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- EMDB-11920: Bacillus subtilis ribosome-associated quality control complex wit... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11920 | ||||||||||||||||||
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Title | Bacillus subtilis ribosome-associated quality control complex with RsfS, derived from RqcP/YabO affinity purification. | ||||||||||||||||||
![]() | Bacillus subtilis ribosome-associated quality control complex with RsfS. Derived from RqcP/YabO affinity purification. Output from RELION Refine3D job. | ||||||||||||||||||
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Function / homology | ![]() RQC complex / positive regulation of rRNA processing / nucleoid / ribosome-associated ubiquitin-dependent protein catabolic process / ribosomal large subunit binding / rescue of stalled ribosome / rRNA processing / large ribosomal subunit / transferase activity / 5S rRNA binding ...RQC complex / positive regulation of rRNA processing / nucleoid / ribosome-associated ubiquitin-dependent protein catabolic process / ribosomal large subunit binding / rescue of stalled ribosome / rRNA processing / large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / DNA binding / RNA binding / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||||||||
![]() | Crowe-McAuliffe C / Wilson DN | ||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structural Basis for Bacterial Ribosome-Associated Quality Control by RqcH and RqcP. Authors: Caillan Crowe-McAuliffe / Hiraku Takada / Victoriia Murina / Christine Polte / Sergo Kasvandik / Tanel Tenson / Zoya Ignatova / Gemma C Atkinson / Daniel N Wilson / Vasili Hauryliuk / ![]() ![]() ![]() Abstract: In all branches of life, stalled translation intermediates are recognized and processed by ribosome-associated quality control (RQC) pathways. RQC begins with the splitting of stalled ribosomes, ...In all branches of life, stalled translation intermediates are recognized and processed by ribosome-associated quality control (RQC) pathways. RQC begins with the splitting of stalled ribosomes, leaving an unfinished polypeptide still attached to the large subunit. Ancient and conserved NEMF family RQC proteins target these incomplete proteins for degradation by the addition of C-terminal "tails." How such tailing can occur without the regular suite of translational components is, however, unclear. Using single-particle cryo-electron microscopy (EM) of native complexes, we show that C-terminal tailing in Bacillus subtilis is mediated by NEMF protein RqcH in concert with RqcP, an Hsp15 family protein. Our structures reveal how these factors mediate tRNA movement across the ribosomal 50S subunit to synthesize polypeptides in the absence of mRNA or the small subunit. | ||||||||||||||||||
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 | ![]() | 224.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21.7 KB 21.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 15 KB | Display | ![]() |
Images | ![]() | 79.8 KB | ||
Others | ![]() ![]() ![]() | 44 MB 225.2 MB 225.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 451.8 KB | Display | ![]() |
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Full document | ![]() | 450.9 KB | Display | |
Data in XML | ![]() | 20.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7as8C ![]() 7as9C ![]() 7asaC C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 358.1 Data #1: Unaligned multiframe micrographs of an affinity-purified RqcP/YabO sample [micrographs - multiframe]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Bacillus subtilis ribosome-associated quality control complex with RsfS. Derived from RqcP/YabO affinity purification. Output from RELION Refine3D job. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Bacillus subtilis ribosome-associated quality control complex with RsfS....
File | emd_11920_additional_1.map | ||||||||||||
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Annotation | Bacillus subtilis ribosome-associated quality control complex with RsfS. Derived from RqcP/YabO affinity purification. Post-processed and sharpened with automatically estimated b-factor. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Bacillus subtilis ribosome-associated quality control complex with RsfS....
File | emd_11920_half_map_1.map | ||||||||||||
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Annotation | Bacillus subtilis ribosome-associated quality control complex with RsfS. Derived from RqcP/YabO affinity purification. Half map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Bacillus subtilis ribosome-associated quality control complex with RsfS....
File | emd_11920_half_map_2.map | ||||||||||||
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Annotation | Bacillus subtilis ribosome-associated quality control complex with RsfS. Derived from RqcP/YabO affinity purification. Half map. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : 50S ribosomal subunit in complex with P-tRNA, YabO/RqcP, and RsfS.
Entire | Name: 50S ribosomal subunit in complex with P-tRNA, YabO/RqcP, and RsfS. |
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Components |
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-Supramolecule #1: 50S ribosomal subunit in complex with P-tRNA, YabO/RqcP, and RsfS.
Supramolecule | Name: 50S ribosomal subunit in complex with P-tRNA, YabO/RqcP, and RsfS. type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#33 Details: Generated by affinity purification of FLAG-tagged RqcP/YabO. |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 1.6 MDa |
-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 R2/2 / Material: COPPER / Mesh: 300 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-20 / Number grids imaged: 2 / Number real images: 5416 / Average exposure time: 4.0 sec. / Average electron dose: 29.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -1.9 µm / Nominal defocus min: -0.4 µm / Nominal magnification: 165000 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |