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- EMDB-28151: Cryo-EM reconstruction of the CS17 bacterial adhesion pili -

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Basic information

Entry
Database: EMDB / ID: EMD-28151
TitleCryo-EM reconstruction of the CS17 bacterial adhesion pili
Map dataPrimary map for the CS17 adhesion pili filament.
Sample
  • Organelle or cellular component: CS17 bacterial adhesion pili
    • Protein or peptide: CS17 fimbriae major subunit
Keywordsenterotoxigenic / adhesion pili / superelastic / helical reconstruction / CELL ADHESION
Function / homologyFimbrial major subunit, CS1-type / CS1 type fimbrial major subunit / pilus / CS17 fimbriae major subunit
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodhelical reconstruction / cryo EM / Resolution: 3.3 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-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28151.png

Downloads & links

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Map

FileDownload / File: emd_28151.map.gz / Format: CCP4 / Size: 29.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary map for the CS17 adhesion pili filament.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 198 pix.
= 213.444 Å		1.08 Å/pix.
x 198 pix.
= 213.444 Å		1.08 Å/pix.
x 198 pix.
= 213.444 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.078 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.038
Minimum - Maximum-0.20454963 - 0.28799662
Average (Standard dev.)0.00000068829763 (±0.013665794)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions198198198
Spacing198198198
CellA=B=C: 213.44398 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28151_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_28151_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_28151_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 : CS17 bacterial adhesion pili

EntireName: CS17 bacterial adhesion pili
Components
  • Organelle or cellular component: CS17 bacterial adhesion pili
    • Protein or peptide: CS17 fimbriae major subunit

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Supramolecule #1: CS17 bacterial adhesion pili

SupramoleculeName: CS17 bacterial adhesion pili / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli) / Strain: LSN 03-016011/A (O8:H-,LT,CS17)

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Macromolecule #1: CS17 fimbriae major subunit

MacromoleculeName: CS17 fimbriae major subunit / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 15.386173 KDa
SequenceString:
VEKNITVRAS VDPKLDLLQA DGTSLPDSIA LTYSSASNNF EVYSLNTAIH TNDKSKGVVV KLSASPVLSN IMKPNSQIPM KVTLGGKTL NTTDTEFTVD TLNFGTSGVE NVSSTQQLTI HADTQGTAPE AGNYQGIISL IMTQKT

UniProtKB: CS17 fimbriae major subunit

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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 on the Pelco EasiGlow machine
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 4921 / Average electron dose: 53.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 8.8 Å
Applied symmetry - Helical parameters - Δ&Phi: 108 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.1) / Number images used: 131194
Segment selectionNumber selected: 5358559 / 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)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-8ehs:
Cryo-EM reconstruction of the CS17 bacterial adhesion pili

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