[English] 日本語
Yorodumi- PDB-6yey: Xenorhabdus nematophila XptA1 in complex with porcine mucosa heparin -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yey | ||||||
---|---|---|---|---|---|---|---|
Title | Xenorhabdus nematophila XptA1 in complex with porcine mucosa heparin | ||||||
Components | A component of insecticidal toxin complex (Tc) | ||||||
Keywords | TOXIN / complex / glycan | ||||||
Function / homology | TcA receptor binding domain / TcA receptor binding domain / Insecticidal toxin complex/plasmid virulence protein / Tc toxin complex TcA, C-terminal TcB-binding domain / Neuraminidase-like domain / Salmonella virulence plasmid 28.1kDa A protein / Tc toxin complex TcA C-terminal TcB-binding domain / Neuraminidase-like domain / A component of insecticidal toxin complex (Tc) Function and homology information | ||||||
Biological species | Xenorhabdus nematophila (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
Authors | Roderer, D. / Broecker, F. / Sitsel, O. / Kaplonek, P. / Leidreiter, F. / Seeberger, P.H. / Raunser, S. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Glycan-dependent cell adhesion mechanism of Tc toxins. Authors: Daniel Roderer / Felix Bröcker / Oleg Sitsel / Paulina Kaplonek / Franziska Leidreiter / Peter H Seeberger / Stefan Raunser / Abstract: Toxin complex (Tc) toxins are virulence factors of pathogenic bacteria. Tcs are composed of three subunits: TcA, TcB and TcC. TcA facilitates receptor-toxin interaction and membrane permeation, TcB ...Toxin complex (Tc) toxins are virulence factors of pathogenic bacteria. Tcs are composed of three subunits: TcA, TcB and TcC. TcA facilitates receptor-toxin interaction and membrane permeation, TcB and TcC form a toxin-encapsulating cocoon. While the mechanisms of holotoxin assembly and pore formation have been described, little is known about receptor binding of TcAs. Here, we identify heparins/heparan sulfates and Lewis antigens as receptors for different TcAs from insect and human pathogens. Glycan array screening reveals that all tested TcAs bind negatively charged heparins. Cryo-EM structures of Morganella morganii TcdA4 and Xenorhabdus nematophila XptA1 reveal that heparins/heparan sulfates unexpectedly bind to different regions of the shell domain, including receptor-binding domains. In addition, Photorhabdus luminescens TcdA1 binds to Lewis antigens with micromolar affinity. Here, the glycan interacts with the receptor-binding domain D of the toxin. Our results suggest a glycan dependent association mechanism of Tc toxins on the host cell surface. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6yey.cif.gz | 1.9 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6yey.ent.gz | 1.6 MB | Display | PDB format |
PDBx/mmJSON format | 6yey.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yey_validation.pdf.gz | 443.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6yey_full_validation.pdf.gz | 584.3 KB | Display | |
Data in XML | 6yey_validation.xml.gz | 238.3 KB | Display | |
Data in CIF | 6yey_validation.cif.gz | 397.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/6yey ftp://data.pdbj.org/pub/pdb/validation_reports/ye/6yey | HTTPS FTP |
-Related structure data
Related structure data | 10797MC 6yewC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 287120.781 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenorhabdus nematophila (bacteria) / Gene: xptA, XNC2_2467 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0R4FN93 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Xenorhabdus nematophila XptA1 pentamer in complex with porcine mucosa heparin Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
---|---|
Molecular weight | Value: 1.4 MDa / Experimental value: NO |
Source (natural) | Organism: Xenorhabdus nematophila (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: 0.10 mg/ml XptA1 were pre-applied on the grid for 30s. Subsequently, the grid was manually blotted and 0.30 mg/ml porcine mucosa heparin was applied and incubated for 4 min. |
Specimen support | Grid material: GOLD / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 285 K |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Alignment procedure: COMA FREE |
Image recording | Electron dose: 52 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 1855 |
-Processing
Software | Name: PHENIX / Version: 1.15.2_3472: / Classification: refinement | ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 346048 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C5 (5 fold cyclic) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 172596 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | B value: 65.8 / Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6RW8 Accession code: 6RW8 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||
Refine LS restraints |
|