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

2026-02-04 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY RCSB RCSB 2025-09-18 2026-02-04 2026-02-04 2026-02-04 Other private Denmark Other government R231-A13832 and R352-A20542 Denmark Australian Research Council (ARC) FL180100019 Australia National Health and Medical Research Council (NHMRC, Australia) APP2000728 Australia Human uPAR bound to the Fab fragment of targeted cancer therapeutic antibody FL1 Anane RF Whisstock JC Engelholm LH Law RHP Ploug M Complex, Targeted cancer therapy, Monoclonal anti-uPAR antibody FL1, Antibody-drug conjugate, IMMUNE SYSTEM Anane RF Kumari A Venugopal H Trepout S Whisstock JC Engelholm LH Law RHP 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. US 35 e70473 e70473 2026 41575054 doi:10.1002/pro.70473 1469-896X 0795 PRCIEI 9yc5 FULLOVERLAP EMDB EMD-72760 associated EM volume

Binary complex of human uPAR and Fab fragment of anti-uPAR antibody FL1 Binary complex of human uPAR and Fab fragment of anti-uPAR antibody FL1 0 1 2 3

Full-length human uPAR, and full-length antibody FL1 (IgG) were mixed to form the protein complex which was used for EM sample.

Homo sapiens Urokinase plasminogen activator surface receptor Homo sapiens 0.031501342 1 Drosophila melanogaster LEVO LRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEELELVEKSCTHSEKTNRTLSYRTGLKITSLTEVVCGLDLCNQGN SGRAVTYSRSRYLECISCGSSDMSCERGRHQSLQCRSPEEQCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNGFH NNDTFHFLKCCNTTKCNEGPILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGPMNQCLVATGTHEPKNQSYMVRG CATASMCQHAHLGDAFSMNHIDVSCCTKSGCNHPDLDVQYRSG Q03405 Anti-uPAR antibody FL1 Fab heavy chain Mus musculus 0.023581258 1 Mus musculus LEVO EVQLQQSGSVLVRPGTSVNLSCKASGYTFTSYWMSWVKQRPGQGLEWIGEIFPKSGRINSNENFRGKATLTVDTSSSTAY INLSSLTSEDSAVYYCSPIYSGDYGFADWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTW NSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC Anti-uPAR antibody FL1 Fab light chain Mus musculus 0.024168817999999998 1 Mus musculus LEVO DIVMTQTPLSLPVSLGDQASISCRSSQSVVSNNGKTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKI SRVEAEDLGVYYCFQGSHVPWTFGGGTKLEVKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSER QNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 2 NAG singleParticle particle 3.5 7.4 20.0 C4H11NO3 Tris(hydroxymethyl)aminomethane 150.0 NaCl Sodium chloride 2.5 C3H8O3 Glycerol 1.0 C10H16N2O8 EDTA

20mM Tris, 150mM NaCl, 2.5% Glycerol, 1mM EDTA, pH 7.4

UltrAuFoil R1.2/1.3 GOLD 300 GLOW DISCHARGE 30 3.9 ETHANE 100 277.15 FEI VITROBOT MARK IV

Full-length human uPAR, and full-length antibody FL1 (IgG) were mixed in 2:1 molar ratio to form the protein complex which was used for EM sample.

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.5 2.0 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN VOLTA PHASE PLATE GIF Bioquantum 10 GATAN K3 BIOQUANTUM (6k x 4k) 5760 4092 1 7181 4.92 10.7

Images were collected at a pixel size of 0.8234

Following motion correction, 4345 images were selected for particle picking

7426690

The 7426690 particles were picked by automated particle picking using blob picker. Several rounds of 2D classification were performed to discard particles of low quality, producing 184642 particles of good quality which were used for 3D reconstruction.

cryoSPARC 4.5.3

CTF corrections were performed after 3D reconstruction to improve the final resolution

PHASE FLIPPING AND AMPLITUDE CORRECTION 16 C1 2.94 FSC 0.143 CUT-OFF cryoSPARC 4.5.3 184642 MAXIMUM LIKELIHOOD cryoSPARC 4.5.3 MAXIMUM LIKELIHOOD cryoSPARC 4.5.3 16 11540.0 cryoSPARC 4.5.3 emd_72760.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 262.4 262.4 262.4 90.0 90.0 90.0 X Y Z -1.6133835 2.8104153 0.0027221134 0.038525105 0.82 0.82 0.82 0.2 AUTHOR ::::EMDATABANK.org::::EMD-72760:::: AF-Q03405-F1-v4 114-299 AlphaFold in silico model FLEXIBLE FIT

An initial local fitting was performed with ISOLDE implemented in ChimeraX prior to real-space refinement in phenix.

cross-correlation coefficient REAL 112.0 emd_72760_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 262.4 262.4 262.4 90.0 90.0 90.0 X Y Z -0.44219926 1.1172537 0.001537305 0.02944081 0.82 0.82 0.82 AUTHOR ::::EMDATABANK.org::::EMD-72760:::: emd_72760_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 262.4 262.4 262.4 90.0 90.0 90.0 X Y Z -0.4341142 1.2392765 0.0015354797 0.029360216 0.82 0.82 0.82 AUTHOR ::::EMDATABANK.org::::EMD-72760::::