+Open data
-Basic information
Entry | Database: PDB / ID: 8cp6 | |||||||||
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Title | Type six secretion system exported effector 5 (Tse5) | |||||||||
Components | (Toxin protein Tse5) x 3 | |||||||||
Keywords | TOXIN / Pore-forming protein / P.aeruginosa / effector / Bacterial Rearrangement hot spot protein / ion channel / type VI secretion system | |||||||||
Function / homology | Function and homology information protein secretion by the type VI secretion system / toxin sequestering activity Similarity search - Function | |||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.45 Å | |||||||||
Authors | Gonzalez-Magana, A. / Tascon, I. / Ubarretxena-Belandia, I. / Albesa-Jove, D. | |||||||||
Funding support | Spain, 2items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structural and functional insights into the delivery of a bacterial Rhs pore-forming toxin to the membrane. Authors: Amaia González-Magaña / Igor Tascón / Jon Altuna-Alvarez / María Queralt-Martín / Jake Colautti / Carmen Velázquez / Maialen Zabala / Jessica Rojas-Palomino / Marité Cárdenas / ...Authors: Amaia González-Magaña / Igor Tascón / Jon Altuna-Alvarez / María Queralt-Martín / Jake Colautti / Carmen Velázquez / Maialen Zabala / Jessica Rojas-Palomino / Marité Cárdenas / Antonio Alcaraz / John C Whitney / Iban Ubarretxena-Belandia / David Albesa-Jové / Abstract: Bacterial competition is a significant driver of toxin polymorphism, which allows continual compensatory evolution between toxins and the resistance developed to overcome their activity. Bacterial ...Bacterial competition is a significant driver of toxin polymorphism, which allows continual compensatory evolution between toxins and the resistance developed to overcome their activity. Bacterial Rearrangement hot spot (Rhs) proteins represent a widespread example of toxin polymorphism. Here, we present the 2.45 Å cryo-electron microscopy structure of Tse5, an Rhs protein central to Pseudomonas aeruginosa type VI secretion system-mediated bacterial competition. This structural insight, coupled with an extensive array of biophysical and genetic investigations, unravels the multifaceted functional mechanisms of Tse5. The data suggest that interfacial Tse5-membrane binding delivers its encapsulated pore-forming toxin fragment to the target bacterial membrane, where it assembles pores that cause cell depolarisation and, ultimately, bacterial death. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cp6.cif.gz | 238 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cp6.ent.gz | 181 KB | Display | PDB format |
PDBx/mmJSON format | 8cp6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cp6_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8cp6_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8cp6_validation.xml.gz | 43 KB | Display | |
Data in CIF | 8cp6_validation.cif.gz | 63.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/8cp6 ftp://data.pdbj.org/pub/pdb/validation_reports/cp/8cp6 | HTTPS FTP |
-Related structure data
Related structure data | 16778MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 7456.322 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: tse5, PA2684 / Plasmid: pet29a / Details (production host): Kanamycin resistance / Production host: Escherichia coli (E. coli) / Strain (production host): Lemo 21 / References: UniProt: Q9I0F4 |
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#2: Protein | Mass: 125970.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: tse5, PA2684 / Plasmid: pert29a / Details (production host): Kanamycin resistance / Production host: Escherichia coli (E. coli) / Strain (production host): Lemo 21 / References: UniProt: Q9I0F4 |
#3: Protein | Mass: 15592.012 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: tse5, PA2684 / Plasmid: pet29a / Details (production host): Kan resistance / Production host: Escherichia coli (E. coli) / Strain (production host): Lemo 21 / References: UniProt: Q9I0F4 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Tse5 / Type: ORGANELLE OR CELLULAR COMPONENT Details: Pseudomonas aeruginosa type VI secretion system (T6SS) exported effector Tse5. The three chains result from the auto-cleavage of Tse5 Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.146 MDa / Experimental value: YES | ||||||||||||||||||||
Source (natural) | Organism: Pseudomonas (RNA similarity group I) | ||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: Lemo 21 | ||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil | ||||||||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 94 % / Chamber temperature: 289 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Alignment procedure: COMA FREE |
Image recording | Average exposure time: 10.84 sec. / Electron dose: 60 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10244 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 4866119 | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 323963 / Num. of class averages: 3 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Details: Buccanner / Source name: Other / Type: in silico model | ||||||||||||||||||||||||||||||||||||||||
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