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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 / homology
Function and homology information


pilus / cell adhesion / membrane
Similarity search - Function
Fimbrial protein pilin / Pilin (bacterial filament) / : / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like
Similarity search - Domain/homology
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: To Be Published
Title: Structure of the Pseudomonas aeruginosa PAO1 Type-IV pilus
Authors: Ochner H / Boehning J / Wang Z / Tarafder A / Caspy I / Bharat TAM
History
DepositionApr 5, 2024-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 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
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

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

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_50025_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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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