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- EMDB-50839: Cryo-EM structure of the type 1 pilus tip-to-rod transition -

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Basic information

Entry
Database: EMDB / ID: EMD-50839
TitleCryo-EM structure of the type 1 pilus tip-to-rod transition
Map dataMap of the type 1 pilus tip-to-rod transition complex (sharpened)
Sample
  • Complex: FimDHGFAnC
    • Protein or peptide: Type-1 fimbrial protein, A chain
    • Protein or peptide: Protein FimF
Keywordsrod / tip / usher / pilus / CELL ADHESION
Function / homology
Function and homology information


pilus assembly / pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / 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 / Protein FimF
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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_50839.png

Downloads & links

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Map

FileDownload / File: emd_50839.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of the type 1 pilus tip-to-rod transition complex (sharpened)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 256 pix.
= 331.776 Å		1.3 Å/pix.
x 256 pix.
= 331.776 Å		1.3 Å/pix.
x 256 pix.
= 331.776 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.296 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.7221657 - 2.421167
Average (Standard dev.)0.00033316918 (±0.061644837)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 331.776 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Map of the type 1 pilus tip-to-rod transition complex (unsharpened)

Fileemd_50839_additional_1.map
AnnotationMap of the type 1 pilus tip-to-rod transition complex (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 tip-to-rod transition complex

Fileemd_50839_half_map_1.map
AnnotationHalf-map A of the type 1 pilus tip-to-rod transition complex
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 tip-to-rod transition complex

Fileemd_50839_half_map_2.map
AnnotationHalf-map B of the type 1 pilus tip-to-rod transition complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : FimDHGFAnC

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

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Supramolecule #1: FimDHGFAnC

SupramoleculeName: FimDHGFAnC / 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: 6 / 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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Macromolecule #2: Protein FimF

MacromoleculeName: Protein FimF / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 16.177095 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ADSTITIRGY VRDNGCSVAA ESTNFTVDLM ENAAKQFNNI GATTPVVPFR ILLSPCGNAV SAVKVGFTGV ADSHNANLLA LENTVSAAS GLGIQLLNEQ QNQIPLNAPS SALSWTTLTP GKPNTLNFYA RLMATQVPVT AGHINATATF TLEYQ

UniProtKB: Protein FimF

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 1.1 sec. / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 127989
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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