7ML7 | pdb_00007ml7

Structural basis for CSPG4 as a receptor for TcdB and a therapeutic target in Clostridioides difficile infection


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.17 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structural basis for CSPG4 as a receptor for TcdB and a therapeutic target in Clostridioides difficile infection.

Chen, P.Zeng, J.Liu, Z.Thaker, H.Wang, S.Tian, S.Zhang, J.Tao, L.Gutierrez, C.B.Xing, L.Gerhard, R.Huang, L.Dong, M.Jin, R.

(2021) Nat Commun 12: 3748-3748

  • DOI: https://doi.org/10.1038/s41467-021-23878-3
  • Primary Citation Related Structures: 
    7ML7

  • PubMed Abstract: 

    C. difficile is a major cause of antibiotic-associated gastrointestinal infections. Two C. difficile exotoxins (TcdA and TcdB) are major virulence factors associated with these infections, and chondroitin sulfate proteoglycan 4 (CSPG4) is a potential receptor for TcdB, but its pathophysiological relevance and the molecular details that govern recognition remain unknown. Here, we determine the cryo-EM structure of a TcdB-CSPG4 complex, revealing a unique binding site spatially composed of multiple discontinuous regions across TcdB. Mutations that selectively disrupt CSPG4 binding reduce TcdB toxicity in mice, while CSPG4-knockout mice show reduced damage to colonic tissues during C. difficile infections. We further show that bezlotoxumab, the only FDA approved anti-TcdB antibody, blocks CSPG4 binding via an allosteric mechanism, but it displays low neutralizing potency on many TcdB variants from epidemic hypervirulent strains due to sequence variations in its epitopes. In contrast, a CSPG4-mimicking decoy neutralizes major TcdB variants, suggesting a strategy to develop broad-spectrum therapeutics against TcdB.


  • Organizational Affiliation
    • Department of Physiology and Biophysics, University of California, Irvine, CA, USA.

Macromolecule Content 

  • Total Structure Weight: 311.12 kDa 
  • Atom Count: 10,913 
  • Modeled Residue Count: 1,354 
  • Deposited Residue Count: 2,774 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Toxin B2,014Clostridioides difficileMutation(s): 0 
Gene Names: tcdBtoxB
EC: 3.4.22
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
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Chondroitin sulfate proteoglycan 4760Homo sapiensMutation(s): 0 
Gene Names: CSPG4MCSP
UniProt & NIH Common Fund Data Resources
Find proteins for Q6UVK1 (Homo sapiens)
Explore Q6UVK1 
Go to UniProtKB:  Q6UVK1
PHAROS:  Q6UVK1
GTEx:  ENSG00000173546 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6UVK1
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
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.17 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-09
    Type: Initial release
  • Version 1.1: 2021-06-30
    Changes: Database references
  • Version 1.2: 2024-10-30
    Changes: Data collection, Database references, Structure summary