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- EMDB-52649: Postprocessed map of the focused refinement of the small ribosoma... -

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Entry
Database: EMDB / ID: EMD-52649
TitlePostprocessed map of the focused refinement of the small ribosomal subunit head of the MLSb sensitive S. aureus strain "KES34"
Map dataPostprocessed map of the focused refinement of the small subunit head obtained after MultiBody refinement in RELION
Sample
  • Complex: Cryo-EM structure of the ribosome of a MSLb sensitive S. aureus strain "KES34" in complex with solithromycin
Keywordsribosome / resistance / rRNA / antibiotic
Biological speciesStaphylococcus aureus subsp. aureus USA300 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.39 Å
AuthorsRivalta A / Yonath A
Funding support1 items
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
DepositionJan 29, 2025-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52649.png

Downloads & links

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Map

FileDownload / File: emd_52649.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed map of the focused refinement of the small subunit head obtained after MultiBody refinement in RELION
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 440 pix.
= 362.56 Å		0.82 Å/pix.
x 440 pix.
= 362.56 Å		0.82 Å/pix.
x 440 pix.
= 362.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.08056676 - 0.17989199
Average (Standard dev.)0.000093074144 (±0.002212914)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 362.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52649_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 of the focused refinement

Fileemd_52649_half_map_1.map
AnnotationHalf map 1 of the focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 of the focused refinement

Fileemd_52649_half_map_2.map
AnnotationHalf map 2 of the focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of the ribosome of a MSLb sensitive S. aureus s...

EntireName: Cryo-EM structure of the ribosome of a MSLb sensitive S. aureus strain "KES34" in complex with solithromycin
Components
  • Complex: Cryo-EM structure of the ribosome of a MSLb sensitive S. aureus strain "KES34" in complex with solithromycin

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Supramolecule #1: Cryo-EM structure of the ribosome of a MSLb sensitive S. aureus s...

SupramoleculeName: Cryo-EM structure of the ribosome of a MSLb sensitive S. aureus strain "KES34" in complex with solithromycin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#28
Source (natural)Organism: Staphylococcus aureus subsp. aureus USA300 (bacteria)

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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 R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Number real images: 4053 / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.5 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: EMDB MAP
EMDB ID:

10079

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION
Details: Resolution of the postprocessed map calculated by RELION
Number images used: 408831
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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