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- EMDB-65144: Cryo-EM structure of the type I pilus from Escherichia Coli and t... -

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Basic information

Entry
Database: EMDB / ID: EMD-65144
TitleCryo-EM structure of the type I pilus from Escherichia Coli and the surrounding water network
Map dataThis map is created by Cryosparc by applying a B-factor. A value of B-factor is estimated by Grinier plot and is equal to 77.4.
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) / Escherichia coli (strain K12) (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 2.09 Å
AuthorsPetrova TE / Glukhov AS / Guskov A / Gabdulkhakov AG
Funding support1 items
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 TE / Glukhov AS / Guskov A / Gabdulkhakov AG
History
DepositionJun 24, 2025-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65144.png

Downloads & links

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Map

FileDownload / File: emd_65144.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis map is created by Cryosparc by applying a B-factor. A value of B-factor is estimated by Grinier plot and is equal to 77.4.
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.836 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.204
Minimum - Maximum-0.80522 - 1.5193
Average (Standard dev.)0.0019156986 (±0.07299836)
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: raw output map from Cryosparc

Fileemd_65144_additional_1.map
Annotationraw output map from Cryosparc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65144_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65144_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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 (strain K12) (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: 1644 / 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: 7.71 Å
Applied symmetry - Helical parameters - Δ&Phi: 114.75 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.09 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1593408
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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