+Open data
-Basic information
Entry | Database: PDB / ID: 6rwb | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of Yersinia pseudotuberculosis TcaA-TcaB | ||||||
Components | Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit,Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit,Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit,Toxin,Toxin complex subunit TcaB,Putative toxin subunit,Putative toxin subunit | ||||||
Keywords | TOXIN / membrane permeation / translocation / complex | ||||||
Biological species | Yersinia pseudotuberculosis (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.25 Å | ||||||
Authors | Roderer, D. / Leidreiter, F. / Gatsogiannis, C. / Meusch, D. / Benz, R. / Raunser, S. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: Sci Adv / Year: 2019 Title: Common architecture of Tc toxins from human and insect pathogenic bacteria. Authors: F Leidreiter / D Roderer / D Meusch / C Gatsogiannis / R Benz / S Raunser / Abstract: Tc toxins use a syringe-like mechanism to penetrate the membrane and translocate toxic enzymes into the host cytosol. They are composed of three components: TcA, TcB, and TcC. Low-resolution ...Tc toxins use a syringe-like mechanism to penetrate the membrane and translocate toxic enzymes into the host cytosol. They are composed of three components: TcA, TcB, and TcC. Low-resolution structures of TcAs from different bacteria suggest a considerable difference in their architecture and possibly in their mechanism of action. Here, we present high-resolution structures of five TcAs from insect and human pathogens, which show a similar overall composition and domain organization. Essential structural features, including a trefoil protein knot, are present in all TcAs, suggesting a common mechanism of action. All TcAs form functional pores and can be combined with TcB-TcC subunits from other species to form active chimeric holotoxins. We identified a conserved ionic pair that stabilizes the shell, likely operating as a strong latch that only springs open after destabilization of other regions. Our results provide new insights into the architecture and mechanism of the Tc toxin family. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6rwb.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6rwb.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 6rwb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rwb_validation.pdf.gz | 848.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6rwb_full_validation.pdf.gz | 907.9 KB | Display | |
Data in XML | 6rwb_validation.xml.gz | 217.5 KB | Display | |
Data in CIF | 6rwb_validation.cif.gz | 332.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rw/6rwb ftp://data.pdbj.org/pub/pdb/validation_reports/rw/6rwb | HTTPS FTP |
-Related structure data
Related structure data | 10037MC 6rw6C 6rw8C 6rw9C 6rwaC C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 231985.031 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pseudotuberculosis (bacteria) / Gene: EGX47_10580, YPP3681, NCTC8580_04191 / Production host: Escherichia coli (E. coli) / Variant (production host): RIPL |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Y. pseudotuberculosis TcaA-TcaB pentamer / Type: COMPLEX / Details: Each protomer is a fusion protein of TcaA and TcaB / Entity ID: all / Source: RECOMBINANT |
---|---|
Molecular weight | Value: 1 MDa / Experimental value: NO |
Source (natural) | Organism: Yersinia pseudotuberculosis (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Average exposure time: 1.5 sec. / Electron dose: 130 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C5 (5 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 237295 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 1VW1 1vw1 Accession code: 1VW1 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
Refine LS restraints |
|