data_8DPZ # _entry.id 8DPZ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.375 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 8DPZ pdb_00008dpz 10.2210/pdb8dpz/pdb WWPDB D_1000266992 ? ? EMDB EMD-27644 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.details _pdbx_database_related.db_id _pdbx_database_related.content_type EMDB 'Trimer map' EMD-27606 'other EM volume' EMDB 'Local refinement of SARS-CoV-2 vaccine induced antibody Ab026500 bound to SARS-CoV-2 HexaPro RBD Spike ectodomain' EMD-27644 'associated EM volume' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 8DPZ _pdbx_database_status.recvd_initial_deposition_date 2022-07-18 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Stalls, V.' 1 0000-0002-1878-0581 'May, A.J.' 2 0000-0003-2262-9750 'Acharya, P.' 3 0000-0002-0089-277X # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country ? _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'To Be Published' _citation.journal_id_ASTM ? _citation.journal_id_CSD 0353 _citation.journal_id_ISSN ? _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume ? _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'Local refinement of SARS-CoV-2 vaccine induced antibody Ab026500 bound to SARS-CoV-2 HexaPro RBD Spike ectodomain' _citation.year ? _citation.database_id_CSD ? _citation.pdbx_database_id_DOI ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Stalls, V.' 1 0000-0002-1878-0581 primary 'Acharya, P.' 2 ? primary 'May, A.J.' 3 ? primary 'Malewana, D.' 4 ? # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 90.00 _cell.angle_gamma_esd ? _cell.entry_id 8DPZ _cell.details ? _cell.formula_units_Z ? _cell.length_a 1.00 _cell.length_a_esd ? _cell.length_b 1.00 _cell.length_b_esd ? _cell.length_c 1.00 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB ? _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? _cell.pdbx_esd_method ? # _symmetry.entry_id 8DPZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man 'Spike protein S1' 23059.967 1 ? ? ? ? 2 polymer man 'DH1338 Fab Heavy Chain' 13910.356 1 ? ? ? ? 3 polymer man 'DH1338 Fab Light Chain' 11864.080 1 ? ? ? ? 4 branched man '2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose' 424.401 1 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 'polypeptide(L)' no no ;IVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGD EVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEG FNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKS ; ;IVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGD EVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEG FNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKS ; B ? 2 'polypeptide(L)' no no ;QLQLQESGPGLVKPSETLSLTCAVSGGSISRKNWSWIRQPPGKGLGWIGRISGSGGSTDYNPSLKSRVTISTDTSKNQFS LKLSSVTAADTAVYYCARVAYYEDDYGYYYTEGAFDFWGQGLRVTVSS ; ;QLQLQESGPGLVKPSETLSLTCAVSGGSISRKNWSWIRQPPGKGLGWIGRISGSGGSTDYNPSLKSRVTISTDTSKNQFS LKLSSVTAADTAVYYCARVAYYEDDYGYYYTEGAFDFWGQGLRVTVSS ; F ? 3 'polypeptide(L)' no no ;EIVMTQSPATLSLSPGERATLSCRTSQSVSSYVAWYQQKPEQTPRLLIYDASSRATGIPDRFSGGGSGTDFTLTISSLEP EDFAVYYCQQYSNWPWTFGQGTKVEIK ; ;EIVMTQSPATLSLSPGERATLSCRTSQSVSSYVAWYQQKPEQTPRLLIYDASSRATGIPDRFSGGGSGTDFTLTISSLEP EDFAVYYCQQYSNWPWTFGQGTKVEIK ; G ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 ILE n 1 2 VAL n 1 3 ARG n 1 4 PHE n 1 5 PRO n 1 6 ASN n 1 7 ILE n 1 8 THR n 1 9 ASN n 1 10 LEU n 1 11 CYS n 1 12 PRO n 1 13 PHE n 1 14 GLY n 1 15 GLU n 1 16 VAL n 1 17 PHE n 1 18 ASN n 1 19 ALA n 1 20 THR n 1 21 ARG n 1 22 PHE n 1 23 ALA n 1 24 SER n 1 25 VAL n 1 26 TYR n 1 27 ALA n 1 28 TRP n 1 29 ASN n 1 30 ARG n 1 31 LYS n 1 32 ARG n 1 33 ILE n 1 34 SER n 1 35 ASN n 1 36 CYS n 1 37 VAL n 1 38 ALA n 1 39 ASP n 1 40 TYR n 1 41 SER n 1 42 VAL n 1 43 LEU n 1 44 TYR n 1 45 ASN n 1 46 SER n 1 47 ALA n 1 48 SER n 1 49 PHE n 1 50 SER n 1 51 THR n 1 52 PHE n 1 53 LYS n 1 54 CYS n 1 55 TYR n 1 56 GLY n 1 57 VAL n 1 58 SER n 1 59 PRO n 1 60 THR n 1 61 LYS n 1 62 LEU n 1 63 ASN n 1 64 ASP n 1 65 LEU n 1 66 CYS n 1 67 PHE n 1 68 THR n 1 69 ASN n 1 70 VAL n 1 71 TYR n 1 72 ALA n 1 73 ASP n 1 74 SER n 1 75 PHE n 1 76 VAL n 1 77 ILE n 1 78 ARG n 1 79 GLY n 1 80 ASP n 1 81 GLU n 1 82 VAL n 1 83 ARG n 1 84 GLN n 1 85 ILE n 1 86 ALA n 1 87 PRO n 1 88 GLY n 1 89 GLN n 1 90 THR n 1 91 GLY n 1 92 LYS n 1 93 ILE n 1 94 ALA n 1 95 ASP n 1 96 TYR n 1 97 ASN n 1 98 TYR n 1 99 LYS n 1 100 LEU n 1 101 PRO n 1 102 ASP n 1 103 ASP n 1 104 PHE n 1 105 THR n 1 106 GLY n 1 107 CYS n 1 108 VAL n 1 109 ILE n 1 110 ALA n 1 111 TRP n 1 112 ASN n 1 113 SER n 1 114 ASN n 1 115 ASN n 1 116 LEU n 1 117 ASP n 1 118 SER n 1 119 LYS n 1 120 VAL n 1 121 GLY n 1 122 GLY n 1 123 ASN n 1 124 TYR n 1 125 ASN n 1 126 TYR n 1 127 LEU n 1 128 TYR n 1 129 ARG n 1 130 LEU n 1 131 PHE n 1 132 ARG n 1 133 LYS n 1 134 SER n 1 135 ASN n 1 136 LEU n 1 137 LYS n 1 138 PRO n 1 139 PHE n 1 140 GLU n 1 141 ARG n 1 142 ASP n 1 143 ILE n 1 144 SER n 1 145 THR n 1 146 GLU n 1 147 ILE n 1 148 TYR n 1 149 GLN n 1 150 ALA n 1 151 GLY n 1 152 SER n 1 153 THR n 1 154 PRO n 1 155 CYS n 1 156 ASN n 1 157 GLY n 1 158 VAL n 1 159 GLU n 1 160 GLY n 1 161 PHE n 1 162 ASN n 1 163 CYS n 1 164 TYR n 1 165 PHE n 1 166 PRO n 1 167 LEU n 1 168 GLN n 1 169 SER n 1 170 TYR n 1 171 GLY n 1 172 PHE n 1 173 GLN n 1 174 PRO n 1 175 THR n 1 176 ASN n 1 177 GLY n 1 178 VAL n 1 179 GLY n 1 180 TYR n 1 181 GLN n 1 182 PRO n 1 183 TYR n 1 184 ARG n 1 185 VAL n 1 186 VAL n 1 187 VAL n 1 188 LEU n 1 189 SER n 1 190 PHE n 1 191 GLU n 1 192 LEU n 1 193 LEU n 1 194 HIS n 1 195 ALA n 1 196 PRO n 1 197 ALA n 1 198 THR n 1 199 VAL n 1 200 CYS n 1 201 GLY n 1 202 PRO n 1 203 LYS n 1 204 LYS n 1 205 SER n 2 1 GLN n 2 2 LEU n 2 3 GLN n 2 4 LEU n 2 5 GLN n 2 6 GLU n 2 7 SER n 2 8 GLY n 2 9 PRO n 2 10 GLY n 2 11 LEU n 2 12 VAL n 2 13 LYS n 2 14 PRO n 2 15 SER n 2 16 GLU n 2 17 THR n 2 18 LEU n 2 19 SER n 2 20 LEU n 2 21 THR n 2 22 CYS n 2 23 ALA n 2 24 VAL n 2 25 SER n 2 26 GLY n 2 27 GLY n 2 28 SER n 2 29 ILE n 2 30 SER n 2 31 ARG n 2 32 LYS n 2 33 ASN n 2 34 TRP n 2 35 SER n 2 36 TRP n 2 37 ILE n 2 38 ARG n 2 39 GLN n 2 40 PRO n 2 41 PRO n 2 42 GLY n 2 43 LYS n 2 44 GLY n 2 45 LEU n 2 46 GLY n 2 47 TRP n 2 48 ILE n 2 49 GLY n 2 50 ARG n 2 51 ILE n 2 52 SER n 2 53 GLY n 2 54 SER n 2 55 GLY n 2 56 GLY n 2 57 SER n 2 58 THR n 2 59 ASP n 2 60 TYR n 2 61 ASN n 2 62 PRO n 2 63 SER n 2 64 LEU n 2 65 LYS n 2 66 SER n 2 67 ARG n 2 68 VAL n 2 69 THR n 2 70 ILE n 2 71 SER n 2 72 THR n 2 73 ASP n 2 74 THR n 2 75 SER n 2 76 LYS n 2 77 ASN n 2 78 GLN n 2 79 PHE n 2 80 SER n 2 81 LEU n 2 82 LYS n 2 83 LEU n 2 84 SER n 2 85 SER n 2 86 VAL n 2 87 THR n 2 88 ALA n 2 89 ALA n 2 90 ASP n 2 91 THR n 2 92 ALA n 2 93 VAL n 2 94 TYR n 2 95 TYR n 2 96 CYS n 2 97 ALA n 2 98 ARG n 2 99 VAL n 2 100 ALA n 2 101 TYR n 2 102 TYR n 2 103 GLU n 2 104 ASP n 2 105 ASP n 2 106 TYR n 2 107 GLY n 2 108 TYR n 2 109 TYR n 2 110 TYR n 2 111 THR n 2 112 GLU n 2 113 GLY n 2 114 ALA n 2 115 PHE n 2 116 ASP n 2 117 PHE n 2 118 TRP n 2 119 GLY n 2 120 GLN n 2 121 GLY n 2 122 LEU n 2 123 ARG n 2 124 VAL n 2 125 THR n 2 126 VAL n 2 127 SER n 2 128 SER n 3 1 GLU n 3 2 ILE n 3 3 VAL n 3 4 MET n 3 5 THR n 3 6 GLN n 3 7 SER n 3 8 PRO n 3 9 ALA n 3 10 THR n 3 11 LEU n 3 12 SER n 3 13 LEU n 3 14 SER n 3 15 PRO n 3 16 GLY n 3 17 GLU n 3 18 ARG n 3 19 ALA n 3 20 THR n 3 21 LEU n 3 22 SER n 3 23 CYS n 3 24 ARG n 3 25 THR n 3 26 SER n 3 27 GLN n 3 28 SER n 3 29 VAL n 3 30 SER n 3 31 SER n 3 32 TYR n 3 33 VAL n 3 34 ALA n 3 35 TRP n 3 36 TYR n 3 37 GLN n 3 38 GLN n 3 39 LYS n 3 40 PRO n 3 41 GLU n 3 42 GLN n 3 43 THR n 3 44 PRO n 3 45 ARG n 3 46 LEU n 3 47 LEU n 3 48 ILE n 3 49 TYR n 3 50 ASP n 3 51 ALA n 3 52 SER n 3 53 SER n 3 54 ARG n 3 55 ALA n 3 56 THR n 3 57 GLY n 3 58 ILE n 3 59 PRO n 3 60 ASP n 3 61 ARG n 3 62 PHE n 3 63 SER n 3 64 GLY n 3 65 GLY n 3 66 GLY n 3 67 SER n 3 68 GLY n 3 69 THR n 3 70 ASP n 3 71 PHE n 3 72 THR n 3 73 LEU n 3 74 THR n 3 75 ILE n 3 76 SER n 3 77 SER n 3 78 LEU n 3 79 GLU n 3 80 PRO n 3 81 GLU n 3 82 ASP n 3 83 PHE n 3 84 ALA n 3 85 VAL n 3 86 TYR n 3 87 TYR n 3 88 CYS n 3 89 GLN n 3 90 GLN n 3 91 TYR n 3 92 SER n 3 93 ASN n 3 94 TRP n 3 95 PRO n 3 96 TRP n 3 97 THR n 3 98 PHE n 3 99 GLY n 3 100 GLN n 3 101 GLY n 3 102 THR n 3 103 LYS n 3 104 VAL n 3 105 GLU n 3 106 ILE n 3 107 LYS n # loop_ _entity_src_gen.entity_id _entity_src_gen.pdbx_src_id _entity_src_gen.pdbx_alt_source_flag _entity_src_gen.pdbx_seq_type _entity_src_gen.pdbx_beg_seq_num _entity_src_gen.pdbx_end_seq_num _entity_src_gen.gene_src_common_name _entity_src_gen.gene_src_genus _entity_src_gen.pdbx_gene_src_gene _entity_src_gen.gene_src_species _entity_src_gen.gene_src_strain _entity_src_gen.gene_src_tissue _entity_src_gen.gene_src_tissue_fraction _entity_src_gen.gene_src_details _entity_src_gen.pdbx_gene_src_fragment _entity_src_gen.pdbx_gene_src_scientific_name _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id _entity_src_gen.pdbx_gene_src_variant _entity_src_gen.pdbx_gene_src_cell_line _entity_src_gen.pdbx_gene_src_atcc _entity_src_gen.pdbx_gene_src_organ _entity_src_gen.pdbx_gene_src_organelle _entity_src_gen.pdbx_gene_src_cell _entity_src_gen.pdbx_gene_src_cellular_location _entity_src_gen.host_org_common_name _entity_src_gen.pdbx_host_org_scientific_name _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id _entity_src_gen.host_org_genus _entity_src_gen.pdbx_host_org_gene _entity_src_gen.pdbx_host_org_organ _entity_src_gen.host_org_species _entity_src_gen.pdbx_host_org_tissue _entity_src_gen.pdbx_host_org_tissue_fraction _entity_src_gen.pdbx_host_org_strain _entity_src_gen.pdbx_host_org_variant _entity_src_gen.pdbx_host_org_cell_line _entity_src_gen.pdbx_host_org_atcc _entity_src_gen.pdbx_host_org_culture_collection _entity_src_gen.pdbx_host_org_cell _entity_src_gen.pdbx_host_org_organelle _entity_src_gen.pdbx_host_org_cellular_location _entity_src_gen.pdbx_host_org_vector_type _entity_src_gen.pdbx_host_org_vector _entity_src_gen.host_org_details _entity_src_gen.expression_system_id _entity_src_gen.plasmid_name _entity_src_gen.plasmid_details _entity_src_gen.pdbx_description 1 1 sample 'Biological sequence' 1 205 ? ? 'S, 2' ? ? ? ? ? ? 'Severe acute respiratory syndrome coronavirus 2' 2697049 ? ? ? ? ? ? ? ? 'Homo sapiens' 9606 ? ? ? ? ? ? ? ? 293F ? ? ? ? ? ? ? ? ? ? ? ? 2 1 sample 'Biological sequence' 1 128 ? ? ? ? ? ? ? ? ? 'Macaca mulatta' 9544 ? ? ? ? ? ? ? ? 'Homo sapiens' 9606 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 3 1 sample 'Biological sequence' 1 107 ? ? ? ? ? ? ? ? ? 'Macaca mulatta' 9544 ? ? ? ? ? ? ? ? 'Homo sapiens' 9606 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 UNP SPIKE_SARS2 P0DTC2 ? 1 ;IVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGD EVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEG FNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKS ; 326 2 PDB 8DPZ 8DPZ ? 2 ? 1 3 PDB 8DPZ 8DPZ ? 3 ? 1 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 8DPZ B 1 ? 205 ? P0DTC2 326 ? 530 ? 326 530 2 2 8DPZ F 1 ? 128 ? 8DPZ 1 ? 113 ? 1 113 3 3 8DPZ G 1 ? 107 ? 8DPZ 1 ? 107 ? 1 107 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 NAG 'D-saccharide, beta linking' . 2-acetamido-2-deoxy-beta-D-glucopyranose ;N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE ; 'C8 H15 N O6' 221.208 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 8DPZ _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _refine.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine.entry_id 8DPZ _refine.pdbx_diffrn_id ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs ? _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low ? _refine.ls_d_res_high . _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'ELECTRON MICROSCOPY' ? 0.004 ? 3413 ? f_bond_d ? ? 'ELECTRON MICROSCOPY' ? 0.763 ? 4642 ? f_angle_d ? ? 'ELECTRON MICROSCOPY' ? 13.085 ? 1218 ? f_dihedral_angle_d ? ? 'ELECTRON MICROSCOPY' ? 0.050 ? 501 ? f_chiral_restr ? ? 'ELECTRON MICROSCOPY' ? 0.007 ? 595 ? f_plane_restr ? ? # _struct.entry_id 8DPZ _struct.title 'Local refinement of SARS-CoV-2 vaccine induced antibody DH1338 bound to SARS-CoV-2 HexaPro RBD Spike ectodomain' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 8DPZ _struct_keywords.text 'SARS-CoV-2, VIRAL PROTEIN, Antibody, Fab, RBD, VIRAL PROTEIN-Immune System complex' _struct_keywords.pdbx_keywords 'VIRAL PROTEIN/Immune System' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 AA1 PRO A 12 ? ASN A 18 ? PRO B 337 ASN B 343 1 ? 7 HELX_P HELX_P2 AA2 ASP A 39 ? ASN A 45 ? ASP B 364 ASN B 370 1 ? 7 HELX_P HELX_P3 AA3 THR A 60 ? LEU A 65 ? THR B 385 LEU B 390 5 ? 6 HELX_P HELX_P4 AA4 GLU A 81 ? ILE A 85 ? GLU B 406 ILE B 410 5 ? 5 HELX_P HELX_P5 AA5 GLY A 91 ? ASN A 97 ? GLY B 416 ASN B 422 1 ? 7 HELX_P HELX_P6 AA6 SER A 113 ? SER A 118 ? SER B 438 SER B 443 1 ? 6 HELX_P HELX_P7 AA7 GLY A 177 ? TYR A 180 ? GLY B 502 TYR B 505 5 ? 4 HELX_P HELX_P8 AA8 THR B 87 ? THR B 91 ? THR F 83 THR F 87 5 ? 5 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role disulf1 disulf ? ? A CYS 11 SG ? ? ? 1_555 A CYS 36 SG ? ? B CYS 336 B CYS 361 1_555 ? ? ? ? ? ? ? 2.032 ? ? disulf2 disulf ? ? A CYS 54 SG ? ? ? 1_555 A CYS 107 SG ? ? B CYS 379 B CYS 432 1_555 ? ? ? ? ? ? ? 2.033 ? ? disulf3 disulf ? ? A CYS 66 SG ? ? ? 1_555 A CYS 200 SG ? ? B CYS 391 B CYS 525 1_555 ? ? ? ? ? ? ? 2.031 ? ? disulf4 disulf ? ? B CYS 22 SG ? ? ? 1_555 B CYS 96 SG ? ? F CYS 22 F CYS 92 1_555 ? ? ? ? ? ? ? 2.031 ? ? disulf5 disulf ? ? C CYS 23 SG ? ? ? 1_555 C CYS 88 SG ? ? G CYS 23 G CYS 88 1_555 ? ? ? ? ? ? ? 2.033 ? ? covale1 covale one ? A ASN 18 ND2 ? ? ? 1_555 D NAG . C1 ? ? B ASN 343 A NAG 1 1_555 ? ? ? ? ? ? ? 1.435 ? N-Glycosylation covale2 covale both ? D NAG . O4 ? ? ? 1_555 D NAG . C1 ? ? A NAG 1 A NAG 2 1_555 ? ? ? ? ? ? ? 1.447 ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference disulf ? ? covale ? ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA1 ? 9 ? AA2 ? 10 ? AA3 ? 2 ? AA4 ? 4 ? AA5 ? 4 ? AA6 ? 6 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense AA1 1 2 ? anti-parallel AA1 2 3 ? anti-parallel AA1 3 4 ? anti-parallel AA1 4 5 ? anti-parallel AA1 5 6 ? anti-parallel AA1 6 7 ? anti-parallel AA1 7 8 ? anti-parallel AA1 8 9 ? parallel AA2 1 2 ? anti-parallel AA2 2 3 ? anti-parallel AA2 3 4 ? anti-parallel AA2 4 5 ? anti-parallel AA2 5 6 ? anti-parallel AA2 6 7 ? anti-parallel AA2 7 8 ? anti-parallel AA2 8 9 ? anti-parallel AA2 9 10 ? anti-parallel AA3 1 2 ? anti-parallel AA4 1 2 ? anti-parallel AA4 2 3 ? anti-parallel AA4 3 4 ? anti-parallel AA5 1 2 ? anti-parallel AA5 2 3 ? anti-parallel AA5 3 4 ? anti-parallel AA6 1 2 ? parallel AA6 2 3 ? anti-parallel AA6 3 4 ? anti-parallel AA6 4 5 ? anti-parallel AA6 5 6 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id AA1 1 ASN A 29 ? ILE A 33 ? ASN B 354 ILE B 358 AA1 2 VAL A 70 ? ARG A 78 ? VAL B 395 ARG B 403 AA1 3 PRO A 182 ? LEU A 188 ? PRO B 507 LEU B 513 AA1 4 CYS A 107 ? ASN A 112 ? CYS B 432 ASN B 437 AA1 5 THR A 51 ? CYS A 54 ? THR B 376 CYS B 379 AA1 6 GLY B 107 C TRP B 118 ? GLY F 100 TRP F 103 AA1 7 ALA B 92 ? GLU B 103 ? ALA F 88 GLU F 99 AA1 8 LEU B 122 ? VAL B 126 ? LEU F 107 VAL F 111 AA1 9 LEU B 11 ? VAL B 12 ? LEU F 11 VAL F 12 AA2 1 ASN A 29 ? ILE A 33 ? ASN B 354 ILE B 358 AA2 2 VAL A 70 ? ARG A 78 ? VAL B 395 ARG B 403 AA2 3 PRO A 182 ? LEU A 188 ? PRO B 507 LEU B 513 AA2 4 CYS A 107 ? ASN A 112 ? CYS B 432 ASN B 437 AA2 5 THR A 51 ? CYS A 54 ? THR B 376 CYS B 379 AA2 6 GLY B 107 C TRP B 118 ? GLY F 100 TRP F 103 AA2 7 ALA B 92 ? GLU B 103 ? ALA F 88 GLU F 99 AA2 8 ASN B 33 ? GLN B 39 ? ASN F 33 GLN F 39 AA2 9 GLY B 46 ? SER B 52 ? GLY F 46 SER F 52 AA2 10 THR B 58 ? TYR B 60 ? THR F 57 TYR F 59 AA3 1 LEU A 127 ? ARG A 129 ? LEU B 452 ARG B 454 AA3 2 LEU A 167 ? SER A 169 ? LEU B 492 SER B 494 AA4 1 GLN B 3 ? SER B 7 ? GLN F 3 SER F 7 AA4 2 THR B 17 ? SER B 25 ? THR F 17 SER F 25 AA4 3 GLN B 78 ? SER B 84 A GLN F 77 SER F 82 AA4 4 VAL B 68 ? ASP B 73 ? VAL F 67 ASP F 72 AA5 1 MET C 4 ? THR C 5 ? MET G 4 THR G 5 AA5 2 ALA C 19 ? THR C 25 ? ALA G 19 THR G 25 AA5 3 ASP C 70 ? ILE C 75 ? ASP G 70 ILE G 75 AA5 4 PHE C 62 ? SER C 67 ? PHE G 62 SER G 67 AA6 1 THR C 10 ? LEU C 13 ? THR G 10 LEU G 13 AA6 2 THR C 102 ? ILE C 106 ? THR G 102 ILE G 106 AA6 3 VAL C 85 ? GLN C 90 ? VAL G 85 GLN G 90 AA6 4 VAL C 33 ? GLN C 38 ? VAL G 33 GLN G 38 AA6 5 ARG C 45 ? TYR C 49 ? ARG G 45 TYR G 49 AA6 6 SER C 53 ? ARG C 54 ? SER G 53 ARG G 54 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id AA1 1 2 N ILE A 33 ? N ILE B 358 O VAL A 70 ? O VAL B 395 AA1 2 3 N ILE A 77 ? N ILE B 402 O TYR A 183 ? O TYR B 508 AA1 3 4 O VAL A 186 ? O VAL B 511 N ILE A 109 ? N ILE B 434 AA1 4 5 O VAL A 108 ? O VAL B 433 N LYS A 53 ? N LYS B 378 AA1 5 6 N PHE A 52 ? N PHE B 377 O TYR B 108 D O TYR F 100 AA1 6 7 O ALA B 114 J O ALA F 100 N ALA B 100 ? N ALA F 96 AA1 7 8 N ALA B 92 ? N ALA F 88 O VAL B 124 ? O VAL F 109 AA1 8 9 O THR B 125 ? O THR F 110 N VAL B 12 ? N VAL F 12 AA2 1 2 N ILE A 33 ? N ILE B 358 O VAL A 70 ? O VAL B 395 AA2 2 3 N ILE A 77 ? N ILE B 402 O TYR A 183 ? O TYR B 508 AA2 3 4 O VAL A 186 ? O VAL B 511 N ILE A 109 ? N ILE B 434 AA2 4 5 O VAL A 108 ? O VAL B 433 N LYS A 53 ? N LYS B 378 AA2 5 6 N PHE A 52 ? N PHE B 377 O TYR B 108 D O TYR F 100 AA2 6 7 O ALA B 114 J O ALA F 100 N ALA B 100 ? N ALA F 96 AA2 7 8 O TYR B 95 ? O TYR F 91 N ILE B 37 ? N ILE F 37 AA2 8 9 N TRP B 34 ? N TRP F 34 O ILE B 51 ? O ILE F 51 AA2 9 10 N ARG B 50 ? N ARG F 50 O ASP B 59 ? O ASP F 58 AA3 1 2 N TYR A 128 ? N TYR B 453 O GLN A 168 ? O GLN B 493 AA4 1 2 N GLN B 5 ? N GLN F 5 O ALA B 23 ? O ALA F 23 AA4 2 3 N CYS B 22 ? N CYS F 22 O PHE B 79 ? O PHE F 78 AA4 3 4 O SER B 80 ? O SER F 79 N SER B 71 ? N SER F 70 AA5 1 2 N THR C 5 ? N THR G 5 O ARG C 24 ? O ARG G 24 AA5 2 3 N CYS C 23 ? N CYS G 23 O PHE C 71 ? O PHE G 71 AA5 3 4 O THR C 74 ? O THR G 74 N SER C 63 ? N SER G 63 AA6 1 2 N LEU C 11 ? N LEU G 11 O LYS C 103 ? O LYS G 103 AA6 2 3 O THR C 102 ? O THR G 102 N TYR C 86 ? N TYR G 86 AA6 3 4 O VAL C 85 ? O VAL G 85 N GLN C 38 ? N GLN G 38 AA6 4 5 N TRP C 35 ? N TRP G 35 O LEU C 47 ? O LEU G 47 AA6 5 6 N TYR C 49 ? N TYR G 49 O SER C 53 ? O SER G 53 # _atom_sites.entry_id 8DPZ _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C H N O S # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 ILE 1 326 ? ? ? B . n A 1 2 VAL 2 327 ? ? ? B . n A 1 3 ARG 3 328 ? ? ? B . n A 1 4 PHE 4 329 ? ? ? B . n A 1 5 PRO 5 330 ? ? ? B . n A 1 6 ASN 6 331 ? ? ? B . n A 1 7 ILE 7 332 ? ? ? B . n A 1 8 THR 8 333 333 THR THR B . n A 1 9 ASN 9 334 334 ASN ASN B . n A 1 10 LEU 10 335 335 LEU LEU B . n A 1 11 CYS 11 336 336 CYS CYS B . n A 1 12 PRO 12 337 337 PRO PRO B . n A 1 13 PHE 13 338 338 PHE PHE B . n A 1 14 GLY 14 339 339 GLY GLY B . n A 1 15 GLU 15 340 340 GLU GLU B . n A 1 16 VAL 16 341 341 VAL VAL B . n A 1 17 PHE 17 342 342 PHE PHE B . n A 1 18 ASN 18 343 343 ASN ASN B . n A 1 19 ALA 19 344 344 ALA ALA B . n A 1 20 THR 20 345 345 THR THR B . n A 1 21 ARG 21 346 346 ARG ARG B . n A 1 22 PHE 22 347 347 PHE PHE B . n A 1 23 ALA 23 348 348 ALA ALA B . n A 1 24 SER 24 349 349 SER SER B . n A 1 25 VAL 25 350 350 VAL VAL B . n A 1 26 TYR 26 351 351 TYR TYR B . n A 1 27 ALA 27 352 352 ALA ALA B . n A 1 28 TRP 28 353 353 TRP TRP B . n A 1 29 ASN 29 354 354 ASN ASN B . n A 1 30 ARG 30 355 355 ARG ARG B . n A 1 31 LYS 31 356 356 LYS LYS B . n A 1 32 ARG 32 357 357 ARG ARG B . n A 1 33 ILE 33 358 358 ILE ILE B . n A 1 34 SER 34 359 359 SER SER B . n A 1 35 ASN 35 360 360 ASN ASN B . n A 1 36 CYS 36 361 361 CYS CYS B . n A 1 37 VAL 37 362 362 VAL VAL B . n A 1 38 ALA 38 363 363 ALA ALA B . n A 1 39 ASP 39 364 364 ASP ASP B . n A 1 40 TYR 40 365 365 TYR TYR B . n A 1 41 SER 41 366 366 SER SER B . n A 1 42 VAL 42 367 367 VAL VAL B . n A 1 43 LEU 43 368 368 LEU LEU B . n A 1 44 TYR 44 369 369 TYR TYR B . n A 1 45 ASN 45 370 370 ASN ASN B . n A 1 46 SER 46 371 371 SER SER B . n A 1 47 ALA 47 372 372 ALA ALA B . n A 1 48 SER 48 373 373 SER SER B . n A 1 49 PHE 49 374 374 PHE PHE B . n A 1 50 SER 50 375 375 SER SER B . n A 1 51 THR 51 376 376 THR THR B . n A 1 52 PHE 52 377 377 PHE PHE B . n A 1 53 LYS 53 378 378 LYS LYS B . n A 1 54 CYS 54 379 379 CYS CYS B . n A 1 55 TYR 55 380 380 TYR TYR B . n A 1 56 GLY 56 381 381 GLY GLY B . n A 1 57 VAL 57 382 382 VAL VAL B . n A 1 58 SER 58 383 383 SER SER B . n A 1 59 PRO 59 384 384 PRO PRO B . n A 1 60 THR 60 385 385 THR THR B . n A 1 61 LYS 61 386 386 LYS LYS B . n A 1 62 LEU 62 387 387 LEU LEU B . n A 1 63 ASN 63 388 388 ASN ASN B . n A 1 64 ASP 64 389 389 ASP ASP B . n A 1 65 LEU 65 390 390 LEU LEU B . n A 1 66 CYS 66 391 391 CYS CYS B . n A 1 67 PHE 67 392 392 PHE PHE B . n A 1 68 THR 68 393 393 THR THR B . n A 1 69 ASN 69 394 394 ASN ASN B . n A 1 70 VAL 70 395 395 VAL VAL B . n A 1 71 TYR 71 396 396 TYR TYR B . n A 1 72 ALA 72 397 397 ALA ALA B . n A 1 73 ASP 73 398 398 ASP ASP B . n A 1 74 SER 74 399 399 SER SER B . n A 1 75 PHE 75 400 400 PHE PHE B . n A 1 76 VAL 76 401 401 VAL VAL B . n A 1 77 ILE 77 402 402 ILE ILE B . n A 1 78 ARG 78 403 403 ARG ARG B . n A 1 79 GLY 79 404 404 GLY GLY B . n A 1 80 ASP 80 405 405 ASP ASP B . n A 1 81 GLU 81 406 406 GLU GLU B . n A 1 82 VAL 82 407 407 VAL VAL B . n A 1 83 ARG 83 408 408 ARG ARG B . n A 1 84 GLN 84 409 409 GLN GLN B . n A 1 85 ILE 85 410 410 ILE ILE B . n A 1 86 ALA 86 411 411 ALA ALA B . n A 1 87 PRO 87 412 412 PRO PRO B . n A 1 88 GLY 88 413 413 GLY GLY B . n A 1 89 GLN 89 414 414 GLN GLN B . n A 1 90 THR 90 415 415 THR THR B . n A 1 91 GLY 91 416 416 GLY GLY B . n A 1 92 LYS 92 417 417 LYS LYS B . n A 1 93 ILE 93 418 418 ILE ILE B . n A 1 94 ALA 94 419 419 ALA ALA B . n A 1 95 ASP 95 420 420 ASP ASP B . n A 1 96 TYR 96 421 421 TYR TYR B . n A 1 97 ASN 97 422 422 ASN ASN B . n A 1 98 TYR 98 423 423 TYR TYR B . n A 1 99 LYS 99 424 424 LYS LYS B . n A 1 100 LEU 100 425 425 LEU LEU B . n A 1 101 PRO 101 426 426 PRO PRO B . n A 1 102 ASP 102 427 427 ASP ASP B . n A 1 103 ASP 103 428 428 ASP ASP B . n A 1 104 PHE 104 429 429 PHE PHE B . n A 1 105 THR 105 430 430 THR THR B . n A 1 106 GLY 106 431 431 GLY GLY B . n A 1 107 CYS 107 432 432 CYS CYS B . n A 1 108 VAL 108 433 433 VAL VAL B . n A 1 109 ILE 109 434 434 ILE ILE B . n A 1 110 ALA 110 435 435 ALA ALA B . n A 1 111 TRP 111 436 436 TRP TRP B . n A 1 112 ASN 112 437 437 ASN ASN B . n A 1 113 SER 113 438 438 SER SER B . n A 1 114 ASN 114 439 439 ASN ASN B . n A 1 115 ASN 115 440 440 ASN ASN B . n A 1 116 LEU 116 441 441 LEU LEU B . n A 1 117 ASP 117 442 442 ASP ASP B . n A 1 118 SER 118 443 443 SER SER B . n A 1 119 LYS 119 444 444 LYS LYS B . n A 1 120 VAL 120 445 445 VAL VAL B . n A 1 121 GLY 121 446 446 GLY GLY B . n A 1 122 GLY 122 447 447 GLY GLY B . n A 1 123 ASN 123 448 448 ASN ASN B . n A 1 124 TYR 124 449 449 TYR TYR B . n A 1 125 ASN 125 450 450 ASN ASN B . n A 1 126 TYR 126 451 451 TYR TYR B . n A 1 127 LEU 127 452 452 LEU LEU B . n A 1 128 TYR 128 453 453 TYR TYR B . n A 1 129 ARG 129 454 454 ARG ARG B . n A 1 130 LEU 130 455 455 LEU LEU B . n A 1 131 PHE 131 456 456 PHE PHE B . n A 1 132 ARG 132 457 457 ARG ARG B . n A 1 133 LYS 133 458 458 LYS LYS B . n A 1 134 SER 134 459 459 SER SER B . n A 1 135 ASN 135 460 460 ASN ASN B . n A 1 136 LEU 136 461 461 LEU LEU B . n A 1 137 LYS 137 462 462 LYS LYS B . n A 1 138 PRO 138 463 463 PRO PRO B . n A 1 139 PHE 139 464 464 PHE PHE B . n A 1 140 GLU 140 465 465 GLU GLU B . n A 1 141 ARG 141 466 466 ARG ARG B . n A 1 142 ASP 142 467 467 ASP ASP B . n A 1 143 ILE 143 468 468 ILE ILE B . n A 1 144 SER 144 469 469 SER SER B . n A 1 145 THR 145 470 470 THR THR B . n A 1 146 GLU 146 471 471 GLU GLU B . n A 1 147 ILE 147 472 472 ILE ILE B . n A 1 148 TYR 148 473 473 TYR TYR B . n A 1 149 GLN 149 474 474 GLN GLN B . n A 1 150 ALA 150 475 475 ALA ALA B . n A 1 151 GLY 151 476 ? ? ? B . n A 1 152 SER 152 477 ? ? ? B . n A 1 153 THR 153 478 ? ? ? B . n A 1 154 PRO 154 479 ? ? ? B . n A 1 155 CYS 155 480 ? ? ? B . n A 1 156 ASN 156 481 ? ? ? B . n A 1 157 GLY 157 482 ? ? ? B . n A 1 158 VAL 158 483 ? ? ? B . n A 1 159 GLU 159 484 ? ? ? B . n A 1 160 GLY 160 485 ? ? ? B . n A 1 161 PHE 161 486 ? ? ? B . n A 1 162 ASN 162 487 ? ? ? B . n A 1 163 CYS 163 488 ? ? ? B . n A 1 164 TYR 164 489 489 TYR TYR B . n A 1 165 PHE 165 490 490 PHE PHE B . n A 1 166 PRO 166 491 491 PRO PRO B . n A 1 167 LEU 167 492 492 LEU LEU B . n A 1 168 GLN 168 493 493 GLN GLN B . n A 1 169 SER 169 494 494 SER SER B . n A 1 170 TYR 170 495 495 TYR TYR B . n A 1 171 GLY 171 496 496 GLY GLY B . n A 1 172 PHE 172 497 497 PHE PHE B . n A 1 173 GLN 173 498 498 GLN GLN B . n A 1 174 PRO 174 499 499 PRO PRO B . n A 1 175 THR 175 500 500 THR THR B . n A 1 176 ASN 176 501 501 ASN ASN B . n A 1 177 GLY 177 502 502 GLY GLY B . n A 1 178 VAL 178 503 503 VAL VAL B . n A 1 179 GLY 179 504 504 GLY GLY B . n A 1 180 TYR 180 505 505 TYR TYR B . n A 1 181 GLN 181 506 506 GLN GLN B . n A 1 182 PRO 182 507 507 PRO PRO B . n A 1 183 TYR 183 508 508 TYR TYR B . n A 1 184 ARG 184 509 509 ARG ARG B . n A 1 185 VAL 185 510 510 VAL VAL B . n A 1 186 VAL 186 511 511 VAL VAL B . n A 1 187 VAL 187 512 512 VAL VAL B . n A 1 188 LEU 188 513 513 LEU LEU B . n A 1 189 SER 189 514 514 SER SER B . n A 1 190 PHE 190 515 515 PHE PHE B . n A 1 191 GLU 191 516 516 GLU GLU B . n A 1 192 LEU 192 517 517 LEU LEU B . n A 1 193 LEU 193 518 518 LEU LEU B . n A 1 194 HIS 194 519 519 HIS HIS B . n A 1 195 ALA 195 520 520 ALA ALA B . n A 1 196 PRO 196 521 521 PRO PRO B . n A 1 197 ALA 197 522 522 ALA ALA B . n A 1 198 THR 198 523 523 THR THR B . n A 1 199 VAL 199 524 524 VAL VAL B . n A 1 200 CYS 200 525 525 CYS CYS B . n A 1 201 GLY 201 526 526 GLY GLY B . n A 1 202 PRO 202 527 527 PRO PRO B . n A 1 203 LYS 203 528 528 LYS LYS B . n A 1 204 LYS 204 529 529 LYS LYS B . n A 1 205 SER 205 530 530 SER SER B . n B 2 1 GLN 1 1 1 GLN GLN F . n B 2 2 LEU 2 2 2 LEU LEU F . n B 2 3 GLN 3 3 3 GLN GLN F . n B 2 4 LEU 4 4 4 LEU LEU F . n B 2 5 GLN 5 5 5 GLN GLN F . n B 2 6 GLU 6 6 6 GLU GLU F . n B 2 7 SER 7 7 7 SER SER F . n B 2 8 GLY 8 8 8 GLY GLY F . n B 2 9 PRO 9 9 9 PRO PRO F . n B 2 10 GLY 10 10 10 GLY GLY F . n B 2 11 LEU 11 11 11 LEU LEU F . n B 2 12 VAL 12 12 12 VAL VAL F . n B 2 13 LYS 13 13 13 LYS LYS F . n B 2 14 PRO 14 14 14 PRO PRO F . n B 2 15 SER 15 15 15 SER SER F . n B 2 16 GLU 16 16 16 GLU GLU F . n B 2 17 THR 17 17 17 THR THR F . n B 2 18 LEU 18 18 18 LEU LEU F . n B 2 19 SER 19 19 19 SER SER F . n B 2 20 LEU 20 20 20 LEU LEU F . n B 2 21 THR 21 21 21 THR THR F . n B 2 22 CYS 22 22 22 CYS CYS F . n B 2 23 ALA 23 23 23 ALA ALA F . n B 2 24 VAL 24 24 24 VAL VAL F . n B 2 25 SER 25 25 25 SER SER F . n B 2 26 GLY 26 26 26 GLY GLY F . n B 2 27 GLY 27 27 27 GLY GLY F . n B 2 28 SER 28 28 28 SER SER F . n B 2 29 ILE 29 29 29 ILE ILE F . n B 2 30 SER 30 30 30 SER SER F . n B 2 31 ARG 31 31 31 ARG ARG F . n B 2 32 LYS 32 32 32 LYS LYS F . n B 2 33 ASN 33 33 33 ASN ASN F . n B 2 34 TRP 34 34 34 TRP TRP F . n B 2 35 SER 35 35 35 SER SER F . n B 2 36 TRP 36 36 36 TRP TRP F . n B 2 37 ILE 37 37 37 ILE ILE F . n B 2 38 ARG 38 38 38 ARG ARG F . n B 2 39 GLN 39 39 39 GLN GLN F . n B 2 40 PRO 40 40 40 PRO PRO F . n B 2 41 PRO 41 41 41 PRO PRO F . n B 2 42 GLY 42 42 42 GLY GLY F . n B 2 43 LYS 43 43 43 LYS LYS F . n B 2 44 GLY 44 44 44 GLY GLY F . n B 2 45 LEU 45 45 45 LEU LEU F . n B 2 46 GLY 46 46 46 GLY GLY F . n B 2 47 TRP 47 47 47 TRP TRP F . n B 2 48 ILE 48 48 48 ILE ILE F . n B 2 49 GLY 49 49 49 GLY GLY F . n B 2 50 ARG 50 50 50 ARG ARG F . n B 2 51 ILE 51 51 51 ILE ILE F . n B 2 52 SER 52 52 52 SER SER F . n B 2 53 GLY 53 52 52 GLY GLY F A n B 2 54 SER 54 53 53 SER SER F . n B 2 55 GLY 55 54 54 GLY GLY F . n B 2 56 GLY 56 55 55 GLY GLY F . n B 2 57 SER 57 56 56 SER SER F . n B 2 58 THR 58 57 57 THR THR F . n B 2 59 ASP 59 58 58 ASP ASP F . n B 2 60 TYR 60 59 59 TYR TYR F . n B 2 61 ASN 61 60 60 ASN ASN F . n B 2 62 PRO 62 61 61 PRO PRO F . n B 2 63 SER 63 62 62 SER SER F . n B 2 64 LEU 64 63 63 LEU LEU F . n B 2 65 LYS 65 64 64 LYS LYS F . n B 2 66 SER 66 65 65 SER SER F . n B 2 67 ARG 67 66 66 ARG ARG F . n B 2 68 VAL 68 67 67 VAL VAL F . n B 2 69 THR 69 68 68 THR THR F . n B 2 70 ILE 70 69 69 ILE ILE F . n B 2 71 SER 71 70 70 SER SER F . n B 2 72 THR 72 71 71 THR THR F . n B 2 73 ASP 73 72 72 ASP ASP F . n B 2 74 THR 74 73 73 THR THR F . n B 2 75 SER 75 74 74 SER SER F . n B 2 76 LYS 76 75 75 LYS LYS F . n B 2 77 ASN 77 76 76 ASN ASN F . n B 2 78 GLN 78 77 77 GLN GLN F . n B 2 79 PHE 79 78 78 PHE PHE F . n B 2 80 SER 80 79 79 SER SER F . n B 2 81 LEU 81 80 80 LEU LEU F . n B 2 82 LYS 82 81 81 LYS LYS F . n B 2 83 LEU 83 82 82 LEU LEU F . n B 2 84 SER 84 82 82 SER SER F A n B 2 85 SER 85 82 82 SER SER F B n B 2 86 VAL 86 82 82 VAL VAL F C n B 2 87 THR 87 83 83 THR THR F . n B 2 88 ALA 88 84 84 ALA ALA F . n B 2 89 ALA 89 85 85 ALA ALA F . n B 2 90 ASP 90 86 86 ASP ASP F . n B 2 91 THR 91 87 87 THR THR F . n B 2 92 ALA 92 88 88 ALA ALA F . n B 2 93 VAL 93 89 89 VAL VAL F . n B 2 94 TYR 94 90 90 TYR TYR F . n B 2 95 TYR 95 91 91 TYR TYR F . n B 2 96 CYS 96 92 92 CYS CYS F . n B 2 97 ALA 97 93 93 ALA ALA F . n B 2 98 ARG 98 94 94 ARG ARG F . n B 2 99 VAL 99 95 95 VAL VAL F . n B 2 100 ALA 100 96 96 ALA ALA F . n B 2 101 TYR 101 97 97 TYR TYR F . n B 2 102 TYR 102 98 98 TYR TYR F . n B 2 103 GLU 103 99 99 GLU GLU F . n B 2 104 ASP 104 100 100 ASP ASP F . n B 2 105 ASP 105 100 100 ASP ASP F A n B 2 106 TYR 106 100 100 TYR TYR F B n B 2 107 GLY 107 100 100 GLY GLY F C n B 2 108 TYR 108 100 100 TYR TYR F D n B 2 109 TYR 109 100 100 TYR TYR F E n B 2 110 TYR 110 100 100 TYR TYR F F n B 2 111 THR 111 100 100 THR THR F G n B 2 112 GLU 112 100 100 GLU GLU F H n B 2 113 GLY 113 100 100 GLY GLY F I n B 2 114 ALA 114 100 100 ALA ALA F J n B 2 115 PHE 115 100 100 PHE PHE F K n B 2 116 ASP 116 101 101 ASP ASP F . n B 2 117 PHE 117 102 102 PHE PHE F . n B 2 118 TRP 118 103 103 TRP TRP F . n B 2 119 GLY 119 104 104 GLY GLY F . n B 2 120 GLN 120 105 105 GLN GLN F . n B 2 121 GLY 121 106 106 GLY GLY F . n B 2 122 LEU 122 107 107 LEU LEU F . n B 2 123 ARG 123 108 108 ARG ARG F . n B 2 124 VAL 124 109 109 VAL VAL F . n B 2 125 THR 125 110 110 THR THR F . n B 2 126 VAL 126 111 111 VAL VAL F . n B 2 127 SER 127 112 112 SER SER F . n B 2 128 SER 128 113 113 SER SER F . n C 3 1 GLU 1 1 1 GLU GLU G . n C 3 2 ILE 2 2 2 ILE ILE G . n C 3 3 VAL 3 3 3 VAL VAL G . n C 3 4 MET 4 4 4 MET MET G . n C 3 5 THR 5 5 5 THR THR G . n C 3 6 GLN 6 6 6 GLN GLN G . n C 3 7 SER 7 7 7 SER SER G . n C 3 8 PRO 8 8 8 PRO PRO G . n C 3 9 ALA 9 9 9 ALA ALA G . n C 3 10 THR 10 10 10 THR THR G . n C 3 11 LEU 11 11 11 LEU LEU G . n C 3 12 SER 12 12 12 SER SER G . n C 3 13 LEU 13 13 13 LEU LEU G . n C 3 14 SER 14 14 14 SER SER G . n C 3 15 PRO 15 15 15 PRO PRO G . n C 3 16 GLY 16 16 16 GLY GLY G . n C 3 17 GLU 17 17 17 GLU GLU G . n C 3 18 ARG 18 18 18 ARG ARG G . n C 3 19 ALA 19 19 19 ALA ALA G . n C 3 20 THR 20 20 20 THR THR G . n C 3 21 LEU 21 21 21 LEU LEU G . n C 3 22 SER 22 22 22 SER SER G . n C 3 23 CYS 23 23 23 CYS CYS G . n C 3 24 ARG 24 24 24 ARG ARG G . n C 3 25 THR 25 25 25 THR THR G . n C 3 26 SER 26 26 26 SER SER G . n C 3 27 GLN 27 27 27 GLN GLN G . n C 3 28 SER 28 28 28 SER SER G . n C 3 29 VAL 29 29 29 VAL VAL G . n C 3 30 SER 30 30 30 SER SER G . n C 3 31 SER 31 31 31 SER SER G . n C 3 32 TYR 32 32 32 TYR TYR G . n C 3 33 VAL 33 33 33 VAL VAL G . n C 3 34 ALA 34 34 34 ALA ALA G . n C 3 35 TRP 35 35 35 TRP TRP G . n C 3 36 TYR 36 36 36 TYR TYR G . n C 3 37 GLN 37 37 37 GLN GLN G . n C 3 38 GLN 38 38 38 GLN GLN G . n C 3 39 LYS 39 39 39 LYS LYS G . n C 3 40 PRO 40 40 40 PRO PRO G . n C 3 41 GLU 41 41 41 GLU GLU G . n C 3 42 GLN 42 42 42 GLN GLN G . n C 3 43 THR 43 43 43 THR THR G . n C 3 44 PRO 44 44 44 PRO PRO G . n C 3 45 ARG 45 45 45 ARG ARG G . n C 3 46 LEU 46 46 46 LEU LEU G . n C 3 47 LEU 47 47 47 LEU LEU G . n C 3 48 ILE 48 48 48 ILE ILE G . n C 3 49 TYR 49 49 49 TYR TYR G . n C 3 50 ASP 50 50 50 ASP ASP G . n C 3 51 ALA 51 51 51 ALA ALA G . n C 3 52 SER 52 52 52 SER SER G . n C 3 53 SER 53 53 53 SER SER G . n C 3 54 ARG 54 54 54 ARG ARG G . n C 3 55 ALA 55 55 55 ALA ALA G . n C 3 56 THR 56 56 56 THR THR G . n C 3 57 GLY 57 57 57 GLY GLY G . n C 3 58 ILE 58 58 58 ILE ILE G . n C 3 59 PRO 59 59 59 PRO PRO G . n C 3 60 ASP 60 60 60 ASP ASP G . n C 3 61 ARG 61 61 61 ARG ARG G . n C 3 62 PHE 62 62 62 PHE PHE G . n C 3 63 SER 63 63 63 SER SER G . n C 3 64 GLY 64 64 64 GLY GLY G . n C 3 65 GLY 65 65 65 GLY GLY G . n C 3 66 GLY 66 66 66 GLY GLY G . n C 3 67 SER 67 67 67 SER SER G . n C 3 68 GLY 68 68 68 GLY GLY G . n C 3 69 THR 69 69 69 THR THR G . n C 3 70 ASP 70 70 70 ASP ASP G . n C 3 71 PHE 71 71 71 PHE PHE G . n C 3 72 THR 72 72 72 THR THR G . n C 3 73 LEU 73 73 73 LEU LEU G . n C 3 74 THR 74 74 74 THR THR G . n C 3 75 ILE 75 75 75 ILE ILE G . n C 3 76 SER 76 76 76 SER SER G . n C 3 77 SER 77 77 77 SER SER G . n C 3 78 LEU 78 78 78 LEU LEU G . n C 3 79 GLU 79 79 79 GLU GLU G . n C 3 80 PRO 80 80 80 PRO PRO G . n C 3 81 GLU 81 81 81 GLU GLU G . n C 3 82 ASP 82 82 82 ASP ASP G . n C 3 83 PHE 83 83 83 PHE PHE G . n C 3 84 ALA 84 84 84 ALA ALA G . n C 3 85 VAL 85 85 85 VAL VAL G . n C 3 86 TYR 86 86 86 TYR TYR G . n C 3 87 TYR 87 87 87 TYR TYR G . n C 3 88 CYS 88 88 88 CYS CYS G . n C 3 89 GLN 89 89 89 GLN GLN G . n C 3 90 GLN 90 90 90 GLN GLN G . n C 3 91 TYR 91 91 91 TYR TYR G . n C 3 92 SER 92 92 92 SER SER G . n C 3 93 ASN 93 93 93 ASN ASN G . n C 3 94 TRP 94 94 94 TRP TRP G . n C 3 95 PRO 95 95 95 PRO PRO G . n C 3 96 TRP 96 96 96 TRP TRP G . n C 3 97 THR 97 97 97 THR THR G . n C 3 98 PHE 98 98 98 PHE PHE G . n C 3 99 GLY 99 99 99 GLY GLY G . n C 3 100 GLN 100 100 100 GLN GLN G . n C 3 101 GLY 101 101 101 GLY GLY G . n C 3 102 THR 102 102 102 THR THR G . n C 3 103 LYS 103 103 103 LYS LYS G . n C 3 104 VAL 104 104 104 VAL VAL G . n C 3 105 GLU 105 105 105 GLU GLU G . n C 3 106 ILE 106 106 106 ILE ILE G . n C 3 107 LYS 107 107 107 LYS LYS G . n # _pdbx_contact_author.id 2 _pdbx_contact_author.email pa98@duke.edu _pdbx_contact_author.name_first Priyamvada _pdbx_contact_author.name_last Acharya _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0002-0089-277X # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation ? _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2023-08-02 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # _software.citation_id ? _software.classification refinement _software.compiler_name ? _software.compiler_version ? _software.contact_author ? _software.contact_author_email ? _software.date ? _software.description ? _software.dependencies ? _software.hardware ? _software.language ? _software.location ? _software.mods ? _software.name PHENIX _software.os ? _software.os_version ? _software.type ? _software.version 1.19.2_4158: _software.pdbx_ordinal 1 # _pdbx_entry_details.entry_id 8DPZ _pdbx_entry_details.has_ligand_of_interest N _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? # _em_3d_fitting.entry_id 8DPZ _em_3d_fitting.id 1 _em_3d_fitting.details ? _em_3d_fitting.overall_b_value ? _em_3d_fitting.ref_protocol 'FLEXIBLE FIT' _em_3d_fitting.ref_space ? _em_3d_fitting.target_criteria ? _em_3d_fitting.method ? # loop_ _em_3d_fitting_list.3d_fitting_id _em_3d_fitting_list.id _em_3d_fitting_list.details _em_3d_fitting_list.pdb_chain_id _em_3d_fitting_list.pdb_chain_residue_range _em_3d_fitting_list.pdb_entry_id 1 1 ? ? ? 7LD1 1 2 ? ? ? 3Q6G # _em_3d_reconstruction.entry_id 8DPZ _em_3d_reconstruction.id 1 _em_3d_reconstruction.algorithm ? _em_3d_reconstruction.details ? _em_3d_reconstruction.refinement_type ? _em_3d_reconstruction.image_processing_id 1 _em_3d_reconstruction.num_class_averages ? _em_3d_reconstruction.num_particles 1103016 _em_3d_reconstruction.resolution 3.38 _em_3d_reconstruction.resolution_method 'FSC 0.143 CUT-OFF' _em_3d_reconstruction.symmetry_type POINT _em_3d_reconstruction.method ? _em_3d_reconstruction.nominal_pixel_size ? _em_3d_reconstruction.actual_pixel_size ? _em_3d_reconstruction.magnification_calibration ? # _em_buffer.id 1 _em_buffer.details ? _em_buffer.pH 8.0 _em_buffer.specimen_id 1 _em_buffer.name ? # _em_entity_assembly.id 1 _em_entity_assembly.parent_id 0 _em_entity_assembly.details ? _em_entity_assembly.name 'Ab026500 Fab bound to SARS-CoV-2 HexaPro Spike S1 local refinement' _em_entity_assembly.source RECOMBINANT _em_entity_assembly.type COMPLEX _em_entity_assembly.entity_id_list '1, 2, 3' _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? # _em_imaging.id 1 _em_imaging.entry_id 8DPZ _em_imaging.accelerating_voltage 300 _em_imaging.alignment_procedure 'COMA FREE' _em_imaging.c2_aperture_diameter ? _em_imaging.calibrated_defocus_max ? _em_imaging.calibrated_defocus_min ? _em_imaging.calibrated_magnification ? _em_imaging.cryogen NITROGEN _em_imaging.details ? _em_imaging.electron_source 'FIELD EMISSION GUN' _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.microscope_model 'FEI TITAN KRIOS' _em_imaging.mode 'BRIGHT FIELD' _em_imaging.nominal_cs 2.7 _em_imaging.nominal_defocus_max 2500 _em_imaging.nominal_defocus_min 700 _em_imaging.nominal_magnification ? _em_imaging.recording_temperature_maximum ? _em_imaging.recording_temperature_minimum ? _em_imaging.residual_tilt ? _em_imaging.specimen_holder_model ? _em_imaging.specimen_id 1 _em_imaging.citation_id ? _em_imaging.date ? _em_imaging.temperature ? _em_imaging.tilt_angle_min ? _em_imaging.tilt_angle_max ? _em_imaging.astigmatism ? _em_imaging.detector_distance ? _em_imaging.electron_beam_tilt_params ? _em_imaging.specimen_holder_type ? # _em_sample_support.id 1 _em_sample_support.specimen_id 1 _em_sample_support.details ? _em_sample_support.grid_material COPPER _em_sample_support.grid_mesh_size 300 _em_sample_support.grid_type 'Quantifoil R1.2/1.3' _em_sample_support.method ? _em_sample_support.film_material ? # _em_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.chamber_temperature ? _em_vitrification.cryogen_name ETHANE _em_vitrification.details ? _em_vitrification.humidity 95 _em_vitrification.instrument 'LEICA EM GP' _em_vitrification.entry_id 8DPZ _em_vitrification.citation_id ? _em_vitrification.method ? _em_vitrification.temp ? _em_vitrification.time_resolved_state ? # _em_experiment.entry_id 8DPZ _em_experiment.id 1 _em_experiment.aggregation_state PARTICLE _em_experiment.reconstruction_method 'SINGLE PARTICLE' _em_experiment.entity_assembly_id 1 # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 PRO B 337 ? ? -77.83 24.06 2 1 ALA B 352 ? ? -98.87 59.98 3 1 ASP B 428 ? ? -92.53 53.42 4 1 ILE F 48 ? ? -95.08 -61.24 5 1 TYR G 32 ? ? -102.49 75.31 6 1 ALA G 51 ? ? 62.74 -1.23 7 1 TYR G 91 ? ? -142.34 31.89 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 B ILE 326 ? A ILE 1 2 1 Y 1 B VAL 327 ? A VAL 2 3 1 Y 1 B ARG 328 ? A ARG 3 4 1 Y 1 B PHE 329 ? A PHE 4 5 1 Y 1 B PRO 330 ? A PRO 5 6 1 Y 1 B ASN 331 ? A ASN 6 7 1 Y 1 B ILE 332 ? A ILE 7 8 1 Y 1 B GLY 476 ? A GLY 151 9 1 Y 1 B SER 477 ? A SER 152 10 1 Y 1 B THR 478 ? A THR 153 11 1 Y 1 B PRO 479 ? A PRO 154 12 1 Y 1 B CYS 480 ? A CYS 155 13 1 Y 1 B ASN 481 ? A ASN 156 14 1 Y 1 B GLY 482 ? A GLY 157 15 1 Y 1 B VAL 483 ? A VAL 158 16 1 Y 1 B GLU 484 ? A GLU 159 17 1 Y 1 B GLY 485 ? A GLY 160 18 1 Y 1 B PHE 486 ? A PHE 161 19 1 Y 1 B ASN 487 ? A ASN 162 20 1 Y 1 B CYS 488 ? A CYS 163 # _em_ctf_correction.id 1 _em_ctf_correction.em_image_processing_id 1 _em_ctf_correction.type 'PHASE FLIPPING AND AMPLITUDE CORRECTION' _em_ctf_correction.details ? # _em_entity_assembly_molwt.entity_assembly_id 1 _em_entity_assembly_molwt.id 1 _em_entity_assembly_molwt.experimental_flag YES _em_entity_assembly_molwt.units MEGADALTONS _em_entity_assembly_molwt.value 0.557 # _em_entity_assembly_naturalsource.id 1 _em_entity_assembly_naturalsource.entity_assembly_id 1 _em_entity_assembly_naturalsource.cell ? _em_entity_assembly_naturalsource.cellular_location ? _em_entity_assembly_naturalsource.ncbi_tax_id 2697049 _em_entity_assembly_naturalsource.organ ? _em_entity_assembly_naturalsource.organelle ? _em_entity_assembly_naturalsource.organism 'Severe acute respiratory syndrome coronavirus 2' _em_entity_assembly_naturalsource.strain ? _em_entity_assembly_naturalsource.tissue ? # _em_entity_assembly_recombinant.id 1 _em_entity_assembly_recombinant.entity_assembly_id 1 _em_entity_assembly_recombinant.cell ? _em_entity_assembly_recombinant.ncbi_tax_id 9606 _em_entity_assembly_recombinant.organism 'Homo sapiens' _em_entity_assembly_recombinant.plasmid ? _em_entity_assembly_recombinant.strain ? # _em_image_processing.id 1 _em_image_processing.image_recording_id 1 _em_image_processing.details ? # _em_image_recording.id 1 _em_image_recording.imaging_id 1 _em_image_recording.avg_electron_dose_per_image 59.4 _em_image_recording.average_exposure_time ? _em_image_recording.details ? _em_image_recording.detector_mode ? _em_image_recording.film_or_detector_model 'GATAN K3 (6k x 4k)' _em_image_recording.num_diffraction_images ? _em_image_recording.num_grids_imaged 1 _em_image_recording.num_real_images 7866 _em_image_recording.avg_electron_dose_per_subtomogram ? # loop_ _em_software.id _em_software.category _em_software.details _em_software.name _em_software.version _em_software.image_processing_id _em_software.fitting_id _em_software.imaging_id 1 'CRYSTALLOGRAPHY MERGING' ? ? ? 1 1 1 2 'IMAGE ACQUISITION' ? EPU ? ? ? 1 3 MASKING ? ? ? ? ? ? 4 'CTF CORRECTION' ? ? ? 1 ? ? 5 'LAYERLINE INDEXING' ? ? ? ? ? ? 6 'DIFFRACTION INDEXING' ? ? ? ? ? ? 7 'MODEL FITTING' ? ? ? ? 1 ? 8 OTHER ? ? ? ? ? ? 9 'INITIAL EULER ASSIGNMENT' ? ? ? 1 ? ? 10 'FINAL EULER ASSIGNMENT' ? ? ? 1 ? ? 11 CLASSIFICATION ? cryoSPARC 3.3.1 1 ? ? 12 RECONSTRUCTION ? Coot ? 1 ? ? 13 RECONSTRUCTION ? ISOLDE ? 1 ? ? 14 RECONSTRUCTION ? PHENIX ? 1 ? ? 15 'MODEL REFINEMENT' ? ? ? ? 1 ? # _em_specimen.id 1 _em_specimen.experiment_id 1 _em_specimen.concentration 1.5 _em_specimen.details 'Fab to spike 6:1 ratio.' _em_specimen.embedding_applied NO _em_specimen.shadowing_applied NO _em_specimen.staining_applied NO _em_specimen.vitrification_applied YES # _pdbx_audit_support.funding_organization 'National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)' _pdbx_audit_support.country 'United States' _pdbx_audit_support.grant_number 'R01 AI165947' _pdbx_audit_support.ordinal 1 # loop_ _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_mon_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.hetero D 4 NAG 1 A NAG 1 B NAG 531 n D 4 NAG 2 A NAG 2 B NAG 532 n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier NAG 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DGlcpNAcb NAG 'COMMON NAME' GMML 1.0 N-acetyl-b-D-glucopyranosamine NAG 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 b-D-GlcpNAc NAG 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 GlcNAc # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_descriptor.ordinal _pdbx_entity_branch_descriptor.entity_id _pdbx_entity_branch_descriptor.descriptor _pdbx_entity_branch_descriptor.type _pdbx_entity_branch_descriptor.program _pdbx_entity_branch_descriptor.program_version 1 4 DGlcpNAcb1-4DGlcpNAcb1-ROH 'Glycam Condensed Sequence' GMML 1.0 2 4 'WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1' WURCS PDB2Glycan 1.1.0 3 4 '[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}' LINUCS PDB-CARE ? # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.entity_id 4 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.value_order sing _pdbx_entity_branch_link.details ? # loop_ _pdbx_entity_branch_list.entity_id _pdbx_entity_branch_list.comp_id _pdbx_entity_branch_list.num _pdbx_entity_branch_list.hetero 4 NAG 1 n 4 NAG 2 n # loop_ _pdbx_initial_refinement_model.id _pdbx_initial_refinement_model.type _pdbx_initial_refinement_model.source_name _pdbx_initial_refinement_model.accession_code 1 'experimental model' PDB 7LD1 2 'experimental model' PDB 3Q6G # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'electron microscopy' _pdbx_struct_assembly_auth_evidence.details ? #