[English] 日本語
Yorodumi- PDB-8tuw: Type IV pilus from Pseudomonas PAO1 strain with PP7 Maturation protein -
+Open data
-Basic information
Entry | Database: PDB / ID: 8tuw | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Type IV pilus from Pseudomonas PAO1 strain with PP7 Maturation protein | ||||||||||||||||||||||||
Components |
| ||||||||||||||||||||||||
Keywords | MEMBRANE PROTEIN / Type IV pilus / T4P / PAO1 | ||||||||||||||||||||||||
Function / homology | Function and homology information type IV pilus / type IV pilus-dependent motility / single-species biofilm formation on inanimate substrate / virion attachment to host cell pilus / cell adhesion involved in single-species biofilm formation / pilus / regulation of calcium-mediated signaling / virion component / host cell endoplasmic reticulum membrane / cell surface ...type IV pilus / type IV pilus-dependent motility / single-species biofilm formation on inanimate substrate / virion attachment to host cell pilus / cell adhesion involved in single-species biofilm formation / pilus / regulation of calcium-mediated signaling / virion component / host cell endoplasmic reticulum membrane / cell surface / plasma membrane / cytosol Similarity search - Function | ||||||||||||||||||||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) Pseudomonas phage PP7 (virus) | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.9 Å | ||||||||||||||||||||||||
Authors | Thongchol, J. / Zhang, J. / Zeng, L. | ||||||||||||||||||||||||
Funding support | United States, 7items
| ||||||||||||||||||||||||
Citation | Journal: Science / Year: 2024 Title: Removal of type IV pili by a small RNA virus. Authors: Jirapat Thongchol / Zihao Yu / Laith Harb / Yiruo Lin / Matthias Koch / Matthew Theodore / Utkarsh Narsaria / Joshua Shaevitz / Zemer Gitai / Yinghao Wu / Junjie Zhang / Lanying Zeng / Abstract: The retractile type IV pilus (T4P) is important for virulence of the opportunistic human pathogen . The single-stranded RNA (ssRNA) phage PP7 binds to T4P and is brought to the cell surface through ...The retractile type IV pilus (T4P) is important for virulence of the opportunistic human pathogen . The single-stranded RNA (ssRNA) phage PP7 binds to T4P and is brought to the cell surface through pilus retraction. Using fluorescence microscopy, we discovered that PP7 detaches T4P, which impairs cell motility and restricts the pathogen's virulence. Using cryo-electron microscopy, mutagenesis, optical trapping, and Langevin dynamics simulation, we resolved the structure of PP7, T4P, and the PP7/T4P complex and showed that T4P detachment is driven by the affinity between the phage maturation protein and its bound pilin, plus the pilus retraction force and speed, and pilus bending. Pilus detachment may be widespread among other ssRNA phages and their retractile pilus systems and offers new prospects for antibacterial prophylaxis and therapeutics. | ||||||||||||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8tuw.cif.gz | 827.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8tuw.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8tuw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/8tuw ftp://data.pdbj.org/pub/pdb/validation_reports/tu/8tuw | HTTPS FTP |
---|
-Related structure data
Related structure data | 41633MC 8tumC 8tuxC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 50763.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage PP7 (virus) / References: UniProt: Q38061 |
---|---|
#2: Protein | Mass: 14878.889 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: pilA, fimA, PA4525 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: P04739 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Type IV twitching pilus / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL |
---|---|
Molecular weight | Value: 0.24 MDa / Experimental value: NO |
Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) / Strain: PAO1 |
Buffer solution | pH: 7.4 Details: 137 mM NaCl, 2.7 mM KCl, 8 mM Na2HPO4, and 2 mM KH2PO4, pH 7.4 |
Buffer component | Conc.: 1 x / Name: PBS |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 80 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
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 / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50.85 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 5085 |
-Processing
EM software | Name: cryoSPARC / Category: 3D reconstruction |
---|---|
CTF correction | Type: NONE |
Particle selection | Num. of particles selected: 25763 |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 7.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40493 / Symmetry type: POINT |