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Yorodumi- PDB-6gq1: Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gq1 | |||||||||||||||
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Title | Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP/sordarin) | |||||||||||||||
Components |
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Keywords | RIBOSOME / Eukaryotic 80S riboosme / mRNA-tRNA translocation / diphthamide | |||||||||||||||
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 / Protein methylation / RMTs methylate histone arginines / positive regulation of translational fidelity / mTORC1-mediated signalling ...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 / Protein methylation / RMTs methylate histone arginines / positive regulation of translational fidelity / 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 / 90S preribosome / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 / protein-RNA complex assembly / ribosomal small subunit export from nucleus / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / translation regulator activity / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / 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) / regulation of translational fidelity / positive regulation of protein kinase activity / rescue of stalled ribosome / translational termination / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation elongation factor activity / maturation of LSU-rRNA / ribosomal large subunit biogenesis / DNA-(apurinic or apyrimidinic site) endonuclease activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cellular response to amino acid starvation / Neutrophil degranulation / 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 small subunit biogenesis / small ribosomal subunit rRNA binding / protein tag activity / rRNA processing / ribosomal small subunit assembly / cytoplasmic stress granule / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / ribosome biogenesis / small ribosomal subunit / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / protein-folding chaperone binding / negative regulation of translation / rRNA binding / protein ubiquitination / ribosome / structural constituent of ribosome / positive regulation of protein phosphorylation / translation / ribonucleoprotein complex / 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 / identical protein binding / metal ion binding / nucleus Similarity search - Function | |||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||||||||
Authors | Pellegrino, S. / Demeshkina, N. / Mancera-Martinez, E. / Melnikov, S. / Simonetti, A. / Myasnikov, A. / Yusupov, M. / Yusupova, G. / Hashem, Y. | |||||||||||||||
Funding support | France, 4items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6gq1.cif.gz | 4.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6gq1.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6gq1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/6gq1 ftp://data.pdbj.org/pub/pdb/validation_reports/gq/6gq1 | HTTPS FTP |
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-Related structure data
Related structure data | 0047MC 0048C 0049C 0055C 6gqbC 6gqvC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 6 types, 6 molecules 1342AXAY
#1: RNA chain | Mass: 1097493.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: REF: 831416132 |
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#2: RNA chain | Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: GenBank: 1329886537 |
#3: RNA chain | Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: GenBank: 1358044889 |
#47: RNA chain | Mass: 578820.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: GenBank: 1329886537 |
#81: RNA chain | Mass: 24518.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: GenBank: 176419 |
#82: RNA chain | Mass: 2449.465 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) |
-Protein , 4 types, 4 molecules P0mAVAZ
#4: Protein | Mass: 20929.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P05317 |
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#43: Protein | Mass: 6032.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P0CH08 |
#79: Protein | Mass: 34710.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P38011 |
#83: Protein | Mass: 93318.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P32324 |
+60S ribosomal protein ... , 41 types, 41 molecules P2ABCDEFGHIJLMNOPQRSTUVWXYZabcd...
+40S ribosomal protein ... , 31 types, 31 molecules qrstuvwxyzAAABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAU
-Protein/peptide , 1 types, 1 molecules AW
#80: Protein/peptide | Mass: 4148.841 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P05759 |
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-Non-polymers , 3 types, 10 molecules
#84: Chemical | ChemComp-ZN / #85: Chemical | ChemComp-SO1 / [ | #86: Chemical | ChemComp-GCP / | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight | Value: 3.4 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: synthetic construct (others) | ||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blot force 4, blot waiting time 30 s |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Average exposure time: 1.5 sec. / Electron dose: 60 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 189700 / Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL |