Structure functional insights on FXIII-B subunit from models and biophysical structures.

Introduction Factor XIII-B (FXIII-B) serves as the binding partner of the Factor XIII-A subunit within the plasma heterotetrameric protransglutaminase complex (FXIII-A₂B₂). Besides its complexed form, FXIII-B also circulates in plasma as a free homodimer. Although protective and regulatory functions have been proposed, including stabilization of FXIII-A and modulation of its secretion, structural and functional knowledge of FXIII-B remains limited because no high-resolution structure has yet been resolved. In this study, we aimed to elucidate structural and conformational features of both the free and bound states of FXIII-B using AlphaFold-based predictions together with available cryo-EM data from the recently reported FXIII complex. Method Monomeric FXIII-B models were obtained from the AlphaFold2 database and dimerized using a combination of blind and guided docking. Dimeric models were also independently generated with the AlphaFold3 prediction server to cross-validate the docking results. For comparison with the bound form, the cryo-EM structure of the partial FXIII complex (PDB ID: 8CMT) was retrieved, and the FXIII-B component was analyzed for conformational features associated with subunit interaction. Recombinantly expressed and purified FXIII-B protein was subjected to preliminary cryo-EM analysis to assess particle integrity and heterogeneity. Results Surface property analyses, including electrostatic potential and solvent accessibility mapping, identified distinct regions of FXIII-B that may mediate interactions with partner proteins such as fibrinogen. Conformational evaluation of both modeled and experimental structures revealed that free FXIII-B exists in a flexible and conformationally heterogeneous state. Upon complex formation, this diversity becomes markedly restricted as specific Sushi domains engage with FXIII-A, introducing greater order and compactness to the overall assembly. Correspondingly, initial cryo-EM micrographs of the isolated subunit displayed broad particle distributions, consistent with the presence of dynamic conformers in solution. Conclusion This integrative structural analysis provides preliminary insights into the conformational landscape of FXIII-B in its free and bound states. The study highlights functionally significant regions that mediate partner binding and contribute to maintaining conformational stability. These findings lay the groundwork for future high-resolution investigations into the structural dynamics and regulatory mechanisms of FXIII-B within the FXIII complex. Publication History Article published online: 17 February 2026 © 2026. Thieme. All rights reserved. Georg Thieme Verlag KG Oswald-Hesse-Straße 50, 70469 Stuttgart, Germany