+Open data
-Basic information
Entry | Database: PDB / ID: 8agw | ||||||
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Title | Yeast RQC complex in state D | ||||||
Components |
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Keywords | TRANSLATION / ribosome-associated quality control / NEMF / Listerin / CAT tailing | ||||||
Function / homology | Function and homology information RQC complex / Antigen processing: Ubiquitination & Proteasome degradation / ribosome-associated ubiquitin-dependent protein catabolic process / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to cycloheximide / maturation of 5.8S rRNA / ribosomal subunit export from nucleus / SRP-dependent cotranslational protein targeting to membrane ...RQC complex / Antigen processing: Ubiquitination & Proteasome degradation / ribosome-associated ubiquitin-dependent protein catabolic process / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to cycloheximide / maturation of 5.8S rRNA / ribosomal subunit export from nucleus / SRP-dependent cotranslational protein targeting to membrane / 90S preribosome / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / ribosomal large subunit binding / 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 / protein-RNA complex assembly / subtelomeric heterochromatin formation / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit export from nucleus / regulation of translational fidelity / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / translation initiation factor activity / assembly of large subunit precursor of preribosome / cytosolic ribosome / cytosolic ribosome assembly / proteasomal protein catabolic process / macroautophagy / protein catabolic process / modification-dependent protein catabolic process / RING-type E3 ubiquitin transferase / ribosomal large subunit assembly / protein tag activity / rRNA processing / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / large ribosomal subunit rRNA binding / ribosome biogenesis / cytoplasmic translation / chromatin organization / 5S rRNA binding / cytosolic large ribosomal subunit / ubiquitin-dependent protein catabolic process / negative regulation of translation / chromosome, telomeric region / rRNA binding / protein ubiquitination / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / zinc ion binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å | ||||||
Authors | Tesina, P. / Buschauer, R. / Beckmann, R. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Mol Cell / Year: 2023 Title: Molecular basis of eIF5A-dependent CAT tailing in eukaryotic ribosome-associated quality control. Authors: Petr Tesina / Shuhei Ebine / Robert Buschauer / Matthias Thoms / Yoshitaka Matsuo / Toshifumi Inada / Roland Beckmann / Abstract: Ribosome-associated quality control (RQC) is a conserved process degrading potentially toxic truncated nascent peptides whose malfunction underlies neurodegeneration and proteostasis decline in aging. ...Ribosome-associated quality control (RQC) is a conserved process degrading potentially toxic truncated nascent peptides whose malfunction underlies neurodegeneration and proteostasis decline in aging. During RQC, dissociation of stalled ribosomes is followed by elongation of the nascent peptide with alanine and threonine residues, driven by Rqc2 independently of mRNA, the small ribosomal subunit and guanosine triphosphate (GTP)-hydrolyzing factors. The resulting CAT tails (carboxy-terminal tails) and ubiquitination by Ltn1 mark nascent peptides for proteasomal degradation. Here we present ten cryogenic electron microscopy (cryo-EM) structures, revealing the mechanistic basis of individual steps of the CAT tailing cycle covering initiation, decoding, peptidyl transfer, and tRNA translocation. We discovered eIF5A as a crucial eukaryotic RQC factor enabling peptidyl transfer. Moreover, we observed dynamic behavior of RQC factors and tRNAs allowing for processivity of the CAT tailing cycle without additional energy input. Together, these results elucidate key differences as well as common principles between CAT tailing and canonical translation. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8agw.cif.gz | 3.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8agw.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8agw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/8agw ftp://data.pdbj.org/pub/pdb/validation_reports/ag/8agw | HTTPS FTP |
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-Related structure data
Related structure data | 15426MC 8aafC 8agtC 8aguC 8agvC 8agxC 8agzC 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
+60S ribosomal protein ... , 42 types, 42 molecules ABCDEFGHIJKLMNOPQRSTUVWXYbcdjk...
-Protein , 5 types, 5 molecules Zaeg0
#26: Protein | Mass: 14583.077 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CH08 |
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#45: Protein | Mass: 119250.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A8H4F709 |
#46: Protein | Mass: 180372.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c References: UniProt: Q04781, RING-type E3 ubiquitin transferase |
#47: Protein | Mass: 26476.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q12522 |
#50: 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 |
-RNA chain , 4 types, 5 molecules fhixy
#30: RNA chain | Mass: 1097086.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) |
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#31: RNA chain | Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1329886537 |
#32: RNA chain | Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1331532632 |
#48: RNA chain | Mass: 24502.477 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) |
-Protein/peptide , 1 types, 1 molecules 1
#51: Protein/peptide | Mass: 1464.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) |
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-Non-polymers , 3 types, 21 molecules
#53: Chemical | ChemComp-MG / #54: Chemical | ChemComp-ZN / #55: Chemical | ChemComp-SPD / | |
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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: Yeast RQC complex in state D / Type: RIBOSOME / Entity ID: #1-#52 / Source: NATURAL |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 6.8 |
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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4000 nm / Nominal defocus min: 400 nm |
Image recording | Electron dose: 46 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: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58513 / Symmetry type: POINT |