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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-10315 | |||||||||
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Title | The cryo-EM structure of SDD1-stalled collided trisome. | |||||||||
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Function / homology | ![]() 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 ...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) / 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 / maturation of SSU-rRNA / 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 / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
![]() | Tesina P / Buschauer R / Cheng J / Becker T / Beckmann R | |||||||||
Funding support | ![]()
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![]() | ![]() Title: RQT complex dissociates ribosomes collided on endogenous RQC substrate SDD1. Authors: Yoshitaka Matsuo / Petr Tesina / Shizuka Nakajima / Masato Mizuno / Akinori Endo / Robert Buschauer / Jingdong Cheng / Okuto Shounai / Ken Ikeuchi / Yasushi Saeki / Thomas Becker / Roland ...Authors: Yoshitaka Matsuo / Petr Tesina / Shizuka Nakajima / Masato Mizuno / Akinori Endo / Robert Buschauer / Jingdong Cheng / Okuto Shounai / Ken Ikeuchi / Yasushi Saeki / Thomas Becker / Roland Beckmann / Toshifumi Inada / ![]() ![]() Abstract: Ribosome-associated quality control (RQC) represents a rescue pathway in eukaryotic cells that is triggered upon translational stalling. Collided ribosomes are recognized for subsequent dissociation ...Ribosome-associated quality control (RQC) represents a rescue pathway in eukaryotic cells that is triggered upon translational stalling. Collided ribosomes are recognized for subsequent dissociation followed by degradation of nascent peptides. However, endogenous RQC-inducing sequences and the mechanism underlying the ubiquitin-dependent ribosome dissociation remain poorly understood. Here, we identified SDD1 messenger RNA from Saccharomyces cerevisiae as an endogenous RQC substrate and reveal the mechanism of its mRNA-dependent and nascent peptide-dependent translational stalling. In vitro translation of SDD1 mRNA enabled the reconstitution of Hel2-dependent polyubiquitination of collided disomes and, preferentially, trisomes. The distinct trisome architecture, visualized using cryo-EM, provides the structural basis for the more-efficient recognition by Hel2 compared with that of disomes. Subsequently, the Slh1 helicase subunit of the RQC trigger (RQT) complex preferentially dissociates the first stalled polyubiquitinated ribosome in an ATP-dependent manner. Together, these findings provide fundamental mechanistic insights into RQC and its physiological role in maintaining cellular protein homeostasis. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 110.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 93.1 KB 93.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() ![]() ![]() | 16 KB 16 KB 16 KB | Display Display Display | ![]() |
Images | ![]() | 81.3 KB | ||
Others | ![]() ![]() ![]() | 149.8 MB 160.4 MB 155.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6sv4MC ![]() 6sntC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.084 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: First stalled ribosome of the trisome (focus-refined)
File | emd_10315_additional_1.map | ||||||||||||
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Annotation | First stalled ribosome of the trisome (focus-refined) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Third stalled ribosome of the trisome (focus-refined)
File | emd_10315_additional_2.map | ||||||||||||
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Annotation | Third stalled ribosome of the trisome (focus-refined) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Second stalled ribosome of the trisome (focus-refined)
File | emd_10315_additional_3.map | ||||||||||||
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Annotation | Second stalled ribosome of the trisome (focus-refined) | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Trisome assembly of yeast collided ribosomes
+Supramolecule #1: Trisome assembly of yeast collided ribosomes
+Macromolecule #1: 25S rRNA
+Macromolecule #2: 5S rRNA
+Macromolecule #3: 5.8S rRNA
+Macromolecule #18: 18S rRNA
+Macromolecule #80: tRNA (P/P)
+Macromolecule #81: tRNA (A/P)
+Macromolecule #82: tRNA (P/E)
+Macromolecule #4: 60S ribosomal protein L2-A
+Macromolecule #5: 60S ribosomal protein L3
+Macromolecule #6: 60S ribosomal protein L4-A
+Macromolecule #7: 60S ribosomal protein L5
+Macromolecule #8: 60S ribosomal protein L6-A
+Macromolecule #9: 60S ribosomal protein L7-A
+Macromolecule #10: 60S ribosomal protein L8-A
+Macromolecule #11: 60S ribosomal protein L9-A
+Macromolecule #12: 60S ribosomal protein L10
+Macromolecule #13: 60S ribosomal protein L11-A
+Macromolecule #14: 60S ribosomal protein L13-A
+Macromolecule #15: 60S ribosomal protein L14-A
+Macromolecule #16: 60S ribosomal protein L15-A
+Macromolecule #17: 60S ribosomal protein L16-A
+Macromolecule #19: 40S ribosomal protein S0-A
+Macromolecule #20: 40S ribosomal protein S1-A
+Macromolecule #21: 40S ribosomal protein S2
+Macromolecule #22: 40S ribosomal protein S3
+Macromolecule #23: 40S ribosomal protein S4-A
+Macromolecule #24: Rps5p
+Macromolecule #25: 40S ribosomal protein S6-A
+Macromolecule #26: 40S ribosomal protein S7-A
+Macromolecule #27: 40S ribosomal protein S8-A
+Macromolecule #28: 40S ribosomal protein S9-A
+Macromolecule #29: 40S ribosomal protein S10-A
+Macromolecule #30: 40S ribosomal protein S11-A
+Macromolecule #31: 40S ribosomal protein S12
+Macromolecule #32: 40S ribosomal protein S13
+Macromolecule #33: 40S ribosomal protein S14-A
+Macromolecule #34: 40S ribosomal protein S15
+Macromolecule #35: 40S ribosomal protein S16-A
+Macromolecule #36: 40S ribosomal protein S17-B
+Macromolecule #37: 40S ribosomal protein S18-A
+Macromolecule #38: 40S ribosomal protein S19-A
+Macromolecule #39: 40S ribosomal protein S20
+Macromolecule #40: 40S ribosomal protein S21-A
+Macromolecule #41: 40S ribosomal protein S22-A
+Macromolecule #42: 40S ribosomal protein S23-A
+Macromolecule #43: 40S ribosomal protein S24-A
+Macromolecule #44: 40S ribosomal protein S25-A
+Macromolecule #45: 40S ribosomal protein S26-A
+Macromolecule #46: 40S ribosomal protein S27-A
+Macromolecule #47: 40S ribosomal protein S28-B
+Macromolecule #48: 40S ribosomal protein S29-A
+Macromolecule #49: 40S ribosomal protein S30-A
+Macromolecule #50: Ubiquitin-40S ribosomal protein S31
+Macromolecule #51: Guanine nucleotide-binding protein subunit beta-like protein
+Macromolecule #52: 60S ribosomal protein L17-A
+Macromolecule #53: 60S ribosomal protein L18-A
+Macromolecule #54: 60S ribosomal protein L19-A
+Macromolecule #55: 60S ribosomal protein L20-A
+Macromolecule #56: 60S ribosomal protein L21-A
+Macromolecule #57: 60S ribosomal protein L22-A
+Macromolecule #58: 60S ribosomal protein L23-A
+Macromolecule #59: 60S ribosomal protein L24-A
+Macromolecule #60: 60S ribosomal protein L25
+Macromolecule #61: 60S ribosomal protein L26-A
+Macromolecule #62: 60S ribosomal protein L27-A
+Macromolecule #63: 60S ribosomal protein L28
+Macromolecule #64: 60S ribosomal protein L29
+Macromolecule #65: 60S ribosomal protein L30
+Macromolecule #66: 60S ribosomal protein L31-A
+Macromolecule #67: 60S ribosomal protein L32
+Macromolecule #68: 60S ribosomal protein L33-A
+Macromolecule #69: 60S ribosomal protein L34-A
+Macromolecule #70: 60S ribosomal protein L35-A
+Macromolecule #71: 60S ribosomal protein L36-A
+Macromolecule #72: 60S ribosomal protein L37-A
+Macromolecule #73: 60S ribosomal protein L38
+Macromolecule #74: 60S ribosomal protein L39
+Macromolecule #75: Ubiquitin-60S ribosomal protein L40
+Macromolecule #76: 60S ribosomal protein L41-B
+Macromolecule #77: 60S ribosomal protein L42-A
+Macromolecule #78: 60S ribosomal protein L43-A
+Macromolecule #79: 60S acidic ribosomal protein P0
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |