+Open data
-Basic information
Entry | Database: PDB / ID: 5vxx | |||||||||||||||
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Title | Cryo-EM reconstruction of Neisseria gonorrhoeae Type IV pilus | |||||||||||||||
Components | Fimbrial protein | |||||||||||||||
Keywords | PROTEIN FIBRIL / Melted helix / type IV pili | |||||||||||||||
Function / homology | Function and homology information protein secretion by the type II secretion system / type II protein secretion system complex / pilus / cell adhesion / membrane Similarity search - Function | |||||||||||||||
Biological species | Neisseria gonorrhoeae (bacteria) | |||||||||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 5.1 Å | |||||||||||||||
Authors | Wang, F. / Orlova, A. / Altindal, T. / Craig, L. / Egelman, E.H. | |||||||||||||||
Funding support | United States, Canada, France, 4items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5vxx.cif.gz | 545 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vxx.ent.gz | 445 KB | Display | PDB format |
PDBx/mmJSON format | 5vxx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vxx_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 5vxx_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 5vxx_validation.xml.gz | 89.1 KB | Display | |
Data in CIF | 5vxx_validation.cif.gz | 110.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vx/5vxx ftp://data.pdbj.org/pub/pdb/validation_reports/vx/5vxx | HTTPS FTP |
-Related structure data
Related structure data | 8739MC 8740C 5vxyC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Details | The full assembly is a helical filament. Only a finite portion of the full filament is represented here. |
-Components
#1: Protein | Mass: 17196.467 Da / Num. of mol.: 21 / Mutation: P69S, S71T / Source method: isolated from a natural source / Source: (natural) Neisseria gonorrhoeae (bacteria) / Strain: C30 / References: UniProt: P02974 #2: Polysaccharide | alpha-D-galactopyranose-(1-3)-2,4-bisacetamido-2,4,6-trideoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-OPE / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Neisseria gonorrhoeae Type IV pilin filament / Type: COMPLEX / Entity ID: #1 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Neisseria gonorrhoeae (bacteria) / Strain: C30 |
Buffer solution | pH: 7.4 / Details: PBS buffer |
Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Average exposure time: 2 sec. / Electron dose: 20 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) 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). |
Image scans | Movie frames/image: 7 |
-Processing
Software | Name: PHENIX / Version: dev_2471: / Classification: refinement | |||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 100.8 ° / Axial rise/subunit: 10.1 Å / Axial symmetry: C1 | |||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 5.1 Å / Resolution method: OTHER / Num. of particles: 9855 / Details: model-map FSC 0.38 cut-off / Symmetry type: HELICAL | |||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL | |||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 5.1 Å | |||||||||||||||||||||||||||||||||
Refine LS restraints |
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