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

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Basic information

Entry
Database: PDB / ID: 9vkv
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 (E. coli)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.09 Å
AuthorsPetrova, T.E. / Glukhov, A.S. / Guskov, A. / Gabdulkhakov, A.G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of the type I pilus from Escherichia Coli and the surrounding water network
Authors: Petrova, T.E. / Glukhov, A.S. / Guskov, A. / Gabdulkhakov, A.G.
History
DepositionJun 24, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data 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
Water29,6171644
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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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 (strain K12) (bacteria) / References: UniProt: P04128
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1644 / 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
1EPU2.10.0particle selection
2PHENIX1.21.1_5286model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 114.75 ° / Axial rise/subunit: 7.71 Å / Axial symmetry: C1
3D reconstructionResolution: 2.09 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1593408 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 32.52 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007416875
ELECTRON MICROSCOPYf_angle_d0.676223070
ELECTRON MICROSCOPYf_chiral_restr0.04892880
ELECTRON MICROSCOPYf_plane_restr0.00463105
ELECTRON MICROSCOPYf_dihedral_angle_d15.24495520

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