Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing nanobodies (Ty1)

2024-10-23 REL PDBe PDBe PDBe 2020-07-30 2020-09-23 2020-09-23 2024-10-23 Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing nanobodies (Ty1) Hallberg BM Das H SARS-CoV-2, spike protein, neutralising antibody, VIRAL PROTEIN Hanke L Vidakovics Perez L Sheward DJ Das H Schulte T Moliner-Morro A Corcoran M Achour A Karlsson Hedestam GB Hallberg BM Murrell B McInerney GM An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction. Nat Commun UK 11 4420 4420 2020 32887876 doi:10.1038/s41467-020-18174-5 2041-1723 Hanke L Vidakovics L Sheward DJ Schulte T Moliner Morro A Corcoran M Achour A Karlsson Hedestam G Hallberg BM Murrell B McInerney GM An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction BioRxiv US 2020 doi:10.1101/2020.06.02.130161 2692-8205 6zxn FULLOVERLAP Ternary complex between Nanobody Ty1 and Spike. Ternary complex between Nanobody Ty1 and Spike. 0 1 2 0.014 Nanobody strongly neutralising and blocks ACE2 binding. 1 1 Severe acute respiratory syndrome coronavirus 2 Nanobody Ty1 1 2 Vicugna pacos Spike glycoprotein Severe acute respiratory syndrome coronavirus 2 0.142399375

Severe acute respiratory syndrome coronavirus 2 spike glykoprotein

3 Homo sapiens LEVO MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFD NPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVY SSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRV QPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSF VIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPC NGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFL PFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGS NVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTI SVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGF NFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAG TITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALN TLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRV DFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNT FVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL QELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHSAWSHPQFEKGGGSGGGGSGGSA WSHPQFEK P0DTC2 Nanobody Ty1 Vicugna pacos 0.014306924

Nanobody Ty1 that neutralises SARS-CoV-2 by blocking the receptor bindings site on the spike glykoprotein

3 Escherichia coli LEVO MAQVQLVETGGGLVQPGGSLRLSCAASGFTFSSVYMNWVRQAPGKGPEWVSRISPNSGNIGYTDSVKGRFTISRDNAKNT LYLQMNNLKPEDTALYYCAIGLNLSSSSVRGQGTQVTVSSGGLPETGGHHHHHH 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 39 NAG singleParticle particle 7.4 NICKEL/TITANIUM GLOW DISCHARGE ETHANE TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 20.0 2.7 0.3 0.3 2.5 165000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 10 GATAN K3 BIOQUANTUM (6k x 4k) 1.5 51.0 1 1 C1 BACK PROJECTION 2.93 FSC 0.143 CUT-OFF cryoSPARC 2.15 131816 PROJECTION MATCHING PROJECTION MATCHING emd_11526.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 428 428 428 0 0 0 428 428 428 436.56 436.56 436.56 90.0 90.0 90.0 Z Y X -43.933025000000001 77.149820000000005 0.00055904285 0.9428028 1.02 1.02 1.02 2.74 AUTHOR ::::EMDATABANK.org::::EMD-11526:::: Composite map of prefusion SARS-CoV-2 spike glycoprotein with a single receptor binding domain up. The spike protein is bound with three neutralizing nanobodies. 6VSB PDB experimental model OTHER REAL