2023-12-13 REL PDBe PDBe PDBe 2023-01-20 2023-02-22 2023-02-22 2023-12-13 Health-Holland LSHM20037 Netherlands Netherlands Organisation for Scientific Research (NWO) 184.034.014 Netherlands Structure of the SARS-CoV-2 spike glycoprotein in complex with the 10D12 heavy-chain-only antibody (3 RBDs up) Serna Martin I Hurdiss DL Complex, Spike, Glycoprotein, Antibody, VIRAL PROTEIN Du W Janssens R Mykytyn AZ Li W Drabek D van Haperen R Chatziandreou M Rissmann M van der Lee J van Dortmondt M Martin IS van Kuppeveld FJM Hurdiss DL Haagmans BL Grosveld F Bosch BJ Avidity engineering of human heavy-chain-only antibodies mitigates neutralization resistance of SARS-CoV-2 variants. Front Immunol CH 14 1111385 1111385 2023 36895554 doi:10.3389/fimmu.2023.1111385 1664-3224 SARS-CoV-2 spike glycoprotein in complex with the 10D12 heavy-chain-only antibody SARS-CoV-2 spike glycoprotein in complex with the 10D12 heavy-chain-only antibody 0 1 2 SARS-CoV-2 spike glycoprotein Severe acute respiratory syndrome coronavirus 2 Homo sapiens LEVO MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPAAARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHSAWSHPQFEKGGGSGGGGSGGSAWSHPQFEK Heavy-chain-only antibody 10D12 Mus musculus Homo sapiens LEVO MEFGLSWLFLVAILKGVQCEVQLVETGGGLIQPGGSLRLSCAVSGFTVSLNYMSWVRQAPGKGLEWVSSIYSGGSTFYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARGLGFGELPPFDFWGQGTLVTVSSEPKSCDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK singleParticle particle 1 8.0
20 mM Tris pH 8, 150 mM NaCl.
 Quantifoil R1.2/1.3 COPPER 200 GLOW DISCHARGE ETHANE FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.6 2.4 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K3 BIOQUANTUM (6k x 4k) 1 5018 50.0 1 1215409
ab initio
 C3 3.1 FSC 0.143 CUT-OFF cryoSPARC 76744 RANDOM ASSIGNMENT cryoSPARC MAXIMUM LIKELIHOOD cryoSPARC emd_16480.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 334.40997 334.40997 334.40997 90.0 90.0 90.0 X Y Z -2.2897136 3.169269 0.0016460426 0.061564717 1.1147 1.1147 1.1147 0.235 AUTHOR Sharpened map emd_16480_msk_1.map emd_16480_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 334.40997 334.40997 334.40997 90.0 90.0 90.0 X Y Z -0.34536928 0.969711 0.0016460423 0.026051579 1.1147 1.1147 1.1147 AUTHOR Unsharpened map emd_16480_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 334.40997 334.40997 334.40997 90.0 90.0 90.0 X Y Z -0.39043722 1.0054735 0.0015803926 0.03665769 1.1147 1.1147 1.1147 AUTHOR Half map A emd_16480_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 334.40997 334.40997 334.40997 90.0 90.0 90.0 X Y Z -0.41085288 1.0197316 0.0015848364 0.03664485 1.1147 1.1147 1.1147 AUTHOR Half map B