2025-05-14 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name DATA_COLLECTION em_admin em_software _em_admin.last_update _em_software.name RCSB RCSB 2023-07-29 2024-01-17 2024-01-17 2025-05-14 National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) R01 AI127521 United States Antibody N3-1 bound to RBD in the up conformation Hsieh C-L McLellan JS SARS-CoV-2 spike, neutralizing antibody, RBD-directed antibody, quaternary epitope, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex Goike J Hsieh CL Horton AP Gardner EC Zhou L Bartzoka F Wang N Javanmardi K Herbert A Abbassi S Xie X Xia H Shi PY Renberg R Segall-Shapiro TH Terrace CI Wu W Shroff R Byrom M Ellington AD Marcotte EM Musser JM Kuchipudi SV Kapur V Georgiou G Weaver SC Dye JM Boutz DR McLellan JS Gollihar JD SARS-COV-2 Omicron variants conformationally escape a rare quaternary antibody binding mode. Commun Biol UK 6 1250 1250 2023 38082099 doi:10.1038/s42003-023-05649-6 2399-3642 8tma FULLOVERLAP The complex of N3-1 Fab bound to one receptor binding domain of the spike The complex of N3-1 Fab bound to one receptor binding domain of the spike 0 1 2 3 Spike glycoprotein 1 1 Severe acute respiratory syndrome coronavirus 2 N3-1 Fab 1 2 3 Homo sapiens Spike glycoprotein Severe acute respiratory syndrome coronavirus 2 0.142427438 1 Homo sapiens LEVO MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFD NPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVY SSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRV QPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSF VIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPC NGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFL PFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGS NVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTI SVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGF NFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAG TITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALN TLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRV DFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNT FVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL QELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHSAWSHPQFEKGGGSGGGGSGGSA WSHPQFEK P0DTC2 N3-1 Fab heavy chain Homo sapiens 0.014455996999999998 1 Homo sapiens LEVO QVQLQQWGPGLVNPSETLSLTCSVSGGSFATENYYWSWIRQHPGEGLEWIGNIYFSGNTYYNPSLNNRFTISFDTSKNHL SLKLPSVTAADTAVYYCARGTIYFDRSGYRRVDPFHIWGQGTMVIVSS N3-1 Fab light chain Homo sapiens 0.011828046 1 Homo sapiens LEVO DIQMTQSPSTLSASVGDRVTITCRASQSISSWLAWYQQKPGKAPKLLIYDASSLESGVPSRFSGSGSGTEFTLTISSLQP DDFATYYCQQYNSYSPWTFGQGTKVEIK singleParticle particle 0.2 8.0
2 mM Tris pH 8.0, 200 mM NaCl, 0.02% NaN3
 UltrAuFoil R1.2/1.3 GOLD ETHANE 100 295 FEI VITROBOT MARK IV
Collected on UltrAuFoil 1.2-1.3 with 0.2 mg/mL HexaPro and 5x fold molar excess FabN3-1 spiked in 30 minutes before freezing.
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.5 2.5 GATAN K3 (6k x 4k) 80.0 1 NONE 3.2 FSC 0.143 CUT-OFF 266553 RANDOM ASSIGNMENT MAXIMUM LIKELIHOOD emd_41382.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 432 432 432 0 0 0 432 432 432 475.2 475.2 475.2 90.0 90.0 90.0 X Y Z -5.798137 11.381121 -0.0090609845 0.098313 1.1 1.1 1.1 2.02 AUTHOR sharpen map emd_41382_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 432 432 432 0 0 0 432 432 432 475.2 475.2 475.2 90.0 90.0 90.0 X Y Z -1.6627003 3.5298402 -0.009060984 0.048096612 1.1 1.1 1.1 AUTHOR map emd_41382_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 432 432 432 0 0 0 432 432 432 475.2 475.2 475.2 90.0 90.0 90.0 X Y Z -0.028874753 2.3090076 0.00015686732 0.0069287233 1.1 1.1 1.1 AUTHOR DeepEMhancer map emd_41382_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 432 432 432 0 0 0 432 432 432 475.2 475.2 475.2 90.0 90.0 90.0 X Y Z -2.062989 3.77601 -0.0032895254 0.062015824 1.1 1.1 1.1 AUTHOR half map emd_41382_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 432 432 432 0 0 0 432 432 432 475.2 475.2 475.2 90.0 90.0 90.0 X Y Z -1.9644414 3.8305874 -0.003271576 0.062028058 1.1 1.1 1.1 AUTHOR half map