+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5976 | |||||||||
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Title | Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class II - 1 tRNA in rotated conformation) | |||||||||
Map data | Reconstruction of a yeast 80S ribosome in the rotated state with 1 tRNA bound. (Class II) | |||||||||
Sample |
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Keywords | 80S ribosome / Kozak sequence / translation | |||||||||
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) / Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.2 Å | |||||||||
Authors | Svidritskiy E / Brilot AF / Koh CS / Grigorieff N / Korostelev AA | |||||||||
Citation | Journal: Structure / Year: 2014 Title: Structures of yeast 80S ribosome-tRNA complexes in the rotated and nonrotated conformations. Authors: Egor Svidritskiy / Axel F Brilot / Cha San Koh / Nikolaus Grigorieff / Andrei A Korostelev / Abstract: The structural understanding of eukaryotic translation lags behind that of translation on bacterial ribosomes. Here, we present two subnanometer resolution structures of S. cerevisiae 80S ribosome ...The structural understanding of eukaryotic translation lags behind that of translation on bacterial ribosomes. Here, we present two subnanometer resolution structures of S. cerevisiae 80S ribosome complexes formed with either one or two tRNAs and bound in response to an mRNA fragment containing the Kozak consensus sequence. The ribosomes adopt two globally different conformations that are related to each other by the rotation of the small subunit. Comparison with bacterial ribosome complexes reveals that the global structures and modes of intersubunit rotation of the yeast ribosome differ significantly from those in the bacterial counterpart, most notably in the regions involving the tRNA, small ribosomal subunit, and conserved helix 69 of the large ribosomal subunit. The structures provide insight into ribosome dynamics implicated in tRNA translocation and help elucidate the role of the Kozak fragment in positioning an open reading frame during translation initiation 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_5976.map.gz | 161.4 MB | EMDB map data format | |
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Header (meta data) | emd-5976-v30.xml emd-5976.xml | 16.1 KB 16.1 KB | Display Display | EMDB header |
Images | 400_5976.gif 80_5976.gif | 60.9 KB 4.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5976 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5976 | HTTPS FTP |
-Validation report
Summary document | emd_5976_validation.pdf.gz | 377.5 KB | Display | EMDB validaton report |
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Full document | emd_5976_full_validation.pdf.gz | 377.1 KB | Display | |
Data in XML | emd_5976_validation.xml.gz | 6.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5976 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5976 | HTTPS FTP |
-Related structure data
Related structure data | 3j77MC 5977C 3j78C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | |
EM raw data | EMPIAR-10016 (Title: Yeast 80S Ribosome - tRNA- Kozak mRNA complexes, Frealign Input Particle Stack Data size: 42.0 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_5976.map.gz / Format: CCP4 / Size: 173.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of a yeast 80S ribosome in the rotated state with 1 tRNA bound. (Class II) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 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 bound to mRNA containing Kozak sequence and to one tRNA
Entire | Name: 80S ribosome bound to mRNA containing Kozak sequence and to one tRNA |
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Components |
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-Supramolecule #1000: 80S ribosome bound to mRNA containing Kozak sequence and to one tRNA
Supramolecule | Name: 80S ribosome bound to mRNA containing Kozak sequence and to one tRNA type: sample / ID: 1000 / Details: Sample was monodisperse. / Number unique components: 3 |
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Molecular weight | Experimental: 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) / synonym: Yeast |
Molecular weight | Experimental: 3.5 MDa |
-Macromolecule #1: mRNA
Macromolecule | Name: mRNA / type: rna / ID: 1 / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 5 KDa |
Sequence | String: AAAAAUGUAA AAAA |
-Macromolecule #2: transfer RNA
Macromolecule | Name: transfer RNA / type: rna / ID: 2 / Name.synonym: tRNA / Details: tRNA fmet / Classification: TRANSFER / Structure: OTHER / Synthetic?: No |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 25 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.2 mg/mL |
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Buffer | pH: 7.5 Details: 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2, 0.3 U/uL RNasin |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK II |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Jan 2, 2013 |
Image recording | Category: CCD / Film or detector model: FEI FALCON I (4k x 4k) / Digitization - Sampling interval: 14 µm / Number real images: 4754 / Average electron dose: 30 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 133333 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 4.844 µm / Nominal defocus min: 1.159 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: 6.2 Å / Resolution method: OTHER / Software - Name: EMAN2, IMAGIC, FREALIGN, RSAMPLE, CTFFIND3 / Number images used: 25136 |
-Atomic model buiding 1
Initial model | PDB ID: 3u5b |
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Software | Name: Chimera, CNS |
Details | 3U5B, 3U5C, 3U5D, and 3U5E were combined prior to fitting. tRNA and mRNA were modeled using individual tRNA and mRNA from the crystal structure (4GD1) of the hybrid-state 70S ribosome containing P/E tRNA. The structure of rpL1 was obtained by homology modeling from PDB ID 3J3B. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: cross-correlation |
Output model | PDB-3j77: |
-Atomic model buiding 2
Initial model | PDB ID: 3u5c |
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Software | Name: Chimera, CNS |
Details | 3U5B, 3U5C, 3U5D, and 3U5E were combined prior to fitting. tRNA and mRNA were modeled using individual tRNA and mRNA from the crystal structure (4GD1) of the hybrid-state 70S ribosome containing P/E tRNA. The structure of rpL1 was obtained by homology modeling from PDB ID 3J3B. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: cross-correlation |
Output model | PDB-3j77: |
-Atomic model buiding 3
Initial model | PDB ID: 3u5d |
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Software | Name: Chimera, CNS |
Details | 3U5B, 3U5C, 3U5D, and 3U5E were combined prior to fitting. tRNA and mRNA were modeled using individual tRNA and mRNA from the crystal structure (4GD1) of the hybrid-state 70S ribosome containing P/E tRNA. The structure of rpL1 was obtained by homology modeling from PDB ID 3J3B. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: cross-correlation |
Output model | PDB-3j77: |
-Atomic model buiding 4
Initial model | PDB ID: 3u5e |
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Software | Name: Chimera, CNS |
Details | 3U5B, 3U5C, 3U5D, and 3U5E were combined prior to fitting. tRNA and mRNA were modeled using individual tRNA and mRNA from the crystal structure (4GD1) of the hybrid-state 70S ribosome containing P/E tRNA. The structure of rpL1 was obtained by homology modeling from PDB ID 3J3B. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: cross-correlation |
Output model | PDB-3j77: |
-Atomic model buiding 5
Initial model | PDB ID: 4gd1 Chain - #0 - Chain ID: V / Chain - #1 - Chain ID: X |
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Software | Name: Chimera, CNS |
Details | 3U5B, 3U5C, 3U5D, and 3U5E were combined prior to fitting. tRNA and mRNA were modeled using individual tRNA and mRNA from the crystal structure (4GD1) of the hybrid-state 70S ribosome containing P/E tRNA. The structure of rpL1 was obtained by homology modeling from PDB ID 3J3B. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: cross-correlation |
Output model | PDB-3j77: |
-Atomic model buiding 6
Initial model | PDB ID: 3j3b |
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Software | Name: Chimera, CNS |
Details | 3U5B, 3U5C, 3U5D, and 3U5E were combined prior to fitting. tRNA and mRNA were modeled using individual tRNA and mRNA from the crystal structure (4GD1) of the hybrid-state 70S ribosome containing P/E tRNA. The structure of rpL1 was obtained by homology modeling from PDB ID 3J3B. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: cross-correlation |
Output model | PDB-3j77: |