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- EMDB-50809: Cryo-EM map of the type 1 chaperone-usher pilus tip and rod - Con... -

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Basic information

Entry
Database: EMDB / ID: EMD-50809
TitleCryo-EM map of the type 1 chaperone-usher pilus tip and rod - Conformer 4
Map dataMap of the type 1 chaperone-usher pilus tip and rod - Conformer 4 (sharpened)
Sample
  • Complex: FimDHGFAnC complex
    • Protein or peptide: Type 1 fimbrin D-mannose specific adhesin
    • Protein or peptide: Protein FimG
    • Protein or peptide: Protein FimF
    • Protein or peptide: Type-1 fimbrial protein, A chain
Keywordspilus / tip / rod / CELL ADHESION
Function / homology
Function and homology information


pilus assembly / pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / D-mannose binding / host cell membrane / cell adhesion / identical protein binding
Similarity search - Function
FimH, mannose-binding domain / FimH, mannose binding / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily
Similarity search - Domain/homology
Type-1 fimbrial protein, A chain / Protein FimF / Protein FimG / Type 1 fimbrin D-mannose specific adhesin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 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 map of the type 1 chaperone-usher pilus tip and rod - Conformer 4
Authors: Bachmann P / Afanasyev P / Boehringer D / Glockshuber R
History
DepositionJun 27, 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_50809.png

Downloads & links

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Map

FileDownload / File: emd_50809.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of the type 1 chaperone-usher pilus tip and rod - Conformer 4 (sharpened)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 400 pix.
= 518.4 Å		1.3 Å/pix.
x 400 pix.
= 518.4 Å		1.3 Å/pix.
x 400 pix.
= 518.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.296 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0045
Minimum - Maximum-0.012413203 - 0.030390974
Average (Standard dev.)0.0000037662148 (±0.00095502107)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 518.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Map of the type 1 chaperone-usher pilus tip...

Fileemd_50809_additional_1.map
AnnotationMap of the type 1 chaperone-usher pilus tip and rod - Conformer 4 (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 chaperone-usher pilus...

Fileemd_50809_half_map_1.map
AnnotationHalf-map A of the type 1 chaperone-usher pilus tip and rod - Conformer 4
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 chaperone-usher pilus...

Fileemd_50809_half_map_2.map
AnnotationHalf-map B of the type 1 chaperone-usher pilus tip and rod - Conformer 4
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : FimDHGFAnC complex

EntireName: FimDHGFAnC complex
Components
  • Complex: FimDHGFAnC complex
    • Protein or peptide: Type 1 fimbrin D-mannose specific adhesin
    • Protein or peptide: Protein FimG
    • Protein or peptide: Protein FimF
    • Protein or peptide: Type-1 fimbrial protein, A chain

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Supramolecule #1: FimDHGFAnC complex

SupramoleculeName: FimDHGFAnC 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 fimbrin D-mannose specific adhesin

MacromoleculeName: Type 1 fimbrin D-mannose specific adhesin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: FACKTANGTA IPIGGGSANV YVNLAPVVNV GQNLVVDLST QIFCHNDYPE TITDYVTLQR GSAYGGVLSN FSGTVKYSGS SYPFPTTSET PRVVYNSRTD KPWPVALYLT PVSSAGGVAI KAGSLIAVLI LRQTNNYNSD DFQFVWNIYA NNDVVVPTGG CDVSARDVTV ...String:
FACKTANGTA IPIGGGSANV YVNLAPVVNV GQNLVVDLST QIFCHNDYPE TITDYVTLQR GSAYGGVLSN FSGTVKYSGS SYPFPTTSET PRVVYNSRTD KPWPVALYLT PVSSAGGVAI KAGSLIAVLI LRQTNNYNSD DFQFVWNIYA NNDVVVPTGG CDVSARDVTV TLPDYPGSVP IPLTVYCAKS QNLGYYLSGT TADAGNSIFT NTASFSPAQG VGVQLTRNGT IIPANNTVSL GAVGTSAVSL GLTANYARTG GQVTAGNVQS IIGVTFVYQ

UniProtKB: Type 1 fimbrin D-mannose specific adhesin

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Macromolecule #2: Protein FimG

MacromoleculeName: Protein FimG / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ADVTITVNGK VVAKPCTVST TNATVDLGDL YSFSLMSAGA ASAWHDVALE LTNCPVGTSR VTASFSGAAD STGYYKNQGT AQNIQLELQD DSGNTLNTGA TKTVQVDDSS QSAHFPLQVR ALTVNGGATQ GTIQAVISIT YTYS

UniProtKB: Protein FimG

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Macromolecule #3: Protein FimF

MacromoleculeName: Protein FimF / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
LAADSTITIR GYVRDNGCSV AAESTNFTVD LMENAAKQFN NIGATTPVVP FRILLSPCGN AVSAVKVGFT GVADSHNANL LALENTVSAA SGLGIQLLNE QQNQIPLNAP SSALSWTTLT PGKPNTLNFY ARLMATQVPV TAGHINATAT FTLEYQ

UniProtKB: Protein FimF

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Macromolecule #4: Type-1 fimbrial protein, A chain

MacromoleculeName: Type-1 fimbrial protein, A chain / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MAATTVNGGT VHFKGEVVNA ACAVDAGSVD QTVQLGQVRT ASLAQEGATS SAVGFNIQLN DCDTNVASKA AVAFLGTAID AGHTNVLALQ SSAAGSATNV GVQILDRTGA ALTLDGATFS SETTLNNGTN TIPFQARYFA TGAATPGAAN ADATFKVQYQ

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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 1.1 sec. / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
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: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 33742
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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