6YEW

Morganella morganii TcdA4 in complex with porcine mucosa heparin

• PDB DOI: https://doi.org/10.2210/pdb6YEW/pdb
• EM Map EMD-10796: EMDB EMDataResource

• Classification: TOXIN
• Organism(s): Morganella morganii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-03-25 Released: 2020-07-08 
• Deposition Author(s): Roderer, D., Broecker, F., Sitsel, O., Kaplonek, P., Leidreiter, F., Seeberger, P.H., Raunser, S.
• Funding Organization(s): European Research Council (ERC)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Glycan-dependent cell adhesion mechanism of Tc toxins.

Roderer, D., Brocker, F., Sitsel, O., Kaplonek, P., Leidreiter, F., Seeberger, P.H., Raunser, S.

(2020) Nat Commun 11: 2694-2694

• PubMed: 32483155 
• DOI: https://doi.org/10.1038/s41467-020-16536-7
• Primary Citation of Related Structures:  
  6YEW, 6YEY


• PubMed 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 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.

---

Organizational Affiliation: 

Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 1,378.29 kDa 
• Atom Count: 88,700 
• Modelled Residue Count: 11,425 
• Deposited Residue Count: 12,345 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insecticidal toxin protein	A, B, C, D, E	2,469	Morganella morganii	Mutation(s): 0  Gene Names: CRX48_03350

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	SPHIRE
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-07-08 
Deposition Author(s): Roderer, D., Broecker, F., Sitsel, O., Kaplonek, P., Leidreiter, F., Seeberger, P.H., Raunser, S.

---

Funding Organization	Location	Grant Number
European Research Council (ERC)	Germany	615984

Revision History  

• Version 1.0: 2020-07-08
  Type: Initial release
  
• Version 1.1: 2020-07-15
  Changes: Database references