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- EMDB-0724: FimA type V pilus from P.gingivalis -

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Basic information

Entry
Database: EMDB / ID: EMD-0724
TitleFimA type V pilus from P.gingivalis
Map dataFimA pilus cryo-EM reconstruction
Sample
  • Complex: Type V pilus (FimA)
    • Protein or peptide: Major fimbrium subunit FimA type-1
KeywordsType V pilus / FimA / Porphyromonas gingivalis / ATCC33277 / CELL ADHESION
Function / homology
Function and homology information


pilus / cell outer membrane / cell adhesion / structural molecule activity
Similarity search - Function
Porphyromonas gingivalis fimbrillin protein / : / FimA4 pilin C-terminal domain / Major fimbrial subunit protein, N-terminal / Major fimbrial subunit protein (FimA) / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Major fimbrium subunit FimA type-1
Similarity search - Component
Biological speciesPorphyromonas gingivalis ATCC 33277 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsShibata S / Shoji M
Funding support Japan, 5 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP18am0101076 Japan
Japan Society for the Promotion of Science (JSPS)JP17K17085 Japan
Japan Society for the Promotion of Science (JSPS)JP19K10083 Japan
Japan Society for the Promotion of Science (JSPS)JP16H05504 Japan
Japan Society for the Promotion of Science (JSPS)JP17K07318 Japan
CitationJournal: Nat Microbiol / Year: 2020
Title: Structure of polymerized type V pilin reveals assembly mechanism involving protease-mediated strand exchange.
Authors: Satoshi Shibata / Mikio Shoji / Kodai Okada / Hideyuki Matsunami / Melissa M Matthews / Katsumi Imada / Koji Nakayama / Matthias Wolf /
Abstract: Bacterial adhesion is a general strategy for host-microbe and microbe-microbe interactions. Adhesive pili are essential for colonization, biofilm formation, virulence and pathogenesis of many ...Bacterial adhesion is a general strategy for host-microbe and microbe-microbe interactions. Adhesive pili are essential for colonization, biofilm formation, virulence and pathogenesis of many environmental and pathogenic bacteria. Members of the class Bacteroidia have unique type V pili, assembled by protease-mediated polymerization. Porphyromonas gingivalis is the main contributor to periodontal disease and its type V pili are a key factor for its virulence. However, the structure of the polymerized pilus and its assembly mechanism are unknown. Here we show structures of polymerized and monomeric states of FimA stalk pilin from P. gingivalis, determined by cryo-electron microscopy and crystallography. The atomic model of assembled FimA shows that the C-terminal strand of a donor subunit is inserted into a groove in the β-sheet of an acceptor subunit after N-terminal cleavage by the protease RgpB. The C terminus of the donor strand is essential for polymerization. We propose that type V pili assemble via a sequential polar assembly mechanism at the cell surface, involving protease-mediated strand exchange, employed by various Gram-negative species belonging to the class Bacteroidia. Our results reveal functional surfaces related to pathogenic properties of polymerized FimA. These insights may facilitate development of antibacterial drugs.
History
DepositionJul 31, 2019-
Header (metadata) releaseFeb 26, 2020-
Map releaseApr 15, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 5.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6kmf
  • Surface level: 5.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6kmf
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0724.png

Downloads & links

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Map

FileDownload / File: emd_0724.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFimA pilus cryo-EM reconstruction
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 384 pix.
= 430.08 Å		1.12 Å/pix.
x 384 pix.
= 430.08 Å		1.12 Å/pix.
x 384 pix.
= 430.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.5 / Movie #1: 5.5
Minimum - Maximum-14.449788 - 22.173960000000001
Average (Standard dev.)0.000000001603835 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 430.08002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.121.121.12
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z430.080430.080430.080
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-14.45022.1740.000

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Supplemental data

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Sample components

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Entire : Type V pilus (FimA)

EntireName: Type V pilus (FimA)
Components
  • Complex: Type V pilus (FimA)
    • Protein or peptide: Major fimbrium subunit FimA type-1

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Supramolecule #1: Type V pilus (FimA)

SupramoleculeName: Type V pilus (FimA) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Porphyromonas gingivalis ATCC 33277 (bacteria)
Molecular weightTheoretical: 6 kDa/nm

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Macromolecule #1: Major fimbrium subunit FimA type-1

MacromoleculeName: Major fimbrium subunit FimA type-1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis ATCC 33277 (bacteria)
Molecular weightTheoretical: 36.488805 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: AFGVGDDESK VAKLTVMVYN GEQQEAIKSA ENATKVEDIK CSAGQRTLVV MANTGAMELV GKTLAEVKAL TTELTAENQE AAGLIMTAE PKTIVLKAGK NYIGYSGTGE GNHIENDPLK IKRVHARMAF TEIKVQMSAA YDNIYTFVPE KIYGLIAKKQ S NLFGATLV ...String:
AFGVGDDESK VAKLTVMVYN GEQQEAIKSA ENATKVEDIK CSAGQRTLVV MANTGAMELV GKTLAEVKAL TTELTAENQE AAGLIMTAE PKTIVLKAGK NYIGYSGTGE GNHIENDPLK IKRVHARMAF TEIKVQMSAA YDNIYTFVPE KIYGLIAKKQ S NLFGATLV NADANYLTGS LTTFNGAYTP ANYANVPWLS RNYVAPAADA PQGFYVLEND YSANGGTIHP TILCVYGKLQ KN GADLAGA DLAAAQAANW VDAEGKTYYP VLVNFNSNNY TYDSNYTPKN KIERNHKYDI KLTITGPGTN NPENPITESA HLN VQCTVA EWVLVGQNAT W

UniProtKB: Major fimbrium subunit FimA type-1

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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

Concentration1.5 mg/mL
BufferpH: 7.5 / Component - Concentration: 20.0 mM / Component - Formula: C4H11NO3 / Component - Name: Tris
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 100.1 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 1e-06 kPa / Details: Gatan Solarus
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV / Details: 3 second blot, 3.0uL.
Detailsmatured, polymerized state

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
TemperatureMin: 77.0 K / Max: 100.0 K
Alignment procedureComa free - Residual tilt: 0.1 mrad
Detailsnanoprobe, parallel beam illumination
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4000 pixel / Digitization - Dimensions - Height: 4000 pixel / Digitization - Frames/image: 1-75 / Number grids imaged: 1 / Number real images: 1153 / Average exposure time: 60.0 sec. / Average electron dose: 46.0 e/Å2
Details: frame alignment and dose weighting using motioncor2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Calibrated magnification: 125000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -2.5 µm / Nominal defocus min: -1.5 µm / Nominal magnification: 92000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Detailsframe alignment and integration with motioncor2 incl. dose weighting
Particle selectionNumber selected: 831459
Startup modelType of model: OTHER / Details: ab initio 3D (cisTEM)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1.0.1-beta) / Details: independent / Number images used: 61728
Initial angle assignmentType: OTHER / Software - Name: cisTEM (ver. 1.0.1-beta) / Details: cisTEM global orientation search
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cisTEM (ver. 1.0.1-beta) / Details: cisTEM
Final 3D classificationNumber classes: 2 / Avg.num./class: 59071 / Software - Name: cisTEM (ver. 1.0.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6jzj


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 128 / Target criteria: CC
Output model

PDB-6kmf:
FimA type V pilus from P.gingivalis

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