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

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Basic information

Entry
Database: PDB / ID: 9y6o
TitleStructure of fimbriae-like lipoprotein by Cryo Electron Microscopy
ComponentsMinor fimbrium subunit Mfa1 C-terminal domain-containing protein
KeywordsCELL ADHESION / ffp1 / porphyromonas gingivalis / pili
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 W83 (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsHanssen, E. / Gorasia, D.G. / Reynolds, E.C.
Funding support Australia, 1items
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, E.C. / Gorasia, D.G. / Slakeski, N. / Gui, M. / Chen, Y.-Y. / Moore, C. / Catmull, D. / Veith, P. / Dashper, S. / Hanssen, E.
History
DepositionSep 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Minor fimbrium subunit Mfa1 C-terminal domain-containing protein
B: Minor fimbrium subunit Mfa1 C-terminal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5014
Polymers93,9072
Non-polymers1,5932
Water00
1
A: Minor fimbrium subunit Mfa1 C-terminal domain-containing protein
B: Minor fimbrium subunit Mfa1 C-terminal domain-containing protein
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)1,146,01148
Polymers1,126,89024
Non-polymers19,12124
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
helical symmetry operation11
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryHelical symmetry: (Circular symmetry: 2 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 6 / Rise per n subunits: 60.43 Å / Rotation per n subunits: 25.86 °)

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Components

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


Mass: 46953.746 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis W83 (bacteria) / References: UniProt: Q7MTR3
#2: Polysaccharide beta-L-fucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-2)-[alpha-L- ...beta-L-fucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-2)-[alpha-L-rhamnopyranose-(1-4)]alpha-D-mannopyranose


Type: oligosaccharide / Mass: 796.719 Da / Num. of mol.: 2 / Source method: isolated from a natural source
DescriptorTypeProgram
LFucpb1-3DGlcpb1-3DGlcpa1-2[LRhapa1-4]DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/5,5,4/[a1122h-1a_1-5][a2122h-1a_1-5][a2122h-1b_1-5][a1221m-1b_1-5][a2211m-1a_1-5]/1-2-3-4-5/a2-b1_a4-e1_b3-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(2+1)][a-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-L-Fucp]{}}}[(4+1)][a-L-Rhap]{}}LINUCSPDB-CARE
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: ffp1 a type V pilin / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Porphyromonas gingivalis (bacteria) / Strain: W83
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMtris-HCLC4H11NO3.HCl1
250 mMSodium ChlorideNaCl1
30.5 %n-Dodecyl-B-D-maltosideC24H46O111
41 MUreaCH4N2O1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15 mA / Grid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 295 K
Details: Blot Force -1 Blot time 3 sec temp 22 degres C sample size 4ul

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 64000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 5.34 sec. / Electron dose: 54 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8909

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7Coot0.9.8.93model fitting
9PHENIX1.19.2_4158model refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Helical symmertyAngular rotation/subunit: 25.86 ° / Axial rise/subunit: 60.43 Å / Axial symmetry: C4
Particle selectionNum. of particles selected: 21738
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20069 / Num. of class averages: 9 / Symmetry type: HELICAL
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingAccession code: AF-Q7MTR3-F1-v4 / Source name: AlphaFold / Type: in silico model
RefinementHighest resolution: 3.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00217185
ELECTRON MICROSCOPYf_angle_d0.50923370
ELECTRON MICROSCOPYf_dihedral_angle_d5.4572405
ELECTRON MICROSCOPYf_chiral_restr0.0432720
ELECTRON MICROSCOPYf_plane_restr0.0042980

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