2024-11-06 REL PDBj PDBj PDBj 2022-11-17 2023-02-01 2023-02-01 2024-11-06 Ministry of Science and Technology (MoST, Taiwan) Taiwan SARS-CoV-2 Omicron BA.1 Spike in complex with IY-2A Chen X Mohapatra A Wu Y-M Spike, Omicron variant, BA.1, RBD, monoclonal antibody, Fab, IY-2A, class 4, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex Huang KA Chen X Mohapatra A Nguyen HTV Schimanski L Tan TK Rijal P Vester SK Hills RA Howarth M Keeffe JR Cohen AA Kakutani LM Wu YM Shahed-Al-Mahmud M Chou YC Bjorkman PJ Townsend AR Ma C Structural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2. Nat Commun UK 14 311 311 2023 36658148 doi:10.1038/s41467-023-35949-8 2041-1723 8hhz FULLOVERLAP Complex of Delta Spike and IY-2A with two Fabs bound to one Spike in 3-RBD-up conformation Complex of Delta Spike and IY-2A with two Fabs bound to one Spike in 3-RBD-up conformation 0 1 2 3 0.55 SARS-CoV-2 Delta Spike protein 1 1 Severe acute respiratory syndrome coronavirus 2 IY-2A 1 2 3 Homo sapiens Spike glycoprotein Severe acute respiratory syndrome coronavirus 2 0.140204906 3 Homo sapiens LEVO MKVKLLVLLCTFTATYAGTQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGT KRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRV YSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITR FQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSN FRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYA DSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGN KPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLKGTGVLTESNK KFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYS TGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTN FTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYF GGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIAQYTSAL LAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNHNAQ ALNTLVKQLSSKFGAISSVLNDIFSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQS KRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITT DNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESL IDLQELGKYEQYIKDIRSLVPRGSPGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGHHHHHH P0DTC2 IY-2A Fab heavy chain Homo sapiens 0.023576565999999997 3 Cricetulus griseus LEVO QVQLVEWGAGLLKPSETLSLTCAVYGGSFSGYYWSWIRQPPGKGLEWIGLINHSGSTNYNPSLKSRVTISLDTSKNQFSL KLTSVTAADTAVYYCARGLGIFGVVTLSDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTV SWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC IY-2A Fab light chain Homo sapiens 0.023078278999999997 3 Cricetulus griseus LEVO NFMLTQPHSVSESPGKTVTISCTGSSGSIASNYVQWYQQRPGSAPTTVIYEDNQRPSGVPDRFSGSIDSSSNSASLTISG LRTEDEADYYCQSYDSGIWVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVK AGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS singleParticle particle 0.8 7.5
20mM Tris pH 7.5 150mM NaCl
 ETHANE 100 258 FEI VITROBOT MARK IV
freshly mixed (3 min at room temperature) for complex formation
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.0 2.0 GATAN K3 BIOQUANTUM (6k x 4k) 1 4685 1.1 1 1405490 7XO5 1 4.28 FSC 0.143 CUT-OFF RELION 3.0 67276 NOT APPLICABLE NOT APPLICABLE 3 25000.0 RELION 3.0 emd_34808.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 324 324 324 0 0 0 324 324 324 343.43997 343.43997 343.43997 90.0 90.0 90.0 X Y Z -0.02604841 0.04447294 0.000013066992 0.0014210356 1.06 1.06 1.06 0.0037 AUTHOR FLEXIBLE FIT REAL emd_34808_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 324 324 324 0 0 0 324 324 324 343.43997 343.43997 343.43997 90.0 90.0 90.0 X Y Z -0.023103366 0.037556626 0.0000138479045 0.0017536219 1.06 1.06 1.06 AUTHOR emd_34808_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 324 324 324 0 0 0 324 324 324 343.43997 343.43997 343.43997 90.0 90.0 90.0 X Y Z -0.024719132 0.03376895 0.00001228607 0.0017610085 1.06 1.06 1.06 AUTHOR