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Yorodumi- PDB-6woo: CryoEM structure of yeast 80S ribosome with Met-tRNAiMet, eIF5B, ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6woo | |||||||||
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Title | CryoEM structure of yeast 80S ribosome with Met-tRNAiMet, eIF5B, and GDP | |||||||||
Components |
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Keywords | RIBOSOME / yeast / initiation / eIF5B / GDP / Met-tRNAiMet | |||||||||
Function / homology | Function and homology information : / formation of cytoplasmic translation initiation complex / protein-synthesizing GTPase / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / eukaryotic 48S preinitiation complex / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Negative regulators of DDX58/IFIH1 signaling / positive regulation of translational fidelity / Protein methylation ...: / formation of cytoplasmic translation initiation complex / protein-synthesizing GTPase / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / eukaryotic 48S preinitiation complex / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Negative regulators of DDX58/IFIH1 signaling / positive regulation of translational fidelity / Protein methylation / RMTs methylate histone arginines / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / regulation of translational initiation / nonfunctional rRNA decay / 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 / 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) / preribosome, small subunit precursor / 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 / Ub-specific processing proteases / ribosomal subunit export from nucleus / translation regulator activity / ribosomal small subunit export from nucleus / translational termination / 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) / DNA-(apurinic or apyrimidinic site) endonuclease activity / translation initiation factor binding / translation initiation factor activity / 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) / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome assembly / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / translational initiation / macroautophagy / protein kinase C binding / 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 / 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 / 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 Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Wang, J. / Wang, J. / Puglisi, J. / Fernandez, I.S. | |||||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Structural basis for the transition from translation initiation to elongation by an 80S-eIF5B complex. Authors: Jinfan Wang / Jing Wang / Byung-Sik Shin / Joo-Ran Kim / Thomas E Dever / Joseph D Puglisi / Israel S Fernández / Abstract: Recognition of a start codon by the initiator aminoacyl-tRNA determines the reading frame of messenger RNA (mRNA) translation by the ribosome. In eukaryotes, the GTPase eIF5B collaborates in the ...Recognition of a start codon by the initiator aminoacyl-tRNA determines the reading frame of messenger RNA (mRNA) translation by the ribosome. In eukaryotes, the GTPase eIF5B collaborates in the correct positioning of the initiator Met-tRNA on the ribosome in the later stages of translation initiation, gating entrance into elongation. Leveraging the long residence time of eIF5B on the ribosome recently identified by single-molecule fluorescence measurements, we determine the cryoEM structure of the naturally long-lived ribosome complex with eIF5B and Met-tRNA immediately before transition into elongation. The structure uncovers an unexpected, eukaryotic specific and dynamic fidelity checkpoint implemented by eIF5B in concert with components of the large ribosomal subunit. | |||||||||
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 | 6woo.cif.gz | 5.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6woo.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6woo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6woo_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 6woo_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 6woo_validation.xml.gz | 349 KB | Display | |
Data in CIF | 6woo_validation.cif.gz | 601.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wo/6woo ftp://data.pdbj.org/pub/pdb/validation_reports/wo/6woo | HTTPS FTP |
-Related structure data
Related structure data | 21859MC 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 578234
#1: RNA chain | Mass: 1057318.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) |
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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 (brewer's yeast) / References: GenBank: 1039024045 |
#3: RNA chain | Mass: 50376.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1675231216 |
#81: RNA chain | Mass: 578475.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1329886537 |
#83: RNA chain | Mass: 24583.705 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 176433 |
#84: RNA chain | Mass: 1923.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) |
+Protein , 76 types, 76 molecules ABCDEFGHIJLMNOPQRSTUVWXYZabcde...
-Protein/peptide , 2 types, 2 molecules ln
#40: Protein/peptide | Mass: 6114.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04650 |
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#42: Protein/peptide | Mass: 3137.985 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) |
-Non-polymers , 4 types, 9 molecules
#85: Chemical | ChemComp-ZN / #86: Chemical | ChemComp-GDP / | #87: Chemical | ChemComp-U6A / | #88: Chemical | ChemComp-MET / | |
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-Details
Has ligand of interest | N |
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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 | Name: 80S ribosome with eIF5B, Met-tRNAiMet, mRNA, and GDP / Type: RIBOSOME / Entity ID: #1-#84 / Source: NATURAL |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k 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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 107000 / Symmetry type: POINT | ||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||
Atomic model building | PDB-ID: 4V8Y Accession code: 4V8Y / Source name: PDB / Type: experimental model |