7V1N

Structure of the Clade 2 C. difficile TcdB in complex with its receptor TFPI


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

TFPI is a colonic crypt receptor for TcdB from hypervirulent clade 2 C. difficile.

Luo, J.Yang, Q.Zhang, X.Zhang, Y.Wan, L.Zhan, X.Zhou, Y.He, L.Li, D.Jin, D.Zhen, Y.Huang, J.Li, Y.Tao, L.

(2022) Cell 185: 980-994.e15

  • DOI: https://doi.org/10.1016/j.cell.2022.02.010
  • Primary Citation of Related Structures:  
    7V1N

  • PubMed Abstract: 

    The emergence of hypervirulent clade 2 Clostridioides difficile is associated with severe symptoms and accounts for >20% of global infections. TcdB is a dominant virulence factor of C. difficile, and clade 2 strains exclusively express two TcdB variants (TcdB2 and TcdB4) that use unknown receptors distinct from the classic TcdB. Here, we performed CRISPR/Cas9 screens for TcdB4 and identified tissue factor pathway inhibitor (TFPI) as its receptor. Using cryo-EM, we determined a complex structure of the full-length TcdB4 with TFPI, defining a common receptor-binding region for TcdB. Residue variations within this region divide major TcdB variants into 2 classes: one recognizes Frizzled (FZD), and the other recognizes TFPI. TFPI is highly expressed in the intestinal glands, and recombinant TFPI protects the colonic epithelium from TcdB2/4. These findings establish TFPI as a colonic crypt receptor for TcdB from clade 2 C. difficile and reveal new mechanisms for CDI pathogenesis.


  • Organizational Affiliation

    Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Toxin B2,375Clostridioides difficileMutation(s): 0 
Gene Names: tcdBtoxB
EC: 3.4.22
UniProt
Find proteins for Q9EXR0 (Clostridioides difficile)
Explore Q9EXR0 
Go to UniProtKB:  Q9EXR0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9EXR0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform Beta of Tissue factor pathway inhibitorB [auth K]251Homo sapiensMutation(s): 0 
Gene Names: TFPILACITFPI1
UniProt & NIH Common Fund Data Resources
Find proteins for P10646 (Homo sapiens)
Explore P10646 
Go to UniProtKB:  P10646
PHAROS:  P10646
GTEx:  ENSG00000003436 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10646
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

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

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31970129
National Natural Science Foundation of China (NSFC)China31800128

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-23
    Type: Initial release
  • Version 1.1: 2022-03-30
    Changes: Database references, Structure summary
  • Version 1.2: 2024-10-30
    Changes: Data collection, Structure summary