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- EMDB-50025: Cryo-EM structure of the Pseudomonas aeruginosa PAO1 Type IV pilus -

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Basic information

Entry
Database: EMDB / ID: EMD-50025
TitleCryo-EM structure of the Pseudomonas aeruginosa PAO1 Type IV pilus
Map data
Sample
  • Complex: Pseudomonas aeruginosa PAO1 Type IV Pilus
    • Protein or peptide: Pilin
KeywordsType IV pilus / CELL ADHESION
Function / homologyFimbrial protein pilin / Pilin (bacterial filament) / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / pilus / cell adhesion / membrane / Pilin
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsOchner H / Boehning J / Wang Z / Tarafder A / Caspy I / Bharat TAM
Funding support United Kingdom, 4 items
OrganizationGrant numberCountry
Wellcome Trust225317/Z/22/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UP_1201/31 United Kingdom
Engineering and Physical Sciences Research CouncilEP/V026623/1 United Kingdom
The Lister Institute of Preventive MedicineLister Prize United Kingdom
CitationJournal: PLoS Pathog / Year: 2024
Title: Structure of the Pseudomonas aeruginosa PAO1 Type IV pilus.
Authors: Hannah Ochner / Jan Böhning / Zhexin Wang / Abul K Tarafder / Ido Caspy / Tanmay A M Bharat /
Abstract: Type IV pili (T4Ps) are abundant in many bacterial and archaeal species, where they play important roles in both surface sensing and twitching motility, with implications for adhesion, biofilm ...Type IV pili (T4Ps) are abundant in many bacterial and archaeal species, where they play important roles in both surface sensing and twitching motility, with implications for adhesion, biofilm formation and pathogenicity. While Type IV pilus (T4P) structures from other organisms have been previously solved, a high-resolution structure of the native, fully assembled T4P of Pseudomonas aeruginosa, a major human pathogen, would be valuable in a drug discovery context. Here, we report a 3.2 Å-resolution structure of the P. aeruginosa PAO1 T4P determined by electron cryomicroscopy (cryo-EM). PilA subunits constituting the T4P exhibit a classical pilin fold featuring an extended N-terminal α-helix linked to a C-terminal globular β-sheet-containing domain, which are packed tightly along the pilus, in line with models derived from previous cryo-EM data of the P. aeruginosa PAK strain. The N-terminal helices constitute the pilus core where they stabilise the tubular assembly via hydrophobic interactions. The α-helical core of the pilus is surrounded by the C-terminal globular domain of PilA that coats the outer surface of the pilus, mediating interactions with the surrounding environment. Comparison of the P. aeruginosa PAO1 T4P with T4P structures from other organisms, both at the level of the pilin subunits and the fully assembled pili, confirms previously described common architectural principles whilst highlighting key differences between members of this abundant class of prokaryotic filaments. This study provides a structural framework for understanding the molecular and cell biology of these important cellular appendages mediating interaction of prokaryotes to surfaces.
History
DepositionApr 5, 2024-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateDec 25, 2024-
Current statusDec 25, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50025.png

Downloads & links

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Map

FileDownload / File: emd_50025.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 400 pix.
= 329.6 Å		0.82 Å/pix.
x 400 pix.
= 329.6 Å		0.82 Å/pix.
x 400 pix.
= 329.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0383
Minimum - Maximum-0.061210725 - 0.11574289
Average (Standard dev.)0.0000031458221 (±0.0054348707)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 329.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_50025_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_50025_half_map_2.map
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Sample components

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Entire : Pseudomonas aeruginosa PAO1 Type IV Pilus

EntireName: Pseudomonas aeruginosa PAO1 Type IV Pilus
Components
  • Complex: Pseudomonas aeruginosa PAO1 Type IV Pilus
    • Protein or peptide: Pilin

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Supramolecule #1: Pseudomonas aeruginosa PAO1 Type IV Pilus

SupramoleculeName: Pseudomonas aeruginosa PAO1 Type IV Pilus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 15 KDa

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Macromolecule #1: Pilin

MacromoleculeName: Pilin / type: protein_or_peptide / ID: 1 / Number of copies: 23 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 14.878889 KDa
SequenceString:
FTLIELMIVV AIIGILAAIA IPQYQNYVAR SEGASALATI NPLKTTVEES LSRGIAGSKI KIGTTASTAT ETYVGVEPDA NKLGVIAVA IEDSGAGDIT FTFQTGTSSP KNATKVITLN RTADGVWACK STQDPMFTPK GCDN

UniProtKB: Pilin

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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

Concentration6.46 mg/mL
BufferpH: 7.5 / Details: 50 mM Tris pH 7.5, 150 mM NaCl
GridModel: Quantifoil R3.5/1 / Material: COPPER/RHODIUM / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 5679 / Average exposure time: 6.66 sec. / Average electron dose: 40.0 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: BRIGHT FIELD / Nominal defocus max: 2.5 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: 10.17 Å
Applied symmetry - Helical parameters - Δ&Phi: 87.39 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 114537
Startup modelType of model: OTHER / Details: Cylinder
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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