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Yorodumi- EMDB-3735: Class 2 of rotated ribosomes (rotated 1 state) with A/A- and P/E-... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3735 | |||||||||
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Title | Class 2 of rotated ribosomes (rotated 1 state) with A/A- and P/E-site tRNAs of the Rqt1-FTP pulldown | |||||||||
Map data | Class 2 of rotated ribosomes (rotated 1 state) with A/A- and P/E-site tRNAs of the Rqt1-FTP pulldown | |||||||||
Sample |
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Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.0 Å | |||||||||
Authors | Matsuo Y / Ikeuchi K / Saeki Y / Iwasaki S / Schmidt C / Udagawa T / Sato F / Tsuchiya H / Becker T / Tanaka K ...Matsuo Y / Ikeuchi K / Saeki Y / Iwasaki S / Schmidt C / Udagawa T / Sato F / Tsuchiya H / Becker T / Tanaka K / Ingolia N / Beckmann R / Inada T | |||||||||
Citation | Journal: Nat Commun / Year: 2017 Title: Ubiquitination of stalled ribosome triggers ribosome-associated quality control. Authors: Yoshitaka Matsuo / Ken Ikeuchi / Yasushi Saeki / Shintaro Iwasaki / Christian Schmidt / Tsuyoshi Udagawa / Fumiya Sato / Hikaru Tsuchiya / Thomas Becker / Keiji Tanaka / Nicholas T Ingolia / ...Authors: Yoshitaka Matsuo / Ken Ikeuchi / Yasushi Saeki / Shintaro Iwasaki / Christian Schmidt / Tsuyoshi Udagawa / Fumiya Sato / Hikaru Tsuchiya / Thomas Becker / Keiji Tanaka / Nicholas T Ingolia / Roland Beckmann / Toshifumi Inada / Abstract: Translation arrest by polybasic sequences induces ribosome stalling, and the arrest product is degraded by the ribosome-mediated quality control (RQC) system. Here we report that ubiquitination of ...Translation arrest by polybasic sequences induces ribosome stalling, and the arrest product is degraded by the ribosome-mediated quality control (RQC) system. Here we report that ubiquitination of the 40S ribosomal protein uS10 by the E3 ubiquitin ligase Hel2 (or RQT1) is required for RQC. We identify a RQC-trigger (RQT) subcomplex composed of the RNA helicase-family protein Slh1/Rqt2, the ubiquitin-binding protein Cue3/Rqt3, and yKR023W/Rqt4 that is required for RQC. The defects in RQC of the RQT mutants correlate with sensitivity to anisomycin, which stalls ribosome at the rotated form. Cryo-electron microscopy analysis reveals that Hel2-bound ribosome are dominantly the rotated form with hybrid tRNAs. Ribosome profiling reveals that ribosomes stalled at the rotated state with specific pairs of codons at P-A sites serve as RQC substrates. Rqt1 specifically ubiquitinates these arrested ribosomes to target them to the RQT complex, allowing subsequent RQC reactions including dissociation of the stalled ribosome into subunits.Several protein quality control mechanisms are in place to trigger the rapid degradation of aberrant polypeptides and mRNAs. Here the authors describe a mechanism of ribosome-mediated quality control that involves the ubiquitination of ribosomal proteins by the E3 ubiquitin ligase Hel2/RQT1. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3735.map.gz | 2.5 MB | EMDB map data format | |
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Header (meta data) | emd-3735-v30.xml emd-3735.xml | 8.4 KB 8.4 KB | Display Display | EMDB header |
Images | emd_3735.png | 197.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3735 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3735 | HTTPS FTP |
-Validation report
Summary document | emd_3735_validation.pdf.gz | 246.6 KB | Display | EMDB validaton report |
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Full document | emd_3735_full_validation.pdf.gz | 245.8 KB | Display | |
Data in XML | emd_3735_validation.xml.gz | 5.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3735 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3735 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_3735.map.gz / Format: CCP4 / Size: 8.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Class 2 of rotated ribosomes (rotated 1 state) with A/A- and P/E-site tRNAs of the Rqt1-FTP pulldown | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.252 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Class 2 of rotated ribosomes (rotated 1 state) with A/A- and P/E-...
Entire | Name: Class 2 of rotated ribosomes (rotated 1 state) with A/A- and P/E-site tRNAs of the Rqt1-FTP pulldown |
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Components |
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-Supramolecule #1: Class 2 of rotated ribosomes (rotated 1 state) with A/A- and P/E-...
Supramolecule | Name: Class 2 of rotated ribosomes (rotated 1 state) with A/A- and P/E-site tRNAs of the Rqt1-FTP pulldown type: complex / ID: 1 / Parent: 0 Details: Third class from classification for dataset in Frealign |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 3.6 MDa |
-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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Vitrification | Cryogen name: ETHANE |
-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: 28.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 31858 |
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Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |