Cryo-EM structure of NTD-directed neutralizing antibody 5-7 in complex with prefusion SARS-CoV-2 spike glycoprotein

2021-09-01 OBS RCSB RCSB RCSB 2021-05-24 2021-08-04 2021-08-04 2021-09-01 2021-09-01 Jack Ma Foundation China Cryo-EM structure of NTD-directed neutralizing antibody 5-7 in complex with prefusion SARS-CoV-2 spike glycoprotein Cerutti G Shapiro L Cerutti G Guo Y Wang P Nair MS Huang Y Yu J Liu L Katsamba PS Bahna F Reddem ER Kwong PD Ho DD Sheng Z Shapiro L Neutralizing antibody 5-7 defines a distinct site of vulnerability in SARS-CoV-2 spike N-terminal domain. Biorxiv US 2021 34230927 doi:10.1101/2021.06.29.450397 EMD-24097 associated EM volume

7n01 FULLOVERLAP Prefusion SARS-CoV-2 spike glycoprotein in complex with 5-7 Fab Prefusion SARS-CoV-2 spike glycoprotein in complex with 5-7 Fab 0 1 2 3 Severe acute respiratory syndrome coronavirus 2 Spike glycoprotein Severe acute respiratory syndrome coronavirus 2 0.142399375 3 Homo sapiens LEVO MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFD NPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVY SSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRV QPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSF VIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPC NGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFL PFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGS NVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTI SVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGF NFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAG TITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALN TLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRV DFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNT FVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL QELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHSAWSHPQFEKGGGSGGGGSGGSA WSHPQFEK 5-7 Fab heavy chain Homo sapiens 0.027018072 1 Homo sapiens LEVO QVQLVQSGAEVKKPGASVKVSCKASGYTFTSYYMHWVRQAPGQGLEWMGVINPSGGSTSYAEKFRGRVTMTRDTSTSTVY MELSSLRSEDTAVYYCARDREPHSDSSGYWDSLKYYYYYALDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALG CLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKT HHHHHHHH 5-7 Fab light chain Homo sapiens 0.023220752 1 Homo sapiens LEVO AIQLTQSPSSLSASVGDRVTITCRASQGISSYLAWYQQKPGKAPELLIYAASTLQSGVPSRFSGSGSGTDFTLTISSLQP EDFATYYCQQLNTYPFTFGPGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQ ESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 43 NAG singleParticle particle 4.5 ETHANE FEI TITAN KRIOS OTHER BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K3 BIOQUANTUM (6k x 4k) 42.0 1 cryoSPARC 3.7 FSC 0.143 CUT-OFF cryoSPARC 150834 MAXIMUM LIKELIHOOD cryoSPARC MAXIMUM LIKELIHOOD cryoSPARC emd_24097.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 428.00003 428.00003 428.00003 90.0 90.0 90.0 X Y Z -2.1428838 2.9549742 -0.00015664333 0.048559256 1.07 1.07 1.07 0.38 AUTHOR ::::EMDATABANK.org::::EMD-24097:::: FLEXIBLE FIT emd_24097_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 428.00003 428.00003 428.00003 90.0 90.0 90.0 X Y Z -0.5555661 1.198722 -0.00015664336 0.029633256 1.07 1.07 1.07 AUTHOR ::::EMDATABANK.org::::EMD-24097:::: Unsharpened map emd_24097_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 428.00003 428.00003 428.00003 90.0 90.0 90.0 X Y Z -0.7721557 1.526276 0.0007790099 0.06530882 1.07 1.07 1.07 AUTHOR ::::EMDATABANK.org::::EMD-24097:::: emd_24097_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 428.00003 428.00003 428.00003 90.0 90.0 90.0 X Y Z -0.8785657 1.5354391 0.0007815489 0.06574238 1.07 1.07 1.07 AUTHOR ::::EMDATABANK.org::::EMD-24097::::