+Open data
-Basic information
Entry | Database: PDB / ID: 6yew | ||||||
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Title | Morganella morganii TcdA4 in complex with porcine mucosa heparin | ||||||
Components | Insecticidal toxin protein | ||||||
Keywords | TOXIN / complex / glycan | ||||||
Biological species | Morganella morganii (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Roderer, D. / Broecker, F. / Sitsel, O. / Kaplonek, P. / Leidreiter, F. / Seeberger, P.H. / Raunser, S. | ||||||
Funding support | Germany, 1items
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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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6yew.cif.gz | 1.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6yew.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 6yew.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yew_validation.pdf.gz | 907.1 KB | Display | wwPDB validaton report |
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Full document | 6yew_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6yew_validation.xml.gz | 286.1 KB | Display | |
Data in CIF | 6yew_validation.cif.gz | 437.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/6yew ftp://data.pdbj.org/pub/pdb/validation_reports/ye/6yew | HTTPS FTP |
-Related structure data
Related structure data | 10796MC 6yeyC 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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-Components
#1: Protein | Mass: 275658.312 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Morganella morganii (bacteria) / Gene: CRX48_03350 / Production host: Escherichia coli (E. coli) |
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-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: Morganella morganii TcdA4 pentamer in complex with porcine mucosa heparin Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 1.4 MDa / Experimental value: NO |
Source (natural) | Organism: Morganella morganii (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: 0.10 mg/ml TcdA4 were pre-applied on the grid for 20s. Subsequently, the grid was manually blotted and 0.30 mg/ml porcine mucosa heparin was applied and incubated for 2 min. |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 293 K |
-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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Alignment procedure: ZEMLIN TABLEAU |
Image recording | Electron dose: 100 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 5549 |
-Processing
Software | Name: PHENIX / Version: 1.15.2_3472: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 477602 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C5 (5 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 182506 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | B value: 127.6 / Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 6RW9 Accession code: 6RW9 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
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