9YC6

Mutant human uPAR bound to the Fab fragment of the targeted cancer therapeutic antibody FL1

This is a non-PDB format compatible entry.

Summary for 9YC6

• Entry DOI: 10.2210/pdb9yc6/pdb
• Related: 9YC5
• EMDB information: 72761
• Descriptor: Anti-uPAR antibody FL1 Fab light chain, Urokinase plasminogen activator surface receptor, Anti-uPAR antibody FL1 Fab heavy chain, ... (6 entities in total)
• Functional Keywords: complex, targeted cancer therapy, monoclonal anti-upar antibody fl1, antibody-drug conjugate, immune system
• Biological source: Mus musculus (Mouse); More
• Total number of polymer chains: 3
• Total formula weight: 80658.81

Authors

Anane, R.F.,Whisstock, J.C.,Engelholm, L.H.,Law, R.H.P.,Ploug, M. (deposition date: 2025-09-18, release date: 2026-02-04)

Primary citation

Anane, R.F.,Kumari, A.,Venugopal, H.,Trepout, S.,Whisstock, J.C.,Engelholm, L.H.,Law, R.H.P.,Ploug, M.
Structural basis for uPAR binding to an antibody developed for targeted cancer therapy. Mechanistic insights into flexibility, ligand recognition, and molecular imaging.
Protein Sci., 35:e70473-e70473, 2026

PubMed Abstract: The urokinase-type plasminogen activator receptor (uPAR) is currently gaining momentum as a promising molecular target for treatment of various solid cancers. For patient stratification, we developed a high-affinity uPAR-targeting peptide (AE105) detecting primary cancer lesions as well as occult metastasis by positron emission tomography (PET) imaging. uPAR-targeting by AE105 is also used for optical imaging in fluorescence-guided surgery of, for example, head-and-neck cancers. Recently, we showed that a monoclonal anti-uPAR antibody (FL1), in the form of an antibody-drug conjugate (FL1-ADC), efficiently eradicate pancreatic ductal carcinomas in surrogate mouse models leading to long-term remissions. In the current study, we solved high-resolution cryo-EM structures of FL1 in complex with two different conformational states of uPAR. Combined with comprehensive kinetic data from surface plasmon resonance studies, our cryo-EM structures provide essential insights into how FL1 binding impacts the interdomain flexibility of uPAR by restricting the movement of its N-terminal LU domain. This constraint from the bound FL1 drives uPAR into its open conformation, which leads to a pronounced reduction in the binding affinity for both its natural protease ligand (300-fold) and the PET imaging probe AE105 (25-fold). Collectively, these consequences of FL1-binding on uPAR conformation are considered beneficial for both targeted cancer treatment with FL1-ADCs and for the accompanying evaluation of treatment efficacy by longitudinal AE105-based PET imaging.

PubMed: 41575054
DOI: 10.1002/pro.70473

Experimental method

ELECTRON MICROSCOPY (4.8 Å)