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- EMDB-16334: Cryo-EM structure of a Staphylococus aureus 30S-RbfA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-16334
TitleCryo-EM structure of a Staphylococus aureus 30S-RbfA complex
Map data
Sample
  • Complex: 30S small ribosomal subunit with ribosome binding factor A
    • Complex: 30S Small ribosomal subunit
      • RNA: x 1 types
      • Protein or peptide: x 19 types
    • Complex: Ribosome-binding factor A
      • Protein or peptide: x 1 types
KeywordsRibosome / RbfA / 30S subunit maturation / cryo-EM / ribosome biogenesis / translation / Staphylococcus aureus
Function / homology
Function and homology information


ribosomal small subunit binding / maturation of SSU-rRNA / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding ...ribosomal small subunit binding / maturation of SSU-rRNA / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosome-binding factor A, conserved site / Ribosome-binding factor A signature. / Ribosome-binding factor A / Ribosome-binding factor A domain superfamily / Ribosome-binding factor A / Ribosomal protein S14, type Z / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. ...Ribosome-binding factor A, conserved site / Ribosome-binding factor A signature. / Ribosome-binding factor A / Ribosome-binding factor A domain superfamily / Ribosome-binding factor A / Ribosomal protein S14, type Z / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S2 signature 2. / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / : / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S2, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S5 / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / S5 double stranded RNA-binding domain profile. / K homology domain superfamily, prokaryotic type / Ribosomal protein S5, N-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal / Ribosomal protein S5, C-terminal domain / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S8 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S15 signature. / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal protein S4/S9 / K homology domain-like, alpha/beta / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / Ribosomal S11, conserved site / Ribosomal protein S11 signature.
Similarity search - Domain/homology
Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS14B / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS11 ...Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS14B / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS15 / Ribosome-binding factor A / Small ribosomal subunit protein uS10
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsBikmullin AG / Fatkhullin B / Stetsenko A / Guskov A / Yusupov M
Funding support Russian Federation, 1 items
OrganizationGrant numberCountry
Russian Foundation for Basic Research20-54-15001 Russian Federation
CitationJournal: Int J Mol Sci / Year: 2023
Title: Yet Another Similarity between Mitochondrial and Bacterial Ribosomal Small Subunit Biogenesis Obtained by Structural Characterization of RbfA from .
Authors: Aydar G Bikmullin / Bulat Fatkhullin / Artem Stetsenko / Azat Gabdulkhakov / Natalia Garaeva / Liliia Nurullina / Evelina Klochkova / Alexander Golubev / Iskander Khusainov / Natalie ...Authors: Aydar G Bikmullin / Bulat Fatkhullin / Artem Stetsenko / Azat Gabdulkhakov / Natalia Garaeva / Liliia Nurullina / Evelina Klochkova / Alexander Golubev / Iskander Khusainov / Natalie Trachtmann / Dmitriy Blokhin / Albert Guskov / Shamil Validov / Konstantin Usachev / Marat Yusupov /
Abstract: Ribosome biogenesis is a complex and highly accurate conservative process of ribosomal subunit maturation followed by association. Subunit maturation comprises sequential stages of ribosomal RNA and ...Ribosome biogenesis is a complex and highly accurate conservative process of ribosomal subunit maturation followed by association. Subunit maturation comprises sequential stages of ribosomal RNA and proteins' folding, modification and binding, with the involvement of numerous RNAses, helicases, GTPases, chaperones, RNA, protein-modifying enzymes, and assembly factors. One such assembly factor involved in bacterial 30S subunit maturation is ribosomal binding factor A (RbfA). In this study, we present the crystal (determined at 2.2 Å resolution) and NMR structures of RbfA as well as the 2.9 Å resolution cryo-EM reconstruction of the 30S-RbfA complex from (). Additionally, we show that the manner of RbfA action on the small ribosomal subunit during its maturation is shared between bacteria and mitochondria. The obtained results clarify the function of RbfA in the 30S maturation process and its role in ribosome functioning in general. Furthermore, given that is a serious human pathogen, this study provides an additional prospect to develop antimicrobials targeting bacterial pathogens.
History
DepositionDec 14, 2022-
Header (metadata) releaseDec 27, 2023-
Map releaseDec 27, 2023-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16334.png

Downloads & links

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Map

FileDownload / File: emd_16334.map.gz / Format: CCP4 / Size: 193.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 370 pix.
= 378.14 Å		1.02 Å/pix.
x 370 pix.
= 378.14 Å		1.02 Å/pix.
x 370 pix.
= 378.14 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.022 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.32598308 - 1.124139
Average (Standard dev.)0.0011898964 (±0.036347304)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions370370370
Spacing370370370
CellA=B=C: 378.13998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_16334_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_16334_half_map_2.map
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Sample components

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Entire : 30S small ribosomal subunit with ribosome binding factor A

EntireName: 30S small ribosomal subunit with ribosome binding factor A
Components
  • Complex: 30S small ribosomal subunit with ribosome binding factor A
    • Complex: 30S Small ribosomal subunit
      • RNA: 16S ribosomal RNA
      • Protein or peptide: 30S ribosomal protein S2
      • Protein or peptide: 30S ribosomal protein S3
      • Protein or peptide: 30S ribosomal protein S4
      • Protein or peptide: 30S ribosomal protein S5
      • Protein or peptide: 30S ribosomal protein S6
      • Protein or peptide: 30S ribosomal protein S7
      • Protein or peptide: 30S ribosomal protein S8
      • Protein or peptide: 30S ribosomal protein S9
      • Protein or peptide: 30S ribosomal protein S10
      • Protein or peptide: 30S ribosomal protein S11
      • Protein or peptide: 30S ribosomal protein S12
      • Protein or peptide: 30S ribosomal protein S13
      • Protein or peptide: 30S ribosomal protein S14 type Z
      • Protein or peptide: 30S ribosomal protein S15
      • Protein or peptide: 30S ribosomal protein S16
      • Protein or peptide: 30S ribosomal protein S17
      • Protein or peptide: 30S ribosomal protein S18
      • Protein or peptide: 30S ribosomal protein S19
      • Protein or peptide: 30S ribosomal protein S20
    • Complex: Ribosome-binding factor A
      • Protein or peptide: Ribosome-binding factor A

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Supramolecule #1: 30S small ribosomal subunit with ribosome binding factor A

SupramoleculeName: 30S small ribosomal subunit with ribosome binding factor A
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: 30S Small ribosomal subunit

SupramoleculeName: 30S Small ribosomal subunit / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#20
Source (natural)Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)

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Supramolecule #3: Ribosome-binding factor A

SupramoleculeName: Ribosome-binding factor A / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #21
Source (natural)Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)

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Macromolecule #1: 16S ribosomal RNA

MacromoleculeName: 16S ribosomal RNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Molecular weightTheoretical: 500.464406 KDa
SequenceString: GGAGAGUUUG AUCCUGGCUC AGGAUGAACG CUGGCGGCGU GCCUAAUACA UGCAAGUCGA GCGAACGGAC GAGAAGCUUG CUUCUCUGA UGUUAGCGGC GGACGGGUGA GUAACACGUG GAUAACCUAC CUAUAAGACU GGGAUAACUU CGGGAAACCG U AGCUAAUA ...String:
GGAGAGUUUG AUCCUGGCUC AGGAUGAACG CUGGCGGCGU GCCUAAUACA UGCAAGUCGA GCGAACGGAC GAGAAGCUUG CUUCUCUGA UGUUAGCGGC GGACGGGUGA GUAACACGUG GAUAACCUAC CUAUAAGACU GGGAUAACUU CGGGAAACCG U AGCUAAUA CCGGAUAAUA UUUUGAACCG CAUGGUUCAA AAGUGAAAGA CGGUCUUGCU GUCACUUAUA GAUGGAUCCG CG CUGCAUU AGCUAGUUGG UAAGGUAACG GCUUACCAAG GCAACGAUGC AUAGCCGACC UGAGAGGGUG AUCGGCCACA CUG GAACUG AGACACGGUC CAGACUCCUA CGGGAGGCAG CAGUAGGGAA UCUUCCGCAA UGGGCGAAAG CCUGACGGAG CAAC GCCGC GUGAGUGAUG AAGGUCUUCG GAUCGUAAAA CUCUGUUAUU AGGGAAGAAC AUAUGUGUAA GUAACUGUGC ACAUC UUGA CGGUACCUAA UCAGAAAGCC ACGGCUAACU ACGUGCCAGC AGCCGCGGUA AUACGUAGGU GGCAAGCGUU AUCCGG AAU UAUUGGGCGU AAAGCGCGCG UAGGCGGUUU UUUAAGUCUG AUGUGAAAGC CCACGGCUCA ACCGUGGAGG GUCAUUG GA AACUGGAAAA CUUGAGUGCA GAAGAGGAAA GUGGAAUUCC AUGUGUAGCG GUGAAAUGCG CAGAGAUAUG GAGGAACA C CAGUGGCGAA GGCGACUUUC UGGUCUGUAA CUGACGCUGA UGUGCGAAAG CGUGGGGAUC AAACAGGAUU AGAUACCCU GGUAGUCCAC GCCGUAAACG AUGAGUGCUA AGUGUUAGGG GGUUUCCCGC CCCUUAGUGC UGCAGCUAAC GCAUUAAGCA CUCCGCCUG GGGAGUACGA CCGCAAGGUU GAAACUCAAA GGAAUUGACG GGGACCCGCA CAAGCGGUGG AGCAUGUGGU U UAAUUCGA AGCAACGCGA AGAACCUUAC CAAAUCUUGA CAUCCUUUGA CAACUCUAGA GAUAGAGCCU UCCCCUUCGG GG GACAAAG UGACAGGUGG UGCAUGGUUG UCGUCAGCUC GUGUCGUGAG AUGUUGGGUU AAGUCCCGCA ACGAGCGCAA CCC UUAAGC UUAGUUGCCA UCAUUAAGUU GGGCACUCUA AGUUGACUGC CGGUGACAAA CCGGAGGAAG GUGGGGAUGA CGUC AAAUC AUCAUGCCCC UUAUGAUUUG GGCUACACAC GUGCUACAAU GGACAAUACA AAGGGCAGCG AAACCGCGAG GUCAA GCAA AUCCCAUAAA GUUGUUCUCA GUUCGGAUUG UAGUCUGCAA CUCGACUACA UGAAGCUGGA AUCGCUAGUA AUCGUA GAU CAGCAUGCUA CGGUGAAUAC GUUCCCGGGU CUUGUACACA CCGCCCGUCA CACCACGAGA GUUUGUAACA CCCGAAG CC GGUGGAGUAA CCUUUUAGGA GCUAGCCGUC GAAGGUGGGA CAAAUGAUUG GGGUGAAGUC GUAACAAGGU AGCCGUAU C GGAAGGUGCG GCUGGAUCAC CUCCUU

GENBANK: GENBANK: CP000253.1

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Macromolecule #2: 30S ribosomal protein S2

MacromoleculeName: 30S ribosomal protein S2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Molecular weightTheoretical: 29.136369 KDa
SequenceString: MAVISMKQLL EAGVHFGHQT RRWNPKMKKY IFTERNGIYI IDLQKTVKKV DEAYNFLKQV SEDGGQVLFV GTKKQAQESV KSEAERAGQ FYINQRWLGG LLTNYKTISK RIKRISEIEK MEEDGLFEVL PKKEVVELKK EYDRLIKFLG GIRDMKSMPQ A LFVVDPRK ...String:
MAVISMKQLL EAGVHFGHQT RRWNPKMKKY IFTERNGIYI IDLQKTVKKV DEAYNFLKQV SEDGGQVLFV GTKKQAQESV KSEAERAGQ FYINQRWLGG LLTNYKTISK RIKRISEIEK MEEDGLFEVL PKKEVVELKK EYDRLIKFLG GIRDMKSMPQ A LFVVDPRK ERNAIAEARK LNIPIVGIVD TNCDPDEIDY VIPANDDAIR AVKLLTAKMA DAILEGQQGV SNEEVAAEQN ID LDEKEKS EETEATEE

UniProtKB: Small ribosomal subunit protein uS2

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Macromolecule #3: 30S ribosomal protein S3

MacromoleculeName: 30S ribosomal protein S3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Molecular weightTheoretical: 24.143867 KDa
SequenceString: MGQKINPIGL RVGIIRDWEA KWYAEKDFAS LLHEDLKIRK FIDNELKEAS VSHVEIERAA NRINIAIHTG KPGMVIGKGG SEIEKLRNK LNALTDKKVH INVIEIKKVD LDARLVAENI ARQLENRASF RRVQKQAITR AMKLGAKGIK TQVSGRLGGA D IARAEQYS ...String:
MGQKINPIGL RVGIIRDWEA KWYAEKDFAS LLHEDLKIRK FIDNELKEAS VSHVEIERAA NRINIAIHTG KPGMVIGKGG SEIEKLRNK LNALTDKKVH INVIEIKKVD LDARLVAENI ARQLENRASF RRVQKQAITR AMKLGAKGIK TQVSGRLGGA D IARAEQYS EGTVPLHTLR ADIDYAHAEA DTTYGKLGVK VWIYRGEVLP TKNTSGGGK

UniProtKB: Small ribosomal subunit protein uS3

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Macromolecule #4: 30S ribosomal protein S4

MacromoleculeName: 30S ribosomal protein S4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Molecular weightTheoretical: 23.051416 KDa
SequenceString: MARFRGSNWK KSRRLGISLS GTGKELEKRP YAPGQHGPNQ RKKLSEYGLQ LREKQKLRYL YGMTERQFRN TFDIAGKKFG VHGENFMIL LASRLDAVVY SLGLARTRRQ ARQLVNHGHI LVDGKRVDIP SYSVKPGQTI SVREKSQKLN IIVESVEINN F VPEYLNFD ...String:
MARFRGSNWK KSRRLGISLS GTGKELEKRP YAPGQHGPNQ RKKLSEYGLQ LREKQKLRYL YGMTERQFRN TFDIAGKKFG VHGENFMIL LASRLDAVVY SLGLARTRRQ ARQLVNHGHI LVDGKRVDIP SYSVKPGQTI SVREKSQKLN IIVESVEINN F VPEYLNFD ADSLTGTFVR LPERSELPAE INEQLIVEYY SR

UniProtKB: Small ribosomal subunit protein uS4

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Macromolecule #5: 30S ribosomal protein S5

MacromoleculeName: 30S ribosomal protein S5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Molecular weightTheoretical: 17.770512 KDa
SequenceString:
MARREEETKE FEERVVTINR VAKVVKGGRR FRFTALVVVG DKNGRVGFGT GKAQEVPEAI KKAVEAAKKD LVVVPRVEGT TPHTITGRY GSGSVFMKPA APGTGVIAGG PVRAVLELAG ITDILSKSLG SNTPINMVRA TIDGLQNLKN AEDVAKLRGK T VEELYN

UniProtKB: Small ribosomal subunit protein uS5

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Macromolecule #6: 30S ribosomal protein S6

MacromoleculeName: 30S ribosomal protein S6 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Molecular weightTheoretical: 11.613146 KDa
SequenceString:
MRTYEVMYIV RPNIEEDAKK ALVERFNGIL ATEGAEVLEA KDWGKRRLAY EINDFKDGFY NIVRVKSDNN KATDEFQRLA KISDDIIRY MVIREDEDK

UniProtKB: Small ribosomal subunit protein bS6

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Macromolecule #7: 30S ribosomal protein S7

MacromoleculeName: 30S ribosomal protein S7 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Molecular weightTheoretical: 17.826555 KDa
SequenceString:
MPRKGSVPKR DVLPDPIHNS KLVTKLINKI MLDGKRGTAQ RILYSAFDLV EQRSGRDALE VFEEAINNIM PVLEVKARRV GGSNYQVPV EVRPERRTTL GLRWLVNYAR LRGEKTMEDR LANEILDAAN NTGGAVKKRE DTHKMAEANK AFAHYRW

UniProtKB: Small ribosomal subunit protein uS7

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Macromolecule #8: 30S ribosomal protein S8

MacromoleculeName: 30S ribosomal protein S8 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Molecular weightTheoretical: 14.854315 KDa
SequenceString:
MTMTDPIADM LTRVRNANMV RHEKLELPAS NIKKEIAEIL KSEGFIKNVE YVEDDKQGVL RLFLKYGQND ERVITGLKRI SKPGLRVYA KASEMPKVLN GLGIALVSTS EGVITDKEAR KRNVGGEIIA YVW

UniProtKB: Small ribosomal subunit protein uS8

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Macromolecule #9: 30S ribosomal protein S9

MacromoleculeName: 30S ribosomal protein S9 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Molecular weightTheoretical: 14.856987 KDa
SequenceString:
MTLAQVEYRG TGRRKNSVAR VRLVPGEGNI TVNNRDVREY LPFESLILDL NQPFDVTETK GNYDVLVNVH GGGFTGQAQA IRHGIARAL LEADPEYRGS LKRAGLLTRD PRMKERKKPG LKAARRSPQF SKR

UniProtKB: Small ribosomal subunit protein uS9

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Macromolecule #10: 30S ribosomal protein S10

MacromoleculeName: 30S ribosomal protein S10 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Molecular weightTheoretical: 11.60052 KDa
SequenceString:
MAKQKIRIRL KAYDHRVIDQ SAEKIVETAK RSGADVSGPI PLPTEKSVYT IIRAVHMYKD SREQFEQRTH KRLIDIVNPT PKTVDALMG LNLPSGVDIE IKL

UniProtKB: Small ribosomal subunit protein uS10

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Macromolecule #11: 30S ribosomal protein S11

MacromoleculeName: 30S ribosomal protein S11 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Molecular weightTheoretical: 13.907978 KDa
SequenceString:
MARKQVSRKR RVKKNIENGV AHIRSTFNNT IVTITDEFGN ALSWSSAGAL GFKGSKKSTP FAAQMASETA SKSAMEHGLK TVEVTVKGP GPGRESAIRA LQSAGLEVTA IRDVTPVPHN GCRPPKRRRV

UniProtKB: Small ribosomal subunit protein uS11

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Macromolecule #12: 30S ribosomal protein S12

MacromoleculeName: 30S ribosomal protein S12 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Molecular weightTheoretical: 15.32087 KDa
SequenceString:
MPTINQLVRK PRQSKIKKSD SPALNKGFNS KKKKFTDLNS PQKRGVCTRV GTMTPKKPNS ALRKYARVRL SNNIEINAYI PGIGHNLQE HSVVLVRGGR VKDLPGVRYH IVRGALDTSG VDGRRQGRSL YGTKKPKN

UniProtKB: Small ribosomal subunit protein uS12

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Macromolecule #13: 30S ribosomal protein S13

MacromoleculeName: 30S ribosomal protein S13 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Molecular weightTheoretical: 13.747919 KDa
SequenceString:
MARIAGVDIP REKRVVISLT YIYGIGTSTA QKILEEANVS ADTRVKDLTD DELGRIREVV DGYKVEGDLR RETNLNIKRL MEISSYRGI RHRRGLPVRG QKTKNNARTR KGPVKTVANK KK

UniProtKB: Small ribosomal subunit protein uS13

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Macromolecule #14: 30S ribosomal protein S14 type Z

MacromoleculeName: 30S ribosomal protein S14 type Z / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Molecular weightTheoretical: 7.317769 KDa
SequenceString:
MAKTSMVAKQ QKKQKYAVRE YTRCERCGRP HSVYRKFKLC RICFRELAYK GQIPGVRKAS W

UniProtKB: Small ribosomal subunit protein uS14B

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Macromolecule #15: 30S ribosomal protein S15

MacromoleculeName: 30S ribosomal protein S15 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Molecular weightTheoretical: 10.63433 KDa
SequenceString:
MAISQERKNE IIKEYRVHET DTGSPEVQIA VLTAEINAVN EHLRTHKKDH HSRRGLLKMV GRRRHLLNYL RSKDIQRYRE LIKSLGIRR

UniProtKB: Small ribosomal subunit protein uS15

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Macromolecule #16: 30S ribosomal protein S16

MacromoleculeName: 30S ribosomal protein S16 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Molecular weightTheoretical: 10.253886 KDa
SequenceString:
MAVKIRLTRL GSKRNPFYRI VVADARSPRD GRIIEQIGTY NPTSANAPEI KVDEALALKW LNDGAKPTDT VHNILSKEGI MKKFDEQKK AK

UniProtKB: Small ribosomal subunit protein bS16

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Macromolecule #17: 30S ribosomal protein S17

MacromoleculeName: 30S ribosomal protein S17 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Molecular weightTheoretical: 10.196888 KDa
SequenceString:
MSERNDRKVY VGKVVSDKMD KTITVLVETY KTHKLYGKRV KYSKKYKTHD ENNSAKLGDI VKIQETRPLS ATKRFRLVEI VEESVII

UniProtKB: Small ribosomal subunit protein uS17

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Macromolecule #18: 30S ribosomal protein S18

MacromoleculeName: 30S ribosomal protein S18 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Molecular weightTheoretical: 9.332018 KDa
SequenceString:
MAGGPRRGGR RRKKVCYFTA NGITHIDYKD TELLKRFISE RGKILPRRVT GTSAKYQRML TTAIKRSRHM ALLPYVKEEQ

UniProtKB: Small ribosomal subunit protein bS18

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Macromolecule #19: 30S ribosomal protein S19

MacromoleculeName: 30S ribosomal protein S19 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Molecular weightTheoretical: 10.639309 KDa
SequenceString:
MARSIKKGPF VDEHLMKKVE AQEGSEKKQV IKTWSRRSTI FPNFIGHTFA VYDGRKHVPV YVTEDMVGHK LGEFAPTRTF KGHVADDKK TRR

UniProtKB: Small ribosomal subunit protein uS19

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Macromolecule #20: 30S ribosomal protein S20

MacromoleculeName: 30S ribosomal protein S20 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Molecular weightTheoretical: 9.039472 KDa
SequenceString:
MANIKSAIKR VKTTEKAEAR NISQKSAMRT AVKNAKTAVS NNADNKNELV SLAVKLVDKA AQSNLIHSNK ADRIKSQLMT ANK

UniProtKB: Small ribosomal subunit protein bS20

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Macromolecule #21: Ribosome-binding factor A

MacromoleculeName: Ribosome-binding factor A / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Molecular weightTheoretical: 13.535722 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSSMRAERVG EQMKKELMDI INNKVKDPRV GFITITDVVL TNDLSQAKVF LTVLGNDKEV ENTFKALDKA KGFIKSELGS RMRLRIMPE LMYEYDQSIE YGNKIERMIQ DLHKQDR

UniProtKB: Ribosome-binding factor A

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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 R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 53.3 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 81421
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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