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Yorodumi- EMDB-11889: Bacillus subtilis ribosome quality control complex state B. Ribos... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11889 | ||||||||||||||||||
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Title | Bacillus subtilis ribosome quality control complex state B. Ribosomal 50S subunit with P-tRNA, RqcH, and RqcP/YabO | ||||||||||||||||||
Map data | Bacillus subtilis 50S in complex with P-tRNA, RqcH, and RqcP/YabO. State B. Map filtered according to local resolution. | ||||||||||||||||||
Sample |
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Keywords | 50S / tRNA / RQC / RqcH / peptidyl-tRNA / translation / RqcP / YabO / alanine tailing | ||||||||||||||||||
Function / homology | Function and homology information RQC complex / positive regulation of rRNA processing / nucleoid / ribosomal large subunit binding / rescue of stalled ribosome / rRNA processing / large ribosomal subunit / ribosomal large subunit assembly / transferase activity / large ribosomal subunit rRNA binding ...RQC complex / positive regulation of rRNA processing / nucleoid / ribosomal large subunit binding / rescue of stalled ribosome / rRNA processing / large ribosomal subunit / ribosomal large subunit assembly / transferase activity / large ribosomal subunit rRNA binding / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / DNA binding / RNA binding / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Bacillus subtilis (strain 168) (bacteria) / Bacillus subtilis subsp. subtilis str. 168 (bacteria) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||||||||||||||
Authors | Crowe-McAuliffe C / Wilson DN | ||||||||||||||||||
Funding support | Germany, Sweden, 5 items
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Citation | Journal: Mol Cell / Year: 2021 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11889.map.gz | 128.5 MB | EMDB map data format | |
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Header (meta data) | emd-11889-v30.xml emd-11889.xml | 59.3 KB 59.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11889_fsc.xml | 14.9 KB | Display | FSC data file |
Images | emd_11889.png | 113.5 KB | ||
Masks | emd_11889_msk_1.map | 282.6 MB | Mask map | |
Filedesc metadata | emd-11889.cif.gz | 11 KB | ||
Others | emd_11889_additional_1.map.gz emd_11889_additional_2.map.gz emd_11889_half_map_1.map.gz emd_11889_half_map_2.map.gz | 224.6 MB 38.3 MB 225.7 MB 225.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11889 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11889 | HTTPS FTP |
-Validation report
Summary document | emd_11889_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_11889_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_11889_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | emd_11889_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11889 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11889 | HTTPS FTP |
-Related structure data
Related structure data | 7as8MC 7as9C 7asaC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10540 (Title: Affinity-purified RqcH-ribosome-associated quality control complexes from Bacillus subtilis Data size: 514.6 Data #1: Unaligned multi-frame micrographs of affinity-purified RqcH ribosome-associated quality control complexes from Bacillus subtilis [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11889.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Bacillus subtilis 50S in complex with P-tRNA, RqcH, and RqcP/YabO. State B. Map filtered according to local resolution. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Mask #1
File | emd_11889_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Bacillus subtilis 50S in complex with P-tRNA, RqcH,...
File | emd_11889_additional_1.map | ||||||||||||
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Annotation | Bacillus subtilis 50S in complex with P-tRNA, RqcH, and RqcP/YabO. State B. Output from RELION Refine3D job. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Bacillus subtilis 50S in complex with P-tRNA, RqcH,...
File | emd_11889_additional_2.map | ||||||||||||
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Annotation | Bacillus subtilis 50S in complex with P-tRNA, RqcH, and RqcP/YabO. State B. Post-processed with automatically estimated b-factor. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Bacillus subtilis 50S in complex with P-tRNA, RqcH,...
File | emd_11889_half_map_1.map | ||||||||||||
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Annotation | Bacillus subtilis 50S in complex with P-tRNA, RqcH, and RqcP/YabO. State B. Half map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Bacillus subtilis 50S in complex with P-tRNA, RqcH,...
File | emd_11889_half_map_2.map | ||||||||||||
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Annotation | Bacillus subtilis 50S in complex with P-tRNA, RqcH, and RqcP/YabO. State B. Half map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 50S ribosomal subunit in complex with RqcH, P-tRNA, and YabO/RqcP
+Supramolecule #1: 50S ribosomal subunit in complex with RqcH, P-tRNA, and YabO/RqcP
+Supramolecule #2: RqcH
+Supramolecule #3: 50S ribosomal subunit in complex with P-tRNA, and YabO/RqcP
+Macromolecule #1: Rqc2 homolog RqcH
+Macromolecule #2: Uncharacterized protein YabO
+Macromolecule #6: 50S ribosomal protein L2
+Macromolecule #7: 50S ribosomal protein L3
+Macromolecule #8: 50S ribosomal protein L4
+Macromolecule #9: 50S ribosomal protein L5
+Macromolecule #10: 50S ribosomal protein L6
+Macromolecule #11: 50S ribosomal protein L11
+Macromolecule #12: 50S ribosomal protein L10
+Macromolecule #13: 50S ribosomal protein L13
+Macromolecule #14: 50S ribosomal protein L14
+Macromolecule #15: 50S ribosomal protein L15
+Macromolecule #16: 50S ribosomal protein L16
+Macromolecule #17: 50S ribosomal protein L17
+Macromolecule #18: 50S ribosomal protein L18
+Macromolecule #19: 50S ribosomal protein L19
+Macromolecule #20: 50S ribosomal protein L20
+Macromolecule #21: 50S ribosomal protein L21
+Macromolecule #22: 50S ribosomal protein L22
+Macromolecule #23: 50S ribosomal protein L23
+Macromolecule #24: 50S ribosomal protein L24
+Macromolecule #25: 50S ribosomal protein L27
+Macromolecule #26: 50S ribosomal protein L28
+Macromolecule #27: 50S ribosomal protein L29
+Macromolecule #28: 50S ribosomal protein L30
+Macromolecule #29: 50S ribosomal protein L32
+Macromolecule #30: 50S ribosomal protein L33 1
+Macromolecule #31: 50S ribosomal protein L34
+Macromolecule #32: 50S ribosomal protein L35
+Macromolecule #33: 50S ribosomal protein L36
+Macromolecule #3: tRNA-Ala-1-1
+Macromolecule #4: 23S rRNA
+Macromolecule #5: 5s rRNA
-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: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 2 / Average electron dose: 29.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |