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- EMDB-19641: YlmH bound to stalled 50S subunits with RqcH and PtRNA -

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Basic information

Entry
Database: EMDB / ID: EMD-19641
TitleYlmH bound to stalled 50S subunits with RqcH and PtRNA
Map data
Sample
  • Complex: 50S ribosomal subunit with stalled P-tRNA-nascent chain, bound by YlmH
    • RNA: x 3 types
    • Protein or peptide: x 29 types
  • Ligand: x 1 types
KeywordsLSU / 50S / RQC / YlmH / RIBOSOME / RqcH
Function / homology
Function and homology information


regulation of mitochondrial transcription / 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 / ribosomal small subunit biogenesis ...regulation of mitochondrial transcription / 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 / ribosomal small subunit biogenesis / small 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 / mRNA binding / DNA binding / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
: / YlmH, N-terminal / YlmH, putative RNA-binding domain / Putative RNA-binding domain in YlmH / NFACT protein RNA binding domain / Rqc2 homolog RqcH, bacterial / NFACT, RNA-binding domain / NFACT protein RNA binding domain / NFACT N-terminal and middle domains / Ribosomal protein L31 type A ...: / YlmH, N-terminal / YlmH, putative RNA-binding domain / Putative RNA-binding domain in YlmH / NFACT protein RNA binding domain / Rqc2 homolog RqcH, bacterial / NFACT, RNA-binding domain / NFACT protein RNA binding domain / NFACT N-terminal and middle domains / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L32p, bacterial type / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / Ribosomal protein L30, bacterial-type / : / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L16 / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal L32p protein family / Ribosomal protein L24 / Ribosomal protein L32p / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L13, bacterial-type / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature. / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. / Ribosomal protein L2 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / : / Ribosomal protein L2, conserved site / Ribosomal protein L15, conserved site / Ribosomal protein L15 signature.
Similarity search - Domain/homology
Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Rqc2 homolog RqcH / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL16 ...Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Rqc2 homolog RqcH / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein uL13 / Putative RNA-binding protein YlmH / Large ribosomal subunit protein bL31
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsPaternoga H / Wilson DN
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)WI3285/11-1 Germany
CitationJournal: Nucleic Acids Res / Year: 2024
Title: A role for the S4-domain containing protein YlmH in ribosome-associated quality control in Bacillus subtilis.
Authors: Hiraku Takada / Helge Paternoga / Keigo Fujiwara / Jose A Nakamoto / Esther N Park / Lyudmila Dimitrova-Paternoga / Bertrand Beckert / Merilin Saarma / Tanel Tenson / Allen R Buskirk / Gemma ...Authors: Hiraku Takada / Helge Paternoga / Keigo Fujiwara / Jose A Nakamoto / Esther N Park / Lyudmila Dimitrova-Paternoga / Bertrand Beckert / Merilin Saarma / Tanel Tenson / Allen R Buskirk / Gemma C Atkinson / Shinobu Chiba / Daniel N Wilson / Vasili Hauryliuk /
Abstract: Ribosomes trapped on mRNAs during protein synthesis need to be rescued for the cell to survive. The most ubiquitous bacterial ribosome rescue pathway is trans-translation mediated by tmRNA and SmpB. ...Ribosomes trapped on mRNAs during protein synthesis need to be rescued for the cell to survive. The most ubiquitous bacterial ribosome rescue pathway is trans-translation mediated by tmRNA and SmpB. Genetic inactivation of trans-translation can be lethal, unless ribosomes are rescued by ArfA or ArfB alternative rescue factors or the ribosome-associated quality control (RQC) system, which in Bacillus subtilis involves MutS2, RqcH, RqcP and Pth. Using transposon sequencing in a trans-translation-incompetent B. subtilis strain we identify a poorly characterized S4-domain-containing protein YlmH as a novel potential RQC factor. Cryo-EM structures reveal that YlmH binds peptidyl-tRNA-50S complexes in a position analogous to that of S4-domain-containing protein RqcP, and that, similarly to RqcP, YlmH can co-habit with RqcH. Consistently, we show that YlmH can assume the role of RqcP in RQC by facilitating the addition of poly-alanine tails to truncated nascent polypeptides. While in B. subtilis the function of YlmH is redundant with RqcP, our taxonomic analysis reveals that in multiple bacterial phyla RqcP is absent, while YlmH and RqcH are present, suggesting that in these species YlmH plays a central role in the RQC.
History
DepositionFeb 16, 2024-
Header (metadata) releaseJun 12, 2024-
Map releaseJun 12, 2024-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19641.png

Downloads & links

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Map

FileDownload / File: emd_19641.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.8 Å
Density
Contour LevelBy AUTHOR: 0.0235
Minimum - Maximum-0.07471768 - 0.11641095
Average (Standard dev.)0.00031740862 (±0.0052734567)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 307.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19641_msk_1.map
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Additional map: #1

Fileemd_19641_additional_1.map
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Half map: #2

Fileemd_19641_half_map_1.map
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Half map: #1

Fileemd_19641_half_map_2.map
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Sample components

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Entire : 50S ribosomal subunit with stalled P-tRNA-nascent chain, bound by YlmH

EntireName: 50S ribosomal subunit with stalled P-tRNA-nascent chain, bound by YlmH
Components
  • Complex: 50S ribosomal subunit with stalled P-tRNA-nascent chain, bound by YlmH
    • RNA: P-tRNA
    • Protein or peptide: 50S ribosomal protein L32
    • Protein or peptide: 50S ribosomal protein L33 1
    • Protein or peptide: 50S ribosomal protein L34
    • Protein or peptide: 50S ribosomal protein L35
    • Protein or peptide: 50S ribosomal protein L36
    • Protein or peptide: 50S ribosomal protein L31
    • RNA: 5S rRNA
    • Protein or peptide: 50S ribosomal protein L2
    • Protein or peptide: 50S ribosomal protein L3
    • Protein or peptide: 50S ribosomal protein L4
    • Protein or peptide: 50S ribosomal protein L5
    • Protein or peptide: Large ribosomal subunit protein uL6
    • Protein or peptide: 50S ribosomal protein L13
    • Protein or peptide: 50S ribosomal protein L14
    • Protein or peptide: 50S ribosomal protein L15
    • Protein or peptide: 50S ribosomal protein L16
    • Protein or peptide: 50S ribosomal protein L17
    • Protein or peptide: 50S ribosomal protein L18
    • Protein or peptide: 50S ribosomal protein L19
    • Protein or peptide: Large ribosomal subunit protein bL20
    • Protein or peptide: 50S ribosomal protein L21
    • Protein or peptide: 50S ribosomal protein L22
    • Protein or peptide: Large ribosomal subunit protein uL23
    • Protein or peptide: 50S ribosomal protein L24
    • Protein or peptide: Putative RNA-binding protein YlmH
    • Protein or peptide: Large ribosomal subunit protein bL27
    • Protein or peptide: 50S ribosomal protein L28
    • Protein or peptide: 50S ribosomal protein L29
    • Protein or peptide: Large ribosomal subunit protein uL30
    • Protein or peptide: Rqc2 homolog RqcH
    • RNA: 23S rRNA
  • Ligand: POTASSIUM ION

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Supramolecule #1: 50S ribosomal subunit with stalled P-tRNA-nascent chain, bound by YlmH

SupramoleculeName: 50S ribosomal subunit with stalled P-tRNA-nascent chain, bound by YlmH
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#32
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)

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Macromolecule #1: P-tRNA

MacromoleculeName: P-tRNA / type: rna / ID: 1 / Number of copies: 2
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 24.491547 KDa
SequenceString:
GGGGCCUUAG CUCAGCUGGG AGAGCGCCUG CUUUGCACGC AGGAGGUCAG CGGUUCGAUC CCGCUAGGCU CCACCA

GENBANK: GENBANK: CP052842.1

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Macromolecule #8: 5S rRNA

MacromoleculeName: 5S rRNA / type: rna / ID: 8 / Number of copies: 1
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 36.15752 KDa
SequenceString:
UGGUGGCGAU AGCGAAGAGG UCACACCCGU UCCCAUACCG AACACGGAAG UUAAGCUCUU CAGCGCCGAU GGUAGUCGGG GGUUUCCCC CUGUGAGAGU AGGACGCCGC CAA

GENBANK: GENBANK: CP019662.1

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Macromolecule #32: 23S rRNA

MacromoleculeName: 23S rRNA / type: rna / ID: 32 / Number of copies: 1
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 949.761375 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 GUAGAA(5MU)GAA CCGGCGAGUU ACG AUCUCG UGCAAGGUUA AGCAGAAGAU GCGGAGCCGC AGCGAAAGCG AGUCUGAAUA GGGCGCAUGA GUACGUGGUC GUAG ACCCG AAACCAGGUG AUCUACCCAU GUCCAGGGUG AAGUUCAGGU AACACUGAAU GGAGGCCCGA ACCCACGCAC GU (5MU)GAAAAG UGCGGGGAUG AGGUGUGGGU AGGGGUGAAA UGCCAAUCGA ACCUGGAGAU AGCUGGUUCU CUCCGAAAU AGCUUUAGGG CUAGCCUCAA GGUAAGAGUC UUGGAGGUAG AGCACUGAUU GGACUAGGGG CCCCUACCGG GUUACCGAAU UCAGUCAAA CUCCGAAUGC CAAUGACUUA UCCUUGGGAG UCAGACUGCG AG(PSU)GAUAAGA UCCGUAGUCG AAAGGGA AA CAGCCCAGAC CGCCAGCUAA GGUCCCAAAG UAUACGUUAA GUGGAAAAGG AUGUGGAGUU GCUUAGACAA CCAGGAUG U UGGCUUAGAA GCAGCCACCA UUUAAAGAGU GCGUAAUAGC UCACUGGUCG AGUGACUCUG CGCCGAAAAU GUACCGGGG CUAAACGUAU CACCGAAGCU GCGGACUGUU CUUCGAACAG UGGUAGGAGA GCGUUCUAAG GGCUGUGAAG CCAGACCGGA AGGACUGGU GGAGCGCUUA GAAGUGAGAA UGCCGGUAUG AGUAGCGAAA GAGGGGUGAG AAUCCCCUCC ACCGAAUGCC U AAGGUUUC CUGAGGAAGG CUCGUCCGCU CAGGGUUAGU CGGGACCUAA GCCGAGGCCG AAAGGCGUAG GCGAUGGACA AC AGGUUGA UAUUCCUGUA CCACCUCCUC ACCAUUUGAG CAAUGGGGGG ACGCAGGAGG AUAGGGUAAG CGCGGUAUUG GAU AUCCGC GUCCAAGCAG UUAGGCUGGG AAAUAGGCAA AUCCGUUUCC CAUAAGGCUG AGCUGUGAUG GCGAGCGAAA UAUA GUAGC GAAGUUCCUG AUUCCACACU GCCAAGAAAA GCCUCUAGCG AGGUGAGAGG UGCCCGUACC GCAAACCGAC ACAGG UAGG CGAGGAGAGA AUCCUAAGGU GAUCGAGAGA ACUCUCGUUA AGGAACUCGG CAAAAUGACC CCGUAACUUC GGGAGA AGG GGUGCUCUGU UAGGGUGCAA GCCCGAGAGA GCCGCAGUGA AUAGGCCCAG GCGACUGUUU AGCAAAAACA CAGGUCU CU GCGAAGCCGU AAGGCGAAGU AUAGGGGCUG ACGCCUGCCC GGUGCUGGAA GGUUAAGAGG AGCGCUUAGC GUAAGCGA A GGUGCGAAUU GAAGCCCCAG UAAACGGCGG CCGUAACUAU AACGGUCCUA AGGUAGCGAA A(5MU)UCCUUGUC GGGUA AGUU CCGACCCGCA CGAAAGGCGC AACGAUCUGG GCACUGUCUC AACGAGAGAC UCGGUGAAAU UAUAGUACCU GUGAAG AUG CAGGUUACCC GCGACAGGAC GGAAAGACCC CGUGGAGCUU UACUGCAGCC UGAUAUUGAA UGUUGGUACA GCUUGUA CA GGAUAGGUAG GAGCCUUGGA AACCGGAGCG CCAGCUUCGG UGGAGGCAUC GGUGGGAUAC UACCCUGGCU GUAUUGAC C UUCUAACCCG CCGCCCUUAU CGGGCGGGGA GACAGUGUCA GGUGGGCAGU UUGACUG(OMG)GG CGGUCGCCUC CUAAA AGGU AACGGAGGCG CCCAAAGGUU CCCUCAGAAU GGUUGGAAAU CAUUCGCAGA GUGUAAAGGC ACAAGGGAGC UUGACU GCG AGACCUACAA GUCGAGCAGG GACGAAAGUC GGGCUUAGUG AUCCGGUGGU UCCGCAUGGA AGGGCCAUCG CUCAACG GA UAAAAGCUAC CCCG(2MG)GGA(H2U)A ACAGGC(PSU)UAU CUCCCCCAAG AGUCCACAUC GACGGGGAGG UUUGGC ACC UCG(2MA)(PSU)GUCGG CUCAUCGCAU CCUGGGGCUG UAGUCGGUCC CAAGGGUUGG GCU(OMG)UUCGCC CAUUA AAGC GGUAC(G7M)CGAG CUGGGUUCAG AACGUCGUGA GACAGUUCGG UCCCUAUCCG UCGCGGGCGC AGGAAAUUUG AG AGGAGCU GUCCUUAGUA CGAGAGGACC GGGAUGGACG CACCGCUGGU GUACCAGUUG UUCUGCCAAG GGCAUCGCUG GGU AGCUAU GUGCGGACGG GAUAAGUGCU GAAAGCAUCU AAGCAUGAAG CCCCCCUCAA GAUGAGAUUU CCCAUUCCGC AAGG AAGUA AGAUCCCUGA AAGAUGAUCA GGUUGAUAGG UCUGAGGUGG AAGUGUGGCG ACACAUGGAG CUGACAGAUA CUAAU CGAU CGAGGACUUA ACCAU

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Macromolecule #2: 50S ribosomal protein L32

MacromoleculeName: 50S ribosomal protein L32 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 6.745073 KDa
SequenceString:
MAVPFRRTSK MKKRLRRTHF KLNVPGMTEC PSCGEMKLSH RVCKACGSYN GKDINVKSN

UniProtKB: Large ribosomal subunit protein bL32

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Macromolecule #3: 50S ribosomal protein L33 1

MacromoleculeName: 50S ribosomal protein L33 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 5.915875 KDa
SequenceString:
MRVNITLACT ECGERNYISK KNKRNNPDRV EFKKYCPRDK KSTLHRETK

UniProtKB: Large ribosomal subunit protein bL33A

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Macromolecule #4: 50S ribosomal protein L34

MacromoleculeName: 50S ribosomal protein L34 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 5.271332 KDa
SequenceString:
MKRTFQPNNR KRSKVHGFRS RMSSKNGRLV LARRRRKGRK VLSA

UniProtKB: Large ribosomal subunit protein bL34

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Macromolecule #5: 50S ribosomal protein L35

MacromoleculeName: 50S ribosomal protein L35 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 7.581128 KDa
SequenceString:
MPKMKTHRGS AKRFKKTGSG KLKRSHAYTS HLFANKSQKQ KRKLRKSAVV SAGDFKRIKQ MLANIK

UniProtKB: Large ribosomal subunit protein bL35

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Macromolecule #6: 50S ribosomal protein L36

MacromoleculeName: 50S ribosomal protein L36 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 4.318422 KDa
SequenceString:
MKVRPSVKPI CEKCKVIRRK GKVMVICENP KHKQKQG

UniProtKB: Large ribosomal subunit protein bL36

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Macromolecule #7: 50S ribosomal protein L31

MacromoleculeName: 50S ribosomal protein L31 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 7.458582 KDa
SequenceString:
MKAGIHPNFK KATVKCACGN EFETGSVKEE VRVEICSECH PFYTGRQKFA SADGRVDRFN KKYGLK

UniProtKB: Large ribosomal subunit protein bL31

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Macromolecule #9: 50S ribosomal protein L2

MacromoleculeName: 50S ribosomal protein L2 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 30.335125 KDa
SequenceString: MAIKKYKPTS NGRRGMTTSD FAEITTDKPE KSLLAPLHKK GGRNNQGKLT VRHQGGGHKR QYRVIDFKRD KDGIPGRVAT VEYDPNRSA NIALINYADG EKRYILAPKG IQVGTEIMSG PEADIKVGNA LPLINIPVGT VVHNIELKPG KGGQLVRSAG T SAQVLGKE ...String:
MAIKKYKPTS NGRRGMTTSD FAEITTDKPE KSLLAPLHKK GGRNNQGKLT VRHQGGGHKR QYRVIDFKRD KDGIPGRVAT VEYDPNRSA NIALINYADG EKRYILAPKG IQVGTEIMSG PEADIKVGNA LPLINIPVGT VVHNIELKPG KGGQLVRSAG T SAQVLGKE GKYVLVRLNS GEVRMILSAC RASIGQVGNE QHELINIGKA GRSRWKGIRP TVRGSVMNPN DHPHGGGEGR AP IGRKSPM SPWGKPTLGF KTRKKKNKSD KFIVRRRKNK

UniProtKB: Large ribosomal subunit protein uL2

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Macromolecule #10: 50S ribosomal protein L3

MacromoleculeName: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 22.723348 KDa
SequenceString: MTKGILGRKI GMTQVFAENG DLIPVTVIEA APNVVLQKKT AENDGYEAIQ LGFDDKREKL SNKPEKGHVA KAETAPKRFV KELRGVEMD AYEVGQEVKV EIFSAGEIVD VTGVSKGKGF QGAIKRHGQS RGPMSHGSRY HRRPGSMGPV DPNRVFKGKL L PGRMGGEQ ...String:
MTKGILGRKI GMTQVFAENG DLIPVTVIEA APNVVLQKKT AENDGYEAIQ LGFDDKREKL SNKPEKGHVA KAETAPKRFV KELRGVEMD AYEVGQEVKV EIFSAGEIVD VTGVSKGKGF QGAIKRHGQS RGPMSHGSRY HRRPGSMGPV DPNRVFKGKL L PGRMGGEQ ITVQNLEIVK VDAERNLLLI KGNVPGAKKS LITVKSAVKS K

UniProtKB: Large ribosomal subunit protein uL3

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Macromolecule #11: 50S ribosomal protein L4

MacromoleculeName: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 22.424951 KDa
SequenceString: MPKVALYNQN GSTAGDIELN ASVFGIEPNE SVVFDAILMQ RASLRQGTHK VKNRSEVRGG GRKPWRQKGT GRARQGSIRS PQWRGGGVV FGPTPRSYSY KLPKKVRRLA IKSVLSSKVI DNNIIVLEDL TLDTAKTKEM AAILKGLSVE KKALIVTADA N EAVALSAR ...String:
MPKVALYNQN GSTAGDIELN ASVFGIEPNE SVVFDAILMQ RASLRQGTHK VKNRSEVRGG GRKPWRQKGT GRARQGSIRS PQWRGGGVV FGPTPRSYSY KLPKKVRRLA IKSVLSSKVI DNNIIVLEDL TLDTAKTKEM AAILKGLSVE KKALIVTADA N EAVALSAR NIPGVTVVEA NGINVLDVVN HEKLLITKAA VEKVEEVLA

UniProtKB: Large ribosomal subunit protein uL4

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Macromolecule #12: 50S ribosomal protein L5

MacromoleculeName: 50S ribosomal protein L5 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 20.177564 KDa
SequenceString:
MNRLKEKYNK EIAPALMTKF NYDSVMQVPK IEKIVINMGV GDAVQNAKAI DSAVEELTFI AGQKPVVTRA KKSIAGFRLR EGMPIGAKV TLRGERMYDF LDKLISVSLP RVRDFRGVSK KSFDGRGNYT LGIKEQLIFP EIDYDKVTKV RGMDIVIVTT A NTDEEARE LLTQVGMPFQ K

UniProtKB: Large ribosomal subunit protein uL5

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Macromolecule #13: Large ribosomal subunit protein uL6

MacromoleculeName: Large ribosomal subunit protein uL6 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 19.543389 KDa
SequenceString:
MSRVGKKLLE IPSDVTVTLN DNNTVAVKGP KGELTRTFHP DMEIKVEDNV LTVARPSDQK EHRALHGTTR SLLGNMVEGV SKGFERGLE LVGVGYRASK SGNKLVLNVG YSHPVEIVPE EGIEIEVPSQ TKVVVKGTDK ERVGAIAANI RAVRSPEPYK G KGIRYEGE VVRRKEGKSA K

UniProtKB: Large ribosomal subunit protein uL6

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Macromolecule #14: 50S ribosomal protein L13

MacromoleculeName: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 16.407104 KDa
SequenceString:
MRTTPMANAS TIERKWLVVD AAGKTLGRLS SEVAAILRGK HKPTYTPHVD TGDHVIIINA EKIELTGKKL TDKIYYRHTQ HPGGLKSRT ALEMRTNYPE KMLELAIKGM LPKGSLGRQM FKKLNVYRGS EHPHEAQKPE VYELRG

UniProtKB: Large ribosomal subunit protein uL13

+
Macromolecule #15: 50S ribosomal protein L14

MacromoleculeName: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 13.175288 KDa
SequenceString:
MIQQETRLKV ADNSGAREVL TIKVLGGSGR KTANIGDVIV CTVKQATPGG VVKKGEVVKA VIVRTKSGAR RSDGSYISFD ENACVIIRD DKSPRGTRIF GPVARELREN NFMKIVSLAP EVI

UniProtKB: Large ribosomal subunit protein uL14

+
Macromolecule #16: 50S ribosomal protein L15

MacromoleculeName: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 15.410694 KDa
SequenceString:
MKLHELKPSE GSRKTRNRVG RGIGSGNGKT AGKGHKGQNA RSGGGVRPGF EGGQMPLFQR LPKRGFTNIN RKEYAVVNLD KLNGFAEGT EVTPELLLET GVISKLNAGV KILGNGKLEK KLTVKANKFS ASAKEAVEAA GGTAEVI

UniProtKB: Large ribosomal subunit protein uL15

+
Macromolecule #17: 50S ribosomal protein L16

MacromoleculeName: 50S ribosomal protein L16 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 16.223049 KDa
SequenceString:
MLLPKRVKYR REHRGKMRGR AKGGTEVHFG EFGIQALEAS WITNRQIEAA RIAMTRYMKR GGKVWIKIFP SKPYTAKPLE VRMGSGKGA PEGWVAVVKP GKVLFEISGV SEEVAREALR LASHKLPIKT KFVKREEIGG ESNES

UniProtKB: Large ribosomal subunit protein uL16

+
Macromolecule #18: 50S ribosomal protein L17

MacromoleculeName: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 13.774806 KDa
SequenceString:
MSYRKLGRTS AQRKAMLRDL TTDLIINERI ETTETRAKEL RSVVEKMITL GKRGDLHARR QAAAYIRNEV ANEENNQDAL QKLFSDIAT RYEERQGGYT RIMKLGPRRG DGAPMAIIEL V

UniProtKB: Large ribosomal subunit protein bL17

+
Macromolecule #19: 50S ribosomal protein L18

MacromoleculeName: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 12.993829 KDa
SequenceString:
MITKTSKNAA RLKRHARVRA KLSGTAERPR LNVFRSNKHI YAQIIDDVNG VTLASASTLD KDLNVESTGD TSAATKVGEL VAKRAAEKG ISDVVFDRGG YLYHGRVKAL ADAAREAGLK F

UniProtKB: Large ribosomal subunit protein uL18

+
Macromolecule #20: 50S ribosomal protein L19

MacromoleculeName: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 13.416853 KDa
SequenceString:
MQKLIEDITK EQLRTDLPAF RPGDTLRVHV KVVEGNRERI QIFEGVVIKR RGGGISETFT VRKISYGVGV ERTFPVHTPK IAKIEVVRY GKVRRAKLYY LRELRGKAAR IKEIRR

UniProtKB: Large ribosomal subunit protein bL19

+
Macromolecule #21: Large ribosomal subunit protein bL20

MacromoleculeName: Large ribosomal subunit protein bL20 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 13.669189 KDa
SequenceString:
MPRVKGGTVT RKRRKKVLKL AKGYFGSKHT LYKVANQQVM KSGNYAFRDR RQKKRDFRKL WITRINAAAR MNGLSYSRLM HGLKLSGIE VNRKMLADLA VNDLTAFNQL ADAAKAQLNK

UniProtKB: Large ribosomal subunit protein bL20

+
Macromolecule #22: 50S ribosomal protein L21

MacromoleculeName: 50S ribosomal protein L21 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 11.296081 KDa
SequenceString:
MYAIIKTGGK QIKVEEGQTV YIEKLAAEAG ETVTFEDVLF VGGDNVKVGN PTVEGATVTA KVEKQGRAKK ITVFRYKPKK NVHKKQGHR QPYTKVTIEK INA

UniProtKB: Large ribosomal subunit protein bL21

+
Macromolecule #23: 50S ribosomal protein L22

MacromoleculeName: 50S ribosomal protein L22 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 12.481608 KDa
SequenceString:
MQAKAVARTV RIAPRKARLV MDLIRGKQVG EAVSILNLTP RAASPIIEKV LKSAIANAEH NYEMDANNLV ISQAFVDEGP TLKRFRPRA MGRASQINKR TSHITIVVSE KKEG

UniProtKB: Large ribosomal subunit protein uL22

+
Macromolecule #24: Large ribosomal subunit protein uL23

MacromoleculeName: Large ribosomal subunit protein uL23 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 10.978813 KDa
SequenceString:
MKDPRDVLKR PVITERSADL MTEKKYTFEV DVRANKTEVK DAVESIFGVK VDKVNIMNYK GKSKRVGRYT GMTSRRRKAI VKLTADSKE IEIFEA

UniProtKB: Large ribosomal subunit protein uL23

+
Macromolecule #25: 50S ribosomal protein L24

MacromoleculeName: 50S ribosomal protein L24 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 11.16612 KDa
SequenceString:
MHVKKGDKVM VISGKDKGKQ GTILAAFPKK DRVLVEGVNM VKKHSKPTQA NPQGGISNQE APIHVSNVMP LDPKTGEVTR VGYKVEDGK KVRVAKKSGQ VLDK

UniProtKB: Large ribosomal subunit protein uL24

+
Macromolecule #26: Putative RNA-binding protein YlmH

MacromoleculeName: Putative RNA-binding protein YlmH / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 30.82384 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString: MSDIYQHFRK DERAFIDQAL EWKRIVQEQY RMKLTDFLDP REQVILSAVT GQADVGLAFS GGYDRAERKR AILFPEYITP EESDFELQA FNVRYADKFV SVDHRSLLGA LMGIGLKRQK FGDIVFSETA VQLIVSADTA DFVAAQLTQA GKAAVSLEKI D LSDLNIPA ...String:
MSDIYQHFRK DERAFIDQAL EWKRIVQEQY RMKLTDFLDP REQVILSAVT GQADVGLAFS GGYDRAERKR AILFPEYITP EESDFELQA FNVRYADKFV SVDHRSLLGA LMGIGLKRQK FGDIVFSETA VQLIVSADTA DFVAAQLTQA GKAAVSLEKI D LSDLNIPA VDVEIRDDTV SSLRLDAVCA SMSRQSRQKS QTLVKNGLVK VNWKVVEDPS YIVAEGDMLS IRGFGRCSLT KI EGKTKKD KWRVTFERQK GSGSGSGSGS DYKDDDDK

UniProtKB: Putative RNA-binding protein YlmH

+
Macromolecule #27: Large ribosomal subunit protein bL27

MacromoleculeName: Large ribosomal subunit protein bL27 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 10.391855 KDa
SequenceString:
MLRLDLQFFA SKKGVGSTKN GRDSEAKRLG AKRADGQFVT GGSILYRQRG TKIYPGENVG RGGDDTLFAK IDGTVKFERF GRDRKKVSV YPVAQ

UniProtKB: Large ribosomal subunit protein bL27

+
Macromolecule #28: 50S ribosomal protein L28

MacromoleculeName: 50S ribosomal protein L28 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 6.826144 KDa
SequenceString:
MARKCVITGK KTTAGNNRSH AMNASKRTWG ANLQKVRILV NGKPKKVYVS ARALKSGKVE RV

UniProtKB: Large ribosomal subunit protein bL28

+
Macromolecule #29: 50S ribosomal protein L29

MacromoleculeName: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 7.728029 KDa
SequenceString:
MKANEIRDLT TAEIEQKVKS LKEELFNLRF QLATGQLENT ARIREVRKAI ARMKTVIRER EIAANK

UniProtKB: Large ribosomal subunit protein uL29

+
Macromolecule #30: Large ribosomal subunit protein uL30

MacromoleculeName: Large ribosomal subunit protein uL30 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 6.650795 KDa
SequenceString:
MAKLEITLKR SVIGRPEDQR VTVRTLGLKK TNQTVVHEDN AAIRGMINKV SHLVSVKEQ

UniProtKB: Large ribosomal subunit protein uL30

+
Macromolecule #31: Rqc2 homolog RqcH

MacromoleculeName: Rqc2 homolog RqcH / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 65.307398 KDa
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 VIKLKKS

UniProtKB: Rqc2 homolog RqcH

+
Macromolecule #33: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 33 / Number of copies: 15 / Formula: K
Molecular weightTheoretical: 39.098 Da

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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
GridModel: Quantifoil R3/3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 3
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 %

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.9 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 2550984
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6ha8


Details: Bacillus subtilis 70S
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.1) / Number images used: 3770
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.1)

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