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- EMDB-11891: Bacillus subtilis ribosome-associated quality control complex sta... -

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Basic information

Entry
Database: EMDB / ID: EMD-11891
TitleBacillus subtilis ribosome-associated quality control complex state B, multibody refinement focussed on RqcH. Ribosomal 50S subunit with P-tRNA, RqcH, and RqcP/YabO
Map dataBacillus subtilis 50S ribosme-associated quality control complex state B. in complex P-tRNA, RqcH and RqcP/YabO
Sample
  • Complex: 50S ribosomal subunit in complex with RqcH, P-tRNA, and YabO/RqcP
    • Complex: RqcH
      • Protein or peptide: Rqc2 homolog RqcH
    • Complex: P-tRNA, and YabO/RqcP
      • Protein or peptide: Uncharacterized protein YabO
      • RNA: tRNA-Ala-1-1
      • RNA: 23S rRNA23S ribosomal RNA
      • Protein or peptide: 50S ribosomal protein L11
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
RNA-binding protein, HP1423 type / NFACT protein RNA binding domain / Rqc2 homolog RqcH, bacterial / NFACT N-terminal and middle domains / NFACT, RNA-binding domain / NFACT protein RNA binding domain / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal ...RNA-binding protein, HP1423 type / NFACT protein RNA binding domain / Rqc2 homolog RqcH, bacterial / NFACT N-terminal and middle domains / NFACT, RNA-binding domain / NFACT protein RNA binding 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, RNA binding domain / Ribosomal protein L11/L12 / S4 RNA-binding domain profile. / S4 RNA-binding domain / S4 domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily
Similarity search - Domain/homology
Rqc2 homolog RqcH / Uncharacterized protein YabO / Large ribosomal subunit protein uL11
Similarity search - Component
Biological speciesBacillus subtilis (strain 168) (bacteria) / Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsCrowe-McAuliffe C / Wilson DN
Funding support Germany, Sweden, 5 items
OrganizationGrant numberCountry
German Research Foundation (DFG)WI3285/8-1 Germany
Swedish Research Council2017-03783 Sweden
German Research Foundation (DFG)SPP-1879 Germany
Swedish Research Council2018-00956 Sweden
Swedish Research Council2019-01085 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, 2020-
Header (metadata) releaseDec 23, 2020-
Map releaseDec 23, 2020-
UpdateJan 20, 2021-
Current statusJan 20, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7asa
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_11891.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBacillus subtilis 50S ribosme-associated quality control complex state B. in complex P-tRNA, RqcH and RqcP/YabO
Voxel sizeX=Y=Z: 0.82 Å
Density
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.031642504 - 0.06652722
Average (Standard dev.)3.6992587e-05 (±0.0009103387)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 344.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z344.400344.400344.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS420420420
D min/max/mean-0.0320.0670.000

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Supplemental data

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Sample components

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Entire : 50S ribosomal subunit in complex with RqcH, P-tRNA, and YabO/RqcP

EntireName: 50S ribosomal subunit in complex with RqcH, P-tRNA, and YabO/RqcP
Components
  • Complex: 50S ribosomal subunit in complex with RqcH, P-tRNA, and YabO/RqcP
    • Complex: RqcH
      • Protein or peptide: Rqc2 homolog RqcH
    • Complex: P-tRNA, and YabO/RqcP
      • Protein or peptide: Uncharacterized protein YabO
      • RNA: tRNA-Ala-1-1
      • RNA: 23S rRNA23S ribosomal RNA
      • Protein or peptide: 50S ribosomal protein L11

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Supramolecule #1: 50S ribosomal subunit in complex with RqcH, P-tRNA, and YabO/RqcP

SupramoleculeName: 50S ribosomal subunit in complex with RqcH, P-tRNA, and YabO/RqcP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Molecular weightTheoretical: 1.6 MDa

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Supramolecule #2: RqcH

SupramoleculeName: RqcH / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Bacillus subtilis (strain 168) (bacteria)
Recombinant expressionOrganism: Bacillus subtilis (strain 168) (bacteria)

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Supramolecule #3: P-tRNA, and YabO/RqcP

SupramoleculeName: P-tRNA, and YabO/RqcP / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#5
Source (natural)Organism: Bacillus subtilis (strain 168) (bacteria)

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Macromolecule #1: Rqc2 homolog RqcH

MacromoleculeName: Rqc2 homolog RqcH / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (strain 168) (bacteria) / Strain: 168
Molecular weightTheoretical: 68.341391 KDa
Recombinant expressionOrganism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
SequenceString: MSFDGMFTYG MTHELNEKIM GGRITKIHQP YKHDVIFHIR AKGKNQKLLL SAHPSYSRVH ITAQAYENPS EPPMFCMLLR KHIEGGFIE KIEQAGLDRI MIFHIKSRNE IGDETVRKLY VEIMGRHSNI ILTDAAENVI IDGLKHLSPS MNSYRTVLPG Q DYKLPPAQ ...String:
MSFDGMFTYG MTHELNEKIM GGRITKIHQP YKHDVIFHIR AKGKNQKLLL SAHPSYSRVH ITAQAYENPS EPPMFCMLLR KHIEGGFIE KIEQAGLDRI MIFHIKSRNE IGDETVRKLY VEIMGRHSNI ILTDAAENVI IDGLKHLSPS MNSYRTVLPG Q DYKLPPAQ DKISPLEASE DDILRHLSFQ EGRLDKQIVD HFSGVSPLFA KEAVHRAGLA NKVTLPKALL ALFAEVKEHR FI PNITTVN GKEYFYLLEL THLKGEARRF DSLSELLDRF YFGKAERDRV KQQAQDLERF VVNERKKNAN KIKKLEKTLE YSE NAKEFQ LYGELLTANL YMLKKGDKQA EVINYYDEES PTITIPLNPN KTPSENAQAY FTKYQKAKNS VAVVEEQIRL AQEE IEYFD QLIQQLSSAS PRDISEIREE LVEGKYLRPK QQKGQKKQKP HNPVLETYES TSGLTILVGK NNRQNEYLTT RVAAR DDIW LHTKDIPGSH VVIRSSEPDE QTIMEAATIA AYFSKAKDSS SVPVDYTKIR HVKKPNGAKP GFVTYDSQHT VFVTPD ADT VIKLKKSGSG GDYKDHDGDY KDHDIDYKDD DDKG

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Macromolecule #2: Uncharacterized protein YabO

MacromoleculeName: Uncharacterized protein YabO / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (strain 168) (bacteria) / Strain: 168
Molecular weightTheoretical: 9.737266 KDa
SequenceString:
MRLDKFLKVS RLIKRRTLAK EVADQGRISI NGNQAKASSD VKPGDELTVR FGQKLVTVQV NELKDTTKKE EAANMYTILK EEKLGE

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Macromolecule #5: 50S ribosomal protein L11

MacromoleculeName: 50S ribosomal protein L11 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (strain 168) (bacteria) / Strain: 168
Molecular weightTheoretical: 14.951442 KDa
SequenceString:
MAKKVVKVVK LQIPAGKANP APPVGPALGQ AGVNIMGFCK EFNARTADQA GLIIPVEISV YEDRSFTFIT KTPPAAVLLK KAAGIESGS GEPNRNKVAT VKRDKVREIA ETKMPDLNAA DVEAAMRMVE GTARSMGIVI ED

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Macromolecule #3: tRNA-Ala-1-1

MacromoleculeName: tRNA-Ala-1-1 / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168
Molecular weightTheoretical: 24.491547 KDa
SequenceString:
GGGGCCUUAG CUCAGCUGGG AGAGCGCCUG CUUUGCACGC AGGAGGUCAG CGGUUCGAUC CCGCUAGGCU CCACCA

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Macromolecule #4: 23S rRNA

MacromoleculeName: 23S rRNA / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168
Molecular weightTheoretical: 949.010938 KDa
SequenceString: GGUUAAGUUA GAAAGGGCGC ACGGUGGAUG CCUUGGCACU AGGAGCCGAU GAAGGACGGG ACGAACACCG AUAUGCUUCG GGGAGCUGU AAGCAAGCUU UGAUCCGGAG AUUUCCGAAU GGGGAAACCC ACCACUCGUA AUGGAGUGGU AUCCAUAUCU G AAUUCAUA ...String:
GGUUAAGUUA GAAAGGGCGC ACGGUGGAUG CCUUGGCACU AGGAGCCGAU GAAGGACGGG ACGAACACCG AUAUGCUUCG GGGAGCUGU AAGCAAGCUU UGAUCCGGAG AUUUCCGAAU GGGGAAACCC ACCACUCGUA AUGGAGUGGU AUCCAUAUCU G AAUUCAUA GGAUAUGAGA AGGCAGACCC GGGGAACUGA AACAUCUAAG UACCCGGAGG AAGAGAAAGC AAAUGCGAUU CC CUGAGUA GCGGCGAGCG AAACGGGAUC AGCCCAAACC AAGAGGCUUG CCUCUUGGGG UUGUAGGACA CUCUGUACGG AGU UACAAA GGAACGAGGU AGAUGAAGAG GUCUGGAAAG GCCCGCCAUA GGAGGUAACA GCCCUGUAGU CAAAACUUCG UUCU CUCCU GAGUGGAUCC UGAGUACGGC GGAACACGUG AAAUUCCGUC GGAAUCCGGG AGGACCAUCU CCCAAGGCUA AAUAC UCCC UAGUGACCGA UAGUGAACCA GUACCGUGAG GGAAAGGUGA AAAGCACCCC GGAAGGGGAG UGAAAGAGAU CCUGAA ACC GUGUGCCUAC AAGUAGUCAG AGCCCGUUAA CGGGUGAUGG CGUGCCUUUU GUAGAAUGAA CCGGCGAGUU ACGAUCU CG UGCAAGGUUA AGCAGAAGAU GCGGAGCCGC AGCGAAAGCG AGUCUGAAUA GGGCGCAUGA GUACGUGGUC GUAGACCC G AAACCAGGUG AUCUACCCAU GUCCAGGGUG AAGUUCAGGU AACACUGAAU GGAGGCCCGA ACCCACGCAC GUUGAAAAG UGCGGGGAUG AGGUGUGGGU AGGGGUGAAA UGCCAAUCGA ACCUGGAGAU AGCUGGUUCU CUCCGAAAUA GCUUUAGGGC UAGCCUCAA GGUAAGAGUC UUGGAGGUAG AGCACUGAUU GGACUAGGGG CCCCUACCGG GUUACCGAAU UCAGUCAAAC U CCGAAUGC CAAUGACUUA UCCUUGGGAG UCAGACUGCG AGUGAUAAGA UCCGUAGUCG AAAGGGAAAC AGCCCAGACC GC CAGCUAA GGUCCCAAAG UAUACGUUAA GUGGAAAAGG AUGUGGAGUU GCUUAGACAA CCAGGAUGUU GGCUUAGAAG CAG CCACCA UUUAAAGAGU GCGUAAUAGC UCACUGGUCG AGUGACUCUG CGCCGAAAAU GUACCGGGGC UAAACGUAUC ACCG AAGCU GCGGACUGUU CUUCGAACAG UGGUAGGAGA GCGUUCUAAG GGCUGUGAAG CCAGACCGGA AGGACUGGUG GAGCG CUUA GAAGUGAGAA UGCCGGUAUG AGUAGCGAAA GAGGGGUGAG AAUCCCCUCC ACCGAAUGCC UAAGGUUUCC UGAGGA AGG CUCGUCCGCU CAGGGUUAGU CGGGACCUAA GCCGAGGCCG AAAGGCGUAG GCGAUGGACA ACAGGUUGAU AUUCCUG UA CCACCUCCUC ACCAUUUGAG CAAUGGGGGG ACGCAGGAGG AUAGGGUAAG CGCGGUAUUG GAUAUCCGCG UCCAAGCA G UUAGGCUGGG AAAUAGGCAA AUCCGUUUCC CAUAAGGCUG AGCUGUGAUG GCGAGCGAAA UAUAGUAGCG AAGUUCCUG AUUCCACACU GCCAAGAAAA GCCUCUAGCG AGGUGAGAGG UGCCCGUACC GCAAACCGAC ACAGGUAGGC GAGGAGAGAA UCCUAAGGU GAUCGAGAGA ACUCUCGUUA AGGAACUCGG CAAAAUGACC CCGUAACUUC GGGAGAAGGG GUGCUCUGUU A GGGUGCAA GCCCGAGAGA GCCGCAGUGA AUAGGCCCAG GCGACUGUUU AGCAAAAACA CAGGUCUCUG CGAAGCCGUA AG GCGAAGU AUAGGGGCUG ACGCCUGCCC GGUGCUGGAA GGUUAAGAGG AGCGCUUAGC GUAAGCGAAG GUGCGAAUUG AAG CCCCAG UAAACGGCGG CCGUAACUAU AACGGUCCUA AGGUAGCGAA AUUCCUUGUC GGGUAAGUUC CGACCCGCAC GAAA GGCGC AACGAUCUGG GCACUGUCUC AACGAGAGAC UCGGUGAAAU UAUAGUACCU GUGAAGAUGC AGGUUACCCG CGACA GGAC GGAAAGACCC CGUGGAGCUU UACUGCAGCC UGAUAUUGAA UGUUGGUACA GCUUGUACAG GAUAGGUAGG AGCCUU GGA AACCGGAGCG CCAGCUUCGG UGGAGGCAUC GGUGGGAUAC UACCCUGGCU GUAUUGACCU UCUAACCCGC CGCCCUU AU CGGGCGGGGA GACAGUGUCA GGUGGGCAGU UUGACUGGGG CGGUCGCCUC CUAAAAGGUA ACGGAGGCGC CCAAAGGU U CCCUCAGAAU GGUUGGAAAU CAUUCGCAGA GUGUAAAGGC ACAAGGGAGC UUGACUGCGA GACCUACAAG UCGAGCAGG GACGAAAGUC GGGCUUAGUG AUCCGGUGGU UCCGCAUGGA AGGGCCAUCG CUCAACGGAU AAAAGCUACC CCGGGGAUAA CAGGCUUAU CUCCCCCAAG AGUCCACAUC GACGGGGAGG UUUGGCACCU CGAUGUCGGC UCAUCGCAUC CUGGGGCUGU A GUCGGUCC CAAGGGUUGG GCUGUUCGCC CAUUAAAGCG GUACGCGAGC UGGGUUCAGA ACGUCGUGAG ACAGUUCGGU CC CUAUCCG UCGCGGGCGC AGGAAAUUUG AGAGGAGCUG UCCUUAGUAC GAGAGGACCG GGAUGGACGC ACCGCUGGUG UAC CAGUUG UUCUGCCAAG GGCAUCGCUG GGUAGCUAUG UGCGGACGGG AUAAGUGCUG AAAGCAUCUA AGCAUGAAGC CCCC CUCAA GAUGAGAUUU CCCAUUCCGC AAGGAAGUAA GAUCCCUGAA AGAUGAUCAG GUUGAUAGGU CUGAGGUGGA AGUGU GGCG ACACAUGGAG CUGACAGAUA CUAAUCGAUC GAGGACUUAA CC

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 2 / Average electron dose: 29.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 74210
FSC plot (resolution estimation)

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