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- EMDB-49649: Structure of Pseudomonas FapC Biofilm-Forming Functional Amyloid -

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Basic information

Entry
Database: EMDB / ID: EMD-49649
TitleStructure of Pseudomonas FapC Biofilm-Forming Functional Amyloid
Map dataCryoSPARC Density.
Sample
  • Complex: FapC
    • Protein or peptide: Functional amyloid subunit FapC
KeywordsFapC Functional Amyloid Pseudomonas C / AMYLOID / FIBRIL / BIOFILM / FUNCTIONAL AMYLOID / STRUCTURAL PROTEIN
Function / homologypilus / cell adhesion / extracellular region / Functional amyloid subunit FapC
Function and homology information
Biological speciesPseudomonas fluorescens (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsHansen KH / Golcuk M / Byeon CB / Plechinger EB / Conway JF / Andreasen M / Gur M / Akbey U
Funding support1 items
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, 2025-
Header (metadata) releaseJun 25, 2025-
Map releaseJun 25, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49649.png

Downloads & links

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Map

FileDownload / File: emd_49649.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoSPARC Density.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 300 pix.
= 216. Å		0.72 Å/pix.
x 300 pix.
= 216. Å		0.72 Å/pix.
x 300 pix.
= 216. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.17482044 - 0.35872656
Average (Standard dev.)0.0019959193 (±0.010005905)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 216.00002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49649_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: DeepEM Enhanced CryoSPARC Density. TitghTarget.

Fileemd_49649_additional_1.map
AnnotationDeepEM Enhanced CryoSPARC Density. TitghTarget.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49649_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49649_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : FapC

EntireName: FapC
Components
  • Complex: FapC
    • Protein or peptide: Functional amyloid subunit FapC

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Supramolecule #1: FapC

SupramoleculeName: FapC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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.
Source (natural)Organism: Pseudomonas fluorescens (bacteria) / Strain: UK4
Molecular weightTheoretical: 23.755 kDa/nm

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Macromolecule #1: Functional amyloid subunit FapC

MacromoleculeName: Functional amyloid subunit FapC / type: protein_or_peptide / ID: 1 / Details: FapC 25-250, without signal peptide (1-24). / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas fluorescens (bacteria) / Strain: UK4
Molecular weightTheoretical: 22.574234 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GPAEKWKPTP APTGTVAAAV TDTQVSKDNK FDDTKTLNNA GANGSLSNSK GNLGANIAAG SGNQQDNAAA ITSSAGDAAT VFAVADIYQ ESKDNKFTNK GTQNNALLNN SANNSSGNVG VNVAAGQGNQ QKNNLAIVTA DGKNVAAASN TEQVSLDNHF L NEASSKHS ...String:
GPAEKWKPTP APTGTVAAAV TDTQVSKDNK FDDTKTLNNA GANGSLSNSK GNLGANIAAG SGNQQDNAAA ITSSAGDAAT VFAVADIYQ ESKDNKFTNK GTQNNALLNN SANNSSGNVG VNVAAGQGNQ QKNNLAIVTA DGKNVAAASN TEQVSLDNHF L NEASSKHS YKPQYVVNNA GLLNSANNAS GNIGVNVAAG AGNQQSNTLT LGSGCTVCAA GTGSKLAF

UniProtKB: Functional amyloid subunit FapC

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.02 kPa / Details: 0.2 mili Bar
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 87.0 K / Max: 91.0 K
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 8870 / Average exposure time: 4.8 sec. / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 14.562 Å
Applied symmetry - Helical parameters - Δ&Phi: -2.266 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Details: Determined by CryoSPARC 4.5. / Number images used: 71848
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionNumber selected: 762000 / Software - Name: cryoSPARC (ver. 4.5)
Startup modelType of model: INSILICO MODEL / In silico model: AF2 model: C4IN70
Final angle assignmentType: NOT APPLICABLE / Software - Name: UCSF ChimeraX (ver. 1.8)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

in70


Chain - Chain ID: 1 / Chain - Residue range: 25-250 / Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 15.3
Output model

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

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