2025-07-09 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name STRUCTURE_SUMMARY em_admin pdbx_entry_details pdbx_modification_feature _em_admin.last_update _pdbx_entry_details.has_protein_modification DATA_COLLECTION em_admin em_software _em_admin.last_update _em_software.name PDBe PDBe 2023-11-30 2024-06-05 2024-06-05 2025-07-09 Innovative Medicines Initiative LSHM19136 Switzerland S1B domain of the PDCoV spike glycoprotein in complex with the 67B12 and 42H3 antibody Fab fragments Debski-Antoniak O Hurdiss DL Hurdiss DL Spike, coronavirus, antibody, complex, RBD, S1B, VIRAL PROTEIN Du W Debski-Antoniak O Drabek D van Haperen R van Dortmondt M van der Lee J Drulyte I van Kuppeveld FJM Grosveld F Hurdiss DL Bosch BJ Neutralizing antibodies reveal cryptic vulnerabilities and interdomain crosstalk in the porcine deltacoronavirus spike protein. Nat Commun UK 15 5330 5330 2024 38909062 doi:10.1038/s41467-024-49693-0 2041-1723 8r9y FULLOVERLAP PDCoV spike S1B domain in complex with the 67B12 and 42H3 antibody Fab fragments PDCoV spike S1B domain in complex with the 67B12 and 42H3 antibody Fab fragments 0 1 2 3 4 5 Homo sapiens 0.10524 Spike protein Porcine deltacoronavirus 0.022919553 1 Homo sapiens LEVO MPMGSLQPLATLYLLGMLVASVLATLPKLPELEVVQLNISAHMDFGEARLDSVTINGNTSYCVTKPYFRLETNFMCTGCT MNLRTDTCSFDLSAVNNGMSFSQFCLSTESGACEMKIIVTYVWNYLLRQRLYVTAVEGQTHTGTTSVHATDTDPDYKDDD DKAGPGWSHPQFEKGGGSGGGSGGGSWSHPQFEKGGGSGGGSGGGSWSHPQFEK A0A513Q8I8 67B12 antibody heavy chain Homo sapiens 0.022964826 1 Homo sapiens LEVO VQLVQSGAEVKKPGSSVKVSCKASGGTFSSLAISWVRQAPGQGLEWMGGIIPTFGTTNYAQNFRGRVTITADKSTSTAYM ELSTLISEDTAVYFCARERSTDTWPGDAFDIWGQGTMVTVSSASTKGPSVFPLAPSSGTAALGCLVKDYFPEPVTVSWNS GALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLLGQTYICNVNHKPSNTKVDKKVEPK 67B12 antibody light chain Homo sapiens 0.023037592 1 Homo sapiens LEVO EILMTQSPATLSVSPGERATLSCWASQSVNSKLAWYQQKPGQAPRLLIYDTSTRATGIPARFSGSGSGAEFTLTISSLQS EDFAVYYCQQYNYWPYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQ ESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSF 42H3 antibody heavy chain Homo sapiens 0.023579699 1 Homo sapiens LEVO QVQLVESGGGVVQPGRSLRLSCAASGFTFSSYDMHWVRQAPGKGLEWVAVIWRDGSNEYYADSVKGRFIISRDNSKNTLY LQMNSLRAEDTAVYYCARRGIIMVRGLLGYWGQGTLVTVSSASTKGPSVFPLAPSSKSGTAALGCLVKDYFPEPVTVSWN SGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 42H3 antibody light chain Homo sapiens 0.023017627 1 Homo sapiens LEVO DIQMTQSPPSLSASVGDRVTITCRASQGISNYLAWHQQKPGKVPKLLIYTASTLQSGVPSRFSGSGSGTDFTLTISSLQP EDVATYYCQKYNSAPFTFGPGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQ ESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 1 NAG singleParticle particle 7.8 ETHANE 90 FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.75 1.5 TFS Selectris FEI FALCON IV (4k x 4k) 50.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION
ab initio
 3.0 FSC 0.143 CUT-OFF cryoSPARC 148945 MAXIMUM LIKELIHOOD cryoSPARC MAXIMUM LIKELIHOOD cryoSPARC
Non-uniform refinement
 emd_19016.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 291.999 291.999 291.999 90.0 90.0 90.0 X Y Z -0.29572603 0.6471517 0.00040390767 0.012780409 0.97332996 0.97332996 0.97332996 0.188 AUTHOR 6BFU A PDB experimental model RIGID BODY FIT
Initial fitting was done using Chimera
Cross-correlation coefficient REAL emd_19016_msk_1.map emd_19016_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 291.999 291.999 291.999 90.0 90.0 90.0 X Y Z -0.43961138 0.84092367 0.0003655483 0.03163246 0.97332996 0.97332996 0.97332996 AUTHOR emd_19016_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 291.999 291.999 291.999 90.0 90.0 90.0 X Y Z -0.43581998 0.8454966 0.00037245362 0.031669565 0.97332996 0.97332996 0.97332996 AUTHOR