data_7XIZ # _entry.id 7XIZ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.359 _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 7XIZ pdb_00007xiz 10.2210/pdb7xiz/pdb WWPDB D_1300028933 ? ? EMDB EMD-33213 ? ? # _pdbx_database_related.db_name EMDB _pdbx_database_related.details 'SARS-CoV-2 Omicron BA.3 variant spike (local)' _pdbx_database_related.db_id EMD-33213 _pdbx_database_related.content_type '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 7XIZ _pdbx_database_status.recvd_initial_deposition_date 2022-04-14 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _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 'Wang, X.' 1 0000-0003-0635-278X 'Wang, L.' 2 0000-0002-8519-0637 # _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 UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Nature _citation.journal_id_ASTM NATUAS _citation.journal_id_CSD 0006 _citation.journal_id_ISSN 1476-4687 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 608 _citation.language ? _citation.page_first 593 _citation.page_last 602 _citation.title 'BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection.' _citation.year 2022 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1038/s41586-022-04980-y _citation.pdbx_database_id_PubMed 35714668 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Cao, Y.' 1 ? primary 'Yisimayi, A.' 2 ? primary 'Jian, F.' 3 ? primary 'Song, W.' 4 ? primary 'Xiao, T.' 5 ? primary 'Wang, L.' 6 ? primary 'Du, S.' 7 ? primary 'Wang, J.' 8 ? primary 'Li, Q.' 9 ? primary 'Chen, X.' 10 ? primary 'Yu, Y.' 11 ? primary 'Wang, P.' 12 ? primary 'Zhang, Z.' 13 ? primary 'Liu, P.' 14 ? primary 'An, R.' 15 ? primary 'Hao, X.' 16 ? primary 'Wang, Y.' 17 ? primary 'Wang, J.' 18 ? primary 'Feng, R.' 19 ? primary 'Sun, H.' 20 ? primary 'Zhao, L.' 21 ? primary 'Zhang, W.' 22 ? primary 'Zhao, D.' 23 ? primary 'Zheng, J.' 24 ? primary 'Yu, L.' 25 ? primary 'Li, C.' 26 ? primary 'Zhang, N.' 27 ? primary 'Wang, R.' 28 ? primary 'Niu, X.' 29 ? primary 'Yang, S.' 30 ? primary 'Song, X.' 31 ? primary 'Chai, Y.' 32 ? primary 'Hu, Y.' 33 ? primary 'Shi, Y.' 34 ? primary 'Zheng, L.' 35 ? primary 'Li, Z.' 36 ? primary 'Gu, Q.' 37 ? primary 'Shao, F.' 38 ? primary 'Huang, W.' 39 ? primary 'Jin, R.' 40 ? primary 'Shen, Z.' 41 ? primary 'Wang, Y.' 42 ? primary 'Wang, X.' 43 ? primary 'Xiao, J.' 44 ? primary 'Xie, X.S.' 45 ? # _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 7XIZ _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 7XIZ _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' 30219.145 1 ? ? ? ? 2 non-polymer syn 2-acetamido-2-deoxy-beta-D-glucopyranose 221.208 2 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'S glycoprotein,E2,Peplomer protein' # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code ;TESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFTFKCYGVSPTKLNDLCFTNVYADSFVI RGNEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNG VAGFNCYFPLRSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPF QQFGRDIADTTDAVRDPQTLEILDITP ; _entity_poly.pdbx_seq_one_letter_code_can ;TESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFTFKCYGVSPTKLNDLCFTNVYADSFVI RGNEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNG VAGFNCYFPLRSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPF QQFGRDIADTTDAVRDPQTLEILDITP ; _entity_poly.pdbx_strand_id B _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 THR n 1 2 GLU n 1 3 SER n 1 4 ILE n 1 5 VAL n 1 6 ARG n 1 7 PHE n 1 8 PRO n 1 9 ASN n 1 10 ILE n 1 11 THR n 1 12 ASN n 1 13 LEU n 1 14 CYS n 1 15 PRO n 1 16 PHE n 1 17 ASP n 1 18 GLU n 1 19 VAL n 1 20 PHE n 1 21 ASN n 1 22 ALA n 1 23 THR n 1 24 ARG n 1 25 PHE n 1 26 ALA n 1 27 SER n 1 28 VAL n 1 29 TYR n 1 30 ALA n 1 31 TRP n 1 32 ASN n 1 33 ARG n 1 34 LYS n 1 35 ARG n 1 36 ILE n 1 37 SER n 1 38 ASN n 1 39 CYS n 1 40 VAL n 1 41 ALA n 1 42 ASP n 1 43 TYR n 1 44 SER n 1 45 VAL n 1 46 LEU n 1 47 TYR n 1 48 ASN n 1 49 PHE n 1 50 ALA n 1 51 PRO n 1 52 PHE n 1 53 PHE n 1 54 THR n 1 55 PHE n 1 56 LYS n 1 57 CYS n 1 58 TYR n 1 59 GLY n 1 60 VAL n 1 61 SER n 1 62 PRO n 1 63 THR n 1 64 LYS n 1 65 LEU n 1 66 ASN n 1 67 ASP n 1 68 LEU n 1 69 CYS n 1 70 PHE n 1 71 THR n 1 72 ASN n 1 73 VAL n 1 74 TYR n 1 75 ALA n 1 76 ASP n 1 77 SER n 1 78 PHE n 1 79 VAL n 1 80 ILE n 1 81 ARG n 1 82 GLY n 1 83 ASN n 1 84 GLU n 1 85 VAL n 1 86 ARG n 1 87 GLN n 1 88 ILE n 1 89 ALA n 1 90 PRO n 1 91 GLY n 1 92 GLN n 1 93 THR n 1 94 GLY n 1 95 ASN n 1 96 ILE n 1 97 ALA n 1 98 ASP n 1 99 TYR n 1 100 ASN n 1 101 TYR n 1 102 LYS n 1 103 LEU n 1 104 PRO n 1 105 ASP n 1 106 ASP n 1 107 PHE n 1 108 THR n 1 109 GLY n 1 110 CYS n 1 111 VAL n 1 112 ILE n 1 113 ALA n 1 114 TRP n 1 115 ASN n 1 116 SER n 1 117 ASN n 1 118 LYS n 1 119 LEU n 1 120 ASP n 1 121 SER n 1 122 LYS n 1 123 VAL n 1 124 SER n 1 125 GLY n 1 126 ASN n 1 127 TYR n 1 128 ASN n 1 129 TYR n 1 130 LEU n 1 131 TYR n 1 132 ARG n 1 133 LEU n 1 134 PHE n 1 135 ARG n 1 136 LYS n 1 137 SER n 1 138 ASN n 1 139 LEU n 1 140 LYS n 1 141 PRO n 1 142 PHE n 1 143 GLU n 1 144 ARG n 1 145 ASP n 1 146 ILE n 1 147 SER n 1 148 THR n 1 149 GLU n 1 150 ILE n 1 151 TYR n 1 152 GLN n 1 153 ALA n 1 154 GLY n 1 155 ASN n 1 156 LYS n 1 157 PRO n 1 158 CYS n 1 159 ASN n 1 160 GLY n 1 161 VAL n 1 162 ALA n 1 163 GLY n 1 164 PHE n 1 165 ASN n 1 166 CYS n 1 167 TYR n 1 168 PHE n 1 169 PRO n 1 170 LEU n 1 171 ARG n 1 172 SER n 1 173 TYR n 1 174 GLY n 1 175 PHE n 1 176 ARG n 1 177 PRO n 1 178 THR n 1 179 TYR n 1 180 GLY n 1 181 VAL n 1 182 GLY n 1 183 HIS n 1 184 GLN n 1 185 PRO n 1 186 TYR n 1 187 ARG n 1 188 VAL n 1 189 VAL n 1 190 VAL n 1 191 LEU n 1 192 SER n 1 193 PHE n 1 194 GLU n 1 195 LEU n 1 196 LEU n 1 197 HIS n 1 198 ALA n 1 199 PRO n 1 200 ALA n 1 201 THR n 1 202 VAL n 1 203 CYS n 1 204 GLY n 1 205 PRO n 1 206 LYS n 1 207 LYS n 1 208 SER n 1 209 THR n 1 210 ASN n 1 211 LEU n 1 212 VAL n 1 213 LYS n 1 214 ASN n 1 215 LYS n 1 216 CYS n 1 217 VAL n 1 218 ASN n 1 219 PHE n 1 220 ASN n 1 221 PHE n 1 222 ASN n 1 223 GLY n 1 224 LEU n 1 225 THR n 1 226 GLY n 1 227 THR n 1 228 GLY n 1 229 VAL n 1 230 LEU n 1 231 THR n 1 232 GLU n 1 233 SER n 1 234 ASN n 1 235 LYS n 1 236 LYS n 1 237 PHE n 1 238 LEU n 1 239 PRO n 1 240 PHE n 1 241 GLN n 1 242 GLN n 1 243 PHE n 1 244 GLY n 1 245 ARG n 1 246 ASP n 1 247 ILE n 1 248 ALA n 1 249 ASP n 1 250 THR n 1 251 THR n 1 252 ASP n 1 253 ALA n 1 254 VAL n 1 255 ARG n 1 256 ASP n 1 257 PRO n 1 258 GLN n 1 259 THR n 1 260 LEU n 1 261 GLU n 1 262 ILE n 1 263 LEU n 1 264 ASP n 1 265 ILE n 1 266 THR n 1 267 PRO n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type 'Biological sequence' _entity_src_gen.pdbx_beg_seq_num 1 _entity_src_gen.pdbx_end_seq_num 267 _entity_src_gen.gene_src_common_name '2019-nCoV, SARS-CoV-2' _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'S, 2' _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 'Severe acute respiratory syndrome coronavirus 2' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 2697049 _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 'Homo sapiens' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 9606 _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 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code SPIKE_SARS2 _struct_ref.pdbx_db_accession P0DTC2 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;TESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVI RGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNG VEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPF QQFGRDIADTTDAVRDPQTLEILDITP ; _struct_ref.pdbx_align_begin 323 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 7XIZ _struct_ref_seq.pdbx_strand_id B _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 267 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P0DTC2 _struct_ref_seq.db_align_beg 323 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 589 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 323 _struct_ref_seq.pdbx_auth_seq_align_end 589 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 7XIZ ASP B 17 ? UNP P0DTC2 GLY 339 variant 339 1 1 7XIZ PHE B 49 ? UNP P0DTC2 SER 371 variant 371 2 1 7XIZ PRO B 51 ? UNP P0DTC2 SER 373 variant 373 3 1 7XIZ PHE B 53 ? UNP P0DTC2 SER 375 variant 375 4 1 7XIZ ASN B 83 ? UNP P0DTC2 ASP 405 variant 405 5 1 7XIZ ASN B 95 ? UNP P0DTC2 LYS 417 variant 417 6 1 7XIZ LYS B 118 ? UNP P0DTC2 ASN 440 variant 440 7 1 7XIZ SER B 124 ? UNP P0DTC2 GLY 446 variant 446 8 1 7XIZ ASN B 155 ? UNP P0DTC2 SER 477 variant 477 9 1 7XIZ LYS B 156 ? UNP P0DTC2 THR 478 variant 478 10 1 7XIZ ALA B 162 ? UNP P0DTC2 GLU 484 variant 484 11 1 7XIZ ARG B 171 ? UNP P0DTC2 GLN 493 variant 493 12 1 7XIZ ARG B 176 ? UNP P0DTC2 GLN 498 variant 498 13 1 7XIZ TYR B 179 ? UNP P0DTC2 ASN 501 variant 501 14 1 7XIZ HIS B 183 ? UNP P0DTC2 TYR 505 variant 505 15 # 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 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 7XIZ _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _refine.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine.entry_id 7XIZ _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' ? 0.005 ? 26743 ? f_bond_d ? ? 'ELECTRON MICROSCOPY' ? 0.810 ? 36413 ? f_angle_d ? ? 'ELECTRON MICROSCOPY' ? 9.182 ? 3774 ? f_dihedral_angle_d ? ? 'ELECTRON MICROSCOPY' ? 0.052 ? 4240 ? f_chiral_restr ? ? 'ELECTRON MICROSCOPY' ? 0.008 ? 4658 ? f_plane_restr ? ? # _struct.entry_id 7XIZ _struct.title 'SARS-CoV-2 Omicron BA.3 variant spike (local)' _struct.pdbx_structure_determination_methodology ? _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 7XIZ _struct_keywords.text 'SARS-CoV-2, Omicron, BA.2, spike, VIRAL PROTEIN' _struct_keywords.pdbx_keywords 'VIRAL PROTEIN' # 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 2 ? # 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 15 ? ASN A 21 ? PRO B 337 ASN B 343 1 ? 7 HELX_P HELX_P2 AA2 LYS A 64 ? LEU A 68 ? LYS B 386 LEU B 390 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 14 SG ? ? ? 1_555 A CYS 39 SG ? ? B CYS 336 B CYS 361 1_555 ? ? ? ? ? ? ? 2.035 ? ? disulf2 disulf ? ? A CYS 57 SG ? ? ? 1_555 A CYS 110 SG ? ? B CYS 379 B CYS 432 1_555 ? ? ? ? ? ? ? 2.032 ? ? disulf3 disulf ? ? A CYS 158 SG ? ? ? 1_555 A CYS 166 SG ? ? B CYS 480 B CYS 488 1_555 ? ? ? ? ? ? ? 2.034 ? ? covale1 covale one ? A ASN 9 ND2 ? ? ? 1_555 B NAG . C1 ? ? B ASN 331 B NAG 601 1_555 ? ? ? ? ? ? ? 1.451 ? N-Glycosylation covale2 covale one ? A ASN 21 ND2 ? ? ? 1_555 C NAG . C1 ? ? B ASN 343 B NAG 602 1_555 ? ? ? ? ? ? ? 1.442 ? N-Glycosylation # 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 ? 4 ? AA2 ? 5 ? AA3 ? 2 ? # 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 AA2 1 2 ? anti-parallel AA2 2 3 ? anti-parallel AA2 3 4 ? anti-parallel AA2 4 5 ? anti-parallel AA3 1 2 ? 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 32 ? ILE A 36 ? ASN B 354 ILE B 358 AA1 2 VAL A 73 ? ILE A 80 ? VAL B 395 ILE B 402 AA1 3 TYR A 186 ? SER A 192 ? TYR B 508 SER B 514 AA1 4 GLY A 109 ? ASN A 115 ? GLY B 431 ASN B 437 AA2 1 CYS A 216 ? VAL A 217 ? CYS B 538 VAL B 539 AA2 2 GLY A 228 ? GLU A 232 ? GLY B 550 GLU B 554 AA2 3 ILE A 262 ? THR A 266 ? ILE B 584 THR B 588 AA2 4 THR A 251 ? ARG A 255 ? THR B 573 ARG B 577 AA2 5 PHE A 243 ? ARG A 245 ? PHE B 565 ARG B 567 AA3 1 ASN A 220 ? PHE A 221 ? ASN B 542 PHE B 543 AA3 2 LEU A 224 ? THR A 225 ? LEU B 546 THR B 547 # 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 36 ? N ILE B 358 O VAL A 73 ? O VAL B 395 AA1 2 3 N TYR A 74 ? N TYR B 396 O SER A 192 ? O SER B 514 AA1 3 4 O VAL A 189 ? O VAL B 511 N ILE A 112 ? N ILE B 434 AA2 1 2 N VAL A 217 ? N VAL B 539 O GLY A 228 ? O GLY B 550 AA2 2 3 N VAL A 229 ? N VAL B 551 O THR A 266 ? O THR B 588 AA2 3 4 O ILE A 265 ? O ILE B 587 N ASP A 252 ? N ASP B 574 AA2 4 5 O ALA A 253 ? O ALA B 575 N GLY A 244 ? N GLY B 566 AA3 1 2 N PHE A 221 ? N PHE B 543 O LEU A 224 ? O LEU B 546 # _atom_sites.entry_id 7XIZ _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 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 THR 1 323 323 THR THR B . n A 1 2 GLU 2 324 324 GLU GLU B . n A 1 3 SER 3 325 325 SER SER B . n A 1 4 ILE 4 326 326 ILE ILE B . n A 1 5 VAL 5 327 327 VAL VAL B . n A 1 6 ARG 6 328 328 ARG ARG B . n A 1 7 PHE 7 329 329 PHE PHE B . n A 1 8 PRO 8 330 330 PRO PRO B . n A 1 9 ASN 9 331 331 ASN ASN B . n A 1 10 ILE 10 332 332 ILE ILE B . n A 1 11 THR 11 333 333 THR THR B . n A 1 12 ASN 12 334 334 ASN ASN B . n A 1 13 LEU 13 335 335 LEU LEU B . n A 1 14 CYS 14 336 336 CYS CYS B . n A 1 15 PRO 15 337 337 PRO PRO B . n A 1 16 PHE 16 338 338 PHE PHE B . n A 1 17 ASP 17 339 339 ASP ASP B . n A 1 18 GLU 18 340 340 GLU GLU B . n A 1 19 VAL 19 341 341 VAL VAL B . n A 1 20 PHE 20 342 342 PHE PHE B . n A 1 21 ASN 21 343 343 ASN ASN B . n A 1 22 ALA 22 344 344 ALA ALA B . n A 1 23 THR 23 345 345 THR THR B . n A 1 24 ARG 24 346 346 ARG ARG B . n A 1 25 PHE 25 347 347 PHE PHE B . n A 1 26 ALA 26 348 348 ALA ALA B . n A 1 27 SER 27 349 349 SER SER B . n A 1 28 VAL 28 350 350 VAL VAL B . n A 1 29 TYR 29 351 351 TYR TYR B . n A 1 30 ALA 30 352 352 ALA ALA B . n A 1 31 TRP 31 353 353 TRP TRP B . n A 1 32 ASN 32 354 354 ASN ASN B . n A 1 33 ARG 33 355 355 ARG ARG B . n A 1 34 LYS 34 356 356 LYS LYS B . n A 1 35 ARG 35 357 357 ARG ARG B . n A 1 36 ILE 36 358 358 ILE ILE B . n A 1 37 SER 37 359 359 SER SER B . n A 1 38 ASN 38 360 360 ASN ASN B . n A 1 39 CYS 39 361 361 CYS CYS B . n A 1 40 VAL 40 362 362 VAL VAL B . n A 1 41 ALA 41 363 363 ALA ALA B . n A 1 42 ASP 42 364 364 ASP ASP B . n A 1 43 TYR 43 365 365 TYR TYR B . n A 1 44 SER 44 366 366 SER SER B . n A 1 45 VAL 45 367 367 VAL VAL B . n A 1 46 LEU 46 368 368 LEU LEU B . n A 1 47 TYR 47 369 369 TYR TYR B . n A 1 48 ASN 48 370 370 ASN ASN B . n A 1 49 PHE 49 371 371 PHE PHE B . n A 1 50 ALA 50 372 372 ALA ALA B . n A 1 51 PRO 51 373 373 PRO PRO B . n A 1 52 PHE 52 374 374 PHE PHE B . n A 1 53 PHE 53 375 375 PHE PHE B . n A 1 54 THR 54 376 376 THR THR B . n A 1 55 PHE 55 377 377 PHE PHE B . n A 1 56 LYS 56 378 378 LYS LYS B . n A 1 57 CYS 57 379 379 CYS CYS B . n A 1 58 TYR 58 380 380 TYR TYR B . n A 1 59 GLY 59 381 381 GLY GLY B . n A 1 60 VAL 60 382 382 VAL VAL B . n A 1 61 SER 61 383 383 SER SER B . n A 1 62 PRO 62 384 384 PRO PRO B . n A 1 63 THR 63 385 385 THR THR B . n A 1 64 LYS 64 386 386 LYS LYS B . n A 1 65 LEU 65 387 387 LEU LEU B . n A 1 66 ASN 66 388 388 ASN ASN B . n A 1 67 ASP 67 389 389 ASP ASP B . n A 1 68 LEU 68 390 390 LEU LEU B . n A 1 69 CYS 69 391 391 CYS CYS B . n A 1 70 PHE 70 392 392 PHE PHE B . n A 1 71 THR 71 393 393 THR THR B . n A 1 72 ASN 72 394 394 ASN ASN B . n A 1 73 VAL 73 395 395 VAL VAL B . n A 1 74 TYR 74 396 396 TYR TYR B . n A 1 75 ALA 75 397 397 ALA ALA B . n A 1 76 ASP 76 398 398 ASP ASP B . n A 1 77 SER 77 399 399 SER SER B . n A 1 78 PHE 78 400 400 PHE PHE B . n A 1 79 VAL 79 401 401 VAL VAL B . n A 1 80 ILE 80 402 402 ILE ILE B . n A 1 81 ARG 81 403 403 ARG ARG B . n A 1 82 GLY 82 404 404 GLY GLY B . n A 1 83 ASN 83 405 405 ASN ASN B . n A 1 84 GLU 84 406 406 GLU GLU B . n A 1 85 VAL 85 407 407 VAL VAL B . n A 1 86 ARG 86 408 408 ARG ARG B . n A 1 87 GLN 87 409 409 GLN GLN B . n A 1 88 ILE 88 410 410 ILE ILE B . n A 1 89 ALA 89 411 411 ALA ALA B . n A 1 90 PRO 90 412 412 PRO PRO B . n A 1 91 GLY 91 413 413 GLY GLY B . n A 1 92 GLN 92 414 414 GLN GLN B . n A 1 93 THR 93 415 415 THR THR B . n A 1 94 GLY 94 416 416 GLY GLY B . n A 1 95 ASN 95 417 417 ASN ASN B . n A 1 96 ILE 96 418 418 ILE ILE B . n A 1 97 ALA 97 419 419 ALA ALA B . n A 1 98 ASP 98 420 420 ASP ASP B . n A 1 99 TYR 99 421 421 TYR TYR B . n A 1 100 ASN 100 422 422 ASN ASN B . n A 1 101 TYR 101 423 423 TYR TYR B . n A 1 102 LYS 102 424 424 LYS LYS B . n A 1 103 LEU 103 425 425 LEU LEU B . n A 1 104 PRO 104 426 426 PRO PRO B . n A 1 105 ASP 105 427 427 ASP ASP B . n A 1 106 ASP 106 428 428 ASP ASP B . n A 1 107 PHE 107 429 429 PHE PHE B . n A 1 108 THR 108 430 430 THR THR B . n A 1 109 GLY 109 431 431 GLY GLY B . n A 1 110 CYS 110 432 432 CYS CYS B . n A 1 111 VAL 111 433 433 VAL VAL B . n A 1 112 ILE 112 434 434 ILE ILE B . n A 1 113 ALA 113 435 435 ALA ALA B . n A 1 114 TRP 114 436 436 TRP TRP B . n A 1 115 ASN 115 437 437 ASN ASN B . n A 1 116 SER 116 438 438 SER SER B . n A 1 117 ASN 117 439 439 ASN ASN B . n A 1 118 LYS 118 440 440 LYS LYS B . n A 1 119 LEU 119 441 441 LEU LEU B . n A 1 120 ASP 120 442 442 ASP ASP B . n A 1 121 SER 121 443 443 SER SER B . n A 1 122 LYS 122 444 444 LYS LYS B . n A 1 123 VAL 123 445 445 VAL VAL B . n A 1 124 SER 124 446 446 SER SER B . n A 1 125 GLY 125 447 447 GLY GLY B . n A 1 126 ASN 126 448 448 ASN ASN B . n A 1 127 TYR 127 449 449 TYR TYR B . n A 1 128 ASN 128 450 450 ASN ASN B . n A 1 129 TYR 129 451 451 TYR TYR B . n A 1 130 LEU 130 452 452 LEU LEU B . n A 1 131 TYR 131 453 453 TYR TYR B . n A 1 132 ARG 132 454 454 ARG ARG B . n A 1 133 LEU 133 455 455 LEU LEU B . n A 1 134 PHE 134 456 456 PHE PHE B . n A 1 135 ARG 135 457 457 ARG ARG B . n A 1 136 LYS 136 458 458 LYS LYS B . n A 1 137 SER 137 459 459 SER SER B . n A 1 138 ASN 138 460 460 ASN ASN B . n A 1 139 LEU 139 461 461 LEU LEU B . n A 1 140 LYS 140 462 462 LYS LYS B . n A 1 141 PRO 141 463 463 PRO PRO B . n A 1 142 PHE 142 464 464 PHE PHE B . n A 1 143 GLU 143 465 465 GLU GLU B . n A 1 144 ARG 144 466 466 ARG ARG B . n A 1 145 ASP 145 467 467 ASP ASP B . n A 1 146 ILE 146 468 468 ILE ILE B . n A 1 147 SER 147 469 469 SER SER B . n A 1 148 THR 148 470 470 THR THR B . n A 1 149 GLU 149 471 471 GLU GLU B . n A 1 150 ILE 150 472 472 ILE ILE B . n A 1 151 TYR 151 473 473 TYR TYR B . n A 1 152 GLN 152 474 474 GLN GLN B . n A 1 153 ALA 153 475 475 ALA ALA B . n A 1 154 GLY 154 476 476 GLY GLY B . n A 1 155 ASN 155 477 477 ASN ASN B . n A 1 156 LYS 156 478 478 LYS LYS B . n A 1 157 PRO 157 479 479 PRO PRO B . n A 1 158 CYS 158 480 480 CYS CYS B . n A 1 159 ASN 159 481 481 ASN ASN B . n A 1 160 GLY 160 482 482 GLY GLY B . n A 1 161 VAL 161 483 483 VAL VAL B . n A 1 162 ALA 162 484 484 ALA ALA B . n A 1 163 GLY 163 485 485 GLY GLY B . n A 1 164 PHE 164 486 486 PHE PHE B . n A 1 165 ASN 165 487 487 ASN ASN B . n A 1 166 CYS 166 488 488 CYS CYS B . n A 1 167 TYR 167 489 489 TYR TYR B . n A 1 168 PHE 168 490 490 PHE PHE B . n A 1 169 PRO 169 491 491 PRO PRO B . n A 1 170 LEU 170 492 492 LEU LEU B . n A 1 171 ARG 171 493 493 ARG ARG B . n A 1 172 SER 172 494 494 SER SER B . n A 1 173 TYR 173 495 495 TYR TYR B . n A 1 174 GLY 174 496 496 GLY GLY B . n A 1 175 PHE 175 497 497 PHE PHE B . n A 1 176 ARG 176 498 498 ARG ARG B . n A 1 177 PRO 177 499 499 PRO PRO B . n A 1 178 THR 178 500 500 THR THR B . n A 1 179 TYR 179 501 501 TYR TYR B . n A 1 180 GLY 180 502 502 GLY GLY B . n A 1 181 VAL 181 503 503 VAL VAL B . n A 1 182 GLY 182 504 504 GLY GLY B . n A 1 183 HIS 183 505 505 HIS HIS B . n A 1 184 GLN 184 506 506 GLN GLN B . n A 1 185 PRO 185 507 507 PRO PRO B . n A 1 186 TYR 186 508 508 TYR TYR B . n A 1 187 ARG 187 509 509 ARG ARG B . n A 1 188 VAL 188 510 510 VAL VAL B . n A 1 189 VAL 189 511 511 VAL VAL B . n A 1 190 VAL 190 512 512 VAL VAL B . n A 1 191 LEU 191 513 513 LEU LEU B . n A 1 192 SER 192 514 514 SER SER B . n A 1 193 PHE 193 515 515 PHE PHE B . n A 1 194 GLU 194 516 516 GLU GLU B . n A 1 195 LEU 195 517 517 LEU LEU B . n A 1 196 LEU 196 518 518 LEU LEU B . n A 1 197 HIS 197 519 519 HIS HIS B . n A 1 198 ALA 198 520 520 ALA ALA B . n A 1 199 PRO 199 521 521 PRO PRO B . n A 1 200 ALA 200 522 522 ALA ALA B . n A 1 201 THR 201 523 523 THR THR B . n A 1 202 VAL 202 524 524 VAL VAL B . n A 1 203 CYS 203 525 525 CYS CYS B . n A 1 204 GLY 204 526 526 GLY GLY B . n A 1 205 PRO 205 527 527 PRO PRO B . n A 1 206 LYS 206 528 528 LYS LYS B . n A 1 207 LYS 207 529 529 LYS LYS B . n A 1 208 SER 208 530 530 SER SER B . n A 1 209 THR 209 531 531 THR THR B . n A 1 210 ASN 210 532 532 ASN ASN B . n A 1 211 LEU 211 533 533 LEU LEU B . n A 1 212 VAL 212 534 534 VAL VAL B . n A 1 213 LYS 213 535 535 LYS LYS B . n A 1 214 ASN 214 536 536 ASN ASN B . n A 1 215 LYS 215 537 537 LYS LYS B . n A 1 216 CYS 216 538 538 CYS CYS B . n A 1 217 VAL 217 539 539 VAL VAL B . n A 1 218 ASN 218 540 540 ASN ASN B . n A 1 219 PHE 219 541 541 PHE PHE B . n A 1 220 ASN 220 542 542 ASN ASN B . n A 1 221 PHE 221 543 543 PHE PHE B . n A 1 222 ASN 222 544 544 ASN ASN B . n A 1 223 GLY 223 545 545 GLY GLY B . n A 1 224 LEU 224 546 546 LEU LEU B . n A 1 225 THR 225 547 547 THR THR B . n A 1 226 GLY 226 548 548 GLY GLY B . n A 1 227 THR 227 549 549 THR THR B . n A 1 228 GLY 228 550 550 GLY GLY B . n A 1 229 VAL 229 551 551 VAL VAL B . n A 1 230 LEU 230 552 552 LEU LEU B . n A 1 231 THR 231 553 553 THR THR B . n A 1 232 GLU 232 554 554 GLU GLU B . n A 1 233 SER 233 555 555 SER SER B . n A 1 234 ASN 234 556 556 ASN ASN B . n A 1 235 LYS 235 557 557 LYS LYS B . n A 1 236 LYS 236 558 558 LYS LYS B . n A 1 237 PHE 237 559 559 PHE PHE B . n A 1 238 LEU 238 560 560 LEU LEU B . n A 1 239 PRO 239 561 561 PRO PRO B . n A 1 240 PHE 240 562 562 PHE PHE B . n A 1 241 GLN 241 563 563 GLN GLN B . n A 1 242 GLN 242 564 564 GLN GLN B . n A 1 243 PHE 243 565 565 PHE PHE B . n A 1 244 GLY 244 566 566 GLY GLY B . n A 1 245 ARG 245 567 567 ARG ARG B . n A 1 246 ASP 246 568 568 ASP ASP B . n A 1 247 ILE 247 569 569 ILE ILE B . n A 1 248 ALA 248 570 570 ALA ALA B . n A 1 249 ASP 249 571 571 ASP ASP B . n A 1 250 THR 250 572 572 THR THR B . n A 1 251 THR 251 573 573 THR THR B . n A 1 252 ASP 252 574 574 ASP ASP B . n A 1 253 ALA 253 575 575 ALA ALA B . n A 1 254 VAL 254 576 576 VAL VAL B . n A 1 255 ARG 255 577 577 ARG ARG B . n A 1 256 ASP 256 578 578 ASP ASP B . n A 1 257 PRO 257 579 579 PRO PRO B . n A 1 258 GLN 258 580 580 GLN GLN B . n A 1 259 THR 259 581 581 THR THR B . n A 1 260 LEU 260 582 582 LEU LEU B . n A 1 261 GLU 261 583 583 GLU GLU B . n A 1 262 ILE 262 584 584 ILE ILE B . n A 1 263 LEU 263 585 585 LEU LEU B . n A 1 264 ASP 264 586 586 ASP ASP B . n A 1 265 ILE 265 587 587 ILE ILE B . n A 1 266 THR 266 588 588 THR THR B . n A 1 267 PRO 267 589 589 PRO PRO B . n # _pdbx_contact_author.id 2 _pdbx_contact_author.email wonder_leilei@163.com _pdbx_contact_author.name_first Lei _pdbx_contact_author.name_last Wang _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0002-8519-0637 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 NAG 1 601 1152 NAG NAG B . C 2 NAG 1 602 1166 NAG NAG B . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C # _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 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2022-07-13 2 'Structure model' 1 1 2022-08-31 # _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 ? # _pdbx_audit_revision_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Database references' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' citation 2 2 'Structure model' citation_author # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_citation.journal_volume' 2 2 'Structure model' '_citation.page_first' 3 2 'Structure model' '_citation.page_last' 4 2 'Structure model' '_citation_author.identifier_ORCID' # _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 1.20.1_4487: _software.pdbx_ordinal 1 # _pdbx_entry_details.entry_id 7XIZ _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest Y # _em_3d_fitting.entry_id 7XIZ _em_3d_fitting.id 1 _em_3d_fitting.details ? _em_3d_fitting.overall_b_value ? _em_3d_fitting.ref_protocol ? _em_3d_fitting.ref_space ? _em_3d_fitting.target_criteria ? _em_3d_fitting.method ? # _em_3d_reconstruction.entry_id 7XIZ _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 185916 _em_3d_reconstruction.resolution 3.74 _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 7.4 _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 'SARS-CoV-2 Omicron BA.2 spike protein' _em_entity_assembly.source RECOMBINANT _em_entity_assembly.type COMPLEX _em_entity_assembly.entity_id_list 1 _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? # _em_imaging.id 1 _em_imaging.entry_id 7XIZ _em_imaging.accelerating_voltage 300 _em_imaging.alignment_procedure ? _em_imaging.c2_aperture_diameter ? _em_imaging.calibrated_defocus_max ? _em_imaging.calibrated_defocus_min ? _em_imaging.calibrated_magnification ? _em_imaging.cryogen ? _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 'DARK FIELD' _em_imaging.nominal_cs ? _em_imaging.nominal_defocus_max 1800 _em_imaging.nominal_defocus_min 1200 _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_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.chamber_temperature ? _em_vitrification.cryogen_name ETHANE _em_vitrification.details ? _em_vitrification.humidity ? _em_vitrification.instrument ? _em_vitrification.entry_id 7XIZ _em_vitrification.citation_id ? _em_vitrification.method ? _em_vitrification.temp ? _em_vitrification.time_resolved_state ? # _em_experiment.entry_id 7XIZ _em_experiment.id 1 _em_experiment.aggregation_state PARTICLE _em_experiment.reconstruction_method 'SINGLE PARTICLE' _em_experiment.entity_assembly_id 1 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 CG B PRO 384 ? ? CD B PRO 384 ? ? 0.960 1.502 -0.542 0.033 N 2 1 CD B PRO 384 ? ? N B PRO 384 ? ? 1.574 1.474 0.100 0.014 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 CA B PRO 384 ? ? N B PRO 384 ? ? CD B PRO 384 ? ? 96.26 111.70 -15.44 1.40 N 2 1 CA B PRO 384 ? ? CB B PRO 384 ? ? CG B PRO 384 ? ? 87.29 104.80 -17.51 1.90 N 3 1 N B PRO 384 ? ? CD B PRO 384 ? ? CG B PRO 384 ? ? 78.55 103.20 -24.65 1.50 N # 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 ALA B 344 ? ? 52.16 -167.88 2 1 THR B 345 ? ? -122.39 -52.92 3 1 ALA B 348 ? ? -177.86 -179.76 4 1 ALA B 372 ? ? -155.15 86.42 5 1 PHE B 377 ? ? 70.86 -15.86 6 1 LYS B 378 ? ? 25.78 60.70 7 1 ASN B 388 ? ? -85.75 43.56 8 1 ARG B 403 ? ? -63.56 -76.83 9 1 ASN B 422 ? ? -147.96 -157.68 10 1 LYS B 444 ? ? 66.62 163.82 11 1 SER B 446 ? ? 55.65 19.60 12 1 LEU B 455 ? ? 60.45 -79.65 13 1 ALA B 475 ? ? 69.92 -3.20 14 1 LYS B 478 ? ? 52.41 77.37 15 1 PRO B 491 ? ? -74.34 -168.72 16 1 LEU B 492 ? ? 62.63 61.28 17 1 VAL B 503 ? ? 62.27 -53.82 18 1 LEU B 518 ? ? 57.78 -112.86 19 1 HIS B 519 ? ? 47.70 -140.74 20 1 ASN B 536 ? ? -143.16 21.12 21 1 ASP B 568 ? ? -124.88 -165.58 22 1 THR B 581 ? ? 66.34 -5.80 # _em_ctf_correction.id 1 _em_ctf_correction.em_image_processing_id 1 _em_ctf_correction.type NONE _em_ctf_correction.details ? # _em_entity_assembly_naturalsource.id 2 _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 2 _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 60 _em_image_recording.average_exposure_time ? _em_image_recording.details ? _em_image_recording.detector_mode ? _em_image_recording.film_or_detector_model 'GATAN K2 BASE (4k x 4k)' _em_image_recording.num_diffraction_images ? _em_image_recording.num_grids_imaged ? _em_image_recording.num_real_images ? _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' ? ? ? ? ? 1 3 MASKING ? ? ? ? ? ? 4 'CTF CORRECTION' ? ? ? 1 ? ? 5 'LAYERLINE INDEXING' ? ? ? ? ? ? 6 'DIFFRACTION INDEXING' ? ? ? ? ? ? 7 'MODEL FITTING' ? ? ? ? ? ? 8 'MODEL REFINEMENT' ? ? ? ? ? ? 9 OTHER ? ? ? ? ? ? 10 'INITIAL EULER ASSIGNMENT' ? ? ? 1 ? ? 11 'FINAL EULER ASSIGNMENT' ? ? ? 1 ? ? 12 CLASSIFICATION ? ? ? 1 ? ? 13 RECONSTRUCTION ? ? ? 1 ? ? # _em_specimen.id 1 _em_specimen.experiment_id 1 _em_specimen.concentration ? _em_specimen.details ? _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 'Not funded' _pdbx_audit_support.country ? _pdbx_audit_support.grant_number ? _pdbx_audit_support.ordinal 1 # 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_instance_feature.ordinal 1 _pdbx_entity_instance_feature.comp_id NAG _pdbx_entity_instance_feature.asym_id ? _pdbx_entity_instance_feature.seq_num ? _pdbx_entity_instance_feature.auth_comp_id NAG _pdbx_entity_instance_feature.auth_asym_id ? _pdbx_entity_instance_feature.auth_seq_num ? _pdbx_entity_instance_feature.feature_type 'SUBJECT OF INVESTIGATION' _pdbx_entity_instance_feature.details ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name 2-acetamido-2-deoxy-beta-D-glucopyranose _pdbx_entity_nonpoly.comp_id NAG # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'gel filtration' _pdbx_struct_assembly_auth_evidence.details ? #