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- PDB-9qeg: Cryo-EM structure of the 70S ribosome of a MLSb sensitive S. aure... -

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Basic information

Entry
Database: PDB / ID: 9qeg
TitleCryo-EM structure of the 70S ribosome of a MLSb sensitive S. aureus strain "KES34" in complex with solithromycin
Components
  • (Large ribosomal subunit protein ...) x 27
  • (Small ribosomal subunit protein ...) x 19
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 50S ribosomal protein L25
  • 5S ribosomal RNA
  • A-site tRNA molecule
  • E-site tRNA molecule
  • P-site tRNA molecule
  • mRNA molecule
KeywordsRIBOSOME / resistance / rRNA / antibiotic
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small ribosomal subunit rRNA binding ...large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L31 type B / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein S14, type Z / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily ...Ribosomal protein L31 type B / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein S14, type Z / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / : / Ribosomal protein L16 signature 1. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / : / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / : / Ribosomal protein S19, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L36 / Ribosomal protein S4, bacterial-type / Ribosomal protein L36 superfamily / Ribosomal protein L36 / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S14/S29 / 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 S2, bacteria/mitochondria/plastid / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / : / L28p-like / Ribosomal protein S15, bacterial-type / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein S12, bacterial-type / Ribosomal protein L20 / Ribosomal L32p protein family / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 superfamily / Ribosomal protein L21 / Ribosomal protein L32p / Ribosomal protein L17
Similarity search - Domain/homology
Chem-EM1 / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL34 ...Chem-EM1 / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS14B / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein bL31B / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein bL33A / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein bL19 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus USA300 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.21 Å
AuthorsRivalta, A. / Yonath, A.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Life Sci Alliance / Year: 2025
Title: Structural studies on ribosomes of differentially macrolide-resistant strains.
Authors: André Rivalta / Aliza Fedorenko / Alexandre Le Scornet / Sophie Thompson / Yehuda Halfon / Elinor Breiner Goldstein / Sude Çavdaroglu / Tal Melenitzky / Disha-Gajanan Hiregange / Ella ...Authors: André Rivalta / Aliza Fedorenko / Alexandre Le Scornet / Sophie Thompson / Yehuda Halfon / Elinor Breiner Goldstein / Sude Çavdaroglu / Tal Melenitzky / Disha-Gajanan Hiregange / Ella Zimmerman / Anat Bashan / Mee-Ngan Frances Yap / Ada Yonath /
Abstract: Antimicrobial resistance is a major global health challenge, diminishing the efficacy of many antibiotics, including macrolides. In , an opportunistic pathogen, macrolide resistance is primarily ...Antimicrobial resistance is a major global health challenge, diminishing the efficacy of many antibiotics, including macrolides. In , an opportunistic pathogen, macrolide resistance is primarily mediated by Erm-family methyltransferases, which mono- or dimethylate A2058 in the 23S ribosomal RNA, reducing drug binding. Although macrolide-ribosome interactions have been characterized in nonpathogenic species, their structural basis in clinically relevant pathogens remains limited. In this study, we investigate the impact of -mediated resistance on drug binding by analyzing ribosomes from strains with varying levels of expression and activity. Using cryo-electron microscopy, we determined the high-resolution structures of solithromycin-bound ribosomes, including those with dimethylated A2058. Our structural analysis reveals the specific interactions that enable solithromycin binding despite double methylation and resistance, as corroborated by microbiological and biochemical data, suggesting that further optimization of ketolide-ribosome interactions could enhance macrolide efficacy against resistant strains.
History
DepositionMar 10, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Large ribosomal subunit protein bL33A
2: Large ribosomal subunit protein bL34
3: Large ribosomal subunit protein bL35
4: Large ribosomal subunit protein bL36
B: 5S ribosomal RNA
C: Large ribosomal subunit protein uL2
D: Large ribosomal subunit protein uL3
E: Large ribosomal subunit protein uL4
G: Large ribosomal subunit protein uL6
H: Large ribosomal subunit protein uL13
I: Large ribosomal subunit protein uL14
J: Large ribosomal subunit protein uL15
K: Large ribosomal subunit protein uL16
L: Large ribosomal subunit protein bL17
M: Large ribosomal subunit protein uL18
N: Large ribosomal subunit protein bL19
O: Large ribosomal subunit protein bL20
P: Large ribosomal subunit protein bL21
Q: Large ribosomal subunit protein uL22
R: Large ribosomal subunit protein uL23
S: Large ribosomal subunit protein uL24
T: 50S ribosomal protein L25
U: Large ribosomal subunit protein bL27
V: Large ribosomal subunit protein bL28
W: Large ribosomal subunit protein uL29
X: Large ribosomal subunit protein uL30
Z: Large ribosomal subunit protein bL32
F: Large ribosomal subunit protein uL5
11: E-site tRNA molecule
A: 23S ribosomal RNA
Ae: Small ribosomal subunit protein uS5
Af: Small ribosomal subunit protein bS6
Ag: Small ribosomal subunit protein uS7
Ai: Small ribosomal subunit protein uS9
Al: Small ribosomal subunit protein uS12
Ao: Small ribosomal subunit protein uS15
Ap: Small ribosomal subunit protein bS16
Aq: Small ribosomal subunit protein uS17
Ar: Small ribosomal subunit protein bS18
At: Small ribosomal subunit protein bS20
Aa: 16S ribosomal RNA
Aj: Small ribosomal subunit protein uS10
Ac: Small ribosomal subunit protein uS3
Am: Small ribosomal subunit protein uS13
Ak: Small ribosomal subunit protein uS11
Ab: Small ribosomal subunit protein uS2
Ah: Small ribosomal subunit protein uS8
Ad: Small ribosomal subunit protein uS4
An: Small ribosomal subunit protein uS14B
As: Small ribosomal subunit protein uS19
d: mRNA molecule
8: P-site tRNA molecule
9: A-site tRNA molecule
13: Large ribosomal subunit protein bL31B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,178,858308
Polymers2,171,43354
Non-polymers7,425254
Water11,187621
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Large ribosomal subunit protein ... , 27 types, 27 molecules 1234CDEGHIJKLMNOPQRSUVWXZF13

#1: Protein Large ribosomal subunit protein bL33A / 50S ribosomal protein L33 1


Mass: 6305.343 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FH98
#2: Protein/peptide Large ribosomal subunit protein bL34 / 50S ribosomal protein L34


Mass: 5454.642 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FDE6
#3: Protein Large ribosomal subunit protein bL35 / 50S ribosomal protein L35


Mass: 7722.368 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FG57
#4: Protein/peptide Large ribosomal subunit protein bL36 / 50S ribosomal protein L36


Mass: 4318.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FER2
#6: Protein Large ribosomal subunit protein uL2 / 50S ribosomal protein L2


Mass: 30217.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FEP2
#7: Protein Large ribosomal subunit protein uL3 / 50S ribosomal protein L3


Mass: 23760.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FEN9
#8: Protein Large ribosomal subunit protein uL4 / 50S ribosomal protein L4


Mass: 22495.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FEP0
#9: Protein Large ribosomal subunit protein uL6 / 50S ribosomal protein L6


Mass: 19818.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FEQ4
#10: Protein Large ribosomal subunit protein uL13 / 50S ribosomal protein L13


Mass: 16359.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FES1
#11: Protein Large ribosomal subunit protein uL14 / 50S ribosomal protein L14


Mass: 13157.342 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FEP9
#12: Protein Large ribosomal subunit protein uL15 / 50S ribosomal protein L15


Mass: 15628.890 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FEQ8
#13: Protein Large ribosomal subunit protein uL16 / 50S ribosomal protein L16


Mass: 16274.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FEP6
#14: Protein Large ribosomal subunit protein bL17 / 50S ribosomal protein L17


Mass: 13771.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FER6
#15: Protein Large ribosomal subunit protein uL18 / 50S ribosomal protein L18


Mass: 13124.093 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FEQ5
#16: Protein Large ribosomal subunit protein bL19 / 50S ribosomal protein L19


Mass: 13392.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FHJ7
#17: Protein Large ribosomal subunit protein bL20 / 50S ribosomal protein L20


Mass: 13720.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FG58
#18: Protein Large ribosomal subunit protein bL21 / 50S ribosomal protein L21


Mass: 11354.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FG80
#19: Protein Large ribosomal subunit protein uL22 / 50S ribosomal protein L22


Mass: 12857.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FEP4
#20: Protein Large ribosomal subunit protein uL23 / 50S ribosomal protein L23


Mass: 10625.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FEP1
#21: Protein Large ribosomal subunit protein uL24 / 50S ribosomal protein L24


Mass: 11561.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FEQ0
#23: Protein Large ribosomal subunit protein bL27 / 50S ribosomal protein L27


Mass: 10334.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FG82
#24: Protein Large ribosomal subunit protein bL28 / 50S ribosomal protein L28


Mass: 6995.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FHL4
#25: Protein Large ribosomal subunit protein uL29


Mass: 8592.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: A0A0H2XHC7
#26: Protein Large ribosomal subunit protein uL30 / 50S ribosomal protein L30


Mass: 6565.683 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FEQ7
#27: Protein Large ribosomal subunit protein bL32 / 50S ribosomal protein L32


Mass: 6500.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FHV3
#28: Protein Large ribosomal subunit protein uL5 / 50S ribosomal protein L5


Mass: 20296.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FEQ1
#54: Protein Large ribosomal subunit protein bL31B / 50S ribosomal protein L31 type B


Mass: 9737.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FF08

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RNA chain , 7 types, 7 molecules B11AAad89

#5: RNA chain 5S ribosomal RNA


Mass: 36975.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: GenBank: 1335862171
#29: RNA chain E-site tRNA molecule


Mass: 4804.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
#30: RNA chain 23S ribosomal RNA


Mass: 946822.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
#41: RNA chain 16S ribosomal RNA


Mass: 502199.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: GenBank: 1733371935
#51: RNA chain mRNA molecule


Mass: 6165.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
#52: RNA chain P-site tRNA molecule


Mass: 22913.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
#53: RNA chain A-site tRNA molecule


Mass: 1554.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)

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Protein , 1 types, 1 molecules T

#22: Protein 50S ribosomal protein L25 / General stress protein CTC


Mass: 23810.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FJE0

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Small ribosomal subunit protein ... , 19 types, 19 molecules AeAfAgAiAlAoApAqArAtAjAcAmAkAbAhAdAnAs

#31: Protein Small ribosomal subunit protein uS5 / 30S ribosomal protein S5


Mass: 17770.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FEQ6
#32: Protein Small ribosomal subunit protein bS6 / 30S ribosomal protein S6


Mass: 11613.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FJP8
#33: Protein Small ribosomal subunit protein uS7 / 30S ribosomal protein S7


Mass: 17826.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FJ94
#34: Protein Small ribosomal subunit protein uS9 / 30S ribosomal protein S9


Mass: 14856.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FES2
#35: Protein Small ribosomal subunit protein uS12 / 30S ribosomal protein S12


Mass: 15320.870 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FJ95
#36: Protein Small ribosomal subunit protein uS15 / 30S ribosomal protein S15


Mass: 10634.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FHG5
#37: Protein Small ribosomal subunit protein bS16 / 30S ribosomal protein S16


Mass: 10253.886 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FHK0
#38: Protein Small ribosomal subunit protein uS17 / 30S ribosomal protein S17


Mass: 10196.888 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FEP8
#39: Protein Small ribosomal subunit protein bS18 / 30S ribosomal protein S18


Mass: 9332.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FJP6
#40: Protein Small ribosomal subunit protein bS20 / 30S ribosomal protein S20


Mass: 9039.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FGD8
#42: Protein Small ribosomal subunit protein uS10 / 30S ribosomal protein S10


Mass: 11598.503 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FEN8
#43: Protein Small ribosomal subunit protein uS3 / 30S ribosomal protein S3


Mass: 24143.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FEP5
#44: Protein Small ribosomal subunit protein uS13 / 30S ribosomal protein S13


Mass: 13747.919 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FER3
#45: Protein Small ribosomal subunit protein uS11 / 30S ribosomal protein S11


Mass: 13907.978 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FER4
#46: Protein Small ribosomal subunit protein uS2 / 30S ribosomal protein S2


Mass: 29136.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FHI2
#47: Protein Small ribosomal subunit protein uS8 / 30S ribosomal protein S8


Mass: 14854.315 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FEQ3
#48: Protein Small ribosomal subunit protein uS4 / 30S ribosomal protein S4


Mass: 23051.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FG18
#49: Protein Small ribosomal subunit protein uS14B / 30S ribosomal protein S14 type Z


Mass: 7317.769 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FEQ2
#50: Protein Small ribosomal subunit protein uS19 / 30S ribosomal protein S19


Mass: 10639.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: UniProt: Q2FEP3

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Non-polymers , 5 types, 875 molecules

#55: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#56: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 231 / Source method: obtained synthetically / Formula: Mg
#57: Chemical ChemComp-EM1 / (3aS,4R,7S,9R,10R,11R,13R,15R,15aR)-1-{4-[4-(3-aminophenyl)-1H-1,2,3-triazol-1-yl]butyl}-4-ethyl-7-fluoro-11-methoxy-3a ,7,9,11,13,15-hexamethyl-2,6,8,14-tetraoxotetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-10-yl 3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranoside / CEM-101


Mass: 845.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H65FN6O10 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#58: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: K
#59: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 621 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Cryo-EM structure of the 70S ribosome of a MLSb sensitive S. aureus strain "KES34" in complex with solithromycin
Type: RIBOSOME / Entity ID: #1-#54 / Source: NATURAL
Source (natural)Organism: Staphylococcus aureus subsp. aureus USA300 (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 1 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
2EPUimage acquisition
11RELIONfinal Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.21 Å / Resolution method: OTHER / Num. of particles: 408831
Details: FSC (model) = 0.5 unmasked resolution calculated using PHENIX Mtriage and the composite map and the model.
Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 29.07 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039140826
ELECTRON MICROSCOPYf_angle_d0.624211347
ELECTRON MICROSCOPYf_chiral_restr0.037627318
ELECTRON MICROSCOPYf_plane_restr0.005111050
ELECTRON MICROSCOPYf_dihedral_angle_d12.944556679

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