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- PDB-6jzk: Structure of FimA type-1 (FimA1) prepilin of the type V major fimbrium -

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Basic information

Entry
Database: PDB / ID: 6jzk
TitleStructure of FimA type-1 (FimA1) prepilin of the type V major fimbrium
ComponentsMajor fimbrium subunit FimA type-1
KeywordsCELL ADHESION / Type V pili / Major fimbrial subunit protein
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
S,R MESO-TARTARIC ACID / Major fimbrium subunit FimA type-1
Similarity search - Component
Biological speciesPorphyromonas gingivalis ATCC 33277 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsOkada, K. / Shoji, M. / Nakayam, K. / Imada, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science16H05504 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
DepositionMay 2, 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 ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 17, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major fimbrium subunit FimA type-1
B: Major fimbrium subunit FimA type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6135
Polymers79,2742
Non-polymers3383
Water6,864381
1
A: Major fimbrium subunit FimA type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7292
Polymers39,6371
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15530 Å2
MethodPISA
2
B: Major fimbrium subunit FimA type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8833
Polymers39,6371
Non-polymers2462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area14940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.840, 85.452, 242.561
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 39637.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis ATCC 33277 (bacteria)
Gene: fimA, PGN_0180 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2RH54
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M Sodium citrate pH5.6, 1.8M ammonium sulfate, 0.2M sodium potassium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 16, 2018
RadiationMonochromator: Double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→48.5 Å / Num. obs: 44884 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 30.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.031 / Rrim(I) all: 0.059 / Net I/σ(I): 21.3
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 3585 / CC1/2: 0.949 / Rpim(I) all: 0.244 / Rrim(I) all: 0.468 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JZJ

6jzj


Resolution: 2.1→42.726 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.02
RfactorNum. reflection% reflection
Rfree0.24 1999 4.46 %
Rwork0.1892 --
obs0.1915 44790 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→42.726 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5231 0 21 381 5633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075345
X-RAY DIFFRACTIONf_angle_d0.8187277
X-RAY DIFFRACTIONf_dihedral_angle_d3.5563185
X-RAY DIFFRACTIONf_chiral_restr0.054839
X-RAY DIFFRACTIONf_plane_restr0.005946
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15250.27891390.24032982X-RAY DIFFRACTION100
2.1525-2.21070.3381410.24112995X-RAY DIFFRACTION100
2.2107-2.27580.31811390.24842997X-RAY DIFFRACTION100
2.2758-2.34920.33481400.24452994X-RAY DIFFRACTION100
2.3492-2.43320.3451430.23063036X-RAY DIFFRACTION100
2.4332-2.53060.29151420.21763033X-RAY DIFFRACTION100
2.5306-2.64570.26741400.2263011X-RAY DIFFRACTION100
2.6457-2.78520.33981410.23413037X-RAY DIFFRACTION100
2.7852-2.95970.28621440.22533053X-RAY DIFFRACTION100
2.9597-3.18810.30161410.21083042X-RAY DIFFRACTION100
3.1881-3.50880.21561440.19473065X-RAY DIFFRACTION100
3.5088-4.01620.22841450.16063111X-RAY DIFFRACTION100
4.0162-5.05870.1521470.13313135X-RAY DIFFRACTION100
5.0587-42.73480.19161530.16543300X-RAY DIFFRACTION100

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