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- EMDB-67574: Mfa1 type V pilus from P.gingivalis -

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Basic information

Entry
Database: EMDB / ID: EMD-67574
TitleMfa1 type V pilus from P.gingivalis
Map data
Sample
  • Complex: Mfa1 minor type V pilus
    • Protein or peptide: Minor fimbrium subunit Mfa1
    • Protein or peptide: Minor fimbrium subunit Mfa1
    • Protein or peptide: Minor fimbrium subunit Mfa1
  • Ligand: CALCIUM ION
KeywordsType V pilus / Mfa1 / Porphyromonas gingivalis / ATCC33277 / CELL ADHESION
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.99 Å
AuthorsShibata S / Matsunami H / Wolf M
Funding support Japan, 6 items
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, 2025-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_67574.png

Downloads & links

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Map

FileReleased
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 400 pix.
= 432. Å		1.08 Å/pix.
x 400 pix.
= 432. Å		1.08 Å/pix.
x 400 pix.
= 432. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.7
Minimum - Maximum-7.3643985 - 13.075332
Average (Standard dev.)-0.000864182 (±0.18626612)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 432.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_67574_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_67574_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 : Mfa1 minor type V pilus

EntireName: Mfa1 minor type V pilus
Components
  • Complex: Mfa1 minor type V pilus
    • Protein or peptide: Minor fimbrium subunit Mfa1
    • Protein or peptide: Minor fimbrium subunit Mfa1
    • Protein or peptide: Minor fimbrium subunit Mfa1
  • Ligand: CALCIUM ION

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Supramolecule #1: Mfa1 minor type V pilus

SupramoleculeName: Mfa1 minor type V pilus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Porphyromonas gingivalis ATCC 33277 (bacteria)

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Macromolecule #1: Minor fimbrium subunit Mfa1

MacromoleculeName: Minor fimbrium subunit Mfa1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis ATCC 33277 (bacteria)
Molecular weightTheoretical: 2.725075 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
QDTFMSVEVT VLPWKVHSYE VDL

UniProtKB: Minor fimbrium subunit Mfa1

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Macromolecule #2: Minor fimbrium subunit Mfa1

MacromoleculeName: Minor fimbrium subunit Mfa1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis ATCC 33277 (bacteria)
Molecular weightTheoretical: 55.633906 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GDGQDQANPD YHYVGEWAGK DKIEKVSIYM VPQGGPGLVE SAEDLDFGTY YENPTIDPAT HNAILKPKKG IKVNSAVGKT VKVYVVLND IAGKAKALLA NVNAADFDAK FKEIIELSTQ AQALGTVADG PNPATAAGKI AKKNGTTDET IMMTCLQPSD A LTIEAAVS ...String:
GDGQDQANPD YHYVGEWAGK DKIEKVSIYM VPQGGPGLVE SAEDLDFGTY YENPTIDPAT HNAILKPKKG IKVNSAVGKT VKVYVVLND IAGKAKALLA NVNAADFDAK FKEIIELSTQ AQALGTVADG PNPATAAGKI AKKNGTTDET IMMTCLQPSD A LTIEAAVS EANAIAGIKN QAKVTVERSV ARAMVSTKAQ SYEIKATTQI GEIAAGSVLA TITDIRWVVA QGERRQYLSK KR GTVPENT WVTPGSGFVP TSSTFHTNAT EYYDYAGLWE DHNTNEAVIS GTQVPTLADY QLQDVTGELA NALSGKFLLP NTH KSGANA ASSDYKRGNT AYVLVRAKFT PKKEAFIDRG KTYSDNTAVP EYVAGEDFFV GENGQFYVSM KSVTDPKVGG VAGM KAHKY VKGKVLYYAW LNPSTTSPDS WWNSPVVRNN IYHIHIKSIK KLGFNWNPLV PDPDPSNPEN PNNPDPNPDE PGTPV PTDP ENPLPDQDTF MSVEVTVLPW KVHSYEVDL

UniProtKB: Minor fimbrium subunit Mfa1

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Macromolecule #3: Minor fimbrium subunit Mfa1

MacromoleculeName: Minor fimbrium subunit Mfa1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis ATCC 33277 (bacteria)
Molecular weightTheoretical: 52.926863 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GDGQDQANPD YHYVGEWAGK DKIEKVSIYM VPQGGPGLVE SAEDLDFGTY YENPTIDPAT HNAILKPKKG IKVNSAVGKT VKVYVVLND IAGKAKALLA NVNAADFDAK FKEIIELSTQ AQALGTVADG PNPATAAGKI AKKNGTTDET IMMTCLQPSD A LTIEAAVS ...String:
GDGQDQANPD YHYVGEWAGK DKIEKVSIYM VPQGGPGLVE SAEDLDFGTY YENPTIDPAT HNAILKPKKG IKVNSAVGKT VKVYVVLND IAGKAKALLA NVNAADFDAK FKEIIELSTQ AQALGTVADG PNPATAAGKI AKKNGTTDET IMMTCLQPSD A LTIEAAVS EANAIAGIKN QAKVTVERSV ARAMVSTKAQ SYEIKATTQI GEIAAGSVLA TITDIRWVVA QGERRQYLSK KR GTVPENT WVTPGSGFVP TSSTFHTNAT EYYDYAGLWE DHNTNEAVIS GTQVPTLADY QLQDVTGELA NALSGKFLLP NTH KSGANA ASSDYKRGNT AYVLVRAKFT PKKEAFIDRG KTYSDNTAVP EYVAGEDFFV GENGQFYVSM KSVTDPKVGG VAGM KAHKY VKGKVLYYAW LNPSTTSPDS WWNSPVVRNN IYHIHIKSIK KLGFNWNPLV PDPDPSNPEN PNNPDPNPDE PGTPV PTDP ENPLPD

UniProtKB: Minor fimbrium subunit Mfa1

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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.25 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5nf2

Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 267383
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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