9P6H | pdb_00009p6h

Structure of P. gingivalis PorK and PorN complexes from cryo electron microscopy


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Insights into type IX secretion from PorKN cogwheel structure bound to PorG and attachment complexes.

Gorasia, D.G.Hanssen, E.Mudaliyar, M.Morton, C.J.Valimehr, S.Seers, C.Zhang, L.Doyle, M.T.Ghosal, D.Veith, P.D.Reynolds, E.C.

(2025) Nat Commun 16: 7735-7735

  • DOI: https://doi.org/10.1038/s41467-025-63163-1
  • Primary Citation of Related Structures:  
    9MYJ, 9P6H

  • PubMed Abstract: 

    The Type IX Secretion System exports proteins across the outer membrane (OM) of bacteria in the Bacteroidota phylum, however, the mechanistic details remain unknown. In Porphyromonas gingivalis the core components of the multi-protein complex are the Sov translocon, Attachment Complexes (PorQ, U, V, Z), PorLM molecular motors and PorKN rings. Here, we present a ~ 3.5 Å cryo-EM structure of the periplasmic rings comprising 32-33 subunits each of PorK and PorN. Additionally, we show the presence of a critical disulfide bond between PorK and the OM protein PorG that is essential for protein secretion and demonstrate that the Attachment Complexes bind to, and are localized above, the PorKN rings. Overall, each ring resembles a cogwheel with PorN forming cog-like projections that we propose engage with the PorLM motor to drive the rotation of the PorKN cogwheel together with PorG and associated Attachment Complexes, thus providing the energy to complete protein secretion and the coordinated cell surface attachment of the secreted cargo.


  • Organizational Affiliation
    • Oral Health Cooperative Research Centre, Melbourne Dental School, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia. gorasiad@unimelb.edu.au.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gliding motility protein GldN254Porphyromonas gingivalis W83Mutation(s): 0 
UniProt
Find proteins for Q7MXB4 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
Explore Q7MXB4 
Go to UniProtKB:  Q7MXB4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7MXB4
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Lipoprotein, putative447Porphyromonas gingivalis W83Mutation(s): 0 
UniProt
Find proteins for Q7MXB7 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
Explore Q7MXB7 
Go to UniProtKB:  Q7MXB7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7MXB7
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-beta-L-fucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-2)-[alpha-L-rhamnopyranose-(1-4)]alpha-D-mannopyranose
C, D
7O-Glycosylation
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-glucopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-2)-[alpha-L-rhamnopyranose-(1-4)]alpha-D-mannopyranose
E
4O-Glycosylation
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.5.1
MODEL REFINEMENTPHENIX1.19.2

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1123866
National Health and Medical Research Council (NHMRC, Australia)Australia1193647

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-16
    Type: Initial release
  • Version 1.1: 2025-09-03
    Changes: Data collection, Database references