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Yorodumi- PDB-7asa: Bacillus subtilis ribosome-associated quality control complex sta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7asa | ||||||||||||||||||
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Title | Bacillus subtilis ribosome-associated quality control complex state B, multibody refinement focussed on RqcH. Ribosomal 50S subunit with P-tRNA, RqcH, and RqcP/YabO | ||||||||||||||||||
Components |
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Keywords | TRANSLATION / 50S / tRNA / RQC / RqcH / peptidyl-tRNA / RqcP / YabO / alanine tailing | ||||||||||||||||||
Function / homology | Function and homology information RQC complex / ribosomal large subunit binding / rescue of stalled ribosome / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / tRNA binding / structural constituent of ribosome / translation / response to antibiotic / RNA binding Similarity search - Function | ||||||||||||||||||
Biological species | Bacillus subtilis (bacteria) Bacillus subtilis subsp. subtilis str. 168 (bacteria) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||||||||
Authors | Crowe-McAuliffe, C. / Wilson, D.N. | ||||||||||||||||||
Funding support | Germany, Sweden, 5items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7asa.cif.gz | 252 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7asa.ent.gz | 160.5 KB | Display | PDB format |
PDBx/mmJSON format | 7asa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7asa_validation.pdf.gz | 763.8 KB | Display | wwPDB validaton report |
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Full document | 7asa_full_validation.pdf.gz | 788 KB | Display | |
Data in XML | 7asa_validation.xml.gz | 37.8 KB | Display | |
Data in CIF | 7asa_validation.cif.gz | 58 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/as/7asa ftp://data.pdbj.org/pub/pdb/validation_reports/as/7asa | HTTPS FTP |
-Related structure data
Related structure data | 11891MC 7as8C 7as9C C: citing same article (ref.) M: map data used to model this data |
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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]) EMPIAR-10541 (Title: Affinity-purified RqcP/YabO-ribosome-associated quality control complexes from Bacillus subtilis Data size: 358.1 Data #1: Unaligned multiframe micrographs of an affinity-purified RqcP/YabO sample [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 68341.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: rqcH, yloA, BSU15640 Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria) Strain (production host): 168 / References: UniProt: O34693 |
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#2: Protein | Mass: 9737.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / Strain: 168 / References: UniProt: P37557 |
#3: RNA chain | Mass: 24491.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Strain: 168 |
#4: RNA chain | Mass: 949010.938 Da / Num. of mol.: 1 / Mutation: Discontinuous sequence / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Strain: 168 |
#5: Protein | Mass: 14951.442 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / Strain: 168 / References: UniProt: Q06796 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight | Value: 1.6 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Bacillus subtilis (strain 168) (bacteria) | ||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 29 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74210 / Symmetry type: POINT |