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
Deposition
May 23, 2017
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Header (metadata) release
May 31, 2017
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Map release
Aug 9, 2017
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Update
Aug 9, 2017
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Current status
Aug 9, 2017
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Download / File: emd_3735.map.gz / Format: CCP4 / Size: 8.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
Class 2 of rotated ribosomes (rotated 1 state) with A/A- and P/E-site tRNAs of the Rqt1-FTP pulldown
Voxel size
X=Y=Z: 3.252 Å
Density
Contour Level
By AUTHOR: 0.027 / Movie #1: 0.027
Minimum - Maximum
-0.07632151 - 0.23760337
Average (Standard dev.)
-0.0006627558 (±0.02365276)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
0
0
0
Dimensions
130
130
130
Spacing
130
130
130
Cell
A=B=C: 422.76 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
3.252
3.252
3.252
M x/y/z
130
130
130
origin x/y/z
0.000
0.000
0.000
length x/y/z
422.760
422.760
422.760
α/β/γ
90.000
90.000
90.000
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
130
130
130
D min/max/mean
-0.076
0.238
-0.001
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Supplemental data
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Sample components
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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
Components
Complex: 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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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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