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- EMDB-66617: Cryo-EM structure of the type I pilus from Escherichia Coli and t... -

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Basic information

Entry
Database: EMDB / ID: EMD-66617
TitleCryo-EM structure of the type I pilus from Escherichia Coli and the surrounding water network
Map dataSharpened map. B-factor=55.7 A**2
Sample
  • Complex: Type 1 pilus rod assembled from FimA monomers
    • Protein or peptide: Type-1 fimbrial protein, A chain
  • Ligand: water
KeywordsType-I pilus rod / 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 K-12 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 1.85 Å
AuthorsPetrova TE / Glukhov AS / Stetsenko A / Guskov A / Gabdulkhakov AG
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: FEBS J / Year: 2026
Title: Determination of the water network surrounding the type I pilus from Escherichia coli by cryo-electron microscopy.
Authors: Tatiana E Petrova / Anatoly S Glukhov / Artem Stetsenko / Albert Guskov / Azat G Gabdulkhakov /
Abstract: Type 1 pili are protein filamentous surface structures of Gram-negative bacteria that mediate adhesion to host and play a crucial role in infection. Here, we report the cryogenic electron microscopy ...Type 1 pili are protein filamentous surface structures of Gram-negative bacteria that mediate adhesion to host and play a crucial role in infection. Here, we report the cryogenic electron microscopy structure of the type 1 pilus from uropathogenic E. coli K-12 comprising 15 subunits of the major protein pilin FimA. The final local resolution of electron microscopy reconstruction was estimated to reach 1.85 Å, which is higher than that of the previously published structure. This improvement in the resolution enabled us to refine side-chain conformations to reliably determine the distances between the side-chain residues participating in the intersubunit interactions and determine a network of water molecules surrounding the pilus rod. The analysis revealed that water contributes to intersubunit stabilization both through discrete bridging interactions and through extended hydrogen-bonded clusters, thereby supporting both the rigidity and flexibility of the filament. Comparison with a homologous high-resolution pilus model from enterotoxigenic E. coli showed that the vast majority of 'conserved' water molecules, that is, those that are present at equivalent positions in different subunits of our model occupy also equivalent positions across the two structures, underscoring their functional relevance. At the same time, sequence-specific differences in hydration patterns were observed. These findings highlight the structural and functional importance of water in pilus architecture and provide a more detailed molecular framework for understanding bacterial adhesion.
History
DepositionOct 15, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66617.png

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Map

FileDownload / File: emd_66617.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map. B-factor=55.7 A**2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 256 pix.
= 214.016 Å		0.84 Å/pix.
x 256 pix.
= 214.016 Å		0.84 Å/pix.
x 256 pix.
= 214.016 Å

Surface

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Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.836 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.077
Minimum - Maximum-0.25072736 - 0.5907155
Average (Standard dev.)0.001251822 (±0.02661117)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 214.016 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map

Fileemd_66617_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_66617_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_66617_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

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Sample components

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Entire : Type 1 pilus rod assembled from FimA monomers

EntireName: Type 1 pilus rod assembled from FimA monomers
Components
  • Complex: Type 1 pilus rod assembled from FimA monomers
    • Protein or peptide: Type-1 fimbrial protein, A chain
  • Ligand: water

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Supramolecule #1: Type 1 pilus rod assembled from FimA monomers

SupramoleculeName: Type 1 pilus rod assembled from FimA monomers / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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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: 15 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 15.835243 KDa
SequenceString:
AATTVNGGTV HFKGEVVNAA CAVDAGSVDQ TVQLGQVRTA SLAQEGATSS AVGFNIQLND CDTNVASKAA VAFLGTAIDA GHTNVLALQ SSAAGSATNV GVQILDRTGA ALTLDGATFS SETTLNNGTN TIPFQARYFA TGAATPGAAN ADATFKVQYQ

UniProtKB: Type-1 fimbrial protein, A chain

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 1903 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 115.0 Å
Applied symmetry - Helical parameters - Δ&Phi: 7.738 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 1.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 770491
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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