2025-06-04 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name DATABASE_REFERENCES citation _citation.journal_volume _citation.pdbx_database_id_DOI _citation.year STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond em_admin pdbx_entry_details pdbx_modification_feature _em_admin.last_update _pdbx_entry_details.has_protein_modification DATA_COLLECTION em_admin em_software _em_admin.last_update _em_software.name RCSB RCSB 2021-10-27 2021-12-08 2021-12-08 2025-06-04 Other private no grant number United States Pan J Abraham J COVID-19, SARS-CoV-2, neutralizing antibody, neutralization escape, IMMUNE SYSTEM Nabel KG Clark SA Shankar S Pan J Clark LE Yang P Coscia A McKay LGA Varnum HH Brusic V Tolan NV Zhou G Desjardins M Turbett SE Kanjilal S Sherman AC Dighe A LaRocque RC Ryan ET Tylek C Cohen-Solal JF Darcy AT Tavella D Clabbers A Fan Y Griffiths A Correia IR Seagal J Baden LR Charles RC Abraham J Science US 375 eabl6251 eabl6251 2022 34855508 doi:10.1126/science.abl6251 1095-9203 0038 SCIEAS 7sn2 FULLOVERLAP SARS-CoV-2_Hexapro in complex with neutralizing antibody C1C-A3 Fab from human patient SARS-CoV-2_Hexapro in complex with neutralizing antibody C1C-A3 Fab from human patient 0 1 2 3

concentration of the SARS-CoV-2 spike protein SARS-CoV-2 Hexapro (trimeric) and human patient antibody C1C-A3 Fab is 0.6 and 0.3 mg/mL in the final complex sample in buffer consisting of 150 mM NaCl and 25 mM Tris-HCl, pH 7.5. structure deposited here is one receptor binding domain (RBD) in complex with on C1C-A3 Fab determined from the relate wwPDB deposit D_1000258559.

Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1 0.05 SARS-CoV-2 spike protein SARS-CoV-2 Hexapro 1 1 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1 C1C-A3 Fab 1 2 3

Fab of C1C-A3 antibody recombinantly expressed using sequence sequenced from single B cells from human patient peripheral blood sample

Homo sapiens Spike glycoprotein Severe acute respiratory syndrome coronavirus 2 0.141192203

Severe acute respiratory syndrome coronavirus 2 surface glycoprotein (residues 1-1208) of GeneBank locus QHD43416.1 (amino acids 1-15 are the endogenous signal peptide, 16-1208 are SARS-CoV-2 spike protein residues 16-1208, 1209-1210+1237-1239+1255-1258 are linkers, 1211-1236 are T4 fibritinn foldon, 1240-1254 are the avi-tag for biotinylation, 1259-1265 are the TEV protease cleavage site, 1266-1273 are the 8xHis tag; mutations include R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P)

1 Homo sapiens LEVO MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFD NPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVY SSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRV QPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSF VIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPC NGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFL PFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGS NVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTI SVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGF NFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAG TITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALN TLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRV DFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNT FVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL QELGKYEQSGYIPEAPRDGQAYVRKDGEWVLLSTFLSAGGLNDIFEAQKIEWHEGASGENLYFQGHHHHHHHH P0DTC2 neutralizing antibody C1C-A3 Fab heavy chain Homo sapiens 0.027022606999999997

amino acids 1-20 are the human tPA signal peptide, 21-22 are a linker, 23-250 are the C1C-A3 Fab heavy chain residues 1-213 (note insertions in CDR loops; numbering should be according to the PDB file).

1 Homo sapiens LEVO MKRGLCCVLLLCGAVFVSPSASQVQLVESGGGVVQPGRSLRLSCAASGFTFSSYGMHWVRQAPGKGLEWVAVIWYDGTNT YYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDLAYRDYVWRYFDLWGRGTLVTVSGASTKGPSVFPLAPSS KSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVD KRVEPKSCDR neutralizing antibody C1C-A3 Fab light chain Homo sapiens 0.025896106999999998

amino acids 1-20 are the human tPA signal peptide, 21-22 are a linker, 23-238 are the C1C-A3 Fab light chain residues 1-212 (note insertions in CDR loops; numbering should be according to the PDB file).

1 Homo sapiens LEVO MKRGLCCVLLLCGAVFVSPSASEIVLTQSPATLSLSPGERATLSCRASQSVSTYLAWYQQKFGQAPRLLIYDASNRATGI PARFSGSGSGTDFTLTISSLEPEDFAVYYCQCRSNWPPGITFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLL NNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC singleParticle particle 0.9 7.5 25.0 C4H11NO3 Tris 150.0 NaCl sodium chloride Quantifoil R1.2/1.3 COPPER 300 CARBON CONTINUOUS 2.0 GLOW DISCHARGE 30 AIR 0.039

Quantifoil Cu 1.2/1.3 2nm carbon 300 mesh grids glowed discharge at 15 mA in Pelco EasiGlow

ETHANE 100 293 FEI VITROBOT MARK IV

blot for 4-6 seconds.

this sample was monodisperse.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.0 2.5 105000.0 60606.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 77.0 77.0 GATAN K3 BIOQUANTUM (6k x 4k) 5760 4092 1 4583 1.9 56.5 1 1296929 CTFFIND 4.1 NONE 2 C1 FOURIER SPACE 4.3 FSC 0.143 CUT-OFF cryoSPARC 2.14.2 344920 RANDOM ASSIGNMENT RELION 3.1.2 MAXIMUM LIKELIHOOD cryoSPARC 2.14.2 5 101973.0 cryoSPARC 2.14.2