Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting novel and conserved epitopes-CovS with NB34

2024-11-13 REL RCSB RCSB RCSB 2021-06-17 2021-08-04 2021-08-04 2024-11-13 National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD) R35 GM137905 United States National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD) R35 GM128641 United States National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD) U24 GM129539 United States Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting novel and conserved epitopes-CovS with NB34 Sun D Zhang C CovS NB34 nanobody, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex Sun D Sang Z Kim YJ Xiang Y Cohen T Belford AK Huet A Conway JF Sun J Taylor DJ Schneidman-Duhovny D Zhang C Huang W Shi Y Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting diverse and conserved epitopes Nat Commun UK 12 4676 2021 doi:10.1038/s41467-021-24963-3 2041-1723 7n9e FULLOVERLAP SARS Cov 2 Spike S with Nanobody Nb34 SARS Cov 2 Spike S with Nanobody Nb34 0 1 2 SARS Cov 2 Spike S 1 2 Severe acute respiratory syndrome coronavirus 2 Nanobody Nb34 1 1 Lama glama Nb34 nanobody Lama glama 0.016951646 1 Escherichia coli LEVO MASMTGGQQMGRDPNSDVQLVESGGGLVQAGGSLRLSCAASGFTFSNYVMYWGRQAPGKGREWVSGIDSDGSDTAYASSV KGRFTISRDNAKNTLYLQMNNLKPEDTALYYCVKSKDPYGSPWTRSEFDDYWGQGTQVTVSSKLAAALEHHHHHH Spike glycoprotein Severe acute respiratory syndrome coronavirus 2 0.15231275

Pre-fusion stabilized HexaPro construct, including six proline substitutions and furin cleavage site RRAR 682-685 mutated to GSAS

3 Homo sapiens LEVO MGGEGLRASPRRRPLLPLQPRGCPRGDGCLRGGRGRAGFGFWRVTGGSSASANHVHAFFFFLQLLGNVLVVVLSHHFGKE LRPSQAEFGTATMFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAI HVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKN NKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVD LPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTV EKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLN DLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDI STEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTG TGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQ LTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPGSASSVASQSIIAYTMSLGAENSVAYS NNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQI YKTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDE MIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKL QDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATK MSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRN FYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNE VAKNLNESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHSAWSHPQFEKG GGSGGGGSGGSAWSHPQFEK P0DTC2 singleParticle particle 7.5 ETHANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K3 (6k x 4k) COUNTING 60.0 1 3.52 FSC 0.143 CUT-OFF 60614 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_24257.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 416 416 416 0 0 0 416 416 416 440.95996 440.95996 440.95996 90.0 90.0 90.0 X Y Z -0.046157576 0.110596426 0.0002284925 0.0037897998 1.06 1.06 1.06 0.015 AUTHOR ::::EMDATABANK.org::::EMD-24257:::: CryoEM map of CovS with NB34