9PZI image
Deposition Date 2025-08-11
Release Date 2025-08-20
Last Version Date 2025-09-24
Entry Detail
PDB ID:
9PZI
Title:
Crystal Structure of synthetic antibody COP-2 in complex with the C-terminal domain of Clostridium perfringens enterotoxin
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.50 Å
R-Value Free:
0.22
R-Value Work:
0.17
Space Group:
I 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:COP-2 Light chain
Chain IDs:A (auth: C), C (auth: A), E
Chain Length:239
Number of Molecules:3
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:COP-2 Heavy chain
Chain IDs:B (auth: D), D (auth: B), F
Chain Length:260
Number of Molecules:3
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Heat-labile enterotoxin B chain
Gene (Uniprot):cpe
Chain IDs:G, H (auth: I), I (auth: H)
Chain Length:134
Number of Molecules:3
Biological Source:Clostridium perfringens
Primary Citation
Structures of a synthetic antibody selected against and bound to the C-terminal domain of Clostridium perfringens enterotoxin.
Protein Sci. 34 e70281 e70281 (2025)
PMID: 40944397 DOI: 10.1002/pro.70281

Abstact

Clostridium perfringens enterotoxin (CpE) causes cytotoxic gastrointestinal disease in mammalian epithelium by binding membrane protein receptors called claudins. Claudins direct the formation of cell/cell tight junctions through oligomerization and govern the transport of molecules between individual cells. CpE binds claudins through its C-terminal domain (cCpE) and induces cytotoxicity through its N-terminal domain. The non-toxic cCpE is a useful tool to study claudins, tight junctions, and for translational applications, such as increasing the permeability of restrictive tissues like the blood-brain barrier or selective targeting of claudin overexpressing cancers. Conversely, there are no specialized molecular tools to study CpE or cCpE, or to modulate or inhibit their functions. We previously reported the development of synthetic antigen-binding fragments (sFabs) that bind cCpE, and low-resolution structures of them bound to claudin/cCpE complexes. Here, we determine high-resolution structures of sFab COP-2 bound to cCpE using X-ray crystallography and cryogenic electron microscopy. The structures and biophysical findings provide the mechanism of COP-2 binding to cCpE and the molecular determinants driving their interactions. These insights can advance the design of new antibody-based tools from our COP-2 scaffold to study or alter cCpE function and give rise to a "Trojan horse" strategy that exploits cCpE's tight junction barrier disrupting function to selectively deliver conjugated therapeutics through normally impermeable tissues.

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