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Yorodumi- EMDB-0049: Cryo-EM recosntruction of yeast 80S ribosome in complex with mRNA... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0049 | |||||||||
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Title | Cryo-EM recosntruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP) | |||||||||
Map data | None | |||||||||
Sample |
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Function / homology | Function and homology information Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / 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 ...Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / 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 / ribosome-associated ubiquitin-dependent protein catabolic process / Protein hydroxylation / GDP-dissociation inhibitor activity / pre-mRNA 5'-splice site binding / 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 / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / translational elongation / 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) / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of mRNA splicing, via spliceosome / ribosomal small subunit export from nucleus / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / translation regulator activity / 90S preribosome / protein-RNA complex assembly / ribosomal large subunit export from nucleus / Ub-specific processing proteases / G-protein alpha-subunit binding / 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 elongation factor activity / translational termination / rescue of stalled ribosome / 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 SSU-rRNA / ribosomal large subunit biogenesis / DNA-(apurinic or apyrimidinic site) endonuclease activity / maturation of LSU-rRNA / Neutrophil degranulation / cellular response to amino acid starvation / ribosome assembly / small-subunit processome / protein kinase C binding / maintenance of translational fidelity / macroautophagy / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / modification-dependent protein catabolic process / ribosomal large subunit assembly / rRNA processing / ribosomal small subunit biogenesis / protein tag activity / small ribosomal subunit rRNA binding / cytoplasmic stress granule / ribosomal small subunit assembly / ribosome binding / ribosome biogenesis / large ribosomal subunit rRNA binding / small ribosomal subunit / cytosolic small ribosomal subunit / 5S rRNA binding / protein-folding chaperone binding / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / protein ubiquitination / ribosome / structural constituent of ribosome / ribonucleoprotein complex / positive regulation of protein phosphorylation / translation / G protein-coupled receptor signaling pathway / response to antibiotic / negative regulation of gene expression / mRNA binding / GTPase activity / ubiquitin protein ligase binding / GTP binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Baker's yeast (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Pellegrino S / Yusupov M / Yusupova G / Hashem Y | |||||||||
Citation | Journal: J Mol Biol / Year: 2018 Title: Structural Insights into the Role of Diphthamide on Elongation Factor 2 in mRNA Reading-Frame Maintenance. Authors: Simone Pellegrino / Natalia Demeshkina / Eder Mancera-Martinez / Sergey Melnikov / Angelita Simonetti / Alexander Myasnikov / Marat Yusupov / Gulnara Yusupova / Yaser Hashem / Abstract: One of the most critical steps of protein biosynthesis is the coupled movement of mRNA, which encodes genetic information, with tRNAs on the ribosome. In eukaryotes, this process is catalyzed by a ...One of the most critical steps of protein biosynthesis is the coupled movement of mRNA, which encodes genetic information, with tRNAs on the ribosome. In eukaryotes, this process is catalyzed by a conserved G-protein, the elongation factor 2 (eEF2), which carries a unique post-translational modification, called diphthamide, found in all eukaryotic species. Here we present near-atomic resolution cryo-electron microscopy structures of yeast 80S ribosome complexes containing mRNA, tRNA and eEF2 trapped in different GTP-hydrolysis states which provide further structural insights into the role of diphthamide in the mechanism of translation fidelity in eukaryotes. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0049.map.gz | 20.5 MB | EMDB map data format | |
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Header (meta data) | emd-0049-v30.xml emd-0049.xml | 103.6 KB 103.6 KB | Display Display | EMDB header |
Images | emd_0049.png | 275.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0049 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0049 | HTTPS FTP |
-Related structure data
Related structure data | 6gqvMC 0047C 0048C 0055C 6gq1C 6gqbC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0049.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : 80S ribosome in complex with mRNA, tRNA and eEF2 in presence of n...
+Supramolecule #1: 80S ribosome in complex with mRNA, tRNA and eEF2 in presence of n...
+Supramolecule #2: 80S ribosome
+Supramolecule #3: mRNA
+Macromolecule #1: 25S ribosomal RNA
+Macromolecule #2: 5S ribosomal RNA
+Macromolecule #3: 5.8S ribosomal RNA
+Macromolecule #47: 18S ribosomal RNA
+Macromolecule #82: Transfer RNA - Phe
+Macromolecule #83: Messenger RNA
+Macromolecule #4: 60S acidic ribosomal protein P0
+Macromolecule #5: 60S ribosomal protein L12-A
+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: 60S ribosomal protein L6-A
+Macromolecule #11: 60S ribosomal protein L7-A
+Macromolecule #12: 60S ribosomal protein L8-A
+Macromolecule #13: 60S ribosomal protein L9-A
+Macromolecule #14: 60S ribosomal protein L10
+Macromolecule #15: 60S ribosomal protein L11-B
+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-B
+Macromolecule #45: 60S ribosomal protein L42-A
+Macromolecule #46: 60S ribosomal protein L43-A
+Macromolecule #48: 40S ribosomal protein S0-A
+Macromolecule #49: 40S ribosomal protein S1-A
+Macromolecule #50: 40S ribosomal protein S2
+Macromolecule #51: 40S ribosomal protein S3
+Macromolecule #52: 40S ribosomal protein S4-A
+Macromolecule #53: 40S ribosomal protein S5
+Macromolecule #54: 40S ribosomal protein S6-A
+Macromolecule #55: 40S ribosomal protein S7-A
+Macromolecule #56: 40S ribosomal protein S8-A
+Macromolecule #57: 40S ribosomal protein S9-A
+Macromolecule #58: 40S ribosomal protein S10-A
+Macromolecule #59: 40S ribosomal protein S11-A
+Macromolecule #60: 40S ribosomal protein S12
+Macromolecule #61: 40S ribosomal protein S13
+Macromolecule #62: 40S ribosomal protein S14-B
+Macromolecule #63: 40S ribosomal protein S15
+Macromolecule #64: 40S ribosomal protein S16-A
+Macromolecule #65: 40S ribosomal protein S17-B
+Macromolecule #66: 40S ribosomal protein S18-A
+Macromolecule #67: 40S ribosomal protein S19-A
+Macromolecule #68: 40S ribosomal protein S20
+Macromolecule #69: 40S ribosomal protein S21-A
+Macromolecule #70: 40S ribosomal protein S22-A
+Macromolecule #71: 40S ribosomal protein S23-A
+Macromolecule #72: 40S ribosomal protein S24-A
+Macromolecule #73: 40S ribosomal protein S25-A
+Macromolecule #74: 40S ribosomal protein S26-B
+Macromolecule #75: 40S ribosomal protein S27-A
+Macromolecule #76: 40S ribosomal protein S28-A
+Macromolecule #77: 40S ribosomal protein S29-A
+Macromolecule #78: 40S ribosomal protein S30-A
+Macromolecule #79: Guanine nucleotide-binding protein subunit beta-like protein
+Macromolecule #80: Ubiquitin-40S ribosomal protein S31
+Macromolecule #81: Elongation factor 2
+Macromolecule #84: 60S ribosomal protein L1-A
+Macromolecule #85: ZINC ION
+Macromolecule #86: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot force 4, blot waiting time 30 s. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average exposure time: 1.5 sec. / Average electron dose: 60.0 e/Å2 |
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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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 86500 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER |
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Output model | PDB-6gqv: |