L15-A
+Macromolecule #49: 60S ribosomal protein L33-A
+Macromolecule #50: 60S ribosomal protein L34-A
+Macromolecule #51: 60S ribosomal protein L35-A
+Macromolecule #52: 60S ribosomal protein L36-A
+Macromolecule #53: 60S ribosomal protein L37-A
+Macromolecule #54: 60S ribosomal protein L38
+Macromolecule #55: 60S ribosomal protein L39
+Macromolecule #56: Ubiquitin-60S ribosomal protein L40
+Macromolecule #57: RPL41A isoform 1
+Macromolecule #58: 60S ribosomal protein L42-A
+Macromolecule #59: 60S ribosomal protein L43-A
+Macromolecule #61: 40S ribosomal protein S0-A
+Macromolecule #62: 40S ribosomal protein S1-A
+Macromolecule #63: 40S ribosomal protein S2
+Macromolecule #64: RPS3 isoform 1
+Macromolecule #65: 40S ribosomal protein S4-A
+Macromolecule #66: 40S ribosomal protein S5
+Macromolecule #67: 40S ribosomal protein S6-A
+Macromolecule #68: 40S ribosomal protein S7-A
+Macromolecule #69: 40S ribosomal protein S8-A
+Macromolecule #70: 40S ribosomal protein S9-A
+Macromolecule #71: 40S ribosomal protein S10-A
+Macromolecule #72: 40S ribosomal protein S11-A
+Macromolecule #73: 40S ribosomal protein S13
+Macromolecule #74: 40S ribosomal protein S14-A
+Macromolecule #75: 40S ribosomal protein S15
+Macromolecule #76: 40S ribosomal protein S16-A
+Macromolecule #77: 40S ribosomal protein S17-A
+Macromolecule #78: 40S ribosomal protein S18-A
+Macromolecule #79: 40S ribosomal protein S19-A
+Macromolecule #80: 40S ribosomal protein S20
+Macromolecule #81: 40S ribosomal protein S21-A
+Macromolecule #82: 40S ribosomal protein S22-A
+Macromolecule #83: 40S ribosomal protein S23-A
+Macromolecule #11: 25S ribosomal RNA
+Macromolecule #14: 5S ribosomal RNA
+Macromolecule #15: Transfer RNA Phe
+Macromolecule #17: 5.8S ribosomal RNA
+Macromolecule #18: Transfer RNA fMet
+Macromolecule #21: Messenger RNA
+Macromolecule #60: 18S ribosomal RNA
+Macromolecule #84: ZINC ION
+Macromolecule #85: MAGNESIUM ION
+Macromolecule #86: POTASSIUM ION
+Macromolecule #87: SPERMIDINE
+Macromolecule #88: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #89: water
-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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Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |