+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8740 | |||||||||||||||
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Title | Cryo-EM reconstruction of PAK pilus from Pseudomonas aeruginosa | |||||||||||||||
Map data | PAK pilus from Pseudomonas aeruginosa | |||||||||||||||
Sample |
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Function / homology | Function and homology information | |||||||||||||||
Biological species | Pseudomonas aeruginosa PAK (bacteria) | |||||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 8.0 Å | |||||||||||||||
Authors | Wang F / Osinksi T / Orlova A / Altindal T / Craig L / Egelman EH | |||||||||||||||
Funding support | United States, France, Canada, 4 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8740.map.gz | 5.7 MB | EMDB map data format | |
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Header (meta data) | emd-8740-v30.xml emd-8740.xml | 12.5 KB 12.5 KB | Display Display | EMDB header |
Images | emd_8740.png | 133.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8740 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8740 | HTTPS FTP |
-Validation report
Summary document | emd_8740_validation.pdf.gz | 333.1 KB | Display | EMDB validaton report |
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Full document | emd_8740_full_validation.pdf.gz | 332.6 KB | Display | |
Data in XML | emd_8740_validation.xml.gz | 4.6 KB | Display | |
Data in CIF | emd_8740_validation.cif.gz | 5.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8740 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8740 | HTTPS FTP |
-Related structure data
Related structure data | 5vxyMC 8739C 5vxxC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8740.map.gz / Format: CCP4 / Size: 13.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | PAK pilus from Pseudomonas aeruginosa | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Pseudomonas aeruginosa Type IV pilin filament
Entire | Name: Pseudomonas aeruginosa Type IV pilin filament |
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Components |
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-Supramolecule #1: Pseudomonas aeruginosa Type IV pilin filament
Supramolecule | Name: Pseudomonas aeruginosa Type IV pilin filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Pseudomonas aeruginosa PAK (bacteria) / Strain: PAK/2pfs |
-Macromolecule #1: Fimbrial protein
Macromolecule | Name: Fimbrial protein / type: protein_or_peptide / ID: 1 / Number of copies: 21 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas aeruginosa PAK (bacteria) / Strain: PAK/2pfs |
Molecular weight | Theoretical: 15.02118 KDa |
Sequence | String: FTLIELMIVV AIIGILAAIA IPQYQNYVAR SEGASALASV NPLKTTVEEA LSRGWSVKSG TGTEDATKKE VPLGVAADAN KLGTIALKP DPADGTADIT LTFTMGGAGP KNKGKIITLT RTAADGLWKC TSDQDEQFIP KGCSR |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 9 / Details: 50 mM CHES buffer |
Grid | Pretreatment - Type: PLASMA CLEANING / Details: unspecified |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film 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) |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied 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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CTF correction | Software - Name: CTFFIND3 |
Startup model | Type of model: OTHER / Details: featureless cylinder |
Final angle assignment | Type: NOT APPLICABLE / Software - Name: SPIDER |
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | PDB-5vxy: |