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- PDB-9ots: Cryo-EM structure of the T9SS PORkN ring complex of P. Gingivalis -

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Basic information

Entry
Database: PDB / ID: 9ots
TitleCryo-EM structure of the T9SS PORkN ring complex of P. Gingivalis
Components
  • Por secretion system protein porK/gldK
  • Por secretion system protein porN/gldN
KeywordsMEMBRANE PROTEIN / T9SS / Type IX SECRETION SYSTEM / PORKN RING COMPLEX / PORPHYROMONAS GINGIVALIS / PROTEIN TRANSPORT
Function / homology
Function and homology information


formylglycine-generating oxidase activity
Similarity search - Function
Gliding motility associated protein GldN / Gliding motility associated protein GldN / : / Sulfatase-modifying factor enzyme / Sulfatase-modifying factor enzyme 1-like domain / Sulfatase-modifying factor enzyme superfamily / C-type lectin fold / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Por secretion system protein porN/gldN / Por secretion system protein porK/gldK
Similarity search - Component
Biological speciesPorphyromonas gingivalis ATCC 33277 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLiu, X. / Song, L. / Zheng, L. / Hu, B.
Funding support United States, 1items
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, R.J. / Cascales, E. / Hu, B.
History
DepositionMay 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0Aug 6, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Por secretion system protein porK/gldK
B: Por secretion system protein porK/gldK
C: Por secretion system protein porK/gldK
D: Por secretion system protein porN/gldN
E: Por secretion system protein porN/gldN
F: Por secretion system protein porN/gldN


Theoretical massNumber of molelcules
Total (without water)292,4966
Polymers292,4966
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Por secretion system protein porK/gldK


Mass: 55979.594 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Porphyromonas gingivalis ATCC 33277 (bacteria)
Strain: ATCC 33277 / References: UniProt: B2RLF0
#2: Protein Por secretion system protein porN/gldN


Mass: 41519.016 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Porphyromonas gingivalis ATCC 33277 (bacteria)
Strain: ATCC 33277 / References: UniProt: B2RLE7
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: T9SS PorKN ring complex / Type: ORGANELLE OR CELLULAR COMPONENT / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Porphyromonas gingivalis ATCC 33277 (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2500000 / Symmetry type: POINT
RefinementHighest resolution: 3.2 Å

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