2024-10-16 REL RCSB RCSB RCSB 2020-09-27 2020-10-21 2020-10-21 2024-10-16 National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) P01-AI138938-S1 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) P50-AI150464-13 United States Structure of the SARS-CoV-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, C121 (State 2) Abernathy ME Barnes CO Bjorkman PJ SARS-CoV-2, spike glycoprotein, COVID-19, monoclonal antibody, neutralizing antibody, PROTEIN-IMMUNE SYSTEM complex, VIRAL PROTEIN-IMMUNE SYSTEM complex Barnes CO Jette CA Abernathy ME Dam KA Esswein SR Gristick HB Malyutin AG Sharaf NG Huey-Tubman KE Lee YE Robbiani DF Nussenzweig MC West Jr AP Bjorkman PJ SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies. Nature UK 588 682 687 2020 33045718 doi:10.1038/s41586-020-2852-1 1476-4687 0006 NATUAS EMD-22729 other EM volume EMD-22730 other EM volume EMD-22731 other EM volume EMD-22732 other EM volume EMD-22733 other EM volume EMD-22736 other EM volume EMD-22737 other EM volume EMD-22734 other EM volume 7k8y FULLOVERLAP Ternary complex of SARS-CoV-2 S 2P trimer with human neutralizing antibody Fab fragment C121 (state 2) Ternary complex of SARS-CoV-2 S 2P trimer with human neutralizing antibody Fab fragment C121 (state 2) 0 1 2 3 0.72 SARS-CoV-2 S 2P glycoprotein 1 1 Severe acute respiratory syndrome coronavirus 2 neutralizing antibody Fab fragment C121 1 2 3 Homo sapiens Spike glycoprotein Severe acute respiratory syndrome coronavirus 2 0.139787969 3 Homo sapiens LEVO MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFD NPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVY SSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRV QPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSF VIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPC NGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFL PFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGS NVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTI SVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGF NFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAG TITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALN TLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRV DFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNT FVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL QELGKYEQYIKWPSGRLVPRGSPGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGHHHHHH P0DTC2 C121 Fab Heavy chain Homo sapiens 0.025965162 1 Homo sapiens LEVO QVQLVQSGAEVKKPGASVKVSCKASGYTFTGYYMHWVRQAPGQGLEWMGWISPVSGGTNYAQKFQGRVTMTRDTSISTAY MELSRLRSDDTAVYYCARAPLFPTGVLAGDYYYYGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKD YFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHHHHH H C121 Fab Light chain Homo sapiens 0.022619984 1 Homo sapiens LEVO QSALTQPASVSGSPGQSITISCTGTSSDVGSYNLVSWYQQHPGKAPKLMIYEGSKRPSGVSNRFSGSKSGNTASLTISGL QAEDEADYYCCSYAGSSTLVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVK AGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 23 NAG singleParticle particle 2.5 8.0 0.02 Tris 0.15 NaCl sodium chlorid GLOW DISCHARGE AIR
0.2 mA
 ETHANE 100 295 FEI VITROBOT MARK IV
3s blot.
Monodisperse sample
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.0 2.5 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K3 BIOQUANTUM (6k x 4k) 1 5481 2.6 60.0 1 892954
generated ab initio in cryoSPARC
 C1 4.4 FSC 0.143 CUT-OFF cryoSPARC 2.15 14999 MAXIMUM LIKELIHOOD cryoSPARC 2.15 MAXIMUM LIKELIHOOD cryoSPARC 2.15 2 cryoSPARC 2.15 emd_22735.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 452 452 452 0 0 0 452 452 452 377.872 377.872 377.872 90.0 90.0 90.0 X Y Z -0.08990264 0.28155127 0.00043788945 0.011951806 0.836 0.836 0.836 0.0555 AUTHOR sharpened main map 6VXX PDB experimental model 6W41 PDB experimental model RIGID BODY FIT REAL emd_22735_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 452 452 452 0 0 0 452 452 452 377.872 377.872 377.872 90.0 90.0 90.0 X Y Z -0.06972304 0.2549492 0.0004378894 0.01097814 0.836 0.836 0.836 AUTHOR un-sharpened main map