+Open data
-Basic information
Entry | Database: PDB / ID: 7zw0 | ||||||||||||
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Title | FAP-80S Complex - Rotated state | ||||||||||||
Components |
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Keywords | RIBOSOME / NRD / Ubiquitination / E3 ligase / Quality Control System | ||||||||||||
Function / homology | Function and homology information Calcineurin activates NFAT / regulation of chaperone-mediated protein folding / regulation of homoserine biosynthetic process / macrolide binding / 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 ...Calcineurin activates NFAT / regulation of chaperone-mediated protein folding / regulation of homoserine biosynthetic process / macrolide binding / 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) / protein folding chaperone / 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 / peptidylprolyl isomerase / maturation of SSU-rRNA / peptidyl-prolyl cis-trans isomerase activity / 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 / protein folding / ribosome biogenesis / chromatin organization / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / nucleic acid binding / cytosolic large ribosomal subunit / transcription by RNA polymerase II / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / DNA-binding transcription factor activity / G protein-coupled receptor signaling pathway / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / nucleolus Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae W303 (yeast) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å | ||||||||||||
Authors | Ikeuchi, K. / Buschauer, R. / Berninghausen, O. / Becker, T. / Beckmann, R. | ||||||||||||
Funding support | Germany, European Union, 3items
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Citation | Journal: Mol Cell / Year: 2022 Title: Sensing of individual stalled 80S ribosomes by Fap1 for nonfunctional rRNA turnover. Authors: Sihan Li / Ken Ikeuchi / Misaki Kato / Robert Buschauer / Takato Sugiyama / Shungo Adachi / Hideo Kusano / Tohru Natsume / Otto Berninghausen / Yoshitaka Matsuo / Thomas Becker / Roland ...Authors: Sihan Li / Ken Ikeuchi / Misaki Kato / Robert Buschauer / Takato Sugiyama / Shungo Adachi / Hideo Kusano / Tohru Natsume / Otto Berninghausen / Yoshitaka Matsuo / Thomas Becker / Roland Beckmann / Toshifumi Inada / Abstract: Cells can respond to stalled ribosomes by sensing ribosome collisions and employing quality control pathways. How ribosome stalling is resolved without collisions, however, has remained elusive. ...Cells can respond to stalled ribosomes by sensing ribosome collisions and employing quality control pathways. How ribosome stalling is resolved without collisions, however, has remained elusive. Here, focusing on noncolliding stalling exhibited by decoding-defective ribosomes, we identified Fap1 as a stalling sensor triggering 18S nonfunctional rRNA decay via polyubiquitination of uS3. Ribosome profiling revealed an enrichment of Fap1 at the translation initiation site but also an association with elongating individual ribosomes. Cryo-EM structures of Fap1-bound ribosomes elucidated Fap1 probing the mRNA simultaneously at both the entry and exit channels suggesting an mRNA stasis sensing activity, and Fap1 sterically hinders the formation of canonical collided di-ribosomes. Our findings indicate that individual stalled ribosomes are the potential signal for ribosome dysfunction, leading to accelerated turnover of the ribosome itself. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zw0.cif.gz | 4.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7zw0.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7zw0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zw0_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7zw0_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7zw0_validation.xml.gz | 329.3 KB | Display | |
Data in CIF | 7zw0_validation.cif.gz | 600.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zw/7zw0 ftp://data.pdbj.org/pub/pdb/validation_reports/zw/7zw0 | HTTPS FTP |
-Related structure data
Related structure data | 14990MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 6 types, 7 molecules LA2smslsnLCLD
#1: RNA chain | Mass: 1097493.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) | ||||
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#3: RNA chain | Mass: 579761.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) | ||||
#39: RNA chain | Mass: 9439.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) | ||||
#40: RNA chain | Mass: 24502.477 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) #41: RNA chain | | Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) #42: RNA chain | | Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) |
+60S ribosomal protein ... , 42 types, 43 molecules LBLELFLGLHLILJLKLLLMLNLOLPLQLRLSLTLULVLWLXLYLZLaLbLcLdLeLfLg...
+40S ribosomal protein ... , 30 types, 30 molecules sPsQsRsAsSsBsTsUsVsWsCsXsDsYsZsFsGsHsIsJsasbscsdsKsesfsgsNsL
-Protein , 6 types, 6 molecules sEsMsOsjsksh
#6: Protein | Mass: 16031.907 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: Q01855 |
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#32: Protein | Mass: 6675.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P41057 |
#35: Protein | Mass: 34841.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P38011 |
#37: Protein | Mass: 27164.072 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P40449 |
#38: Protein | Mass: 12169.823 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P20081, peptidylprolyl isomerase |
#84: Protein | Mass: 108662.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: A0A8H4BXZ5 |
-Non-polymers , 3 types, 359 molecules
#85: Chemical | ChemComp-MG / #86: Chemical | ChemComp-SPD / | #87: Chemical | ChemComp-ZN / |
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-Details
Has ligand of interest | N |
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-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 | Name: Fap1-Yil161w-Fpr1-bound yeast 80S ribosome in rotated state Type: RIBOSOME / Entity ID: #1-#84 / Source: NATURAL |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: W303 |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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 / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 43.4 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 114964 / Symmetry type: POINT |