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- PDB-7asa: Bacillus subtilis ribosome-associated quality control complex sta... -

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Basic information

Entry
Database: PDB / ID: 7asa
TitleBacillus subtilis ribosome-associated quality control complex state B, multibody refinement focussed on RqcH. Ribosomal 50S subunit with P-tRNA, RqcH, and RqcP/YabO
Components
  • 23S rRNA
  • 50S ribosomal protein L11
  • Rqc2 homolog RqcH
  • Uncharacterized protein YabO
  • tRNA-Ala-1-1
KeywordsTRANSLATION / 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 cytosolic ribosome / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / translation / response to antibiotic
Similarity search - Function
ibrinogen binding protein from staphylococcus aureus fold / ibrinogen binding protein from staphylococcus aureus domain / RNA-binding protein, HP1423 type / Rqc2 homolog RqcH, bacterial / : / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / NFACT, RNA-binding domain / NFACT protein RNA binding domain / NFACT N-terminal and middle domains ...ibrinogen binding protein from staphylococcus aureus fold / ibrinogen binding protein from staphylococcus aureus domain / RNA-binding protein, HP1423 type / Rqc2 homolog RqcH, bacterial / : / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / NFACT, RNA-binding domain / NFACT protein RNA binding domain / NFACT N-terminal and middle domains / Ribosomal protein L11/L12, C-terminal domain / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / S4 RNA-binding domain profile. / S4 RNA-binding domain / S4 domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / Arc Repressor Mutant, subunit A / Roll / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Rqc2 homolog RqcH / RQC P-site tRNA stabilizing factor / Large ribosomal subunit protein uL11
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Bacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsCrowe-McAuliffe, C. / Wilson, D.N.
Funding support Germany, Sweden, 5items
OrganizationGrant numberCountry
German Research Foundation (DFG)WI3285/8-1 Germany
German Research Foundation (DFG)SPP-1879 Germany
Swedish Research Council2017-03783 Sweden
Swedish Research Council2019-01085 Sweden
Swedish Research Council2018-00956 Sweden
CitationJournal: 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
DepositionOct 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 20, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
0: Rqc2 homolog RqcH
1: Uncharacterized protein YabO
2: tRNA-Ala-1-1
A: 23S rRNA
K: 50S ribosomal protein L11


Theoretical massNumber of molelcules
Total (without water)1,066,5335
Polymers1,066,5335
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area8720 Å2
ΔGint-55 kcal/mol
Surface area56710 Å2
MethodPISA

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Components

#1: Protein Rqc2 homolog RqcH / RqcH


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
#2: Protein Uncharacterized protein YabO


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 tRNA-Ala-1-1


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 23S rRNA


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 50S ribosomal protein L11 / BL11


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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
150S ribosomal subunit in complex with RqcH, P-tRNA, and YabO/RqcPRIBOSOMEall0MULTIPLE SOURCES
2RqcHRIBOSOME#11RECOMBINANT
3P-tRNA, and YabO/RqcPRIBOSOME#2-#51NATURAL
Molecular weightValue: 1.6 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Bacillus subtilis (strain 168) (bacteria)224308
23Bacillus subtilis (strain 168) (bacteria)224308
Source (recombinant)Organism: Bacillus subtilis (strain 168) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 29 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74210 / Symmetry type: POINT

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