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- EMDB-71238: YsxC-GMPPNP treated 44.5SYsxC particles. Class 1. -

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Basic information

Entry
Database: EMDB / ID: EMD-71238
TitleYsxC-GMPPNP treated 44.5SYsxC particles. Class 1.
Map dataYsxC-GMPPNP treated 44.5SYsxC particles. Class 1
Sample
  • Complex: YsxC-GMPPNP treated 44.5SYsxC particles. Class 1.
    • RNA: x 1 types
    • Protein or peptide: x 17 types
KeywordsRibosome / 44.5S particle / YsxC
Function / homology
Function and homology information


division septum assembly / large ribosomal subunit / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation ...division septum assembly / large ribosomal subunit / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / GTP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
GTP-binding protein, ribosome biogenesis, YsxC / EngB-type guanine nucleotide-binding (G) domain profile. / EngB-type guanine nucleotide-binding (G) domain / 50S ribosome-binding GTPase / GTP binding domain / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / : / Ribosomal protein L17 signature. / Ribosomal protein L32p, bacterial type ...GTP-binding protein, ribosome biogenesis, YsxC / EngB-type guanine nucleotide-binding (G) domain profile. / EngB-type guanine nucleotide-binding (G) domain / 50S ribosome-binding GTPase / GTP binding domain / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / : / Ribosomal protein L17 signature. / Ribosomal protein L32p, bacterial type / : / : / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L30, bacterial-type / : / Ribosomal protein L20 / Ribosomal L32p protein family / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L21 / Ribosomal protein L32p / Large ribosomal subunit protein uL24, C-terminal domain / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L24 / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L13, bacterial-type / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Ribosomal protein L15, conserved site / Ribosomal protein L15 signature. / Small GTP-binding protein domain / Ribosomal protein L13 signature. / Ribosomal protein L13, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L22 signature. / Ribosomal protein L14P, conserved site / Ribosomal protein L14 signature. / Ribosomal L29 protein / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal protein L24 signature. / Ribosomal protein L24/L26, conserved site / KOW (Kyprides, Ouzounis, Woese) motif. / Ribosomal protein L23 / Ribosomal protein L13 / Ribosomal protein L13 / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L30p/L7e / Ribosomal protein L25/L23 / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L15 / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal protein L14p/L23e / Ribosomal protein L14P / Ribosomal protein L14 superfamily / Ribosomal protein L14p/L23e / Ribosomal protein L22/L17 / Ribosomal protein L22p/L17e / Ribosomal protein L22/L17 superfamily / Ribosomal protein L26/L24, KOW domain / Ribosomal protein L3, conserved site / Ribosomal protein L3 signature. / Ribosomal protein L3 / Ribosomal protein L3 / Ribosomal protein L18e/L15P / Ribosomal L18e/L15P superfamily / Ribosomal protein L4/L1e / Ribosomal protein L4 domain superfamily / Ribosomal protein L4/L1 family / Translation protein SH3-like domain superfamily / Ribosomal protein L23/L15e core domain superfamily / Zinc-binding ribosomal protein / KOW motif / KOW / Translation protein, beta-barrel domain superfamily / Ribosomal protein L2, domain 2 / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL34 / Probable GTP-binding protein EngB / Large ribosomal subunit protein bL20 ...Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL34 / Probable GTP-binding protein EngB / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL29
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsOrtega J / Seffouh A
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Nucleic Acids Res / Year: 2025
Title: YsxC is a placeholder for ribosomal protein uL2 during 50S ribosomal subunit assembly.
Authors: Amal Seffouh / Dominic Arpin / Kaustuv Basu / Joaquin Ortega /
Abstract: The maturation of the functional core of the 50S ribosomal subunit in Bacillus subtilis is assisted by assembly factors that enhance the efficiency of the process. Two essential assembly factors, the ...The maturation of the functional core of the 50S ribosomal subunit in Bacillus subtilis is assisted by assembly factors that enhance the efficiency of the process. Two essential assembly factors, the GTPases RbgA and YphC, bind at or near the functional sites of the 50S subunit to promote the folding of ribosomal RNA helices that play key functional roles. YsxC is another GTPase involved in the maturation of the 50S subunit, whose function remains unknown. We demonstrate that YsxC aids 50S assembly through a drastically different mechanism. YsxC binds in the body of the 44.5S large ribosome assembly intermediate, occupying the site where uL2 binds and controls the timing in the folding of rRNA helices forming the binding site for uL2. It creates a "primordial" binding site that includes six out of the eleven rRNA helices forming the uL2 mature binding site. Once YsxC is released, uL2 binds to this "primordial" binding site, and the remaining helices that stabilize uL2 fold, and the entire region adopts the mature conformation. This role of YsxC functioning as a placeholder factor for ribosomal protein uL2 provides the first example of such a factor's involvement in the ribosome assembly process in bacteria.
History
DepositionJun 13, 2025-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71238.png

Downloads & links

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Map

FileDownload / File: emd_71238.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationYsxC-GMPPNP treated 44.5SYsxC particles. Class 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 420 pix.
= 359.1 Å		0.86 Å/pix.
x 420 pix.
= 359.1 Å		0.86 Å/pix.
x 420 pix.
= 359.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.23
Minimum - Maximum-0.5183467 - 2.0656364
Average (Standard dev.)0.012089491 (±0.083094455)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 359.1 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_71238_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_71238_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : YsxC-GMPPNP treated 44.5SYsxC particles. Class 1.

EntireName: YsxC-GMPPNP treated 44.5SYsxC particles. Class 1.
Components
  • Complex: YsxC-GMPPNP treated 44.5SYsxC particles. Class 1.
    • RNA: 23S rRNA
    • Protein or peptide: 50S ribosomal protein L3
    • Protein or peptide: 50S ribosomal protein L4
    • 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 L17
    • Protein or peptide: 50S ribosomal protein L19
    • Protein or peptide: 50S ribosomal protein L20
    • Protein or peptide: 50S ribosomal protein L21
    • Protein or peptide: 50S ribosomal protein L22
    • Protein or peptide: 50S ribosomal protein L23
    • Protein or peptide: 50S ribosomal protein L24
    • Protein or peptide: 50S ribosomal protein L30
    • Protein or peptide: 50S ribosomal protein L32
    • Protein or peptide: 50S ribosomal protein L29
    • Protein or peptide: 50S ribosomal protein L34
    • Protein or peptide: Probable GTP-binding protein EngB

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Supramolecule #1: YsxC-GMPPNP treated 44.5SYsxC particles. Class 1.

SupramoleculeName: YsxC-GMPPNP treated 44.5SYsxC particles. Class 1. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus subtilis (bacteria)

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Macromolecule #1: 23S rRNA

MacromoleculeName: 23S rRNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 949.300062 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 CAUAAGCCUG 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 CCA

GENBANK: GENBANK: CP061870.1

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Macromolecule #2: 50S ribosomal protein L3

MacromoleculeName: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 22.723348 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
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 #3: 50S ribosomal protein L4

MacromoleculeName: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 22.424951 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
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 #4: 50S ribosomal protein L13

MacromoleculeName: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 16.407104 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString:
MRTTPMANAS TIERKWLVVD AAGKTLGRLS SEVAAILRGK HKPTYTPHVD TGDHVIIINA EKIELTGKKL TDKIYYRHTQ HPGGLKSRT ALEMRTNYPE KMLELAIKGM LPKGSLGRQM FKKLNVYRGS EHPHEAQKPE VYELRG

UniProtKB: Large ribosomal subunit protein uL13

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Macromolecule #5: 50S ribosomal protein L14

MacromoleculeName: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 13.175288 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString:
MIQQETRLKV ADNSGAREVL TIKVLGGSGR KTANIGDVIV CTVKQATPGG VVKKGEVVKA VIVRTKSGAR RSDGSYISFD ENACVIIRD DKSPRGTRIF GPVARELREN NFMKIVSLAP EVI

UniProtKB: Large ribosomal subunit protein uL14

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Macromolecule #6: 50S ribosomal protein L15

MacromoleculeName: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 15.410694 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString:
MKLHELKPSE GSRKTRNRVG RGIGSGNGKT AGKGHKGQNA RSGGGVRPGF EGGQMPLFQR LPKRGFTNIN RKEYAVVNLD KLNGFAEGT EVTPELLLET GVISKLNAGV KILGNGKLEK KLTVKANKFS ASAKEAVEAA GGTAEVI

UniProtKB: Large ribosomal subunit protein uL15

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Macromolecule #7: 50S ribosomal protein L17

MacromoleculeName: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 13.774806 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString:
MSYRKLGRTS AQRKAMLRDL TTDLIINERI ETTETRAKEL RSVVEKMITL GKRGDLHARR QAAAYIRNEV ANEENNQDAL QKLFSDIAT RYEERQGGYT RIMKLGPRRG DGAPMAIIEL V

UniProtKB: Large ribosomal subunit protein bL17

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Macromolecule #8: 50S ribosomal protein L19

MacromoleculeName: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 13.416853 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString:
MQKLIEDITK EQLRTDLPAF RPGDTLRVHV KVVEGNRERI QIFEGVVIKR RGGGISETFT VRKISYGVGV ERTFPVHTPK IAKIEVVRY GKVRRAKLYY LRELRGKAAR IKEIRR

UniProtKB: Large ribosomal subunit protein bL19

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Macromolecule #9: 50S ribosomal protein L20

MacromoleculeName: 50S ribosomal protein L20 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 13.537993 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString:
PRVKGGTVTR KRRKKVLKLA KGYFGSKHTL YKVANQQVMK SGNYAFRDRR QKKRDFRKLW ITRINAAARM NGLSYSRLMH GLKLSGIEV NRKMLADLAV NDLTAFNQLA DAAKAQLNK

UniProtKB: Large ribosomal subunit protein bL20

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Macromolecule #10: 50S ribosomal protein L21

MacromoleculeName: 50S ribosomal protein L21 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 11.296081 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString:
MYAIIKTGGK QIKVEEGQTV YIEKLAAEAG ETVTFEDVLF VGGDNVKVGN PTVEGATVTA KVEKQGRAKK ITVFRYKPKK NVHKKQGHR QPYTKVTIEK INA

UniProtKB: Large ribosomal subunit protein bL21

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Macromolecule #11: 50S ribosomal protein L22

MacromoleculeName: 50S ribosomal protein L22 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 12.481608 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString:
MQAKAVARTV RIAPRKARLV MDLIRGKQVG EAVSILNLTP RAASPIIEKV LKSAIANAEH NYEMDANNLV ISQAFVDEGP TLKRFRPRA MGRASQINKR TSHITIVVSE KKEG

UniProtKB: Large ribosomal subunit protein uL22

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Macromolecule #12: 50S ribosomal protein L23

MacromoleculeName: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 10.978813 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString:
MKDPRDVLKR PVITERSADL MTEKKYTFEV DVRANKTEVK DAVESIFGVK VDKVNIMNYK GKSKRVGRYT GMTSRRRKAI VKLTADSKE IEIFEA

UniProtKB: Large ribosomal subunit protein uL23

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Macromolecule #13: 50S ribosomal protein L24

MacromoleculeName: 50S ribosomal protein L24 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 11.16612 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString:
MHVKKGDKVM VISGKDKGKQ GTILAAFPKK DRVLVEGVNM VKKHSKPTQA NPQGGISNQE APIHVSNVMP LDPKTGEVTR VGYKVEDGK KVRVAKKSGQ VLDK

UniProtKB: Large ribosomal subunit protein uL24

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Macromolecule #14: 50S ribosomal protein L30

MacromoleculeName: 50S ribosomal protein L30 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 6.650795 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString:
MAKLEITLKR SVIGRPEDQR VTVRTLGLKK TNQTVVHEDN AAIRGMINKV SHLVSVKEQ

UniProtKB: Large ribosomal subunit protein uL30

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Macromolecule #15: 50S ribosomal protein L32

MacromoleculeName: 50S ribosomal protein L32 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 6.745073 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString:
MAVPFRRTSK MKKRLRRTHF KLNVPGMTEC PSCGEMKLSH RVCKACGSYN GKDINVKSN

UniProtKB: Large ribosomal subunit protein bL32

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Macromolecule #16: 50S ribosomal protein L29

MacromoleculeName: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 7.728029 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString:
MKANEIRDLT TAEIEQKVKS LKEELFNLRF QLATGQLENT ARIREVRKAI ARMKTVIRER EIAANK

UniProtKB: Large ribosomal subunit protein uL29

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Macromolecule #17: 50S ribosomal protein L34

MacromoleculeName: 50S ribosomal protein L34 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 5.271332 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString:
MKRTFQPNNR KRSKVHGFRS RMSSKNGRLV LARRRRKGRK VLSA

UniProtKB: Large ribosomal subunit protein bL34

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Macromolecule #18: Probable GTP-binding protein EngB

MacromoleculeName: Probable GTP-binding protein EngB / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 22.060414 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString: MKVTKSEIVI SAVKPEQYPE GGLPEIALAG RSNVGKSSFI NSLINRKNLA RTSSKPGKTQ TLNFYIINDE LHFVDVPGYG FAKVSKSER EAWGRMIETY ITTREELKAV VQIVDLRHAP SNDDVQMYEF LKYYGIPVIV IATKADKIPK GKWDKHAKVV R QTLNIDPE ...String:
MKVTKSEIVI SAVKPEQYPE GGLPEIALAG RSNVGKSSFI NSLINRKNLA RTSSKPGKTQ TLNFYIINDE LHFVDVPGYG FAKVSKSER EAWGRMIETY ITTREELKAV VQIVDLRHAP SNDDVQMYEF LKYYGIPVIV IATKADKIPK GKWDKHAKVV R QTLNIDPE DELILFSSET KKGKDEAWGA IKKMINR

UniProtKB: Probable GTP-binding protein EngB

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k 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: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 873768
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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