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- EMDB-49649: Structural Basis of Pseudomonas FapC Biofilm-Forming Functional A... -

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Basic information

Entry
Database: EMDB / ID: EMD-49649
TitleStructural Basis of Pseudomonas FapC Biofilm-Forming Functional Amyloid Formation
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: To Be Published
Title: Structural Basis of Pseudomonas FapC Biofilm-Forming Functional Amyloid Formation
Authors: Hansen KH / Golcuk M / Byeon CB / Plechinger EB / Conway JF / Andreasen M / Gur M / Akbey U
History
DepositionMar 12, 2025-
Header (metadata) releaseJun 25, 2025-
Map releaseJun 25, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 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:
Structural Basis of Pseudomonas FapC Biofilm-Forming Functional Amyloid Formation

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