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- EMDB-63855: Structure of the functional amyloid FapC from Pseudomonas sp.UK4 -

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Basic information

Entry
Database: EMDB / ID: EMD-63855
TitleStructure of the functional amyloid FapC from Pseudomonas sp.UK4
Map data
Sample
  • Complex: Recombinant FapC protein
    • Protein or peptide: Functional amyloid subunit FapC
KeywordsFunctional amyloid / PROTEIN FIBRIL
Function / homologypilus / cell adhesion / extracellular region / Functional amyloid subunit FapC
Function and homology information
Biological speciesPseudomonas sp. UK4 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsCao Q / Yanting J / Wang H
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Adv Mater / Year: 2025
Title: Natural Design of a Stabilized Cross-β Fold: Structure of the FuA FapC from Pseudomonas Sp. UK4 Reveals a Critical Role for Stacking of Imperfect Repeats.
Authors: Yanting Jiang / Samuel Peña-Díaz / Zhefei Zhang / Anders Ogechi Hostrup Daugberg / Marcos López Hernández / Janni Nielsen / Qiaojie Huang / Shenghan Qin / Morten K D Dueholm / Mingdong ...Authors: Yanting Jiang / Samuel Peña-Díaz / Zhefei Zhang / Anders Ogechi Hostrup Daugberg / Marcos López Hernández / Janni Nielsen / Qiaojie Huang / Shenghan Qin / Morten K D Dueholm / Mingdong Dong / Jan Skov Pedersen / Qin Cao / Daniel E Otzen / Huabing Wang /
Abstract: An essential structural component of bacterial biofilms is functional amyloid (FuA), which also has great potential as an engineerable nano-biomaterial. However, experimentally based high resolution ...An essential structural component of bacterial biofilms is functional amyloid (FuA), which also has great potential as an engineerable nano-biomaterial. However, experimentally based high resolution structures of FuA that resolve individual residues are lacking. A fully experimentally based 3.2 Å resolution cryo-electron microscopy density map of the FuA protein FapC from Pseudomonas sp. UK4 is presented, which reveals a Greek key-shaped protofilament. The structure supports bioinformatic identification of conserved motifs and is broadly consistent with the AlphaFold prediction but with important modifications. Each FapC monomer consists of three imperfect repeats (IRs), with each repeat forming one cross-β layer. An array of highly conserved Asn and Gln residues with an extensive H-bonding network underpins this conserved Greek key-shape and reveals the role of heterogeneous cross-β stacking in amyloid cross-seeding. The covariation of residues in the hydrophobic core among different IRs suggests a cooperative monomer folding process during fibril elongation, while heterogeneous stacking of IRs reduces charge repulsion between layers to stabilize the monomer fold. The FapC fibrils show intrinsic catalytic activity and strain-dependent nanomechanical properties. Combined with mutagenesis data, the structure provides mechanistic insights into formation of FapC FuA from disordered monomers and a structural foundation for the design of novel biomaterials.
History
DepositionMar 20, 2025-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63855.png

Downloads & links

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Map

FileDownload / File: emd_63855.map.gz / Format: CCP4 / Size: 5.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.93 Å/pix.
x 110 pix.
= 102.52 Å		0.93 Å/pix.
x 110 pix.
= 102.52 Å		0.93 Å/pix.
x 110 pix.
= 102.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.6
Minimum - Maximum-6.234381 - 11.336028000000001
Average (Standard dev.)0.000000000030992 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin-55-55-55
Dimensions110110110
Spacing110110110
CellA=B=C: 102.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63855_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_63855_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 : Recombinant FapC protein

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

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Supramolecule #1: Recombinant FapC protein

SupramoleculeName: Recombinant FapC protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas sp. UK4 (bacteria)

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Macromolecule #1: Functional amyloid subunit FapC

MacromoleculeName: Functional amyloid subunit FapC / type: protein_or_peptide / ID: 1
Details: Sequence reference for strain 'Pseudomonas sp. UK4' is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id P0DXF5.
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas sp. UK4 (bacteria)
Molecular weightTheoretical: 25.016334 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKPTMALKPL VFALAALMAV AAQAGPAEKW KPTPAPTGTV AAAVTDTQVS KDNKFDDTKT LNNAGANGSL SNSKGNLGAN IAAGSGNQQ DNAAAITSSA GDAATVFAVA DIYQESKDNK FTNKGTQNNA LLNNSANNSS GNVGVNVAAG QGNQQKNNLA I VTADGKNV ...String:
MKPTMALKPL VFALAALMAV AAQAGPAEKW KPTPAPTGTV AAAVTDTQVS KDNKFDDTKT LNNAGANGSL SNSKGNLGAN IAAGSGNQQ DNAAAITSSA GDAATVFAVA DIYQESKDNK FTNKGTQNNA LLNNSANNSS GNVGVNVAAG QGNQQKNNLA I VTADGKNV AAASNTEQVS LDNHFLNEAS SKHSYKPQYV VNNAGLLNSA NNASGNIGVN VAAGAGNQQS NTLTLGSGCT VC AAGTGSK LAF

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

Concentration2 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 14.4 Å
Applied symmetry - Helical parameters - Δ&Phi: -6 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 35507
CTF correctionType: NONE
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9u4u:
Structure of the functional amyloid FapC from Pseudomonas sp.UK4

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