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- EMDB-24227: Porphyromonas gingivalis type IX secretion system -

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Basic information

Entry
Database: EMDB / ID: EMD-24227
TitlePorphyromonas gingivalis type IX secretion system
Map dataIntact T9SS
Sample
  • Complex: T9SS
Biological speciesPorphyromonas gingivalis (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 32.0 Å
AuthorsHu B
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM138301 United States
Welch FoundationAU-1953-20180324 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: A unique bacterial secretion machinery with multiple secretion centers.
Authors: Liqiang Song / John D Perpich / Chenggang Wu / Thierry Doan / Zuzanna Nowakowska / Jan Potempa / Peter J Christie / Eric Cascales / Richard J Lamont / Bo Hu /
Abstract: The Porphyromonas gingivalis type IX secretion system (T9SS) promotes periodontal disease by secreting gingipains and other virulence factors. By in situ cryoelectron tomography, we report that the P. ...The Porphyromonas gingivalis type IX secretion system (T9SS) promotes periodontal disease by secreting gingipains and other virulence factors. By in situ cryoelectron tomography, we report that the P. gingivalis T9SS consists of 18 PorM dimers arranged as a large, caged ring in the periplasm. Near the outer membrane, PorM dimers interact with a PorKN ring complex of ∼52 nm in diameter. PorMKN translocation complexes of a given T9SS adopt distinct conformations energized by the proton motive force, suggestive of different activation states. At the inner membrane, PorM associates with a cytoplasmic complex that exhibits 12-fold symmetry and requires both PorM and PorL for assembly. Activated motors deliver substrates across the outer membrane via one of eight Sov translocons arranged in a ring. The T9SSs are unique among known secretion systems in bacteria and eukaryotes in their assembly as supramolecular machines composed of apparently independently functioning translocation motors and export pores.
History
DepositionJun 10, 2021-
Header (metadata) releaseMay 11, 2022-
Map releaseMay 11, 2022-
UpdateMay 11, 2022-
Current statusMay 11, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24227.png

Downloads & links

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Map

FileDownload / File: emd_24227.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIntact T9SS
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
9 Å/pix.
x 80 pix.
= 720. Å		9 Å/pix.
x 68 pix.
= 612. Å		9 Å/pix.
x 68 pix.
= 612. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 9 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.36
Minimum - Maximum-3.7332988 - 4.069277
Average (Standard dev.)-2.8300564e-09 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-34-34-40
Dimensions686880
Spacing686880
CellA: 612.0 Å / B: 612.0 Å / C: 720.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : T9SS

EntireName: T9SS
Components
  • Complex: T9SS

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Supramolecule #1: T9SS

SupramoleculeName: T9SS / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Porphyromonas gingivalis (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C18 (18 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 32.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 694
ExtractionNumber tomograms: 516 / Number images used: 694
Final angle assignmentType: OTHER

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