21CO | pdb_000021co

Mfa1 type V pilus from P.gingivalis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.99 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history

Literature

Cryo-EM structure of the native assembled Mfa type V pilus from the periodontal pathogen Porphyromonas gingivalis.

Shibata, S.Matsunami, H.Ouhara, K.Taniguchi, Y.Schreiber, M.T.Villar-Brillones, A.Nakayama, K.Shoji, M.Wolf, M.

(2026) Commun Biol 

  • DOI: https://doi.org/10.1038/s42003-026-10515-2
  • Primary Citation Related Structures: 
    21CO

  • PubMed Abstract: 

    Porphyromonas gingivalis is a primary pathogen causing periodontal disease. The cell has two kinds of type V pili, the Fim pilus and the Mfa pilus, both of which play essential roles in colonization, biofilm formation, and pathogenicity. The functional polymerized structure of the Fim pilus is known, whereas the structure and assembly mechanism of the Mfa pilus remain unclear. Here, we show the structure of the polymerized recombinant Mfa1 stalk pilin determined by cryo-electron microscopy at 3.0 Å resolution. The atomic model of the Mfa1 filament reveals that Mfa1 pilins polymerize by protease-mediated strand exchange and retain a Ca 2+ ion in the metal-binding pocket, which modulates immune recognition of the Mfa pilus by human cells. Furthermore, we elucidated the three-dimensional architecture of the streptococcal-binding region on the Mfa pilus. Our results further strengthen evidence that protease-mediated strand exchange is the universal assembly mechanism of type V pili. Our structure of the polymerized Mfa pilus, which represents the functional state on the cell surface, provides targets for antimicrobial drug design to treat periodontal disease and P. gingivalis-related systemic diseases.


  • Organizational Affiliation
    • Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan. sshibata@tottori-u.ac.jp.

Macromolecule Content 

  • Total Structure Weight: 111.37 kDa 
  • Atom Count: 7,850 
  • Modeled Residue Count: 1,026 
  • Deposited Residue Count: 1,026 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Minor fimbrium subunit Mfa123Porphyromonas gingivalis ATCC 33277Mutation(s): 0 
Gene Names: mfa1PGN_0287
UniProt
Find proteins for B2RHG1 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561))
Explore B2RHG1 
Go to UniProtKB:  B2RHG1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2RHG1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Minor fimbrium subunit Mfa1513Porphyromonas gingivalis ATCC 33277Mutation(s): 0 
Gene Names: mfa1PGN_0287
UniProt
Find proteins for B2RHG1 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561))
Explore B2RHG1 
Go to UniProtKB:  B2RHG1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2RHG1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Minor fimbrium subunit Mfa1490Porphyromonas gingivalis ATCC 33277Mutation(s): 0 
Gene Names: mfa1PGN_0287
UniProt
Find proteins for B2RHG1 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561))
Explore B2RHG1 
Go to UniProtKB:  B2RHG1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2RHG1
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.99 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)JapanJP18am0101076
Japan Society for the Promotion of Science (JSPS)JapanJP19K10083
Japan Society for the Promotion of Science (JSPS)Japan23K006530
Japan Society for the Promotion of Science (JSPS)JapanJP17K07318
Japan Society for the Promotion of Science (JSPS)Japan20K06581
Japan Agency for Medical Research and Development (AMED)JapanJP25ama121037

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-08
    Type: Initial release