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- EMDB-72625: Structure of fimbriae-like lipoprotein by Cryo Electron Microscopy -

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Basic information

Entry
Database: EMDB / ID: EMD-72625
TitleStructure of fimbriae-like lipoprotein by Cryo Electron Microscopy
Map data
Sample
  • Complex: ffp1 a type V pilin
    • Protein or peptide: Minor fimbrium subunit Mfa1 C-terminal domain-containing protein
Keywordsffp1 / porphyromonas gingivalis / pili / CELL ADHESION
Function / homologyFimbrial subunit protein, C-terminal / Major fimbrial subunit protein type IV, Fimbrillin, C-terminal / Prokaryotic membrane lipoprotein lipid attachment site profile. / Minor fimbrium subunit Mfa1 C-terminal domain-containing protein
Function and homology information
Biological speciesPorphyromonas gingivalis (bacteria) / Porphyromonas gingivalis W83 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsHanssen E / Gorasia DG / Reynolds EC / Veith PD
Funding support Australia, 1 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1193647 Australia
CitationJournal: Res Sq / Year: 2026
Title: Novel quadruple helical assembly of a Type V pilin in Porphyromonas gingivalis
Authors: Reynolds EC / Gorasia DG / Slakeski N / Gui M / Chen Y-Y / Moore C / Catmull D / Veith P / Dashper S / Hanssen E
History
DepositionSep 9, 2025-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72625.png

Downloads & links

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Map

FileDownload / File: emd_72625.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 400 pix.
= 528. Å		1.32 Å/pix.
x 400 pix.
= 528. Å		1.32 Å/pix.
x 400 pix.
= 528. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.31675744 - 0.9247663
Average (Standard dev.)0.0027998532 (±0.030896334)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 528.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72625_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72625_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_72625_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 : ffp1 a type V pilin

EntireName: ffp1 a type V pilin
Components
  • Complex: ffp1 a type V pilin
    • Protein or peptide: Minor fimbrium subunit Mfa1 C-terminal domain-containing protein

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Supramolecule #1: ffp1 a type V pilin

SupramoleculeName: ffp1 a type V pilin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Porphyromonas gingivalis (bacteria) / Strain: W83

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Macromolecule #1: Minor fimbrium subunit Mfa1 C-terminal domain-containing protein

MacromoleculeName: Minor fimbrium subunit Mfa1 C-terminal domain-containing protein
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis W83 (bacteria)
Molecular weightTheoretical: 46.953746 KDa
SequenceString: KGGTHDPLQS VRRITFLFFH ETDSKLLLSR TVEPTSDLSF DLKIPKQNYR LAVLVNSGSS YAAIIPEILL PTTAIQATSQ TLFESFAAY ETGNITSESE HSVTMANDQG LIKLLSTQIV DKKSQLSEAS RLSVNVEPCL ARVLVVGKPT ISGGEYTGDV S CYVIDVVP ...String:
KGGTHDPLQS VRRITFLFFH ETDSKLLLSR TVEPTSDLSF DLKIPKQNYR LAVLVNSGSS YAAIIPEILL PTTAIQATSQ TLFESFAAY ETGNITSESE HSVTMANDQG LIKLLSTQIV DKKSQLSEAS RLSVNVEPCL ARVLVVGKPT ISGGEYTGDV S CYVIDVVP QRIYPLRHLA KLSSGTNEAY GDNSPLADRY ASSWAEESIA AGVAYNNVYG YVKADMFDNP VAATKMQEKK TD FNLNQVA IYTKESTVNP KNYFTAYVPR VVLRAKYVPH GIPGVKPDEG WIEFQGRKMS LEQFKKYVDN PVSAGMALAD SIK KAKADN SLVYTGGFVS HGIQFYYKSQ NYYAIPIRHF DDEKAPNKDS YGRFGLVRNN EYILSVKSIT GAGSPIVPPV STTE AIEKE GYLPASIAVN QTTAHEQDVD L

UniProtKB: Minor fimbrium subunit Mfa1 C-terminal domain-containing protein

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMC4H11NO3.HCltris-HCL
50.0 mMNaClSodium Chloride
0.5 %C24H46O11n-Dodecyl-B-D-maltoside
1.0 MCH4N2OUrea
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR / Details: 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV
Details: Blot Force -1 Blot time 3 sec temp 22 degres C sample size 4ul.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 8909 / Average exposure time: 5.34 sec. / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 64000
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

Final reconstructionNumber classes used: 9
Applied symmetry - Helical parameters - Δz: 60.43 Å
Applied symmetry - Helical parameters - Δ&Phi: 25.86 °
Applied symmetry - Helical parameters - Axial symmetry: C4 (4 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 20069
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING ONLY
Segment selectionNumber selected: 21738 / Software - Name: cryoSPARC
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1-v4


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9y6o:
Structure of fimbriae-like lipoprotein by Cryo Electron Microscopy

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