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

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Basic information

Entry
Database: PDB / ID: 9u4u
TitleStructure of the functional amyloid FapC from Pseudomonas sp.UK4
ComponentsFunctional amyloid subunit FapC
KeywordsPROTEIN FIBRIL / Functional amyloid
Function / homologypilus / cell adhesion / extracellular region / Functional amyloid subunit FapC
Function and homology information
Biological speciesPseudomonas sp. UK4 (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsCao, Q. / Yanting, J. / Wang, H.
Funding support China, 1items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2025Group: Data collection / Database references / Category: citation / em_admin / Item: _citation.journal_volume / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Functional amyloid subunit FapC
B: Functional amyloid subunit FapC
C: Functional amyloid subunit FapC


Theoretical massNumber of molelcules
Total (without water)75,0493
Polymers75,0493
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: 25016.334 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
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.
Source: (gene. exp.) Pseudomonas sp. UK4 (bacteria) / Gene: fapC, HZ99_04090, PSUK4_00030 / Production host: Escherichia coli (E. coli) / 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: Recombinant FapC protein / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Pseudomonas sp. UK4 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE

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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 defocus max: 3500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: -6 ° / Axial rise/subunit: 14.4 Å / Axial symmetry: C1
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35507 / Symmetry type: HELICAL
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0033201
ELECTRON MICROSCOPYf_angle_d0.5464323
ELECTRON MICROSCOPYf_dihedral_angle_d4.307435
ELECTRON MICROSCOPYf_chiral_restr0.039510
ELECTRON MICROSCOPYf_plane_restr0.002612

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