9FXT

L2A5 Fab in complex with STn-Ser

Summary for 9FXT

• Entry DOI: 10.2210/pdb9fxt/pdb
• Related: 9FY8
• Related PRD ID: PRD_002573
• Descriptor: L2A5 Fab Heavy Chain, Anti kappa Variable Heavy Chain, L2A5 Fab Light Chain, ... (8 entities in total)
• Functional Keywords: antibody, fab, sugar binding protein
• Biological source: Homo sapiens; More
• Total number of polymer chains: 6
• Total formula weight: 119585.97

Authors

Laugieri, M.E.,Ereno Orbea, J.,Jimenez Barbero, J.,Oyenarte, I. (deposition date: 2024-07-02, release date: 2025-02-12)

Primary citation

Soares, C.O.,Laugieri, M.E.,Grosso, A.S.,Natale, M.,Coelho, H.,Behren, S.,Yu, J.,Cai, H.,Franconetti, A.,Oyenarte, I.,Magnasco, M.,Gimeno, A.,Ramos, N.,Chai, W.,Corzana, F.,Westerlind, U.,Jimenez-Barbero, J.,Palma, A.S.,Videira, P.A.,Ereno-Orbea, J.,Marcelo, F.
Decoding the Molecular Basis of the Specificity of an Anti-sTn Antibody.
Jacs Au, 5:225-236, 2025

PubMed Abstract: The mucin -glycan sialyl Tn antigen (sTn, Neu5Acα2-6GalNAcα1--Ser/Thr) is an antigen associated with different types of cancers, often linked with a higher risk of metastasis and poor prognosis. Despite efforts to develop anti-sTn antibodies with high specificity for diagnostics and immunotherapy, challenges in eliciting high-affinity antibodies for glycan structures have limited their effectiveness, leading to low titers and short protection durations. Experimental structural insights into anti-sTn antibody specificity are lacking, hindering their optimization for cancer cell recognition. In this study, we used a comprehensive structural approach, combining X-ray crystallography, NMR spectroscopy, computational methods, glycan/glycopeptide microarrays, and biophysical techniques, to thoroughly investigate the molecular basis of sTn recognition by L2A5, a novel preclinical anti-sTn monoclonal antibody (mAb). Our data unequivocally show that the L2A5 fragment antigen-binding (Fab) specifically binds to core sTn moieties. NMR and X-ray structural data suggest a similar binding mode for the complexes formed by the sTn moiety linked to Ser or Thr and the L2A5 Fab. The sugar moieties are similarly oriented in the paratope of mAb, with the Neu5Ac moiety establishing key interactions with the receptor and the GalNAc moiety providing additional contacts. Furthermore, L2A5 exhibits fine specificity toward cancer-related MUC1 and MUC4 mucin-derived sTn glycopeptides, which might contribute to its selective targeting against tumor cells. This newfound knowledge holds promise for the rational improvement and potential application of this anti-sTn antibody in diagnosis and targeted therapy against sTn expressing cancers such as breast, colorectal, and bladder cancer, improving patient care.

PubMed: 39886580
DOI: 10.1021/jacsau.4c00921

Experimental method

X-RAY DIFFRACTION (2.3 Å)