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- PDB-9qeh: Cryo-EM structure of the A2085-methylated 50S ribosome of a MLSb ... -

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Basic information

Entry
Database: PDB / ID: 9qeh
TitleCryo-EM structure of the A2085-methylated 50S ribosome of a MLSb resistant S. aureus strain "MNY196" in complex with solithromycin
Components
  • (Large ribosomal subunit protein ...) x 26
  • 23S rRNA
  • 50S ribosomal protein L25
  • 5S rRNA
  • E_site tRNA
  • P_site tRNA
KeywordsRIBOSOME
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding ...large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large 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 / cytoplasm
Similarity search - Function
Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / : / Ribosomal protein L16 signature 1. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site ...Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / : / 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 L6, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 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 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 L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L30, bacterial-type / : / L28p-like / Ribosomal protein L27 / Ribosomal L27 protein / 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 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L24 / Ribosomal protein L13, bacterial-type / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. / Ribosomal protein L2 signature. / Ribosomal protein L2, conserved site / : / Ribosomal protein L5, N-terminal / Ribosomal protein L5 / Ribosomal protein L15, conserved site / Ribosomal protein L15 signature. / Ribosomal protein L5, C-terminal / ribosomal L5P family C-terminus / Ribosomal protein L5 / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e / Ribosomal protein L5 domain superfamily / Ribosomal protein L6, alpha-beta domain
Similarity search - Domain/homology
Chem-EM1 / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL3 ...Chem-EM1 / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus USA300 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.08 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 / _citation_author.identifier_ORCID / _citation_author.name / _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
L: Large ribosomal subunit protein bL17
A: 23S rRNA
B: 5S rRNA
C: Large ribosomal subunit protein uL2
D: Large ribosomal subunit protein uL3
E: Large ribosomal subunit protein uL4
F: Large ribosomal subunit protein uL5
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
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
8: P_site tRNA
11: E_site tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,383,107278
Polymers1,375,98331
Non-polymers7,125247
Water11,980665
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 ... , 26 types, 26 molecules 1234LCDEFGHIJKMNOPQRSUVWXZ

#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
#5: 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
#8: 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
#9: 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
#10: 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
#11: 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
#12: 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
#13: 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
#14: 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
#15: 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
#16: 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
#17: 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
#18: 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
#19: 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
#20: 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
#21: 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
#22: 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
#23: 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
#25: 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
#26: 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
#27: 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
#28: 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
#29: 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

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RNA chain , 4 types, 4 molecules AB811

#6: RNA chain 23S rRNA


Mass: 946850.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
#7: RNA chain 5S rRNA


Mass: 36974.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
References: GenBank: 1760048038
#30: RNA chain P_site tRNA


Mass: 22969.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus USA300 (bacteria)
#31: RNA chain E_site tRNA


Mass: 4170.574 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

#24: 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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Non-polymers , 5 types, 912 molecules

#32: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#33: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 231 / Source method: obtained synthetically / Formula: Mg
#34: 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
#35: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: K
#36: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 665 / 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: A2085-methylated 50S ribosome of a MLSb resistant S. aureus strain "MNY196" in complex with solithromycin
Type: RIBOSOME / Entity ID: #1-#31 / 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 material: COPPER / Grid type: Quantifoil R2/2
VitrificationCryogen 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: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
2EPUimage acquisition
7Cootmodel fitting
12RELION3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 263087
Details: Resolution refers to gold-standard FSC 0.143 cutoff calculated on the postprocessed, solvent mask map
Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 24.94 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004188789
ELECTRON MICROSCOPYf_angle_d0.6659133693
ELECTRON MICROSCOPYf_chiral_restr0.039417350
ELECTRON MICROSCOPYf_plane_restr0.00546684
ELECTRON MICROSCOPYf_dihedral_angle_d13.206936547

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