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

2026-02-11 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY REFINEMENT_DESCRIPTION em_3d_fitting_list em_admin pdbx_initial_refinement_model _em_3d_fitting_list.initial_refinement_model_id _em_admin.last_update _pdbx_initial_refinement_model.accession_code _pdbx_initial_refinement_model.source_name _pdbx_initial_refinement_model.type REFINEMENT_DESCRIPTION em_3d_fitting_list em_admin pdbx_initial_refinement_model _em_3d_fitting_list.initial_refinement_model_id _em_admin.last_update _pdbx_initial_refinement_model.accession_code _pdbx_initial_refinement_model.source_name _pdbx_initial_refinement_model.type RCSB RCSB 2025-09-18 2026-02-04 2026-02-04 2026-02-11 Other private Other government R231-A13832 R352-A20542 Australian Research Council (ARC) FL180100019 Australia National Health and Medical Research Council (NHMRC, Australia) APP2000728 Australia Mutant human uPAR bound to the Fab fragment of the 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 9yc6 FULLOVERLAP PDB 9YC5 unspecified

9YC5 contain the same protein complex with wild type human uPAR

EMDB EMD-72761 associated EM volume

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

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

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

Homo sapiens Anti-uPAR antibody FL1 Fab light chain Mus musculus 0.024168817999999998 1 Mus musculus LEVO DIVMTQTPLSLPVSLGDQASISCRSSQSVVSNNGKTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKI SRVEAEDLGVYYCFQGSHVPWTFGGGTKLEVKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSER QNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC Urokinase plasminogen activator surface receptor Homo sapiens 0.031455377 1 Drosophila melanogaster LEVO LRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEELELVEKSCTCSEKTNRTLSYRTGLKITSLTEVVCGLDLCNQGN SGRAVTYSRSRYLECISCGSSDMSCERGRHQSLQCRSPEEQCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNGFH NNDTFHFLKCCNTTKCNEGPILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGPMNQCLVATGTHEPKNQSYMVRG CATASMCQHAHLGDAFSMCHIDVSCCTKSGCNHPDLDVQYRSG Q03405 Anti-uPAR antibody FL1 Fab heavy chain Mus musculus 0.023581258 1 Mus musculus LEVO EVQLQQSGSVLVRPGTSVNLSCKASGYTFTSYWMSWVKQRPGQGLEWIGEIFPKSGRINSNENFRGKATLTVDTSSSTAY INLSSLTSEDSAVYYCSPIYSGDYGFADWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTW NSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC 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 GOLD HOLEY ETHANE 100 277.15 FEI VITROBOT MARK IV

Full-length mutant 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 0.8 2.0 165000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN VOLTA PHASE PLATE GIF Bioquantum 10 TFS FALCON 4i (4k x 4k) 4092 4092 1 6669 12.06

Images were collected at a pixel size of 0.75

Following motion correction, 4668 images were selected for particle picking

8296036

The 8296036 particles were picked by automated particle picking using blob picker. Several rounds of 2D classification were performed to discard particles of low quality, producing 86404 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 14 C1 FOURIER SPACE 4.8 FSC 0.143 CUT-OFF cryoSPARC 4.5.3 86404 MAXIMUM LIKELIHOOD cryoSPARC 4.5.3 MAXIMUM LIKELIHOOD cryoSPARC 4.5.3 16 11540.0 cryoSPARC 4.5.3 emd_72761.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 270.0 270.0 270.0 90.0 90.0 90.0 X Y Z -0.52656204 0.42939013 0.001471229 0.018643325 0.75 0.75 0.75 0.08 AUTHOR ::::EMDATABANK.org::::EMD-72761:::: 3u74 23-301 PDB experimental 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 92.0 emd_72761_msk_1.map emd_72761_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 270.0 270.0 270.0 90.0 90.0 90.0 X Y Z -0.25635636 0.35543525 0.00086918066 0.016432371 0.75 0.75 0.75 AUTHOR ::::EMDATABANK.org::::EMD-72761:::: emd_72761_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 270.0 270.0 270.0 90.0 90.0 90.0 X Y Z -0.24599329 0.3693371 0.0008528564 0.016504092 0.75 0.75 0.75 AUTHOR ::::EMDATABANK.org::::EMD-72761::::