+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15426 | |||||||||
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Title | Yeast RQC complex in state D | |||||||||
Map data | Yeast RQC complex in state D, half map B | |||||||||
Sample |
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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) / baker's yeast (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||
Authors | Tesina P / Buschauer R / Beckmann R | |||||||||
Funding support | Germany, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15426.map.gz | 20.8 MB | EMDB map data format | |
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Header (meta data) | emd-15426-v30.xml emd-15426.xml | 68.3 KB 68.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15426_fsc.xml | 15.6 KB | Display | FSC data file |
Images | emd_15426.png | 62.3 KB | ||
Others | emd_15426_half_map_1.map.gz emd_15426_half_map_2.map.gz | 322.6 MB 322.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15426 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15426 | HTTPS FTP |
-Related structure data
Related structure data | 8agwMC 8aafC 8agtC 8aguC 8agvC 8agxC 8agzC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_15426.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Yeast RQC complex in state D, half map B | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.059 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Yeast RQC complex in state D, half map A
File | emd_15426_half_map_1.map | ||||||||||||
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Annotation | Yeast RQC complex in state D, half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Yeast RQC complex in state D
File | emd_15426_half_map_2.map | ||||||||||||
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Annotation | Yeast RQC complex in state D | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Yeast RQC complex in state D
+Supramolecule #1: Yeast RQC complex in state D
+Macromolecule #1: 60S ribosomal protein L15-A
+Macromolecule #2: 60S ribosomal protein L16-A
+Macromolecule #3: 60S ribosomal protein L17-A
+Macromolecule #4: 60S ribosomal protein L18-A
+Macromolecule #5: 60S ribosomal protein L19-A
+Macromolecule #6: 60S ribosomal protein L20-A
+Macromolecule #7: 60S ribosomal protein L21-A
+Macromolecule #8: 60S ribosomal protein L22-A
+Macromolecule #9: 60S ribosomal protein L23-A
+Macromolecule #10: 60S ribosomal protein L24-A
+Macromolecule #11: 60S ribosomal protein L25
+Macromolecule #12: 60S ribosomal protein L26-A
+Macromolecule #13: 60S ribosomal protein L27-A
+Macromolecule #14: 60S ribosomal protein L28
+Macromolecule #15: 60S ribosomal protein L29
+Macromolecule #16: 60S ribosomal protein L30
+Macromolecule #17: 60S ribosomal protein L31-A
+Macromolecule #18: 60S ribosomal protein L32
+Macromolecule #19: 60S ribosomal protein L33-A
+Macromolecule #20: 60S ribosomal protein L34-A
+Macromolecule #21: 60S ribosomal protein L35-A
+Macromolecule #22: 60S ribosomal protein L36-A
+Macromolecule #23: 60S ribosomal protein L37-A
+Macromolecule #24: 60S ribosomal protein L38
+Macromolecule #25: 60S ribosomal protein L39
+Macromolecule #26: Ubiquitin-60S ribosomal protein L40
+Macromolecule #27: 60S ribosomal protein L42-A
+Macromolecule #28: 60S ribosomal protein L43-A
+Macromolecule #29: 60S ribosomal protein L41-A
+Macromolecule #33: 60S ribosomal protein L2-A
+Macromolecule #34: 60S ribosomal protein L3
+Macromolecule #35: 60S ribosomal protein L4-A
+Macromolecule #36: 60S ribosomal protein L5
+Macromolecule #37: 60S ribosomal protein L6-B
+Macromolecule #38: 60S ribosomal protein L7-A
+Macromolecule #39: 60S ribosomal protein L8-A
+Macromolecule #40: 60S ribosomal protein L9-A
+Macromolecule #41: 60S ribosomal protein L10
+Macromolecule #42: 60S ribosomal protein L11-A
+Macromolecule #43: 60S ribosomal protein L13-A
+Macromolecule #44: 60S ribosomal protein L14-A
+Macromolecule #45: RQC2 isoform 1
+Macromolecule #46: E3 ubiquitin-protein ligase listerin
+Macromolecule #47: Eukaryotic translation initiation factor 6
+Macromolecule #49: 60S ribosomal protein L12-A
+Macromolecule #50: 60S acidic ribosomal protein P0
+Macromolecule #51: CAT-tailed nascent peptide
+Macromolecule #52: 60S ribosomal protein L1-A
+Macromolecule #30: 25S rRNA
+Macromolecule #31: 5S rRNA
+Macromolecule #32: 5.8S rRNA
+Macromolecule #48: Ala tRNA
+Macromolecule #53: MAGNESIUM ION
+Macromolecule #54: ZINC ION
+Macromolecule #55: SPERMIDINE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.4 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 46.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |