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- EMDB-14861: Structure of the RQT-bound 80S ribosome from S. cerevisiae (C1) -
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Open data
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Basic information
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Title | Structure of the RQT-bound 80S ribosome from S. cerevisiae (C1) | ||||||||||||
![]() | Composite map of ribosome and ligand | ||||||||||||
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Function / homology | ![]() : / primary metabolic process / ribosomal subunit / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / ribosome disassembly / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity ...: / primary metabolic process / ribosomal subunit / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / ribosome disassembly / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / pre-mRNA 5'-splice site binding / 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) / 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 / preribosome, large subunit precursor / ribosomal large subunit export from nucleus / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / G-protein alpha-subunit binding / positive regulation of protein kinase activity / protein-RNA complex assembly / regulation of translational fidelity / translation regulator activity / ribosomal subunit export from nucleus / 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) / 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) / helicase activity / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / ubiquitin binding / maturation of SSU-rRNA / macroautophagy / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / maintenance of translational fidelity / ribosomal large subunit assembly / cytoplasmic stress granule / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / gene expression / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / nucleic acid binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / hydrolase activity / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / 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 / regulation of DNA-templated transcription / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.47 Å | ||||||||||||
![]() | Best KM / Ikeuchi K / Kater L / Best DM / Musial J / Matsuo Y / Berninghausen O / Becker T / Inada T / Beckmann R | ||||||||||||
Funding support | European Union, ![]()
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![]() | ![]() Title: Structural basis for clearing of ribosome collisions by the RQT complex. Authors: Katharina Best / Ken Ikeuchi / Lukas Kater / Daniel Best / Joanna Musial / Yoshitaka Matsuo / Otto Berninghausen / Thomas Becker / Toshifumi Inada / Roland Beckmann / ![]() ![]() ![]() Abstract: Translation of aberrant messenger RNAs can cause stalling of ribosomes resulting in ribosomal collisions. Collided ribosomes are specifically recognized to initiate stress responses and quality ...Translation of aberrant messenger RNAs can cause stalling of ribosomes resulting in ribosomal collisions. Collided ribosomes are specifically recognized to initiate stress responses and quality control pathways. Ribosome-associated quality control facilitates the degradation of incomplete translation products and requires dissociation of the stalled ribosomes. A central event is therefore the splitting of collided ribosomes by the ribosome quality control trigger complex, RQT, by an unknown mechanism. Here we show that RQT requires accessible mRNA and the presence of a neighboring ribosome. Cryogenic electron microscopy of RQT-ribosome complexes reveals that RQT engages the 40S subunit of the lead ribosome and can switch between two conformations. We propose that the Ski2-like helicase 1 (Slh1) subunit of RQT applies a pulling force on the mRNA, causing destabilizing conformational changes of the small ribosomal subunit, ultimately resulting in subunit dissociation. Our findings provide conceptual framework for a helicase-driven ribosomal splitting mechanism. #1: ![]() Title: Real-space refinement in PHENIX for cryo-EM and crystallography. Authors: Afonine PV / Poon BK / Read RJ / Sobolev OV / Terwilliger TC / Urzhumtsev A / Adams PD | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 25.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 120.4 KB 120.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() ![]() | 18.6 KB 18.4 KB | Display Display | ![]() |
Images | ![]() | 100.4 KB | ||
Masks | ![]() ![]() | 669.9 MB 669.9 MB | ![]() | |
Others | ![]() ![]() ![]() ![]() ![]() ![]() | 621.6 MB 621.7 MB 5.2 MB 29.5 MB 622.4 MB 622.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 765.3 KB | Display | ![]() |
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Full document | ![]() | 764.8 KB | Display | |
Data in XML | ![]() | 28.3 KB | Display | |
Data in CIF | ![]() | 37.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7zpqMC ![]() 7zrsC ![]() 7zs5C ![]() 7zuwC ![]() 7zuxC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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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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Annotation | Composite map of ribosome and ligand | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.045 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Mask #2
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Density Histograms |
-Additional map: halfmap 1 of the ligand
File | emd_14861_additional_1.map | ||||||||||||
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Annotation | halfmap 1 of the ligand | ||||||||||||
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-Additional map: halfmap 2 of the ligand
File | emd_14861_additional_2.map | ||||||||||||
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Annotation | halfmap 2 of the ligand | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: locally refined and filtered map of the ligand
File | emd_14861_additional_3.map | ||||||||||||
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Annotation | locally refined and filtered map of the ligand | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: locally refined and filtered map of the ribosome
File | emd_14861_additional_4.map | ||||||||||||
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Annotation | locally refined and filtered map of the ribosome | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: halfmap 1 of the ribosome
File | emd_14861_half_map_1.map | ||||||||||||
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Annotation | halfmap 1 of the ribosome | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: halfmap 2 of the ribosome
File | emd_14861_half_map_2.map | ||||||||||||
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Annotation | halfmap 2 of the ribosome | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : ribosome with bound RQT components (Slh1, Cue3 and Rqt4)
+Supramolecule #1: ribosome with bound RQT components (Slh1, Cue3 and Rqt4)
+Supramolecule #2: RQT complex (Slh1, Cue3 and Rqt4)
+Supramolecule #3: ribosome
+Macromolecule #1: 18S ribosomal RNA
+Macromolecule #2: 5.8S ribosomal RNA
+Macromolecule #3: 5S ribosomal RNA
+Macromolecule #4: 25S ribosomal RNA
+Macromolecule #5: tRNA
+Macromolecule #6: 40S ribosomal protein S0-A
+Macromolecule #7: 40S ribosomal protein S1
+Macromolecule #8: RPS2 isoform 1
+Macromolecule #9: RPS3 isoform 1
+Macromolecule #10: 40S ribosomal protein S4-A
+Macromolecule #11: Rps5p
+Macromolecule #12: 40S ribosomal protein S6-A
+Macromolecule #13: 40S ribosomal protein S7-A
+Macromolecule #14: 40S ribosomal protein S8
+Macromolecule #15: 40S ribosomal protein S9-A
+Macromolecule #16: 40S ribosomal protein S10-A
+Macromolecule #17: 40S ribosomal protein S11-A
+Macromolecule #18: 40S ribosomal protein S12
+Macromolecule #19: 40S ribosomal protein S13
+Macromolecule #20: 40S ribosomal protein S14-B
+Macromolecule #21: RPS15 isoform 1
+Macromolecule #22: 40S ribosomal protein S16-A
+Macromolecule #23: 40S ribosomal protein S17-B
+Macromolecule #24: 40S ribosomal protein S18-A
+Macromolecule #25: 40S ribosomal protein S19-A
+Macromolecule #26: RPS20 isoform 1
+Macromolecule #27: 40S ribosomal protein S21-A
+Macromolecule #28: RPS22A isoform 1
+Macromolecule #29: 40S ribosomal protein S23-A
+Macromolecule #30: 40S ribosomal protein S24-A
+Macromolecule #31: 40S ribosomal protein S25
+Macromolecule #32: RPS26B isoform 1
+Macromolecule #33: 40S ribosomal protein S27-A
+Macromolecule #34: RPS28A isoform 1
+Macromolecule #35: RPS29A isoform 1
+Macromolecule #36: 40S ribosomal protein S30-A
+Macromolecule #37: RPS31 isoform 1
+Macromolecule #38: Guanine nucleotide-binding protein subunit beta-like protein
+Macromolecule #39: 60S ribosomal protein L2-A
+Macromolecule #40: 60S ribosomal protein L3
+Macromolecule #41: RPL4A isoform 1
+Macromolecule #42: RPL5 isoform 1
+Macromolecule #43: 60S ribosomal protein L6-B
+Macromolecule #44: 60S ribosomal protein L7-A
+Macromolecule #45: 60S ribosomal protein L8-A
+Macromolecule #46: 60S ribosomal protein L9-A
+Macromolecule #47: RPL10 isoform 1
+Macromolecule #48: RPL11B isoform 1
+Macromolecule #49: 60S ribosomal protein L13-A
+Macromolecule #50: 60S ribosomal protein L14-A
+Macromolecule #51: 60S ribosomal protein L15-A
+Macromolecule #52: 60S ribosomal protein L16-A
+Macromolecule #53: 60S ribosomal protein L17-A
+Macromolecule #54: 60S ribosomal protein L18-A
+Macromolecule #55: 60S ribosomal protein L19-A
+Macromolecule #56: 60S ribosomal protein L20-A
+Macromolecule #57: 60S ribosomal protein L21-A
+Macromolecule #58: 60S ribosomal protein L22-A
+Macromolecule #59: 60S ribosomal protein L23-A
+Macromolecule #60: RPL24A isoform 1
+Macromolecule #61: 60S ribosomal protein L25
+Macromolecule #62: 60S ribosomal protein L26-A
+Macromolecule #63: 60S ribosomal protein L27-A
+Macromolecule #64: 60S ribosomal protein L28
+Macromolecule #65: 60S ribosomal protein L29
+Macromolecule #66: 60S ribosomal protein L30
+Macromolecule #67: 60S ribosomal protein L31-A
+Macromolecule #68: RPL32 isoform 1
+Macromolecule #69: 60S ribosomal protein L33-A
+Macromolecule #70: 60S ribosomal protein L34-A
+Macromolecule #71: 60S ribosomal protein L35-A
+Macromolecule #72: 60S ribosomal protein L36-A
+Macromolecule #73: 60S ribosomal protein L37-A
+Macromolecule #74: RPL38 isoform 1
+Macromolecule #75: 60S ribosomal protein L39
+Macromolecule #76: 60S ribosomal protein L40-A
+Macromolecule #77: RPL41A isoform 1
+Macromolecule #78: 60S ribosomal protein L42-A
+Macromolecule #79: 60S ribosomal protein L43-A
+Macromolecule #80: SLH1 isoform 1
+Macromolecule #81: RQC trigger complex subunit CUE3
+Macromolecule #82: RQT4 isoform 1
+Macromolecule #83: MAGNESIUM ION
+Macromolecule #84: ZINC ION
-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: 7.5 |
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Grid | Model: Quantifoil R3/3 / Material: COPPER / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK II |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 43.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |