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Yorodumi- EMDB-5942: Cryo-EM Map of a yeast ribosome bound to the TSV IRES (Class II) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5942 | |||||||||
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Title | Cryo-EM Map of a yeast ribosome bound to the TSV IRES (Class II) | |||||||||
Map data | Reconstruction of yeast 80S ribosome bound with the Taura Syndrome Virus IRES | |||||||||
Sample |
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Keywords | Translation Initiation / Internal Ribosome Entry Site | |||||||||
Function / homology | Function and homology information 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 / Protein methylation / RMTs methylate histone arginines / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process ...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 / Protein methylation / RMTs methylate histone arginines / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / 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 / 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) / 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 / mRNA binding / ubiquitin protein ligase binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Taura syndrome virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.1 Å | |||||||||
Authors | Koh CS / Brilot AF / Grigorieff N / Korostelev AA | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2014 Title: Taura syndrome virus IRES initiates translation by binding its tRNA-mRNA-like structural element in the ribosomal decoding center. Authors: Cha San Koh / Axel F Brilot / Nikolaus Grigorieff / Andrei A Korostelev / Abstract: In cap-dependent translation initiation, the open reading frame (ORF) of mRNA is established by the placement of the AUG start codon and initiator tRNA in the ribosomal peptidyl (P) site. Internal ...In cap-dependent translation initiation, the open reading frame (ORF) of mRNA is established by the placement of the AUG start codon and initiator tRNA in the ribosomal peptidyl (P) site. Internal ribosome entry sites (IRESs) promote translation of mRNAs in a cap-independent manner. We report two structures of the ribosome-bound Taura syndrome virus (TSV) IRES belonging to the family of Dicistroviridae intergenic IRESs. Intersubunit rotational states differ in these structures, suggesting that ribosome dynamics play a role in IRES translocation. Pseudoknot I of the IRES occupies the ribosomal decoding center at the aminoacyl (A) site in a manner resembling that of the tRNA anticodon-mRNA codon. The structures reveal that the TSV IRES initiates translation by a previously unseen mechanism, which is conceptually distinct from initiator tRNA-dependent mechanisms. Specifically, the ORF of the IRES-driven mRNA is established by the placement of the preceding tRNA-mRNA-like structure in the A site, whereas the 40S P site remains unoccupied during this initial step. | |||||||||
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_5942.map.gz | 253.9 MB | EMDB map data format | |
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Header (meta data) | emd-5942-v30.xml emd-5942.xml | 14.2 KB 14.2 KB | Display Display | EMDB header |
Images | 400_5942.gif 80_5942.gif | 70.5 KB 4.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5942 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5942 | HTTPS FTP |
-Validation report
Summary document | emd_5942_validation.pdf.gz | 346.6 KB | Display | EMDB validaton report |
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Full document | emd_5942_full_validation.pdf.gz | 346.2 KB | Display | |
Data in XML | emd_5942_validation.xml.gz | 7.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5942 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5942 | HTTPS FTP |
-Related structure data
Related structure data | 3j6xMC 5943C 3j6yC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | |
EM raw data | EMPIAR-10015 (Title: Yeast 80S Ribosome-Taura Syndrome Virus IRES complex, Frealign Input Particle Stack Data size: 273.6 Data #1: Frealign input particle stack [picked particles - multiframe - processed]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_5942.map.gz / Format: CCP4 / Size: 276 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of yeast 80S ribosome bound with the Taura Syndrome Virus IRES | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0595 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 with TSV IRES
Entire | Name: Saccharomyces cerevisiae 80S ribosome bound with TSV IRES |
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Components |
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-Supramolecule #1000: Saccharomyces cerevisiae 80S ribosome bound with TSV IRES
Supramolecule | Name: Saccharomyces cerevisiae 80S ribosome bound with TSV IRES type: sample / ID: 1000 / Number unique components: 2 |
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Molecular weight | Experimental: 3.5 MDa / Theoretical: 3.5 MDa |
-Supramolecule #1: 80S ribosome
Supramolecule | Name: 80S 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) / Strain: W303 / synonym: Yeast |
Molecular weight | Experimental: 3.4 MDa / Theoretical: 3.4 MDa |
-Macromolecule #1: Internal Ribosome Entry Site
Macromolecule | Name: Internal Ribosome Entry Site / type: rna / ID: 1 / Name.synonym: IRES / Classification: OTHER / Structure: DOUBLE HELIX / Synthetic?: Yes |
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Source (natural) | Organism: Taura syndrome virus |
Molecular weight | Experimental: 80 KDa / Theoretical: 80 KDa |
Sequence | String: UAGCACCACC CGAUCGUAAA CUCCAUGUAU UGGUUACCCA UCUGCAUCGA AAACUCUCCG AACACUAGGU GCAGUAAGGC UUUCAUGGAG UGGUUUGCUA UUUAGCGUAC GUGUACCAUA GGCAGCCCCA AAAACACGUG UGAGGAGAAA GUCCCAGUCA CUUUGGGCAA ...String: UAGCACCACC CGAUCGUAAA CUCCAUGUAU UGGUUACCCA UCUGCAUCGA AAACUCUCCG AACACUAGGU GCAGUAAGGC UUUCAUGGAG UGGUUUGCUA UUUAGCGUAC GUGUACCAUA GGCAGCCCCA AAAACACGUG UGAGGAGAAA GUCCCAGUCA CUUUGGGCAA AGUAGACAGC CGCGCUUGCG UGGUGGGACU UAAUUAAUGC CUGCUAACCC AGUUGAAAUU GAUAAUUUUG AUACAACAAC |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.044 mg/mL |
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Buffer | pH: 7.5 Details: 45 mM HEPES/KOH, 10 mM MgCl2, 100 mM KCl, 2.5 mM spermine, 2 mM BME, 0.5 U/ul RNasin |
Grid | Details: C-flat 1.2-1.3 400C |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK II / Method: Fresh glow discharge, 7 second blot |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Alignment procedure | Legacy - Astigmatism: Corrected using FEI software bundled with Titan Krios/Cs Corrector. |
Date | Dec 26, 2012 |
Image recording | Category: CCD / Film or detector model: FEI FALCON I (4k x 4k) / Digitization - Sampling interval: 14.0 µm / Number real images: 11498 / Average electron dose: 30 e/Å2 / Bits/pixel: 32 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 132138 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 6.53 µm / Nominal defocus min: 1.15 µm / Nominal magnification: 133333 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: CTFFIND3, FREALIGN per micrograph |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.1 Å / Resolution method: OTHER / Software - Name: EMAN2, IMAGIC, FREALIGN, RSAMPLE, CTFFIND3 / Number images used: 52444 |
-Atomic model buiding 1
Initial model | PDB ID: 3u5b |
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Software | Name: Chimera, CNS |
Details | 1. TSV IRES was modeled with iFoldRNA and ModeRNA programs and then fitted into the cryo-EM map in Chimera. 2. The 80S-IRES complex was refined against the map, using stereochemically restrained real-space refinement in RSRef. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation |
Output model | PDB-3j6x: |
-Atomic model buiding 2
Initial model | PDB ID: 3u5c |
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Software | Name: Chimera, CNS |
Details | 1. TSV IRES was modeled with iFoldRNA and ModeRNA programs and then fitted into the cryo-EM map in Chimera. 2. The 80S-IRES complex was refined against the map, using stereochemically restrained real-space refinement in RSRef. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation |
Output model | PDB-3j6x: |
-Atomic model buiding 3
Initial model | PDB ID: 3u5d |
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Software | Name: Chimera, CNS |
Details | 1. TSV IRES was modeled with iFoldRNA and ModeRNA programs and then fitted into the cryo-EM map in Chimera. 2. The 80S-IRES complex was refined against the map, using stereochemically restrained real-space refinement in RSRef. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation |
Output model | PDB-3j6x: |
-Atomic model buiding 4
Initial model | PDB ID: 3u5e |
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Software | Name: Chimera, CNS |
Details | 1. TSV IRES was modeled with iFoldRNA and ModeRNA programs and then fitted into the cryo-EM map in Chimera. 2. The 80S-IRES complex was refined against the map, using stereochemically restrained real-space refinement in RSRef. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation |
Output model | PDB-3j6x: |