Cryo-EM Structure of SARS-CoV-2 Spike : H11-D4 Nanobody Complex

2024-10-16 REL PDBe PDBe PDBe 2020-05-22 2020-06-03 2020-06-03 2024-10-16 Engineering and Physical Sciences Research Council EP/S025243/1 United Kingdom Wellcome Trust 100209/Z/12/Z United Kingdom Cancer Research UK C20724/A14414 United Kingdom Cancer Research UK C20724/A26752 United Kingdom Wellcome Trust 101122/Z/13/Z United Kingdom Medical Research Council (MRC, United Kingdom) MR/N00065X/1 United Kingdom Cryo-EM Structure of SARS-CoV-2 Spike : H11-D4 Nanobody Complex Ruza RR Duyvesteyn HME Spike, nanobody, VHH, SARS-CoV-2, COVID-19, VIRAL PROTEIN Huo J Le Bas A Ruza RR Duyvesteyn HME Mikolajek H Malinauskas T Tan T Rijal P Dumoux M Ward PN Ren J Zhou D Harrison PJ Radecke J Zhao Y Jaramillo JG Knight M Carrique L Shah P James W Townsend A Stuart DI Owens RJ Naismith JH Structural basis for a potent neutralising single-domain antibody that blocks SARS-CoV-2 binding to its receptor ACE2 To Be Published 0353 6z43 FULLOVERLAP Spike glycoprotein in complex with H11-D4 nanobodies Spike glycoprotein in complex with H11-D4 nanobodies 0 1 2 0.48 Spike glycoprotein 1 1 Severe acute respiratory syndrome coronavirus 2 Nanobody 1 2 Lama glama 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 QELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHGSAWSHPQFEKGGGSGGGSGGSA WSHPQFEK P0DTC2 Nanobody Lama glama 0.016679453 3 Escherichia coli LEVO QVQLVESGGGLMQAGGSLRLSCAVSGRTFSTAAMGWFRQAPGKEREFVAAIRWSGGSAYYADSVKGRFTISRDKAKNTVY LQMNSLKYEDTAVYYCARTENVRSLLSDYATWPYDYWGQGTQVTVSSGPGGQHHHHHHGAEQKLISEEDLS 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 26 NAG singleParticle particle 0.25 8.0 20.0 C4H11NO3 Tris 200.0 NaCl Sodium Chloride 0.02 NaN3 Sodium Azide C-flat-2/1 COPPER 200 CARBON HOLEY GLOW DISCHARGE 20 AIR ETHANE 100 277.65 FEI VITROBOT MARK IV

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FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 (6k x 4k) 42.8 1 C1 BACK PROJECTION 3.3 FSC 0.143 CUT-OFF RELION 3.1 305513 RANDOM ASSIGNMENT cryoSPARC MAXIMUM LIKELIHOOD cryoSPARC emd_11068.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 528 528 528 0 0 0 528 528 528 438.24 438.24 438.24 90.0 90.0 90.0 X Y Z -0.10291079 0.17046817 0.00008132132 0.002073685 0.83 0.83 0.83 0.015 AUTHOR ::::EMDATABANK.org::::EMD-11068:::: Structure of SARS-CoV-2 Spike : H11-D4 Nanobody Complex 6VXX PDB experimental model RIGID BODY FIT REAL