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Open data
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Basic information
| Entry | Database: PDB / ID: 7b7d | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| Title | Yeast 80S ribosome bound to eEF3 and A/A- and P/P-tRNAs | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Keywords | TRANSLATION / eukaryotic Elongation Factor 3 / eEF3 / YEF3 / Elongation / ABCF | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Function / homology | Function and homology informationcytoplasmic translational elongation / cytoplasmic translational termination / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / Negative regulators of DDX58/IFIH1 signaling / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / RMTs methylate histone arginines / Protein methylation / mTORC1-mediated signalling ...cytoplasmic translational elongation / cytoplasmic translational termination / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / Negative regulators of DDX58/IFIH1 signaling / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / 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 / pre-mRNA 5'-splice site binding / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / nonfunctional rRNA decay / response to cycloheximide / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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) / negative regulation of translational frameshifting / Formation of a pool of free 40S subunits / negative regulation of mRNA splicing, via spliceosome / preribosome, large subunit precursor / positive regulation of protein kinase activity / L13a-mediated translational silencing of Ceruloplasmin expression / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit export from nucleus / translational elongation / G-protein alpha-subunit binding / 90S preribosome / Ub-specific processing proteases / translation elongation factor activity / ribosomal subunit export from nucleus / regulation of translational fidelity / 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) / protein-RNA complex assembly / translational termination / maturation of LSU-rRNA / ribosomal small subunit export from nucleus / translation regulator activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / cytosolic ribosome / rescue of stalled ribosome / cellular response to amino acid starvation / protein kinase C binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / ribosome assembly / 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 / maintenance of translational fidelity / modification-dependent protein catabolic process / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein tag activity / cytoplasmic stress granule / rRNA processing / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / protein ubiquitination / structural constituent of ribosome / ribosome / translation / G protein-coupled receptor signaling pathway / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / nucleolus / ATP hydrolysis activity / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytosol Similarity search - Function | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Biological species | ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Authors | Ranjan, N. / Pochopien, A.A. / Wu, C.C. / Beckert, B. / Blanchet, S. / Green, R. / Rodnina, M.V. / Wilson, D.N. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Funding support | Germany, 4items
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Citation | Journal: To Be PublishedTitle: eEF3 promotes late stages of tRNA translocation including E-tRNA release from the ribosome Authors: Ranjan, N. / Pochopien, A.A. / Wu, C.C. / Beckert, B. / Blanchet, S. / Green, R. / Rodnina, M.V. / Wilson, D.N. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
| History |
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Structure visualization
| Movie |
Movie viewer |
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| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 7b7d.cif.gz | 4.6 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb7b7d.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 7b7d.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 7b7d_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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| Full document | 7b7d_full_validation.pdf.gz | 2.4 MB | Display | |
| Data in XML | 7b7d_validation.xml.gz | 381.7 KB | Display | |
| Data in CIF | 7b7d_validation.cif.gz | 654.5 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/7b7d ftp://data.pdbj.org/pub/pdb/validation_reports/b7/7b7d | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 12081MC M: map data used to model this data C: citing same article ( |
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| Similar structure data |
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Links
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Assembly
| Deposited unit | ![]()
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| 1 |
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Components
-RNA chain , 6 types, 7 molecules 21LALBLCSnSm
| #1: RNA chain | Mass: 570585.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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| #2: RNA chain | Mass: 2206.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #36: RNA chain | Mass: 1041699.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #37: RNA chain | Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #38: RNA chain | Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #80: RNA chain | Mass: 24222.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
+40S ribosomal protein ... , 31 types, 31 molecules PQERASBTUVWCXDYZFGHIJabcdKefMgL
-Protein , 4 types, 4 molecules NOLiEF
| #33: Protein | Mass: 8329.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 204508 / S288c / References: UniProt: P05759 |
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| #34: Protein | Mass: 34151.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 204508 / S288c / References: UniProt: P38011 |
| #76: Protein | Mass: 6032.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 204508 / S288c / References: UniProt: P0CH08 |
| #81: Protein | Mass: 116367.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 204508 / S288c / References: UniProt: P16521 |
+60S ribosomal protein ... , 40 types, 40 molecules LDLELFLGLHLILJLKLLLMLNLOLPLQLRLmLnLoLpLqLrLSLTLULVLWLXLYLZLa...
-Non-polymers , 1 types, 2 molecules 
| #82: Chemical |
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-Details
| Has ligand of interest | N |
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| Has protein modification | Y |
-Experimental details
-Experiment
| Experiment | Method: ELECTRON MICROSCOPY |
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| EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
| Component | Name: Yeast 80S ribosome bound to eEF3 and A/A- and P/P-tRNAs Type: RIBOSOME / Entity ID: #1-#81 / Source: NATURAL |
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| Molecular weight | Experimental value: NO |
| Source (natural) | Organism: ![]() |
| Buffer solution | pH: 6.5 |
| Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
| Vitrification | Cryogen name: ETHANE-PROPANE |
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Electron microscopy imaging
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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| Microscopy | Model: FEI TITAN KRIOS |
| Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
| Electron lens | Mode: BRIGHT FIELD |
| Image recording | Electron dose: 25 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
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Processing
| CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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| 3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45000 / Symmetry type: POINT |
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About Yorodumi






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