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- EMDB-28150: Cryo-EM reconstruction of the CFA/I bacterial adhesion pili -

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Basic information

Entry
Database: EMDB / ID: EMD-28150
TitleCryo-EM reconstruction of the CFA/I bacterial adhesion pili
Map dataPrimary map for the CFA/1 adhesion pili filament.
Sample
  • Organelle or cellular component: CFA/I bacterial adhesion pili
    • Protein or peptide: CFA/I fimbrial subunit B
Function / homologyFimbrial major subunit, CS1-type / CS1 type fimbrial major subunit / pilus / CFA/I fimbrial subunit B
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodhelical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsDoran MH / Bullitt E
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R21AI156236-01 United States
CitationJournal: Structure / Year: 2023
Title: Three structural solutions for bacterial adhesion pilus stability and superelasticity.
Authors: Matthew H Doran / Joseph L Baker / Tobias Dahlberg / Magnus Andersson / Esther Bullitt /
Abstract: Bacterial adhesion pili are key virulence factors that mediate host-pathogen interactions in diverse epithelial environments. Deploying a multimodal approach, we probed the structural basis ...Bacterial adhesion pili are key virulence factors that mediate host-pathogen interactions in diverse epithelial environments. Deploying a multimodal approach, we probed the structural basis underpinning the biophysical properties of pili originating from enterotoxigenic (ETEC) and uropathogenic bacteria. Using cryo-electron microscopy we solved the structures of three vaccine target pili from ETEC bacteria, CFA/I, CS17, and CS20. Pairing these and previous pilus structures with force spectroscopy and steered molecular dynamics simulations, we find a strong correlation between subunit-subunit interaction energies and the force required for pilus unwinding, irrespective of genetic similarity. Pili integrate three structural solutions for stabilizing their assemblies: layer-to-layer interactions, N-terminal interactions to distant subunits, and extended loop interactions from adjacent subunits. Tuning of these structural solutions alters the biophysical properties of pili and promotes the superelastic behavior that is essential for sustained bacterial attachment.
History
DepositionSep 14, 2022-
Header (metadata) releaseMar 22, 2023-
Map releaseMar 22, 2023-
UpdateMay 17, 2023-
Current statusMay 17, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28150.png

Downloads & links

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Map

FileDownload / File: emd_28150.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary map for the CFA/1 adhesion pili filament.
Voxel sizeX=Y=Z: 1.078 Å
Density
Contour LevelBy AUTHOR: 0.036
Minimum - Maximum-0.1415716 - 0.22948536
Average (Standard dev.)0.000108274486 (±0.011622449)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 215.59999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28150_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1.

Fileemd_28150_half_map_1.map
AnnotationHalf map 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2.

Fileemd_28150_half_map_2.map
AnnotationHalf map 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CFA/I bacterial adhesion pili

EntireName: CFA/I bacterial adhesion pili
Components
  • Organelle or cellular component: CFA/I bacterial adhesion pili
    • Protein or peptide: CFA/I fimbrial subunit B

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Supramolecule #1: CFA/I bacterial adhesion pili

SupramoleculeName: CFA/I bacterial adhesion pili / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli) / Strain: BL21-AI

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Macromolecule #1: CFA/I fimbrial subunit B

MacromoleculeName: CFA/I fimbrial subunit B / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 14.968839 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
VEKNITVTAS VDPAIDLLQA DGNALPSAVK LAYSPASKTF ESYRVMTQVH TNDATKKVIV KLADTPQLTD VLNSTVQMPI SVSWGGQVL STTAKEFEAA ALGYSASGVN GVSSSQELVI SAAPKTAGTA PTAGNYSGVV SLVMTLG

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.4
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Details: 15 mA with the Pelco EasiGlow Machine
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 4809 / Average electron dose: 53.7 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Segment selectionNumber selected: 6094726 / Software - Name: RELION (ver. 3.1.1)
Startup modelType of model: OTHER / Details: solid featureless cylinder
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.1.1)
Final reconstructionApplied symmetry - Helical parameters - Δz: 8.505 Å
Applied symmetry - Helical parameters - Δ&Phi: 113.37 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.1) / Number images used: 325069
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6nrv

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-8ehr:
Cryo-EM reconstruction of the CFA/I bacterial adhesion pili

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