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- EMDB-52768: Focus refined 30S body map of 70S P. gingivalis ribosome W83 strain -

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Basic information

Entry
Database: EMDB / ID: EMD-52768
TitleFocus refined 30S body map of 70S P. gingivalis ribosome W83 strain
Map dataFocus refined 30S body map of 70S P. gingivalis ribosome W83 strain
Sample
  • Complex: Porphyromonas gingivalis 70S ribosome (W83 Strain)
KeywordsAntibiotic / Lefamulin / RIBOSOME
Biological speciesPorphyromonas gingivalis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsHiregange DG / Bashan A / Yonath A
Funding support Israel, 1 items
OrganizationGrant numberCountry
Other privateTHE HELEN AND MILTON A. KIMMELMAN CENTER FOR BIOMOLECULAR STRUCTURE AND ASSEMBLY Israel
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Structural studies of ribosome from an anaerobic Bacteroidetes human pathogen Porphyromonas gingivalis.
Authors: Disha-Gajanan Hiregange / Sarit Samiya / Danuta Mizgalska / Efrat Ben-Zeev / Miriam Waghalter / Andre Rivalta / K Shanmugha Rajan / Yehuda Halfon / Elinor Breiner-Goldstein / Igor ...Authors: Disha-Gajanan Hiregange / Sarit Samiya / Danuta Mizgalska / Efrat Ben-Zeev / Miriam Waghalter / Andre Rivalta / K Shanmugha Rajan / Yehuda Halfon / Elinor Breiner-Goldstein / Igor Kaczmarczyk / Aneta Sroka / Masato Taoka / Yuko Nobe / Toshiaki Isobe / Susanne Paukner / Ella Zimmerman / Anat Bashan / Jan Potempa / Ada Yonath /
Abstract: Porphyromonas gingivalis, an anaerobic pathogen in chronic periodontitis, belongs to the Bacteroidota phylum and is associated with various virulence factors. Its antibiotic-resistant strains and its ...Porphyromonas gingivalis, an anaerobic pathogen in chronic periodontitis, belongs to the Bacteroidota phylum and is associated with various virulence factors. Its antibiotic-resistant strains and its propensity to form biofilms pose a challenge to effective treatment. To explore therapeutic avenues, we studied the high-resolution cryogenic electron microscope structures of ribosomes from the wild-type P. gingivalis W83 and the macrolide-resistant mutant strain ermΔporN. The structural analysis revealed unique features primarily at the ribosome periphery. Together with the distinctive distribution of ribosomal RNA modifications, these findings offer insights into the therapeutical potential, such as creation of novel therapeutic compounds inhibiting the specific cellular functions of the P. gingivalis ribosomes. Moreover, the high-resolution structure of the ermΔporN ribosome in its complex with the approved antibiotic lefamulin suggests its repurposing against P. gingivalis. Furthermore, we provide a foundation for additional effective strategies to treat periodontitis and associated systemic diseases.
History
DepositionFeb 7, 2025-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52768.png

Downloads & links

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Map

FileDownload / File: emd_52768.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocus refined 30S body map of 70S P. gingivalis ribosome W83 strain
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 460 pix.
= 387.32 Å		0.84 Å/pix.
x 460 pix.
= 387.32 Å		0.84 Å/pix.
x 460 pix.
= 387.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.842 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.040375035 - 0.09154484
Average (Standard dev.)0.00008851749 (±0.0014035848)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 387.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_52768_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52768_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Porphyromonas gingivalis 70S ribosome (W83 Strain)

EntireName: Porphyromonas gingivalis 70S ribosome (W83 Strain)
Components
  • Complex: Porphyromonas gingivalis 70S ribosome (W83 Strain)

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Supramolecule #1: Porphyromonas gingivalis 70S ribosome (W83 Strain)

SupramoleculeName: Porphyromonas gingivalis 70S ribosome (W83 Strain) / type: complex / ID: 1 / Parent: 0
Macromolecule list: #2-#3, #46, #4-#14, #48, #47, #15-#28, #44, #29-#43, #45, #1
Details: 70S ribosome of W83 strain
Source (natural)Organism: Porphyromonas gingivalis (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: Quantifoi / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / 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: 1.5 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 129576
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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