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Yorodumi- EMDB-6643: Ensemble cryo-EM uncovers inchworm-like translocation of a viral ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6643 | |||||||||
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Title | Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome | |||||||||
Map data | Saccharomyces cerevisiae 80S ribosome bound to eEF2-GDP-sordarin and TSV IRES, Structure I. For classification, 2D masking around the A site was used, including PKI of the IRES and domain IV of eEF2. | |||||||||
Sample |
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Keywords | cryo-EM / translocation / IRES / ribosome / eEF2 | |||||||||
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 / positive regulation of translational fidelity / RMTs methylate histone arginines / Protein methylation ...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 / positive regulation of translational fidelity / RMTs methylate histone arginines / Protein methylation / 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 / nonfunctional rRNA decay / pre-mRNA 5'-splice site binding / preribosome, small subunit precursor / 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 / response to cycloheximide / 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 / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / negative regulation of mRNA splicing, via spliceosome / preribosome, large subunit precursor / regulation of amino acid metabolic process / L13a-mediated translational silencing of Ceruloplasmin expression / translational elongation / ribosomal large subunit export from nucleus / 90S preribosome / G-protein alpha-subunit binding / positive regulation of protein kinase activity / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity / Ub-specific processing proteases / protein-RNA complex assembly / translation elongation factor activity / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / translational termination / translation regulator 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) / DNA-(apurinic or apyrimidinic site) endonuclease activity / maturation of LSU-rRNA / Neutrophil degranulation / cellular response to amino acid starvation / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / rescue of stalled ribosome / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / translational initiation / macroautophagy / protein kinase C binding / maintenance of translational fidelity / cytoplasmic stress granule / modification-dependent protein catabolic process / protein tag activity / rRNA processing / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosome binding / ribosomal small subunit assembly / protein-folding chaperone binding / large ribosomal subunit rRNA binding / 5S rRNA binding / small ribosomal subunit / cytosolic small ribosomal subunit / ribosomal large subunit assembly / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / translation / ribonucleoprotein complex / 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 Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Taura syndrome virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Abeyrathne PD / Koh CS / Grant T / Grigorieff N / Korostelev AA | |||||||||
Citation | Journal: Elife / Year: 2016 Title: Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome. Authors: Priyanka D Abeyrathne / Cha San Koh / Timothy Grant / Nikolaus Grigorieff / Andrei A Korostelev / Abstract: Internal ribosome entry sites (IRESs) mediate cap-independent translation of viral mRNAs. Using electron cryo-microscopy of a single specimen, we present five ribosome structures formed with the ...Internal ribosome entry sites (IRESs) mediate cap-independent translation of viral mRNAs. Using electron cryo-microscopy of a single specimen, we present five ribosome structures formed with the Taura syndrome virus IRES and translocase eEF2•GTP bound with sordarin. The structures suggest a trajectory of IRES translocation, required for translation initiation, and provide an unprecedented view of eEF2 dynamics. The IRES rearranges from extended to bent to extended conformations. This inchworm-like movement is coupled with ribosomal inter-subunit rotation and 40S head swivel. eEF2, attached to the 60S subunit, slides along the rotating 40S subunit to enter the A site. Its diphthamide-bearing tip at domain IV separates the tRNA-mRNA-like pseudoknot I (PKI) of the IRES from the decoding center. This unlocks 40S domains, facilitating head swivel and biasing IRES translocation via hitherto-elusive intermediates with PKI captured between the A and P sites. The structures suggest missing links in our understanding of tRNA translocation. | |||||||||
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_6643.map.gz | 163.5 MB | EMDB map data format | |
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Header (meta data) | emd-6643-v30.xml emd-6643.xml | 11.6 KB 11.6 KB | Display Display | EMDB header |
Images | 400_6643.gif 80_6643.gif | 77.5 KB 4.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6643 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6643 | HTTPS FTP |
-Validation report
Summary document | emd_6643_validation.pdf.gz | 389.9 KB | Display | EMDB validaton report |
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Full document | emd_6643_full_validation.pdf.gz | 389.5 KB | Display | |
Data in XML | emd_6643_validation.xml.gz | 7.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6643 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6643 | HTTPS FTP |
-Related structure data
Related structure data | 5juoMC 6644C 6645C 6646C 6647C 6648C 6649C 6650C 6651C 6652C 6653C 5jupC 5jusC 5jutC 5juuC M: atomic model generated by this map C: citing same article (ref.) |
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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_6643.map.gz / Format: CCP4 / Size: 500 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Saccharomyces cerevisiae 80S ribosome bound to eEF2-GDP-sordarin and TSV IRES, Structure I. For classification, 2D masking around the A site was used, including PKI of the IRES and domain IV of eEF2. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 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 : Saccharomyces cerevisiae 80S ribosome bound to elongation factor ...
Entire | Name: Saccharomyces cerevisiae 80S ribosome bound to elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure I |
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Components |
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-Supramolecule #1000: Saccharomyces cerevisiae 80S ribosome bound to elongation factor ...
Supramolecule | Name: Saccharomyces cerevisiae 80S ribosome bound to elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure I type: sample / ID: 1000 / Number unique components: 3 |
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Molecular weight | Theoretical: 3.2 MDa |
-Supramolecule #1: Ribosome
Supramolecule | Name: Ribosome / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-eukaryote: ALL |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Yeast |
Molecular weight | Theoretical: 3.2 MDa |
-Macromolecule #1: Internal Ribosome Entry Site
Macromolecule | Name: Internal Ribosome Entry Site / type: rna / ID: 1 / Name.synonym: IRES / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: Yes |
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Source (natural) | Organism: Taura syndrome virus |
Molecular weight | Theoretical: 80 KDa |
-Macromolecule #2: eukaryotic elongation factor 2
Macromolecule | Name: eukaryotic elongation factor 2 / type: protein_or_peptide / ID: 2 / Name.synonym: eEF2 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Yeast |
Molecular weight | Theoretical: 94 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL |
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Grid | Details: Quantifoil Cu 200 mesh |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 103 K / Instrument: FEI VITROBOT MARK II |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 120,000 times magnification. Legacy - Electron beam tilt params: 0 |
Details | 10 electrons/physical pixel/second |
Date | Nov 11, 2015 |
Image recording | Category: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Sampling interval: 5 µm / Number real images: 2662 / Average electron dose: 70 e/Å2 Details: Images recorded as movies in super-resolution mode. Bits/pixel: 8 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 30487 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 18000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | FREALIGN |
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CTF correction | Details: Each particle |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: OTHER / Software - Name: Unblur, CTFFIND4, FREALIGN Details: The highest resolution included in the refinement was 7 Angstrom. Number images used: 1105737 |