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- EMDB-50846: Cryo-EM structure of the type 1 pilus rod as part of the FimI-bou... -

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Basic information

Entry
Database: EMDB / ID: EMD-50846
TitleCryo-EM structure of the type 1 pilus rod as part of the FimI-bound usher complex (FimDHGFAnIC - body 1)
Map dataMap of the type 1 pilus rod as part of the FimI-bound usher complex FimDHGFAnIC - body 1 (sharpened)
Sample
  • Complex: FimDHGFAnIChis complex
    • Protein or peptide: Type-1 fimbrial protein, A chain
Keywordsrod / pilus / usher / termination / CELL ADHESION
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsBachmann P / Afanasyev P / Boehringer D / Glockshuber R
Funding support Switzerland, 1 items
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
DepositionJul 1, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50846.png

Downloads & links

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Map

FileDownload / File: emd_50846.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of the type 1 pilus rod as part of the FimI-bound usher complex FimDHGFAnIC - body 1 (sharpened)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 300 pix.
= 306. Å		1.02 Å/pix.
x 300 pix.
= 306. Å		1.02 Å/pix.
x 300 pix.
= 306. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.015381239 - 0.023557292
Average (Standard dev.)0.000021707103 (±0.00082176545)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 306.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Map of the type 1 pilus rod as...

Fileemd_50846_additional_1.map
AnnotationMap of the type 1 pilus rod as part of the FimI-bound usher complex FimDHGFAnIC - body 1 (unsharpened)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map A of the type 1 pilus rod...

Fileemd_50846_half_map_1.map
AnnotationHalf-map A of the type 1 pilus rod as part of the FimI-bound usher complex FimDHGFAnIC - body 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B of the type 1 pilus rod...

Fileemd_50846_half_map_2.map
AnnotationHalf-map B of the type 1 pilus rod as part of the FimI-bound usher complex FimDHGFAnIC - body 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : FimDHGFAnIChis complex

EntireName: FimDHGFAnIChis complex
Components
  • Complex: FimDHGFAnIChis complex
    • Protein or peptide: Type-1 fimbrial protein, A chain

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Supramolecule #1: FimDHGFAnIChis complex

SupramoleculeName: FimDHGFAnIChis complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Type-1 fimbrial protein, A chain

MacromoleculeName: Type-1 fimbrial protein, A chain / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 15.96644 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MAATTVNGGT VHFKGEVVNA ACAVDAGSVD QTVQLGQVRT ASLAQEGATS SAVGFNIQLN DCDTNVASKA AVAFLGTAID AGHTNVLAL QSSAAGSATN VGVQILDRTG AALTLDGATF SSETTLNNGT NTIPFQARYF ATGAATPGAA NADATFKVQY Q

UniProtKB: Type-1 fimbrial protein, A chain

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average exposure time: 0.6 sec. / Average electron dose: 68.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 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

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 32594
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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