9CM5

CryoEM Strucuture of TcdB in complex with De Novo Minibinder fzd48

Summary for 9CM5

• Entry DOI: 10.2210/pdb9cm5/pdb
• EMDB information: 45739
• Descriptor: De Novo Minibinder fzd48, Toxin B (2 entities in total)
• Functional Keywords: tcdb, clostridium difficile, c. diff., fzd48, de novo minibinder, toxin
• Biological source: synthetic construct; More
• Total number of polymer chains: 2
• Total formula weight: 250156.04

Authors

Weidle, C.,Carr, K.D.,Borst, A.J. (deposition date: 2024-07-12, release date: 2025-05-21, Last modification date: 2025-10-08)

Primary citation

Ragotte, R.J.,Liang, H.,Tam, J.,Miletic, S.,Berman, J.M.,Palou, R.,Weidle, C.,Li, Z.,Glogl, M.,Beilhartz, G.L.,Carr, K.D.,Borst, A.J.,Coventry, B.,Wang, X.,Rubinstein, J.L.,Tyers, M.,Schramek, D.,Melnyk, R.A.,Baker, D.
De novo design of potent inhibitors of clostridial family toxins.
Proc.Natl.Acad.Sci.USA, 122:e2509329122-e2509329122, 2025

PubMed Abstract: remains a leading cause of hospital-acquired infections, with its primary virulence factor, toxin B (TcdB), responsible for severe colitis and recurrent disease. The closely related toxin, TcsL, from , causes a rarer but often fatal toxic shock syndrome, particularly in gynecological and obstetric contexts. We report the de novo design of small protein minibinders that directly neutralize TcdB and TcsL by preventing their entry into host cells. Using deep learning and Rosetta-based approaches, we generated high-affinity minibinders that protect cells from intoxication with picomolar potency and, in the case of TcsL, prolonged survival following lethal toxin challenge in mice. The designed proteins against TcdB demonstrate exceptional stability in proteolytic and acidic environments, making them well-suited for oral delivery-a valuable feature for treating infections localized to the gastrointestinal tract. For TcsL, potent inhibitors were identified from 48 initial designs and 48 optimized designs, highlighting the potential of computational design for rapidly developing countermeasures against life-threatening bacterial toxins.

PubMed: 40982695
DOI: 10.1073/pnas.2509329122

Experimental method

ELECTRON MICROSCOPY (4.61 Å)