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

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Basic information

Entry
Database: PDB / ID: 6kmf
TitleFimA type V pilus from P.gingivalis
ComponentsMajor fimbrium subunit FimA type-1
KeywordsCELL ADHESION / Type V pilus / FimA / Porphyromonas gingivalis / ATCC33277
Function / homology
Function and homology information


pilus / cell outer membrane / cell adhesion / structural molecule activity
Similarity search - Function
Porphyromonas gingivalis fimbrillin protein / Fimbrial subunit protein, C-terminal / Major fimbrial subunit protein type IV, Fimbrillin, C-terminal / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsShibata, S. / Shoji, M. / Matsunami, H. / Matthews, M. / Imada, K. / Nakayama, K. / Wolf, M.
Funding support Japan, 5items
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, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 17, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Assembly

Deposited unit
A: Major fimbrium subunit FimA type-1
B: Major fimbrium subunit FimA type-1
C: Major fimbrium subunit FimA type-1
D: Major fimbrium subunit FimA type-1


Theoretical massNumber of molelcules
Total (without water)145,9554
Polymers145,9554
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Major fimbrium subunit FimA type-1 / Fimbrillin / Fimbrilin / Major fimbrial subunit protein type I


Mass: 36488.805 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis ATCC 33277 (bacteria)
Gene: fimA, PGN_0180 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: B2RH54

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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: Type V pilus (FimA) / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 6 kDa/nm / Experimental value: NO
Source (natural)Organism: Porphyromonas gingivalis ATCC 33277 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21 (bacteria) / Strain: BL21
Buffer solutionpH: 7.5
Buffer componentConc.: 20 mM / Name: Tris / Formula: C4H11NO3
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: matured, polymerized state
Specimen supportDetails: Gatan Solarus / Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 289 K / Details: 3 second blot, 3.0uL

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA / Details: nanoprobe, parallel beam illumination
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 92000 X / Calibrated magnification: 125000 X / Nominal defocus max: -2500 nm / Nominal defocus min: -1500 nm / Cs: 2.7 mm / C2 aperture diameter: 30 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 K / Temperature (min): 77 K / Residual tilt: 0.1 mradians
Image recordingAverage exposure time: 60 sec. / Electron dose: 46 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1153
Details: frame alignment and dose weighting using motioncor2
Image scansSampling size: 14 µm / Width: 4000 / Height: 4000 / Movie frames/image: 75 / Used frames/image: 1-75

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Processing

EM software
IDNameVersionCategoryDetails
2EPU2.1.0image acquisition
4CTFFIND4.1CTF correction
7Coot0.8.9model fitting
9cisTEM1.0.1-betainitial Euler assignment
10cisTEM1.0.1-betafinal Euler assignment
11cisTEM1.0.1classification
12cisTEM1.0.1-beta3D reconstruction
13PHENIX1.14-3260model refinementphenix.real_space_refine
Image processingDetails: frame alignment and integration with motioncor2 incl. dose weighting
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 831459
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61728 / Algorithm: FOURIER SPACE / Details: independent / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 128 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: CC
Atomic model buildingPDB-ID: 6JZJ

6jzj


Pdb chain-ID: A / Accession code: 6JZJ / Source name: PDB / Type: experimental model

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