2024-10-23 REL PDBe PDBe PDBe 2022-02-08 2022-04-20 2022-04-20 2024-10-23 European Commission 101003651 European Union German Research Foundation (DFG) 398066876/GRK 2485/1 Germany German Federal Ministry for Education and Research 01KI1723G Germany Structure of the SARS-CoV-2 spike glycoprotein in complex with the 87G7 antibody Fab fragment Hurdiss DL Drulyte I Coronavirus, Spike, Antibody, Complex, VIRAL PROTEIN Du W Hurdiss DL Drabek D Mykytyn AZ Kaiser FK Gonzalez-Hernandez M Munoz-Santos D Lamers MM van Haperen R Li W Drulyte I Wang C Sola I Armando F Beythien G Ciurkiewicz M Baumgartner W Guilfoyle K Smits T van der Lee J van Kuppeveld FJM van Amerongen G Haagmans BL Enjuanes L Osterhaus ADME Grosveld F Bosch BJ An ACE2-blocking antibody confers broad neutralization and protection against Omicron and other SARS-CoV-2 variants of concern. Sci Immunol US 7 eabp9312 eabp9312 2022 35471062 doi:10.1126/sciimmunol.abp9312 2470-9468 7r40 FULLOVERLAP SARS-CoV-2 spike glycoprotein in complex with the 87G7 antibody Fab fragment SARS-CoV-2 spike glycoprotein in complex with the 87G7 antibody Fab fragment 0 1 2 3 0.5 SARS-CoV-2 spike glycoprotein 1 1 Severe acute respiratory syndrome coronavirus 2 87G7 antibody Fab fragment 1 2 3 Homo sapiens Spike glycoprotein Severe acute respiratory syndrome coronavirus 2 0.14104873399999998 3 Homo sapiens LEVO QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFA STEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQ PFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD SSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNIT NLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPG QTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQ SYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTT DAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGA EHVNNSYECDIPIGAGICASYQTQTNSPAAARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTK TSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPS KRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPA LQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALNTLVKQLSSNFGAI SSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFP QSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIV NNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYI PEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHSAWSHPQFEKGGGSGGGGSGGSAWSHPQFEK P0DTC2 87G7 light chain variable region Homo sapiens 0.023550206999999997 3 Homo sapiens LEVO EIVLTQSPATLSLSPGERATLSCRASQSFHNYLAWYQQKPGRAPRLLIFDASNRATGIPARFSGSGSGTDFTLTISSLEP EDFAVYYCQQRFNWPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQ ESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 87G7 heavy chain variable region Homo sapiens 0.023915703 3 Homo sapiens LEVO EVQLLESGGGLVQPGGSLRLSCVASGFTFSSYVMSWVRQAPGKGLEWVAAISGSGGNTYYADSVKGRFTISRDNSKNTLY LQMNSLRAEDTAVYYCAKEGTYYYGSGSFWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVS WNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 27 NAG singleParticle particle 4 8.0 Quantifoil R1.2/1.3 COPPER ETHANE FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 0.5 1.5 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN TFS Selectris X 10 FEI FALCON IV (4k x 4k) 4096 4096 2 3831 51.5
1331 images collected from grid 1 (0.02% FOM) and 2500 images collected from grid 2 (0% FOM)
 1 934811
313636 particles were picked from 1331 images from 0.02% FOM dataset and 621175 particles were picked from 2500 images without FOM.
Generated ab initio using cryoSPARC
 C3 2.9 FSC 0.143 CUT-OFF cryoSPARC 133550 RANDOM ASSIGNMENT MAXIMUM LIKELIHOOD cryoSPARC emd_14250.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 372.0 372.0 372.0 90.0 90.0 90.0 X Y Z -0.004284906 3.62477 0.0013926498 0.027411383 1.24 1.24 1.24 0.1 AUTHOR Composite map 7B62 A 14-308 PDB experimental model 7K4N A 309-332 PDB experimental model 7K4N A 527-1145 PDB experimental model 6M0J E 333-526 PDB experimental model emd_14250_msk_1.map emd_14250_additional_5.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 372.0 372.0 372.0 90.0 90.0 90.0 X Y Z -3.459593 5.3024416 -0.000076429584 0.079155415 1.24 1.24 1.24 AUTHOR Sharpened map emd_14250_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 372.0 372.0 372.0 90.0 90.0 90.0 X Y Z -0.5487913 1.4057845 -0.00007642957 0.038419846 1.24 1.24 1.24 AUTHOR Unsharpened map emd_14250_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 372.0 372.0 372.0 90.0 90.0 90.0 X Y Z -0.0018736022 1.8731486 0.0010350884 0.020762417 1.24 1.24 1.24 AUTHOR DeepEMhancer sharpened map emd_14250_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 372.0 372.0 372.0 90.0 90.0 90.0 X Y Z -6.3861237 11.925616 0.001683307 0.13282745 1.24 1.24 1.24 AUTHOR Local resolution filtered map emd_14250_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 372.0 372.0 372.0 90.0 90.0 90.0 X Y Z 0.0 1.0 0.038613923 0.18546957 1.24 1.24 1.24 AUTHOR Mask used for refinement emd_14250_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 372.0 372.0 372.0 90.0 90.0 90.0 X Y Z -0.642128 1.5151323 0.0018135281 0.045139223 1.24 1.24 1.24 AUTHOR Half map 2 emd_14250_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 372.0 372.0 372.0 90.0 90.0 90.0 X Y Z -0.5781136 1.6066352 0.0018187319 0.045414526 1.24 1.24 1.24 AUTHOR Half map 1