SARS-CoV-2 Delta Spike in complex with IS-9A

2026-09-09 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY STRUCTURE_SUMMARY em_admin em_entity_assembly em_imaging em_software entity entity_poly entity_src_gen struct_ref struct_ref_seq struct_ref_seq_dif _em_admin.last_update _em_entity_assembly.entity_id_list _em_imaging.microscope_model _entity.formula_weight _entity.pdbx_description _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_src_gen.pdbx_end_seq_num _entity_src_gen.pdbx_gene_src_gene _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id _entity_src_gen.pdbx_gene_src_scientific_name _entity_src_gen.pdbx_host_org_cell_line _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id _entity_src_gen.pdbx_host_org_scientific_name _struct_ref.db_code _struct_ref.db_name _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_accession _struct_ref.pdbx_seq_one_letter_code _struct_ref_seq.db_align_beg _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end _struct_ref_seq.pdbx_db_accession _struct_ref_seq.pdbx_strand_id _struct_ref_seq.ref_id _struct_ref_seq.seq_align_beg _struct_ref_seq.seq_align_end _struct_ref_seq_dif.align_id COORDINATE_REPLACEMENT AUTHOR Model orientation/position

We identified an issue with the Fab coordinates in the originally deposited structure. We have carefully corrected the Fab model and would like to replace the Fab coordinates in PDB 8HHY. In addition, I have changed the chain ID of all hetatom: NAG of chains A, B, C, as the mismatch occurred during sequence alignment. The experimental data are unchanged.

STRUCTURE_SUMMARY atom_site audit_author em_admin em_entity_assembly em_imaging em_software entity entity_name_com entity_poly entity_poly_seq entity_src_gen pdbx_contact_author pdbx_modification_feature pdbx_nonpoly_scheme pdbx_poly_seq_scheme pdbx_struct_assembly pdbx_struct_oper_list pdbx_struct_sheet_hbond pdbx_unobs_or_zero_occ_atoms pdbx_unobs_or_zero_occ_residues pdbx_validate_close_contact pdbx_validate_peptide_omega pdbx_validate_rmsd_angle pdbx_validate_torsion refine refine_ls_restr struct_asym struct_conf struct_conn struct_mon_prot_cis struct_ref struct_ref_seq struct_ref_seq_dif struct_sheet struct_sheet_order struct_sheet_range _em_admin.last_update _em_entity_assembly.entity_id_list _em_imaging.microscope_model _entity.formula_weight _entity.pdbx_description _entity_name_com.entity_id _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly_seq.entity_id _entity_poly_seq.mon_id _entity_poly_seq.num _entity_src_gen.pdbx_end_seq_num _entity_src_gen.pdbx_gene_src_gene _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id _entity_src_gen.pdbx_gene_src_scientific_name _entity_src_gen.pdbx_host_org_cell_line _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id _entity_src_gen.pdbx_host_org_scientific_name _pdbx_modification_feature.auth_asym_id _pdbx_modification_feature.auth_seq_id _pdbx_modification_feature.label_asym_id _pdbx_modification_feature.label_seq_id _pdbx_modification_feature.modified_residue_auth_asym_id _pdbx_modification_feature.modified_residue_auth_seq_id _pdbx_modification_feature.modified_residue_label_asym_id _pdbx_modification_feature.modified_residue_label_seq_id _pdbx_nonpoly_scheme.auth_seq_num _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.seq_id _pdbx_struct_assembly.details _pdbx_struct_oper_list.symmetry_operation _refine.pdbx_stereochemistry_target_values _struct_asym.entity_id _struct_conn.pdbx_dist_value _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_seq_id _struct_mon_prot_cis.auth_asym_id _struct_mon_prot_cis.label_asym_id _struct_mon_prot_cis.pdbx_auth_asym_id_2 _struct_mon_prot_cis.pdbx_label_asym_id_2 _struct_mon_prot_cis.pdbx_omega_angle _struct_ref.db_code _struct_ref.db_name _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_accession _struct_ref.pdbx_seq_one_letter_code _struct_ref_seq.db_align_beg _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end _struct_ref_seq.pdbx_db_accession _struct_ref_seq.pdbx_strand_id _struct_ref_seq.ref_id _struct_ref_seq.seq_align_beg _struct_ref_seq.seq_align_end _struct_ref_seq_dif.align_id PDBj PDBj 2022-11-17 2023-02-01 2023-02-01 2026-09-09 Ministry of Science and Technology (MoST, Taiwan) Taiwan SARS-CoV-2 Delta Spike in complex with IS-9A Mohapatra A Wu Y-M Spike, Delta variant, RBD, monoclonal antibody, Fab, IS-9A, 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 8hhy FULLOVERLAP EMDB EMD-34807 associated EM volume

Complex of Delta Spike and IS-9A with two Fabs bound to one Spike in 3-RBD-up conformation Complex of Delta Spike and IS-9A with two Fabs bound to one Spike in 3-RBD-up conformation 0 2 3 0.55 IS-9A Fab 1 2 3 Homo sapiens Spike glycoprotein 1 1 Severe acute respiratory syndrome coronavirus 2 Spike glycoprotein Severe acute respiratory syndrome coronavirus 2 0.13942154699999998 3 Homo sapiens LEVO MKVKLLVLLCTFTATYAGTQCVNLRTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTN GTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWME SGVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINIT RFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTS NFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVY ADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAG SKPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESN KKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVY STGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSRGSAGSVASQSIIAYTMSLGAENSVAYSNNSIAIPT NFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKD FGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSA LLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQNVVNQNA QALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQ SKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIIT TDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNES LIDLQELGKYEQDIRSLVPRGSPGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGHHHHHH P0DTC2 IS-9A Fab heavy chain Homo sapiens 0.024225161999999998 3 Cricetulus griseus LEVO QVQLVQSGAEVKKPGESLRISCKGSGYSFTNYWISWVRQMPGKGLEWMGRIDPSDSYINYSPSFQGHATISADKSISTAY LQWGSLKASDTAMYYCARGRNYLDSRGRFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVT VSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC IS-9A Fab light chain Homo sapiens 0.023403809 3 Cricetulus griseus LEVO DIVMTQSPSSLSASVGDRVTITCQASQDISNYLNWYQQKSGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQP EDIATYYCQQYDSLGFTFGPGTKVEIRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQ ESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 24 NAG 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 POLARA 300 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.0 2.0 GATAN K3 BIOQUANTUM (6k x 4k) 1 4457 1.1 1 1542976 NONE 7ZDH 1 2.77 FSC 0.143 CUT-OFF RELION 2 296356 NOT APPLICABLE NOT APPLICABLE 6 80000.0 emd_34807.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 318.72 318.72 318.72 90.0 90.0 90.0 X Y Z -3.6532578 4.6102676 0.0012028585 0.07703812 0.83 0.83 0.83 0.17 AUTHOR ::::EMDATABANK.org::::EMD-34807:::: FLEXIBLE FIT REAL emd_34807_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 318.72 318.72 318.72 90.0 90.0 90.0 X Y Z -0.4168707 1.3239735 0.0020869565 0.0394077 0.83 0.83 0.83 AUTHOR ::::EMDATABANK.org::::EMD-34807:::: emd_34807_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 318.72 318.72 318.72 90.0 90.0 90.0 X Y Z -0.47580865 1.3685278 0.002086017 0.039414562 0.83 0.83 0.83 AUTHOR ::::EMDATABANK.org::::EMD-34807::::