CryoEM map of SARS-CoV-2 S protein in complex with N-terminal domain antibody DH1050.1

2024-11-13 REL RCSB RCSB RCSB 2021-01-11 2021-01-27 2021-01-27 2024-11-13 National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) AI145687 United States CryoEM map of SARS-CoV-2 S protein in complex with N-terminal domain antibody DH1050.1 Manne K Acharya P RBD antibody, DH1050.1, SARS, COVID-19, SARS-CoV-2 2P S ectodomain, VIRAL PROTEIN, IMMUNE SYSTEM Li D Edwards RJ Manne K Martinez DR Schafer A Alam SM Wiehe K Lu X Parks R Sutherland LL Oguin 3rd TH McDanal C Perez LG Mansouri K Gobeil SMC Janowska K Stalls V Kopp M Cai F Lee E Foulger A Hernandez GE Sanzone A Tilahun K Jiang C Tse LV Bock KW Minai M Nagata BM Cronin K Gee-Lai V Deyton M Barr M Von Holle T Macintyre AN Stover E Feldman J Hauser BM Caradonna TM Scobey TD Rountree W Wang Y Moody MA Cain DW DeMarco CT Denny TN Woods CW Petzold EW Schmidt AG Teng IT Zhou T Kwong PD Mascola JR Graham BS Moore IN Seder R Andersen H Lewis MG Montefiori DC Sempowski GD Baric RS Acharya P Haynes BF Saunders KO In vitro and in vivo functions of SARS-CoV-2 infection-enhancing and neutralizing antibodies. Cell 184 4203 2021 34242577 doi:10.1016/j.cell.2021.06.021 1097-4172 Li D Edwards RJ Manne K Martinez DR Schafer A Alam SM Wiehe K Lu X Parks R Sutherland LL Oguin TH McDanal C Perez LG Mansouri K Gobeil SMC Janowska K Stalls V Kopp M Cai F Lee E Foulger A Hernandez GE Sanzone A Tilahun K Jiang C Tse LV Bock KW Minai M Nagata BM Cronin K Gee-Lai V Deyton M Barr M Von Holle T Macintyre AN Stover E Feldman J Hauser BM Caradonna TM Scobey TD Moody MA Cain DW DeMarco CT Denny TN Woods CW Petzold EW Schmidt AG Teng IT Zhou T Kwong PD Mascola JR Graham BS Moore IN Seder R Andersen H Lewis MG Montefiori DC Sempowski GD Baric RS Acharya P Haynes BF Saunders KO The functions of SARS-CoV-2 neutralizing and infection-enhancing antibodies in vitro and in mice and nonhuman primates. Biorxiv US 2021 33442694 doi:10.1101/2020.12.31.424729 2692-8205 7lcn FULLOVERLAP Severe acute respiratory syndrome-related coronavirus spike glycoprotein in complex with NTD antibody DH1050.1 Severe acute respiratory syndrome-related coronavirus spike glycoprotein in complex with NTD antibody DH1050.1 0 1 2 3 Spike glycoprotein 1 1 Severe acute respiratory syndrome coronavirus 2 Antibody DH1050.1 1 2 3 Homo sapiens Spike glycoprotein Severe acute respiratory syndrome coronavirus 2 0.124124477 3 Homo sapiens LEVO AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIF GTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNF KNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYY VGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATR FASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLP DDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQ PYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILD ITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPI GAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDS TECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKV TLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRF NGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDP PEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVT YVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELD S P0DTC2 DH1050.1 heavy chain Homo sapiens 0.023722615 3 Homo sapiens LEVO QVQLVQSGAEVKKPGASVKVSCKVSGYTLPELSMHWVRQAPGKGLEWMGGFHPEDGETIYAQKFQGRVTMTEDTSTDTAY MELSSLRSEDTAVYYCATGSPFGVVTDWFDPWGRGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVT VSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK DH1050.1 light chain Homo sapiens 0.022834096 3 Homo sapiens LEVO QSALTQPPSASGSPGQSVTISCTGTSSDVGGYNYVSWYQQHPGKAPKLMIYEVSKRPSGVPDRFSGSKSGNTASLTVSGL QAEDEADYYCSSYAGSNNPYVFGTGTKVTVLGQPKANPTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPV KAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTEC 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 33 NAG singleParticle particle 7.4 Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY GLOW DISCHARGE ETHANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 93.15 93.15 GATAN K3 (6k x 4k) 2154 65.09 1 6VXX 3.35 FSC 0.143 CUT-OFF cryoSPARC 426025 MAXIMUM LIKELIHOOD cryoSPARC MAXIMUM LIKELIHOOD cryoSPARC cryoSPARC emd_23277.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 338.56 338.56 338.56 90.0 90.0 90.0 X Y Z -0.6978386 1.7047557 -0.0007424302 0.043502446 1.058 1.058 1.058 0.194 AUTHOR ::::EMDATABANK.org::::EMD-23277:::: Structure of SARS-CoV-2 S protein in complex with N-terminal domain antibody DH1050.1 6VXX PDB experimental model AB INITIO MODEL