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- EMDB-52648: Postprocessed map of the focused refinement of the small ribosoma... -

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Basic information

Entry
Database: EMDB / ID: EMD-52648
TitlePostprocessed map of the focused refinement of the small ribosomal subunit body of a MLSb sensitive S. aureus strain "KES34"
Map dataPostprocessed map of the focused refinement of the small subunit body obtained after MultiBody refinement in RELION
Sample
  • Complex: Cryo-EM structure of the ribosome of a MLSb 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: To Be Published
Title: Structural studies on ribosomes of differentially macrolide-resistant Staphylococcus aureus strains
Authors: Rivalta A / Fedorenko A / Le Scornet A / Thompson S / Halfon Y / Breiner Goldstein E / Cavdaroglu S / Melenitzky T / Hiregange DG / Zimmerman E / Bashan A / Yap MNF / Yonath A
History
DepositionJan 29, 2025-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52648.png

Downloads & links

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Map

FileDownload / File: emd_52648.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 body 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-0.10694795 - 0.23768592
Average (Standard dev.)0.00017122347 (±0.0033061998)
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_52648_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_52648_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_52648_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 MLSb sensitive S. aureus s...

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

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

SupramoleculeName: Cryo-EM structure of the ribosome of a MLSb 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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