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- PDB-9x67: Cryo-EM structure of the type I pilus from Escherichia Coli and t... -

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Basic information

Entry
Database: PDB / ID: 9x67
TitleCryo-EM structure of the type I pilus from Escherichia Coli and the surrounding water network
ComponentsType-1 fimbrial protein, A chain
KeywordsCELL ADHESION / Type-I 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 K-12 (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 1.85 Å
AuthorsPetrova, T.E. / Glukhov, A.S. / Stetsenko, A. / Guskov, A. / Gabdulkhakov, A.G.
Funding support1items
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, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type-1 fimbrial protein, A chain
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
L: Type-1 fimbrial protein, A chain
M: Type-1 fimbrial protein, A chain
N: Type-1 fimbrial protein, A chain
O: Type-1 fimbrial protein, A chain


Theoretical massNumber of molelcules
Total (without water)237,52915
Polymers237,52915
Non-polymers00
Water34,2831903
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: 15835.243 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P04128
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1903 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: Type 1 pilus rod assembled from FimA monomers / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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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: DIFFRACTION / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.1_5286model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 7.738 ° / Axial rise/subunit: 115 Å / Axial symmetry: C1
3D reconstructionResolution: 1.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 770491 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 20.93 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006416875
ELECTRON MICROSCOPYf_angle_d0.651923070
ELECTRON MICROSCOPYf_chiral_restr0.04582880
ELECTRON MICROSCOPYf_plane_restr0.00413105
ELECTRON MICROSCOPYf_dihedral_angle_d15.00495520

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