+Open data
-Basic information
Entry | Database: PDB / ID: 8agu | ||||||
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Title | Yeast RQC complex in state E | ||||||
Components |
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Keywords | TRANSLATION / ribosome-associated quality control / NEMF / Listerin / CAT tailing | ||||||
Function / homology | Function and homology information positive regulation of cytoplasmic translational elongation through polyproline stretches / Hypusine synthesis from eIF5A-lysine / CAT tailing / translational frameshifting / RQC complex / positive regulation of translational termination / positive regulation of translational elongation / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome-associated ubiquitin-dependent protein catabolic process / pre-mRNA 5'-splice site binding ...positive regulation of cytoplasmic translational elongation through polyproline stretches / Hypusine synthesis from eIF5A-lysine / CAT tailing / translational frameshifting / RQC complex / positive regulation of translational termination / positive regulation of translational elongation / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome-associated ubiquitin-dependent protein catabolic process / 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) / translational elongation / response to cycloheximide / maturation of 5.8S rRNA / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / ribosomal large subunit binding / 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 / Antigen processing: Ubiquitination & Proteasome degradation / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / ribosomal large subunit export from nucleus / subtelomeric heterochromatin formation / proteasomal protein catabolic process / positive regulation of translational initiation / regulation of translational fidelity / protein-RNA complex assembly / translation elongation factor activity / ribosomal subunit export from nucleus / cytosolic ribosome / translation initiation factor activity / rescue of stalled ribosome / 90S preribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / assembly of large subunit precursor of preribosome / maturation of LSU-rRNA / cytosolic ribosome assembly / ribosomal large subunit biogenesis / macroautophagy / protein catabolic process / RING-type E3 ubiquitin transferase / ribosomal large subunit assembly / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / ribosome biogenesis / ribosome binding / chromatin organization / 5S rRNA binding / large ribosomal subunit rRNA binding / ubiquitin-dependent protein catabolic process / cytosolic large ribosomal subunit / chromosome, telomeric region / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / nucleolus / perinuclear region of cytoplasm / mitochondrion / RNA binding / zinc ion binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 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 | 8agu.cif.gz | 3.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8agu.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8agu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8agu_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8agu_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8agu_validation.xml.gz | 262.5 KB | Display | |
Data in CIF | 8agu_validation.cif.gz | 464.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/8agu ftp://data.pdbj.org/pub/pdb/validation_reports/ag/8agu | HTTPS FTP |
-Related structure data
Related structure data | 15424MC 8aafC 8agtC 8agvC 8agwC 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 ... , 38 types, 38 molecules ABCDEFGHIJKLMNOPQRSTUVWYbcjkmn...
-Protein , 7 types, 7 molecules XZlsae0
#24: Protein | Mass: 8845.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PUL8 |
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#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 |
#35: Protein | Mass: 39159.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q3W0 |
#42: Protein | Mass: 19755.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q7I9 |
#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 |
#52: 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 |
-Protein/peptide , 2 types, 2 molecules d1
#29: Protein/peptide | Mass: 3354.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A8H8UMB4 |
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#53: Protein/peptide | Mass: 1549.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) |
-RNA chain , 4 types, 4 molecules fhiy
#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 |
#50: RNA chain | Mass: 24502.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) |
-Eukaryotic translation initiation factor ... , 2 types, 2 molecules gv
#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 |
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#48: Protein | Mass: 17222.406 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: P23301 |
-Non-polymers , 3 types, 21 molecules
#54: Chemical | ChemComp-MG / #55: Chemical | ChemComp-ZN / #56: 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 E / Type: RIBOSOME / Entity ID: #1-#53 / 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 FIELD / 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: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44241 / Symmetry type: POINT |