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- EMDB-8740: Cryo-EM reconstruction of PAK pilus from Pseudomonas aeruginosa -

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Basic information

Entry
Database: EMDB / ID: EMD-8740
TitleCryo-EM reconstruction of PAK pilus from Pseudomonas aeruginosa
Map dataPAK pilus from Pseudomonas aeruginosa
Sample
  • Complex: Pseudomonas aeruginosa Type IV pilin filament
    • Protein or peptide: Fimbrial protein
Function / homology
Function and homology information


pilus / cell adhesion / membrane
Similarity search - Function
Fimbrial protein pilin / Pilin (bacterial filament) / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa PAK (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 8.0 Å
AuthorsWang F / Osinksi T / Orlova A / Altindal T / Craig L / Egelman EH
Funding support United States, France, Canada, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI114902 United States
French National Research AgencyANR14CE14001002 France
Canadian Institutes of Health Research (CIHR)MOP125959 Canada
Fondation pour la Recherche Medicale France
CitationJournal: Structure / Year: 2017
Title: Cryoelectron Microscopy Reconstructions of the Pseudomonas aeruginosa and Neisseria gonorrhoeae Type IV Pili at Sub-nanometer Resolution.
Authors: Fengbin Wang / Mathieu Coureuil / Tomasz Osinski / Albina Orlova / Tuba Altindal / Gaël Gesbert / Xavier Nassif / Edward H Egelman / Lisa Craig /
Abstract: We report here cryoelectron microscopy reconstructions of type IV pili (T4P) from two important human pathogens, Pseudomonas aeruginosa and Neisseria gonorrhoeae, at ∼ 8 and 5 Å resolution, ...We report here cryoelectron microscopy reconstructions of type IV pili (T4P) from two important human pathogens, Pseudomonas aeruginosa and Neisseria gonorrhoeae, at ∼ 8 and 5 Å resolution, respectively. The two structures reveal distinct arrangements of the pilin globular domains on the pilus surfaces, which impart different helical parameters, but similar packing of the conserved N-terminal α helices, α1, in the filament core. In contrast to the continuous α helix seen in the X-ray crystal structures of the P. aeruginosa and N. gonorrhoeae pilin subunits, α1 in the pilus filaments has a melted segment located between conserved helix-breaking residues Gly14 and Pro22, as seen for the Neisseria meningitidis T4P. Using mutagenesis we show that Pro22 is critical for pilus assembly, as are Thr2 and Glu5, which are positioned to interact in the hydrophobic filament core. These structures provide a framework for understanding T4P assembly, function, and biophysical properties.
History
DepositionMay 24, 2017-
Header (metadata) releaseJun 14, 2017-
Map releaseJul 12, 2017-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5vxy
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5vxy
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8740.png

Downloads & links

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Map

FileDownload / File: emd_8740.map.gz / Format: CCP4 / Size: 13.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPAK pilus from Pseudomonas aeruginosa
Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy EMDB: 0.6 / Movie #1: 0.6
Minimum - Maximum-0.6075344 - 1.1473567
Average (Standard dev.)0.10802666 (±0.24889718)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-175
Dimensions100100350
Spacing100100350
CellA: 104.99999 Å / B: 104.99999 Å / C: 367.49997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z100100350
origin x/y/z0.0000.0000.000
length x/y/z105.000105.000367.500
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS-50-50-175
NC/NR/NS100100350
D min/max/mean-0.6081.1470.108

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Supplemental data

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Sample components

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Entire : Pseudomonas aeruginosa Type IV pilin filament

EntireName: Pseudomonas aeruginosa Type IV pilin filament
Components
  • Complex: Pseudomonas aeruginosa Type IV pilin filament
    • Protein or peptide: Fimbrial protein

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Supramolecule #1: Pseudomonas aeruginosa Type IV pilin filament

SupramoleculeName: Pseudomonas aeruginosa Type IV pilin filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas aeruginosa PAK (bacteria) / Strain: PAK/2pfs

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Macromolecule #1: Fimbrial protein

MacromoleculeName: Fimbrial protein / type: protein_or_peptide / ID: 1 / Number of copies: 21 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAK (bacteria) / Strain: PAK/2pfs
Molecular weightTheoretical: 15.02118 KDa
SequenceString:
FTLIELMIVV AIIGILAAIA IPQYQNYVAR SEGASALASV NPLKTTVEEA LSRGWSVKSG TGTEDATKKE VPLGVAADAN KLGTIALKP DPADGTADIT LTFTMGGAGP KNKGKIITLT RTAADGLWKC TSDQDEQFIP KGCSR

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 9 / Details: 50 mM CHES buffer
GridPretreatment - Type: PLASMA CLEANING / Details: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK IV

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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
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average exposure time: 2.0 sec. / Average electron dose: 20.0 e/Å2
Details: Images were stored containing seven parts, where each part represented a set of frames corresponding to a dose of ~20 electrons per Angstrom^2. The full dose image stack was used for the ...Details: Images were stored containing seven parts, where each part represented a set of frames corresponding to a dose of ~20 electrons per Angstrom^2. The full dose image stack was used for the estimation of the CTF as well as for boxing filaments. Only the first two parts were used for the reconstruction (~5 electrons per Angstrom^2)
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND3
Startup modelType of model: OTHER / Details: featureless cylinder
Final angle assignmentType: NOT APPLICABLE / Software - Name: SPIDER
Final reconstructionApplied symmetry - Helical parameters - Δz: 10.5 Å
Applied symmetry - Helical parameters - Δ&Phi: 87.3 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: OTHER / Software - Name: SPIDER / Details: model-map FSC 0.38 cut-off / Number images used: 31231

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-5vxy:
Cryo-EM reconstruction of PAK pilus from Pseudomonas aeruginosa

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