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Yorodumi- EMDB-14926: Structure of 60S ribosomal subunit from S. cerevisiae with eIF6 a... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14926 | ||||||||||||
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Title | Structure of 60S ribosomal subunit from S. cerevisiae with eIF6 and tRNA | ||||||||||||
Map data | locally filtered and refined map of the ribosomal 60S subunit | ||||||||||||
Sample |
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Function / homology | Function and homology information 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 / 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) ...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 / 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 / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / ribosomal large subunit export from nucleus / protein-RNA complex assembly / regulation of translational fidelity / ribosomal subunit export from nucleus / translational termination / translation initiation factor activity / 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 / maintenance of translational fidelity / ribosomal large subunit assembly / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosome biogenesis / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / baker's yeast (brewer's yeast) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
Authors | Best KM / Ikeuchi K / Kater L / Best DM / Musial J / Matsuo Y / Berninghausen O / Becker T / Inada T / Beckmann R | ||||||||||||
Funding support | European Union, Germany, 3 items
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Citation | Journal: Nat Commun / Year: 2023 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: Journal: Acta Crystallogr D Struct Biol / Year: 2018 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 | emd_14926.map.gz | 25.3 MB | EMDB map data format | |
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Header (meta data) | emd-14926-v30.xml emd-14926.xml | 68.9 KB 68.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14926_fsc.xml | 18.6 KB | Display | FSC data file |
Images | emd_14926.png | 101.2 KB | ||
Masks | emd_14926_msk_1.map | 669.9 MB | Mask map | |
Others | emd_14926_half_map_1.map.gz emd_14926_half_map_2.map.gz | 622.5 MB 622.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14926 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14926 | HTTPS FTP |
-Validation report
Summary document | emd_14926_validation.pdf.gz | 916.7 KB | Display | EMDB validaton report |
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Full document | emd_14926_full_validation.pdf.gz | 916.3 KB | Display | |
Data in XML | emd_14926_validation.xml.gz | 28.5 KB | Display | |
Data in CIF | emd_14926_validation.cif.gz | 37.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14926 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14926 | HTTPS FTP |
-Related structure data
Related structure data | 7zs5MC 7zpqC 7zrsC 7zuwC 7zuxC 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_14926.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | locally filtered and refined map of the ribosomal 60S subunit | ||||||||||||||||||||||||||||||||||||
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
File | emd_14926_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: halfmap 1 of the 60S
File | emd_14926_half_map_1.map | ||||||||||||
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Annotation | halfmap 1 of the 60S | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: halfmap 2 of the 60S
File | emd_14926_half_map_2.map | ||||||||||||
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Annotation | halfmap 2 of the 60S | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 60S ribosome
+Supramolecule #1: 60S ribosome
+Supramolecule #2: rRNA
+Supramolecule #3: ribosomal proteins
+Macromolecule #1: 25S ribosomal RNA
+Macromolecule #2: 5S ribosomal RNA
+Macromolecule #3: 5.8S ribosomal RNA
+Macromolecule #5: tRNA
+Macromolecule #4: Eukaryotic translation initiation factor 6
+Macromolecule #6: 60S ribosomal protein L42-A
+Macromolecule #7: 60S ribosomal protein L43-A
+Macromolecule #8: 60S ribosomal protein L2-A
+Macromolecule #9: 60S ribosomal protein L3
+Macromolecule #10: 60S ribosomal protein L4-A
+Macromolecule #11: 60S ribosomal protein L5
+Macromolecule #12: 60S ribosomal protein L6-A
+Macromolecule #13: 60S ribosomal protein L7-A
+Macromolecule #14: 60S ribosomal protein L8-A
+Macromolecule #15: 60S ribosomal protein L9-A
+Macromolecule #16: 60S ribosomal protein L11-B
+Macromolecule #17: 60S ribosomal protein L13-A
+Macromolecule #18: 60S ribosomal protein L14-A
+Macromolecule #19: 60S ribosomal protein L15-A
+Macromolecule #20: 60S ribosomal protein L16-A
+Macromolecule #21: 60S ribosomal protein L17-A
+Macromolecule #22: 60S ribosomal protein L18-A
+Macromolecule #23: 60S ribosomal protein L19-A
+Macromolecule #24: 60S ribosomal protein L20-A
+Macromolecule #25: 60S ribosomal protein L21-A
+Macromolecule #26: 60S ribosomal protein L22-A
+Macromolecule #27: 60S ribosomal protein L23-A
+Macromolecule #28: 60S ribosomal protein L24-A
+Macromolecule #29: 60S ribosomal protein L25
+Macromolecule #30: 60S ribosomal protein L26-A
+Macromolecule #31: 60S ribosomal protein L27-A
+Macromolecule #32: 60S ribosomal protein L28
+Macromolecule #33: 60S ribosomal protein L29
+Macromolecule #34: 60S ribosomal protein L30
+Macromolecule #35: 60S ribosomal protein L31-A
+Macromolecule #36: 60S ribosomal protein L32
+Macromolecule #37: 60S ribosomal protein L33-A
+Macromolecule #38: 60S ribosomal protein L34-A
+Macromolecule #39: 60S ribosomal protein L35-A
+Macromolecule #40: 60S ribosomal protein L36-A
+Macromolecule #41: 60S ribosomal protein L37-A
+Macromolecule #42: 60S ribosomal protein L38
+Macromolecule #43: 60S ribosomal protein L39
+Macromolecule #44: 60S ribosomal protein L40-A
+Macromolecule #45: 60S ribosomal protein L10
+Macromolecule #46: UNKNOWN
+Macromolecule #47: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R3/3 / Support film - Material: CARBON |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK II |
-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: FIELD EMISSION GUN |
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 |