8QEN

cryo-EM structure of apo Clostridioides difficile toxin B


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural and functional insight into the interaction of Clostridioides difficile toxin B and FZD 7.

Kinsolving, J.Bous, J.Kozielewicz, P.Kosenina, S.Shekhani, R.Gratz, L.Masuyer, G.Wang, Y.Stenmark, P.Dong, M.Schulte, G.

(2024) Cell Rep 43: 113727-113727

  • DOI: https://doi.org/10.1016/j.celrep.2024.113727
  • Primary Citation of Related Structures:  
    8QEN, 8QEO

  • PubMed Abstract: 

    The G protein-coupled receptors of the Frizzled (FZD) family, in particular FZD 1,2,7 , are receptors that are exploited by Clostridioides difficile toxin B (TcdB), the major virulence factor responsible for pathogenesis associated with Clostridioides difficile infection. We employ a live-cell assay examining the affinity between full-length FZDs and TcdB. Moreover, we present cryoelectron microscopy structures of TcdB alone and in complex with full-length FZD 7 , which reveal that large structural rearrangements of the combined repetitive polypeptide domain are required for interaction with FZDs and other TcdB receptors, constituting a first step for receptor recognition. Furthermore, we show that bezlotoxumab, an FDA-approved monoclonal antibody to treat Clostridioides difficile infection, favors the apo-TcdB structure and thus disrupts binding with FZD 7 . The dynamic transition between the two conformations of TcdB also governs the stability of the pore-forming region. Thus, our work provides structural and functional insight into how conformational dynamics of TcdB determine receptor binding.


  • Organizational Affiliation

    Karolinska Institutet, Department Physiology & Pharmacology, Sec. Receptor Biology & Signaling, Biomedicum, 17165 Stockholm, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Toxin B2,397Clostridioides difficileMutation(s): 0 
Gene Names: tcdB
UniProt
Find proteins for P18177 (Clostridioides difficile)
Explore P18177 
Go to UniProtKB:  P18177
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18177
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.2.1
MODEL REFINEMENTRosetta
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2019-01190
CancerfondenSweden20 1102 PjF
Novo Nordisk FoundationDenmarkNNF21OC0070008
Novo Nordisk FoundationDenmarkNNF22OC0078104
Other government2021-00430
Other government2018-01562
Swedish Research CouncilSweden2022-03681
Swedish Research CouncilSweden2018-03406
CancerfondenSweden20 1287 PjF
CancerfondenSweden202 0264 PjF
Swedish Research CouncilSweden2022-01398

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-20
    Type: Initial release