2023-12-13 REL PDBe PDBe PDBe 2022-02-08 2022-04-20 2022-04-20 2023-12-13 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 (local refinement) 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 EMD-14250 other EM volume
Global refinment of same data and composite map
 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 protein 1 1 Severe acute respiratory syndrome coronavirus 2 Fab 1 2 3 Homo sapiens SARS-CoV-2 spike protein Severe acute respiratory syndrome coronavirus 2 Homo sapiens LEVO MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPAAARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHSAWSHPQFEKGGGSGGGGSGGSAWSHPQFEK 87G7 heavy chain variable domain Homo sapiens Homo sapiens LEVO EVQLLESGGGLVQPGGSLRLSCVASGFTFSSYVMSWVRQAPGKGLEWVAAISGSGGNTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKEGTYYYGSGSFWGQGTLVTVSS 87G7 light chain variable domain Homo sapiens Homo sapiens LEVO EIVLTQSPATLSLSPGERATLSCRASQSFHNYLAWYQQKPGRAPRLLIFDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQRFNWPLTFGGGTKVEIK singleParticle particle 4 8.0 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
 1 C1 4.9 FSC 0.143 CUT-OFF cryoSPARC 72118 RANDOM ASSIGNMENT MAXIMUM LIKELIHOOD cryoSPARC Local refinement job 5 RELION 3.1
Particles were imported into Relion 3.1 and, using the relion particle symmetry expand tool, each particle from the C3 symmetry imposed reconstruction was assigned three orientations corresponding to its symmetry related views. The soft mask was placed over a single RBD Fab region of the map, and the symmetry expanded particles were subjected to masked 3D classification without alignment using a regularization parameter (T number) of 20. Following a single round of focused classification, the best particle stack consisting of 72,118 particles was imported back to cryoSPARC for local refinement.
 emd_14271.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 -0.0018065077 3.370331 0.00022597187 0.011496915 1.24 1.24 1.24 0.08 AUTHOR DeepEMhancer sharpened map emd_14271_msk_1.map emd_14271_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 -7.9036794 14.04974 0.00342056 0.0904376 1.24 1.24 1.24 AUTHOR Local resolution filtered map emd_14271_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 -1.109202 2.6074586 0.0013166515 0.04107833 1.24 1.24 1.24 AUTHOR Unsharpened map emd_14271_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 -7.109889 11.202742000000001 0.0013166517 0.06473924 1.24 1.24 1.24 AUTHOR Sharpened map emd_14271_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 -1.394246 3.2883987 0.0031050812 0.057647474 1.24 1.24 1.24 AUTHOR Half map 1 emd_14271_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 -1.4229244 3.2087152 0.0030367465 0.057800107 1.24 1.24 1.24 AUTHOR Half map 2