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- PDB-9nqd: Structure of Pseudomonas FapC Biofilm-Forming Functional Amyloid -

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Basic information

Entry
Database: PDB / ID: 9nqd
TitleStructure of Pseudomonas FapC Biofilm-Forming Functional Amyloid
ComponentsFunctional amyloid subunit FapC
KeywordsSTRUCTURAL PROTEIN / FapC Functional Amyloid Pseudomonas C / AMYLOID / FIBRIL / BIOFILM / FUNCTIONAL AMYLOID
Function / homologypilus / cell adhesion / extracellular region / Functional amyloid subunit FapC
Function and homology information
Biological speciesPseudomonas fluorescens (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsHansen, K.H. / Golcuk, M. / Byeon, C.B. / Plechinger, E.B. / Conway, J.F. / Andreasen, M. / Gur, M. / Akbey, U.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Adv / Year: 2025
Title: Structural basis of biofilm-forming functional amyloid FapC formation.
Authors: Kasper Holst Hansen / Mert Golcuk / Chang Hyeock Byeon / Abdulkadir Tunc / Emilie Buhl Plechinger / Morten K D Dueholm / James F Conway / Maria Andreasen / Mert Gur / Ümit Akbey /
Abstract: Biofilm-protected causes chronic infections that are difficult to treat. FapC, the major biofilm-forming functional amyloid in , is essential for biofilm integrity, yet its structural details remain ...Biofilm-protected causes chronic infections that are difficult to treat. FapC, the major biofilm-forming functional amyloid in , is essential for biofilm integrity, yet its structural details remain unresolved. Using an integrative structural biology approach, we combine a solution nuclear magnetic resonance-based structural ensemble of unfolded monomeric FapC, a ~3.3-angstrom-resolution cryo-electron microscopy (cryo-EM) density map of FapC fibril, and all-atom molecular dynamics (MD) simulations to capture the transition from the unfolded to folded monomer to the fibrillar fold, providing a complete structural view of FapC biogenesis. Cryo-EM reveals a unique irregular triple-layer β solenoid cross-β fibril composed of a single protofilament. MD simulations initiated from monomeric and fibrillar FapC mapped structural transitions, offering mechanistic insights into amyloid assembly and disassembly. Understanding FapC reveals how exploits functional amyloids for biofilm formation, and establishes a structural and mechanistic foundation for developing therapeutics targeting biofilm-related infection and antimicrobial resistance.
History
DepositionMar 12, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2025Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / struct
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
3: Functional amyloid subunit FapC
4: Functional amyloid subunit FapC
5: Functional amyloid subunit FapC
6: Functional amyloid subunit FapC
7: Functional amyloid subunit FapC
8: Functional amyloid subunit FapC
9: Functional amyloid subunit FapC
0: Functional amyloid subunit FapC
AA: Functional amyloid subunit FapC
AB: Functional amyloid subunit FapC
AC: Functional amyloid subunit FapC
AD: Functional amyloid subunit FapC


Theoretical massNumber of molelcules
Total (without water)270,89112
Polymers270,89112
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Functional amyloid subunit FapC / Amyloid-like fimbrin subunit FapC / ALF subunit FapC / Fibril amyloid subunit FapC


Mass: 22574.234 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: FapC 25-250, without signal peptide (1-24). / Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: UK4 / Gene: fapC, HZ99_04090, PSUK4_00030 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DXF5
Has protein modificationN

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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: FapC / Type: COMPLEX
Details: FapC. Residue between 25-250, without signal peptide. Additional methionine on the N-terminus and a histidine purification tag of LEHHHHHH at the C-terminus.
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 23.755 kDa/nm / Experimental value: YES
Source (natural)Organism: Pseudomonas fluorescens (bacteria) / Strain: UK4
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3)
Buffer solutionpH: 7.4
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 0.2 mili Bar / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 95 % / Chamber temperature: 295 K

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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: 165000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 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 / Temperature (max): 91 K / Temperature (min): 87 K
Image recordingAverage exposure time: 4.8 sec. / Electron dose: 45 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8870
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV
Image scansSampling size: 15 µm / Width: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.5particle selection
2EPU3.2image acquisitionTFS
4cryoSPARC4.5CTF correction
7UCSF ChimeraX1.8model fitting
9UCSF ChimeraX1.8initial Euler assignment
10UCSF ChimeraX1.8final Euler assignment
11cryoSPARC4.5classification
12cryoSPARC4.53D reconstruction
13UCSF ChimeraX1.8model refinement
14PHENIX1.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -2.266 ° / Axial rise/subunit: 14.562 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 762000
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71848 / Details: Determined by CryoSPARC 4.5. / Symmetry type: HELICAL
Atomic model buildingB value: 15.3 / Protocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingAccession code: C4IN70 / Chain residue range: 25-250 / Source name: AlphaFold / Type: in silico model

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