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- PDB-9ftt: Cryo-EM structure of the type 1 pilus rod as part of the FimA-bou... -

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Basic information

Entry
Database: PDB / ID: 9ftt
TitleCryo-EM structure of the type 1 pilus rod as part of the FimA-bound usher complex (FimDHGFAnC)
ComponentsType-1 fimbrial protein, A chain
KeywordsCELL ADHESION / chaperone / usher / pilus / rod
Function / homology
Function and homology information


cell adhesion involved in single-species biofilm formation / pilus / cell adhesion / identical protein binding
Similarity search - Function
Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily
Similarity search - Domain/homology
Type-1 fimbrial protein, A chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsBachmann, P. / Afanasyev, P. / Boehringer, D. / Glockshuber, R.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_201234 Switzerland
CitationJournal: Nat Commun / Year: 2025
Title: Structures of the Escherichia coli type 1 pilus during pilus rod assembly and after assembly termination.
Authors: Paul Bachmann / Pavel Afanasyev / Daniel Boehringer / Rudi Glockshuber /
Abstract: Uropathogenic Escherichia coli strains use filamentous type 1 pili to adhere to and invade uroepithelial cells. The pilus consists of a flexible tip fibrillum, formed by the adhesin FimH and the ...Uropathogenic Escherichia coli strains use filamentous type 1 pili to adhere to and invade uroepithelial cells. The pilus consists of a flexible tip fibrillum, formed by the adhesin FimH and the subunits FimG and FimF. The pilus rod is a helical assembly of up to 3000 copies of the main subunit FimA, terminated by a single copy of the subunit FimI that anchors the rod to the assembly platform FimD in the outer membrane. Although type 1 pilus assembly can be completely reconstituted in vitro, the precise mechanism of assembly termination on FimD is still unknown. Here, we present cryo-electron microscopy structures of the fully assembled pilus with all its components prior to and after incorporation of FimI, capped with the assembly chaperone FimC. The structures reveal that FimD positions the proximal end of the pilus rod at an angle of ca. 50 degrees relative to the plane of the outer membrane. Specific interactions between FimI and FimC, absent in the equivalent FimA-FimC interface of the non-terminated pilus, stabilize the assembly-terminated state. In addition, we present structures of the transition region between the tip fibrillum and the helical rod, showing how FimF aligns the tip fibrillum along the rod axis.
History
DepositionJun 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
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Revision 1.1Dec 17, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Type-1 fimbrial protein, A chain
C: Type-1 fimbrial protein, A chain
D: Type-1 fimbrial protein, A chain
E: Type-1 fimbrial protein, A chain
F: Type-1 fimbrial protein, A chain
G: Type-1 fimbrial protein, A chain
H: Type-1 fimbrial protein, A chain
I: Type-1 fimbrial protein, A chain
J: Type-1 fimbrial protein, A chain
K: Type-1 fimbrial protein, A chain


Theoretical massNumber of molelcules
Total (without water)159,66410
Polymers159,66410
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
Type-1 fimbrial protein, A chain / Type-1A pilin


Mass: 15966.440 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fimA, pilA, b4314, JW4277 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04128
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: FimDHGFAnC complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2800 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.1 sec. / Electron dose: 64 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2PHENIX1.21.1_5286:model refinement
3EPUimage acquisition
5cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11RELIONfinal Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119055 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00210171
ELECTRON MICROSCOPYf_angle_d0.38913897
ELECTRON MICROSCOPYf_dihedral_angle_d3.331472
ELECTRON MICROSCOPYf_chiral_restr0.0391738
ELECTRON MICROSCOPYf_plane_restr0.0021861

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