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- EMDB-70851: C32 reconstruction for the PorKN (single) ring complex of Type IX... -

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Basic information

Entry
Database: EMDB / ID: EMD-70851
TitleC32 reconstruction for the PorKN (single) ring complex of Type IX Secretion System (T9SS)
Map data
Sample
  • Organelle or cellular component: T9SS PorKN ring complex
KeywordsT9SS / Type IX SECRETION SYSTEM / PORKN RING COMPLEX / PORPHYROMONAS GINGIVALIS / PROTEIN TRANSPORT / MEMBRANE PROTEIN
Biological speciesPorphyromonas gingivalis ATCC 33277 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.4 Å
AuthorsLiu X / Song L / Hu B
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: The structure of the T9SS ring complex reveals conformational plasticity based on the repurposed FGE fold
Authors: Liu X / Perpich J / Song L / Cambillau C / Doan T / Zheng L / Lamont RJ / Cascales E / Hu B
History
DepositionMay 27, 2025-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70851.png

Downloads & links

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Map

FileDownload / File: emd_70851.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 720 pix.
= 792. Å		1.1 Å/pix.
x 720 pix.
= 792. Å		1.1 Å/pix.
x 720 pix.
= 792. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.21
Minimum - Maximum-0.28856587 - 0.6614272
Average (Standard dev.)0.0008997782 (±0.029238947)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720720720
Spacing720720720
CellA=B=C: 792.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70851_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_70851_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_70851_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 : T9SS PorKN ring complex

EntireName: T9SS PorKN ring complex
Components
  • Organelle or cellular component: T9SS PorKN ring complex

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Supramolecule #1: T9SS PorKN ring complex

SupramoleculeName: T9SS PorKN ring complex / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Porphyromonas gingivalis ATCC 33277 (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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C32 (32 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 8.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 10300
Initial angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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