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- PDB-21co: Mfa1 type V pilus from P.gingivalis -

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Basic information

Entry
Database: PDB / ID: 21co
TitleMfa1 type V pilus from P.gingivalis
Components(Minor fimbrium subunit Mfa1) x 3
KeywordsCELL ADHESION / Type V pilus / Mfa1 / Porphyromonas gingivalis / ATCC33277
Function / homologypilus shaft / : / Fimbrial subunit protein, C-terminal / Major fimbrial subunit protein type IV, Fimbrillin, C-terminal / outer membrane / cell outer membrane / cell-cell adhesion / Prokaryotic membrane lipoprotein lipid attachment site profile. / Minor fimbrium subunit Mfa1
Function and homology information
Biological speciesPorphyromonas gingivalis ATCC 33277 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.99 Å
AuthorsShibata, S. / Matsunami, H. / Wolf, M.
Funding support Japan, 6items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP18am0101076 Japan
Japan Society for the Promotion of Science (JSPS)JP19K10083 Japan
Japan Society for the Promotion of Science (JSPS)23K006530 Japan
Japan Society for the Promotion of Science (JSPS)JP17K07318 Japan
Japan Society for the Promotion of Science (JSPS)20K06581 Japan
Japan Agency for Medical Research and Development (AMED)JP25ama121037 Japan
CitationJournal: Commun Biol / Year: 2026
Title: Cryo-EM structure of the native assembled Mfa type V pilus from the periodontal pathogen Porphyromonas gingivalis.
Authors: Satoshi Shibata / Hideyuki Matsunami / Kazuhisa Ouhara / Yuri Taniguchi / Makoto Tokoro Schreiber / Alejandro Villar-Brillones / Koji Nakayama / Mikio Shoji / Matthias Wolf /
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, ...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 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.
History
DepositionDec 8, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Minor fimbrium subunit Mfa1
B: Minor fimbrium subunit Mfa1
C: Minor fimbrium subunit Mfa1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,3665
Polymers111,2863
Non-polymers802
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/peptide Minor fimbrium subunit Mfa1 / Pg-II fim a


Mass: 2725.075 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis ATCC 33277 (bacteria)
Gene: mfa1, PGN_0287 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2RHG1
#2: Protein Minor fimbrium subunit Mfa1 / Pg-II fim a


Mass: 55633.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis ATCC 33277 (bacteria)
Gene: mfa1, PGN_0287 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2RHG1
#3: Protein Minor fimbrium subunit Mfa1 / Pg-II fim a


Mass: 52926.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis ATCC 33277 (bacteria)
Gene: mfa1, PGN_0287 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2RHG1
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Mfa1 minor type V pilus / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Porphyromonas gingivalis ATCC 33277 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE-PROPANE

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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: 2250 nm / Nominal defocus min: 1500 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 32 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 267383 / Algorithm: FOURIER SPACE / Symmetry type: POINT

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