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- EMDB-50846: Cryo-EM structure of the type 1 pilus rod as part of the FimI-bou... -

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Basic information

Entry
Database: EMDB / ID: EMD-50846
TitleCryo-EM structure of the type 1 pilus rod as part of the FimI-bound usher complex (FimDHGFAnIC - body 1)
Map dataMap of the type 1 pilus rod as part of the FimI-bound usher complex FimDHGFAnIC - body 1 (sharpened)
Sample
  • Complex: FimDHGFAnIChis complex
    • Protein or peptide: Type-1 fimbrial protein, A chain
Keywordsrod / pilus / usher / termination / 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 (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsBachmann P / Afanasyev P / Boehringer D / Glockshuber R
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_201234 Switzerland
CitationJournal: To Be Published
Title: Cryo-EM structure of the type 1 pilus rod as part of the FimI-bound usher complex (FimDHGFAnIC - body 1)
Authors: Bachmann P / Afanasyev P / Boehringer D / Glockshuber R
History
DepositionJul 1, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50846.png

Downloads & links

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Map

FileDownload / File: emd_50846.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of the type 1 pilus rod as part of the FimI-bound usher complex FimDHGFAnIC - body 1 (sharpened)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 300 pix.
= 306. Å		1.02 Å/pix.
x 300 pix.
= 306. Å		1.02 Å/pix.
x 300 pix.
= 306. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.015381239 - 0.023557292
Average (Standard dev.)0.000021707103 (±0.00082176545)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 306.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Map of the type 1 pilus rod as...

Fileemd_50846_additional_1.map
AnnotationMap of the type 1 pilus rod as part of the FimI-bound usher complex FimDHGFAnIC - body 1 (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 rod...

Fileemd_50846_half_map_1.map
AnnotationHalf-map A of the type 1 pilus rod as part of the FimI-bound usher complex FimDHGFAnIC - body 1
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 rod...

Fileemd_50846_half_map_2.map
AnnotationHalf-map B of the type 1 pilus rod as part of the FimI-bound usher complex FimDHGFAnIC - body 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : FimDHGFAnIChis complex

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

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Supramolecule #1: FimDHGFAnIChis complex

SupramoleculeName: FimDHGFAnIChis complex / 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: 10 / 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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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average exposure time: 0.6 sec. / Average electron dose: 68.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
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: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 32594
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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