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Yorodumi- PDB-3j78: Structures of yeast 80S ribosome-tRNA complexes in the rotated an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3j78 | |||||||||
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Title | Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class I - non-rotated ribosome with 2 tRNAs) | |||||||||
Components |
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Keywords | RIBOSOME / 80S ribosome / Kozak sequence / translation / tRNA / hybrid-state / classical-state | |||||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.3 Å | |||||||||
Authors | Svidritskiy, E. / Brilot, A.F. / Koh, C.S. / Grigorieff, N. / Korostelev, A.A. | |||||||||
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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3j78.cif.gz | 4.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3j78.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 3j78.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3j78_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 3j78_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 3j78_validation.xml.gz | 447.5 KB | Display | |
Data in CIF | 3j78_validation.cif.gz | 714.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/3j78 ftp://data.pdbj.org/pub/pdb/validation_reports/j7/3j78 | HTTPS FTP |
-Related structure data
Related structure data | 5977MC 5976C 3j77C M: map data used to model this data C: citing same article (ref.) |
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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
-Assembly
Deposited unit |
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1 |
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-Components
+60S ribosomal protein ... , 43 types, 43 molecules L1L2L3L4L5L6L7L8L9606162636465666768697071727374757677787980...
-Protein , 2 types, 2 molecules P0RC
#44: Protein | Mass: 33749.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05317 |
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#45: Protein | Mass: 34841.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38011 |
+40S ribosomal protein ... , 32 types, 32 molecules S0S1S2S3S4S5S6S7S8S910111213141516171819202122232425262728293031
-RNA chain , 6 types, 7 molecules 1S2S8S5SETPTMR
#78: RNA chain | Mass: 579126.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) | ||
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#79: RNA chain | Mass: 1097148.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) | ||
#80: RNA chain | Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) | ||
#81: RNA chain | Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) | ||
#82: RNA chain | Mass: 24802.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) #83: RNA chain | | Mass: 4533.844 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) |
-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: 3.5 MDa / Experimental value: YES | ||||||||||||||||||||
Buffer solution | Name: 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2 / pH: 7.5 / Details: 20 mM Tris-HCl, 50 mM NH4Cl, 20 mM MgCl2 | ||||||||||||||||||||
Specimen | Conc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 95 % / Details: Plunged into liquid ethane (FEI VITROBOT MARK II) |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Jan 2, 2013 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 133333 X / Calibrated magnification: 133333 X / Nominal defocus max: 4844 nm / Nominal defocus min: 1159 nm / Cs: 0.01 mm / Camera length: 0 mm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: FEI FALCON I (4k x 4k) |
Image scans | Num. digital images: 4754 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: CTFFIND3, FREALIGN per micrograph | |||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Method: Projection Matching / Resolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23163 / Nominal pixel size: 1.05 Å / Actual pixel size: 1.05 Å / Details: (Single particle--Applied symmetry: C1) / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: cross-correlation Details: REFINEMENT PROTOCOL--rigid body DETAILS--3U5B, 3U5C, 3U5D, and 3U5E were combined prior to fitting. tRNAs and mRNA were modeled using individual tRNAs and mRNA from the crystal structure ...Details: REFINEMENT PROTOCOL--rigid body DETAILS--3U5B, 3U5C, 3U5D, and 3U5E were combined prior to fitting. tRNAs and mRNA were modeled using individual tRNAs and mRNA from the crystal structure (3I9B) of the classical-state 70S ribosome. The structure of rpL1 was obtained by homology modeling from PDB ID 3J3B. | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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