data_7YD1 # _entry.id 7YD1 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.373 _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 7YD1 pdb_00007yd1 10.2210/pdb7yd1/pdb WWPDB D_1300030441 ? ? EMDB EMD-33745 ? ? # _pdbx_database_related.db_name EMDB _pdbx_database_related.details 'Local refinement of SARS-CoV-2 Omicron S trimer complexed with XG005' _pdbx_database_related.db_id EMD-33745 _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 7YD1 _pdbx_database_status.recvd_initial_deposition_date 2022-07-02 _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 'Zhan, W.Q.' 1 ? 'Zhang, X.' 2 ? 'Chen, Z.G.' 3 ? 'Sun, L.' 4 ? # _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 OS-XG005 _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 'Zhan, W.Q.' 1 ? primary 'Zhang, X.' 2 ? # _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 7YD1 _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 7YD1 _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' 22523.479 1 ? ? RBD ? 2 polymer nat XG005-VH 13282.048 1 ? ? ? ? 3 polymer nat XG005-VL 11206.302 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 ;NITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQI APGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYF PLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPK ; ;NITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQI APGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYF PLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPK ; C ? 2 'polypeptide(L)' no no ;QVTLRESGPTLVKPKQTLTLTCTFSGFSLSTPGGGVGWIRQPPGKALEWLALIYWDDDKRYSPSLKSSLTITKDTSKNQV VLTMTNMDPVDTATYYCARLTAADTIFDCWGQGTLVTVSSAS ; ;QVTLRESGPTLVKPKQTLTLTCTFSGFSLSTPGGGVGWIRQPPGKALEWLALIYWDDDKRYSPSLKSSLTITKDTSKNQV VLTMTNMDPVDTATYYCARLTAADTIFDCWGQGTLVTVSSAS ; A ? 3 'polypeptide(L)' no no ;ALTQPASVSGSPGLSITISCTATSSDVGAYNYVSWYQQHPGQAPKLMIYDVSKRPSGVSNRFSGSKSANTASLTISGLQA EDEADYYCSSYTTTSVVFGGGTKLTVLG ; ;ALTQPASVSGSPGLSITISCTATSSDVGAYNYVSWYQQHPGQAPKLMIYDVSKRPSGVSNRFSGSKSANTASLTISGLQA EDEADYYCSSYTTTSVVFGGGTKLTVLG ; B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 ASN n 1 2 ILE n 1 3 THR n 1 4 ASN n 1 5 LEU n 1 6 CYS n 1 7 PRO n 1 8 PHE n 1 9 ASP n 1 10 GLU n 1 11 VAL n 1 12 PHE n 1 13 ASN n 1 14 ALA n 1 15 THR n 1 16 ARG n 1 17 PHE n 1 18 ALA n 1 19 SER n 1 20 VAL n 1 21 TYR n 1 22 ALA n 1 23 TRP n 1 24 ASN n 1 25 ARG n 1 26 LYS n 1 27 ARG n 1 28 ILE n 1 29 SER n 1 30 ASN n 1 31 CYS n 1 32 VAL n 1 33 ALA n 1 34 ASP n 1 35 TYR n 1 36 SER n 1 37 VAL n 1 38 LEU n 1 39 TYR n 1 40 ASN n 1 41 LEU n 1 42 ALA n 1 43 PRO n 1 44 PHE n 1 45 PHE n 1 46 THR n 1 47 PHE n 1 48 LYS n 1 49 CYS n 1 50 TYR n 1 51 GLY n 1 52 VAL n 1 53 SER n 1 54 PRO n 1 55 THR n 1 56 LYS n 1 57 LEU n 1 58 ASN n 1 59 ASP n 1 60 LEU n 1 61 CYS n 1 62 PHE n 1 63 THR n 1 64 ASN n 1 65 VAL n 1 66 TYR n 1 67 ALA n 1 68 ASP n 1 69 SER n 1 70 PHE n 1 71 VAL n 1 72 ILE n 1 73 ARG n 1 74 GLY n 1 75 ASP n 1 76 GLU n 1 77 VAL n 1 78 ARG n 1 79 GLN n 1 80 ILE n 1 81 ALA n 1 82 PRO n 1 83 GLY n 1 84 GLN n 1 85 THR n 1 86 GLY n 1 87 ASN n 1 88 ILE n 1 89 ALA n 1 90 ASP n 1 91 TYR n 1 92 ASN n 1 93 TYR n 1 94 LYS n 1 95 LEU n 1 96 PRO n 1 97 ASP n 1 98 ASP n 1 99 PHE n 1 100 THR n 1 101 GLY n 1 102 CYS n 1 103 VAL n 1 104 ILE n 1 105 ALA n 1 106 TRP n 1 107 ASN n 1 108 SER n 1 109 ASN n 1 110 LYS n 1 111 LEU n 1 112 ASP n 1 113 SER n 1 114 LYS n 1 115 VAL n 1 116 SER n 1 117 GLY n 1 118 ASN n 1 119 TYR n 1 120 ASN n 1 121 TYR n 1 122 LEU n 1 123 TYR n 1 124 ARG n 1 125 LEU n 1 126 PHE n 1 127 ARG n 1 128 LYS n 1 129 SER n 1 130 ASN n 1 131 LEU n 1 132 LYS n 1 133 PRO n 1 134 PHE n 1 135 GLU n 1 136 ARG n 1 137 ASP n 1 138 ILE n 1 139 SER n 1 140 THR n 1 141 GLU n 1 142 ILE n 1 143 TYR n 1 144 GLN n 1 145 ALA n 1 146 GLY n 1 147 ASN n 1 148 LYS n 1 149 PRO n 1 150 CYS n 1 151 ASN n 1 152 GLY n 1 153 VAL n 1 154 ALA n 1 155 GLY n 1 156 PHE n 1 157 ASN n 1 158 CYS n 1 159 TYR n 1 160 PHE n 1 161 PRO n 1 162 LEU n 1 163 ARG n 1 164 SER n 1 165 TYR n 1 166 SER n 1 167 PHE n 1 168 ARG n 1 169 PRO n 1 170 THR n 1 171 TYR n 1 172 GLY n 1 173 VAL n 1 174 GLY n 1 175 HIS n 1 176 GLN n 1 177 PRO n 1 178 TYR n 1 179 ARG n 1 180 VAL n 1 181 VAL n 1 182 VAL n 1 183 LEU n 1 184 SER n 1 185 PHE n 1 186 GLU n 1 187 LEU n 1 188 LEU n 1 189 HIS n 1 190 ALA n 1 191 PRO n 1 192 ALA n 1 193 THR n 1 194 VAL n 1 195 CYS n 1 196 GLY n 1 197 PRO n 1 198 LYS n 2 1 GLN n 2 2 VAL n 2 3 THR n 2 4 LEU n 2 5 ARG n 2 6 GLU n 2 7 SER n 2 8 GLY n 2 9 PRO n 2 10 THR n 2 11 LEU n 2 12 VAL n 2 13 LYS n 2 14 PRO n 2 15 LYS n 2 16 GLN n 2 17 THR n 2 18 LEU n 2 19 THR n 2 20 LEU n 2 21 THR n 2 22 CYS n 2 23 THR n 2 24 PHE n 2 25 SER n 2 26 GLY n 2 27 PHE n 2 28 SER n 2 29 LEU n 2 30 SER n 2 31 THR n 2 32 PRO n 2 33 GLY n 2 34 GLY n 2 35 GLY n 2 36 VAL n 2 37 GLY n 2 38 TRP n 2 39 ILE n 2 40 ARG n 2 41 GLN n 2 42 PRO n 2 43 PRO n 2 44 GLY n 2 45 LYS n 2 46 ALA n 2 47 LEU n 2 48 GLU n 2 49 TRP n 2 50 LEU n 2 51 ALA n 2 52 LEU n 2 53 ILE n 2 54 TYR n 2 55 TRP n 2 56 ASP n 2 57 ASP n 2 58 ASP n 2 59 LYS n 2 60 ARG n 2 61 TYR n 2 62 SER n 2 63 PRO n 2 64 SER n 2 65 LEU n 2 66 LYS n 2 67 SER n 2 68 SER n 2 69 LEU n 2 70 THR n 2 71 ILE n 2 72 THR n 2 73 LYS n 2 74 ASP n 2 75 THR n 2 76 SER n 2 77 LYS n 2 78 ASN n 2 79 GLN n 2 80 VAL n 2 81 VAL n 2 82 LEU n 2 83 THR n 2 84 MET n 2 85 THR n 2 86 ASN n 2 87 MET n 2 88 ASP n 2 89 PRO n 2 90 VAL n 2 91 ASP n 2 92 THR n 2 93 ALA n 2 94 THR n 2 95 TYR n 2 96 TYR n 2 97 CYS n 2 98 ALA n 2 99 ARG n 2 100 LEU n 2 101 THR n 2 102 ALA n 2 103 ALA n 2 104 ASP n 2 105 THR n 2 106 ILE n 2 107 PHE n 2 108 ASP n 2 109 CYS n 2 110 TRP n 2 111 GLY n 2 112 GLN n 2 113 GLY n 2 114 THR n 2 115 LEU n 2 116 VAL n 2 117 THR n 2 118 VAL n 2 119 SER n 2 120 SER n 2 121 ALA n 2 122 SER n 3 1 ALA n 3 2 LEU n 3 3 THR n 3 4 GLN n 3 5 PRO n 3 6 ALA n 3 7 SER n 3 8 VAL n 3 9 SER n 3 10 GLY n 3 11 SER n 3 12 PRO n 3 13 GLY n 3 14 LEU n 3 15 SER n 3 16 ILE n 3 17 THR n 3 18 ILE n 3 19 SER n 3 20 CYS n 3 21 THR n 3 22 ALA n 3 23 THR n 3 24 SER n 3 25 SER n 3 26 ASP n 3 27 VAL n 3 28 GLY n 3 29 ALA n 3 30 TYR n 3 31 ASN n 3 32 TYR n 3 33 VAL n 3 34 SER n 3 35 TRP n 3 36 TYR n 3 37 GLN n 3 38 GLN n 3 39 HIS n 3 40 PRO n 3 41 GLY n 3 42 GLN n 3 43 ALA n 3 44 PRO n 3 45 LYS n 3 46 LEU n 3 47 MET n 3 48 ILE n 3 49 TYR n 3 50 ASP n 3 51 VAL n 3 52 SER n 3 53 LYS n 3 54 ARG n 3 55 PRO n 3 56 SER n 3 57 GLY n 3 58 VAL n 3 59 SER n 3 60 ASN n 3 61 ARG n 3 62 PHE n 3 63 SER n 3 64 GLY n 3 65 SER n 3 66 LYS n 3 67 SER n 3 68 ALA n 3 69 ASN n 3 70 THR n 3 71 ALA n 3 72 SER n 3 73 LEU n 3 74 THR n 3 75 ILE n 3 76 SER n 3 77 GLY n 3 78 LEU n 3 79 GLN n 3 80 ALA n 3 81 GLU n 3 82 ASP n 3 83 GLU n 3 84 ALA n 3 85 ASP n 3 86 TYR n 3 87 TYR n 3 88 CYS n 3 89 SER n 3 90 SER n 3 91 TYR n 3 92 THR n 3 93 THR n 3 94 THR n 3 95 SER n 3 96 VAL n 3 97 VAL n 3 98 PHE n 3 99 GLY n 3 100 GLY n 3 101 GLY n 3 102 THR n 3 103 LYS n 3 104 LEU n 3 105 THR n 3 106 VAL n 3 107 LEU n 3 108 GLY 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 198 _entity_src_gen.gene_src_common_name ? _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 ? # loop_ _entity_src_nat.entity_id _entity_src_nat.pdbx_src_id _entity_src_nat.pdbx_alt_source_flag _entity_src_nat.pdbx_beg_seq_num _entity_src_nat.pdbx_end_seq_num _entity_src_nat.common_name _entity_src_nat.pdbx_organism_scientific _entity_src_nat.pdbx_ncbi_taxonomy_id _entity_src_nat.genus _entity_src_nat.species _entity_src_nat.strain _entity_src_nat.tissue _entity_src_nat.tissue_fraction _entity_src_nat.pdbx_secretion _entity_src_nat.pdbx_fragment _entity_src_nat.pdbx_variant _entity_src_nat.pdbx_cell_line _entity_src_nat.pdbx_atcc _entity_src_nat.pdbx_cellular_location _entity_src_nat.pdbx_organ _entity_src_nat.pdbx_organelle _entity_src_nat.pdbx_cell _entity_src_nat.pdbx_plasmid_name _entity_src_nat.pdbx_plasmid_details _entity_src_nat.details 2 1 sample 1 122 ? 'Homo sapiens' 9606 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 3 1 sample 1 108 ? '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 ;NITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQI APGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYF PLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPK ; 331 2 PDB 7YD1 7YD1 ? 2 ? 1 3 PDB 7YD1 7YD1 ? 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 7YD1 C 1 ? 198 ? P0DTC2 331 ? 528 ? 331 528 2 2 7YD1 A 1 ? 122 ? 7YD1 1 ? 122 ? 1 122 3 3 7YD1 B 1 ? 108 ? 7YD1 3 ? 110 ? 3 110 # 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 7YD1 ASP C 9 ? UNP P0DTC2 GLY 339 variant 339 1 1 7YD1 LEU C 41 ? UNP P0DTC2 SER 371 variant 371 2 1 7YD1 PRO C 43 ? UNP P0DTC2 SER 373 variant 373 3 1 7YD1 PHE C 45 ? UNP P0DTC2 SER 375 variant 375 4 1 7YD1 ASN C 87 ? UNP P0DTC2 LYS 417 variant 417 5 1 7YD1 LYS C 110 ? UNP P0DTC2 ASN 440 variant 440 6 1 7YD1 SER C 116 ? UNP P0DTC2 GLY 446 variant 446 7 1 7YD1 ASN C 147 ? UNP P0DTC2 SER 477 variant 477 8 1 7YD1 LYS C 148 ? UNP P0DTC2 THR 478 variant 478 9 1 7YD1 ALA C 154 ? UNP P0DTC2 GLU 484 variant 484 10 1 7YD1 ARG C 163 ? UNP P0DTC2 GLN 493 variant 493 11 1 7YD1 SER C 166 ? UNP P0DTC2 GLY 496 variant 496 12 1 7YD1 ARG C 168 ? UNP P0DTC2 GLN 498 variant 498 13 1 7YD1 TYR C 171 ? UNP P0DTC2 ASN 501 variant 501 14 1 7YD1 HIS C 175 ? 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 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 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 7YD1 _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _refine.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine.entry_id 7YD1 _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' ? 0.002 ? 3389 ? f_bond_d ? ? 'ELECTRON MICROSCOPY' ? 0.465 ? 4619 ? f_angle_d ? ? 'ELECTRON MICROSCOPY' ? 15.591 ? 1199 ? f_dihedral_angle_d ? ? 'ELECTRON MICROSCOPY' ? 0.039 ? 516 ? f_chiral_restr ? ? 'ELECTRON MICROSCOPY' ? 0.004 ? 590 ? f_plane_restr ? ? # _struct.entry_id 7YD1 _struct.title 'Local refinement of SARS-CoV-2 Omicron S trimer complexed with XG005' _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 7YD1 _struct_keywords.text 'SARS-COV-2, Spike, Antibody, 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 3 ? # 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 PHE A 8 ? ASN A 13 ? PHE C 338 ASN C 343 1 ? 6 HELX_P HELX_P2 AA2 ASP A 34 ? ASN A 40 ? ASP C 364 ASN C 370 5 ? 7 HELX_P HELX_P3 AA3 GLU A 76 ? ILE A 80 ? GLU C 406 ILE C 410 5 ? 5 HELX_P HELX_P4 AA4 ASN A 87 ? ASN A 92 ? ASN C 417 ASN C 422 1 ? 6 HELX_P HELX_P5 AA5 GLN C 79 ? GLU C 83 ? GLN B 81 GLU B 85 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 6 SG ? ? ? 1_555 A CYS 31 SG ? ? C CYS 336 C CYS 361 1_555 ? ? ? ? ? ? ? 2.031 ? ? disulf2 disulf ? ? A CYS 49 SG ? ? ? 1_555 A CYS 102 SG ? ? C CYS 379 C CYS 432 1_555 ? ? ? ? ? ? ? 2.031 ? ? disulf3 disulf ? ? A CYS 61 SG ? ? ? 1_555 A CYS 195 SG ? ? C CYS 391 C CYS 525 1_555 ? ? ? ? ? ? ? 2.032 ? ? disulf4 disulf ? ? A CYS 150 SG ? ? ? 1_555 A CYS 158 SG ? ? C CYS 480 C CYS 488 1_555 ? ? ? ? ? ? ? 2.031 ? ? disulf5 disulf ? ? B CYS 22 SG ? ? ? 1_555 B CYS 97 SG ? ? A CYS 22 A CYS 97 1_555 ? ? ? ? ? ? ? 2.033 ? ? disulf6 disulf ? ? C CYS 20 SG ? ? ? 1_555 C CYS 88 SG ? ? B CYS 22 B CYS 90 1_555 ? ? ? ? ? ? ? 2.032 ? ? # _struct_conn_type.id disulf _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA1 ? 5 ? AA2 ? 2 ? AA3 ? 2 ? AA4 ? 4 ? AA5 ? 3 ? AA6 ? 3 ? AA7 ? 2 ? AA8 ? 3 ? AA9 ? 4 ? # 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 AA2 1 2 ? parallel AA3 1 2 ? anti-parallel AA4 1 2 ? anti-parallel AA4 2 3 ? anti-parallel AA4 3 4 ? anti-parallel AA5 1 2 ? parallel AA5 2 3 ? anti-parallel AA6 1 2 ? anti-parallel AA6 2 3 ? anti-parallel AA7 1 2 ? parallel AA8 1 2 ? anti-parallel AA8 2 3 ? anti-parallel AA9 1 2 ? anti-parallel AA9 2 3 ? anti-parallel AA9 3 4 ? 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 24 ? ILE A 28 ? ASN C 354 ILE C 358 AA1 2 VAL A 65 ? ILE A 72 ? VAL C 395 ILE C 402 AA1 3 TYR A 178 ? PHE A 185 ? TYR C 508 PHE C 515 AA1 4 GLY A 101 ? ASN A 107 ? GLY C 431 ASN C 437 AA1 5 THR A 46 ? CYS A 49 ? THR C 376 CYS C 379 AA2 1 CYS A 31 ? VAL A 32 ? CYS C 361 VAL C 362 AA2 2 VAL A 194 ? CYS A 195 ? VAL C 524 CYS C 525 AA3 1 TYR A 143 ? GLN A 144 ? TYR C 473 GLN C 474 AA3 2 CYS A 158 ? TYR A 159 ? CYS C 488 TYR C 489 AA4 1 THR B 3 ? GLU B 6 ? THR A 3 GLU A 6 AA4 2 LEU B 20 ? SER B 25 ? LEU A 20 SER A 25 AA4 3 GLN B 79 ? THR B 83 ? GLN A 79 THR A 83 AA4 4 THR B 70 ? LYS B 73 ? THR A 70 LYS A 73 AA5 1 LEU B 11 ? VAL B 12 ? LEU A 11 VAL A 12 AA5 2 THR B 114 ? VAL B 118 ? THR A 114 VAL A 118 AA5 3 ALA B 93 ? TYR B 95 ? ALA A 93 TYR A 95 AA6 1 GLY B 37 ? ARG B 40 ? GLY A 37 ARG A 40 AA6 2 GLU B 48 ? ILE B 53 ? GLU A 48 ILE A 53 AA6 3 LYS B 59 ? TYR B 61 ? LYS A 59 TYR A 61 AA7 1 SER C 7 ? GLY C 10 ? SER B 9 GLY B 12 AA7 2 LYS C 103 ? VAL C 106 ? LYS B 105 VAL B 108 AA8 1 ILE C 16 ? THR C 21 ? ILE B 18 THR B 23 AA8 2 THR C 70 ? ILE C 75 ? THR B 72 ILE B 77 AA8 3 PHE C 62 ? LYS C 66 ? PHE B 64 LYS B 68 AA9 1 LYS C 45 ? ILE C 48 ? LYS B 47 ILE B 50 AA9 2 VAL C 33 ? GLN C 38 ? VAL B 35 GLN B 40 AA9 3 ASP C 85 ? TYR C 91 ? ASP B 87 TYR B 93 AA9 4 VAL C 96 ? VAL C 97 ? VAL B 98 VAL B 99 # 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 LYS A 26 ? N LYS C 356 O ALA A 67 ? O ALA C 397 AA1 2 3 N ASP A 68 ? N ASP C 398 O VAL A 182 ? O VAL C 512 AA1 3 4 O VAL A 181 ? O VAL C 511 N ILE A 104 ? N ILE C 434 AA1 4 5 O ALA A 105 ? O ALA C 435 N THR A 46 ? N THR C 376 AA2 1 2 N CYS A 31 ? N CYS C 361 O CYS A 195 ? O CYS C 525 AA3 1 2 N TYR A 143 ? N TYR C 473 O TYR A 159 ? O TYR C 489 AA4 1 2 N ARG B 5 ? N ARG A 5 O THR B 23 ? O THR A 23 AA4 2 3 N CYS B 22 ? N CYS A 22 O VAL B 80 ? O VAL A 80 AA4 3 4 O THR B 83 ? O THR A 83 N THR B 70 ? N THR A 70 AA5 1 2 N VAL B 12 ? N VAL A 12 O THR B 117 ? O THR A 117 AA5 2 3 O VAL B 116 ? O VAL A 116 N ALA B 93 ? N ALA A 93 AA6 1 2 N ARG B 40 ? N ARG A 40 O GLU B 48 ? O GLU A 48 AA6 2 3 N LEU B 52 ? N LEU A 52 O ARG B 60 ? O ARG A 60 AA7 1 2 N VAL C 8 ? N VAL B 10 O LYS C 103 ? O LYS B 105 AA8 1 2 N ILE C 16 ? N ILE B 18 O ILE C 75 ? O ILE B 77 AA8 2 3 O SER C 72 ? O SER B 74 N SER C 65 ? N SER B 67 AA9 1 2 O LYS C 45 ? O LYS B 47 N GLN C 37 ? N GLN B 39 AA9 2 3 N SER C 34 ? N SER B 36 O SER C 89 ? O SER B 91 AA9 3 4 N SER C 90 ? N SER B 92 O VAL C 97 ? O VAL B 99 # _atom_sites.entry_id 7YD1 _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 ASN 1 331 331 ASN ASN C . n A 1 2 ILE 2 332 332 ILE ILE C . n A 1 3 THR 3 333 333 THR THR C . n A 1 4 ASN 4 334 334 ASN ASN C . n A 1 5 LEU 5 335 335 LEU LEU C . n A 1 6 CYS 6 336 336 CYS CYS C . n A 1 7 PRO 7 337 337 PRO PRO C . n A 1 8 PHE 8 338 338 PHE PHE C . n A 1 9 ASP 9 339 339 ASP ASP C . n A 1 10 GLU 10 340 340 GLU GLU C . n A 1 11 VAL 11 341 341 VAL VAL C . n A 1 12 PHE 12 342 342 PHE PHE C . n A 1 13 ASN 13 343 343 ASN ASN C . n A 1 14 ALA 14 344 344 ALA ALA C . n A 1 15 THR 15 345 345 THR THR C . n A 1 16 ARG 16 346 346 ARG ARG C . n A 1 17 PHE 17 347 347 PHE PHE C . n A 1 18 ALA 18 348 348 ALA ALA C . n A 1 19 SER 19 349 349 SER SER C . n A 1 20 VAL 20 350 350 VAL VAL C . n A 1 21 TYR 21 351 351 TYR TYR C . n A 1 22 ALA 22 352 352 ALA ALA C . n A 1 23 TRP 23 353 353 TRP TRP C . n A 1 24 ASN 24 354 354 ASN ASN C . n A 1 25 ARG 25 355 355 ARG ARG C . n A 1 26 LYS 26 356 356 LYS LYS C . n A 1 27 ARG 27 357 357 ARG ARG C . n A 1 28 ILE 28 358 358 ILE ILE C . n A 1 29 SER 29 359 359 SER SER C . n A 1 30 ASN 30 360 360 ASN ASN C . n A 1 31 CYS 31 361 361 CYS CYS C . n A 1 32 VAL 32 362 362 VAL VAL C . n A 1 33 ALA 33 363 363 ALA ALA C . n A 1 34 ASP 34 364 364 ASP ASP C . n A 1 35 TYR 35 365 365 TYR TYR C . n A 1 36 SER 36 366 366 SER SER C . n A 1 37 VAL 37 367 367 VAL VAL C . n A 1 38 LEU 38 368 368 LEU LEU C . n A 1 39 TYR 39 369 369 TYR TYR C . n A 1 40 ASN 40 370 370 ASN ASN C . n A 1 41 LEU 41 371 371 LEU LEU C . n A 1 42 ALA 42 372 372 ALA ALA C . n A 1 43 PRO 43 373 373 PRO PRO C . n A 1 44 PHE 44 374 374 PHE PHE C . n A 1 45 PHE 45 375 375 PHE PHE C . n A 1 46 THR 46 376 376 THR THR C . n A 1 47 PHE 47 377 377 PHE PHE C . n A 1 48 LYS 48 378 378 LYS LYS C . n A 1 49 CYS 49 379 379 CYS CYS C . n A 1 50 TYR 50 380 380 TYR TYR C . n A 1 51 GLY 51 381 381 GLY GLY C . n A 1 52 VAL 52 382 382 VAL VAL C . n A 1 53 SER 53 383 383 SER SER C . n A 1 54 PRO 54 384 384 PRO PRO C . n A 1 55 THR 55 385 385 THR THR C . n A 1 56 LYS 56 386 386 LYS LYS C . n A 1 57 LEU 57 387 387 LEU LEU C . n A 1 58 ASN 58 388 388 ASN ASN C . n A 1 59 ASP 59 389 389 ASP ASP C . n A 1 60 LEU 60 390 390 LEU LEU C . n A 1 61 CYS 61 391 391 CYS CYS C . n A 1 62 PHE 62 392 392 PHE PHE C . n A 1 63 THR 63 393 393 THR THR C . n A 1 64 ASN 64 394 394 ASN ASN C . n A 1 65 VAL 65 395 395 VAL VAL C . n A 1 66 TYR 66 396 396 TYR TYR C . n A 1 67 ALA 67 397 397 ALA ALA C . n A 1 68 ASP 68 398 398 ASP ASP C . n A 1 69 SER 69 399 399 SER SER C . n A 1 70 PHE 70 400 400 PHE PHE C . n A 1 71 VAL 71 401 401 VAL VAL C . n A 1 72 ILE 72 402 402 ILE ILE C . n A 1 73 ARG 73 403 403 ARG ARG C . n A 1 74 GLY 74 404 404 GLY GLY C . n A 1 75 ASP 75 405 405 ASP ASP C . n A 1 76 GLU 76 406 406 GLU GLU C . n A 1 77 VAL 77 407 407 VAL VAL C . n A 1 78 ARG 78 408 408 ARG ARG C . n A 1 79 GLN 79 409 409 GLN GLN C . n A 1 80 ILE 80 410 410 ILE ILE C . n A 1 81 ALA 81 411 411 ALA ALA C . n A 1 82 PRO 82 412 412 PRO PRO C . n A 1 83 GLY 83 413 413 GLY GLY C . n A 1 84 GLN 84 414 414 GLN GLN C . n A 1 85 THR 85 415 415 THR THR C . n A 1 86 GLY 86 416 416 GLY GLY C . n A 1 87 ASN 87 417 417 ASN ASN C . n A 1 88 ILE 88 418 418 ILE ILE C . n A 1 89 ALA 89 419 419 ALA ALA C . n A 1 90 ASP 90 420 420 ASP ASP C . n A 1 91 TYR 91 421 421 TYR TYR C . n A 1 92 ASN 92 422 422 ASN ASN C . n A 1 93 TYR 93 423 423 TYR TYR C . n A 1 94 LYS 94 424 424 LYS LYS C . n A 1 95 LEU 95 425 425 LEU LEU C . n A 1 96 PRO 96 426 426 PRO PRO C . n A 1 97 ASP 97 427 427 ASP ASP C . n A 1 98 ASP 98 428 428 ASP ASP C . n A 1 99 PHE 99 429 429 PHE PHE C . n A 1 100 THR 100 430 430 THR THR C . n A 1 101 GLY 101 431 431 GLY GLY C . n A 1 102 CYS 102 432 432 CYS CYS C . n A 1 103 VAL 103 433 433 VAL VAL C . n A 1 104 ILE 104 434 434 ILE ILE C . n A 1 105 ALA 105 435 435 ALA ALA C . n A 1 106 TRP 106 436 436 TRP TRP C . n A 1 107 ASN 107 437 437 ASN ASN C . n A 1 108 SER 108 438 438 SER SER C . n A 1 109 ASN 109 439 439 ASN ASN C . n A 1 110 LYS 110 440 440 LYS LYS C . n A 1 111 LEU 111 441 441 LEU LEU C . n A 1 112 ASP 112 442 442 ASP ASP C . n A 1 113 SER 113 443 443 SER SER C . n A 1 114 LYS 114 444 444 LYS LYS C . n A 1 115 VAL 115 445 445 VAL VAL C . n A 1 116 SER 116 446 446 SER SER C . n A 1 117 GLY 117 447 447 GLY GLY C . n A 1 118 ASN 118 448 448 ASN ASN C . n A 1 119 TYR 119 449 449 TYR TYR C . n A 1 120 ASN 120 450 450 ASN ASN C . n A 1 121 TYR 121 451 451 TYR TYR C . n A 1 122 LEU 122 452 452 LEU LEU C . n A 1 123 TYR 123 453 453 TYR TYR C . n A 1 124 ARG 124 454 454 ARG ARG C . n A 1 125 LEU 125 455 455 LEU LEU C . n A 1 126 PHE 126 456 456 PHE PHE C . n A 1 127 ARG 127 457 457 ARG ARG C . n A 1 128 LYS 128 458 458 LYS LYS C . n A 1 129 SER 129 459 459 SER SER C . n A 1 130 ASN 130 460 460 ASN ASN C . n A 1 131 LEU 131 461 461 LEU LEU C . n A 1 132 LYS 132 462 462 LYS LYS C . n A 1 133 PRO 133 463 463 PRO PRO C . n A 1 134 PHE 134 464 464 PHE PHE C . n A 1 135 GLU 135 465 465 GLU GLU C . n A 1 136 ARG 136 466 466 ARG ARG C . n A 1 137 ASP 137 467 467 ASP ASP C . n A 1 138 ILE 138 468 468 ILE ILE C . n A 1 139 SER 139 469 469 SER SER C . n A 1 140 THR 140 470 470 THR THR C . n A 1 141 GLU 141 471 471 GLU GLU C . n A 1 142 ILE 142 472 472 ILE ILE C . n A 1 143 TYR 143 473 473 TYR TYR C . n A 1 144 GLN 144 474 474 GLN GLN C . n A 1 145 ALA 145 475 475 ALA ALA C . n A 1 146 GLY 146 476 476 GLY GLY C . n A 1 147 ASN 147 477 477 ASN ASN C . n A 1 148 LYS 148 478 478 LYS LYS C . n A 1 149 PRO 149 479 479 PRO PRO C . n A 1 150 CYS 150 480 480 CYS CYS C . n A 1 151 ASN 151 481 481 ASN ASN C . n A 1 152 GLY 152 482 482 GLY GLY C . n A 1 153 VAL 153 483 483 VAL VAL C . n A 1 154 ALA 154 484 484 ALA ALA C . n A 1 155 GLY 155 485 485 GLY GLY C . n A 1 156 PHE 156 486 486 PHE PHE C . n A 1 157 ASN 157 487 487 ASN ASN C . n A 1 158 CYS 158 488 488 CYS CYS C . n A 1 159 TYR 159 489 489 TYR TYR C . n A 1 160 PHE 160 490 490 PHE PHE C . n A 1 161 PRO 161 491 491 PRO PRO C . n A 1 162 LEU 162 492 492 LEU LEU C . n A 1 163 ARG 163 493 493 ARG ARG C . n A 1 164 SER 164 494 494 SER SER C . n A 1 165 TYR 165 495 495 TYR TYR C . n A 1 166 SER 166 496 496 SER SER C . n A 1 167 PHE 167 497 497 PHE PHE C . n A 1 168 ARG 168 498 498 ARG ARG C . n A 1 169 PRO 169 499 499 PRO PRO C . n A 1 170 THR 170 500 500 THR THR C . n A 1 171 TYR 171 501 501 TYR TYR C . n A 1 172 GLY 172 502 502 GLY GLY C . n A 1 173 VAL 173 503 503 VAL VAL C . n A 1 174 GLY 174 504 504 GLY GLY C . n A 1 175 HIS 175 505 505 HIS HIS C . n A 1 176 GLN 176 506 506 GLN GLN C . n A 1 177 PRO 177 507 507 PRO PRO C . n A 1 178 TYR 178 508 508 TYR TYR C . n A 1 179 ARG 179 509 509 ARG ARG C . n A 1 180 VAL 180 510 510 VAL VAL C . n A 1 181 VAL 181 511 511 VAL VAL C . n A 1 182 VAL 182 512 512 VAL VAL C . n A 1 183 LEU 183 513 513 LEU LEU C . n A 1 184 SER 184 514 514 SER SER C . n A 1 185 PHE 185 515 515 PHE PHE C . n A 1 186 GLU 186 516 516 GLU GLU C . n A 1 187 LEU 187 517 517 LEU LEU C . n A 1 188 LEU 188 518 518 LEU LEU C . n A 1 189 HIS 189 519 519 HIS HIS C . n A 1 190 ALA 190 520 520 ALA ALA C . n A 1 191 PRO 191 521 521 PRO PRO C . n A 1 192 ALA 192 522 522 ALA ALA C . n A 1 193 THR 193 523 523 THR THR C . n A 1 194 VAL 194 524 524 VAL VAL C . n A 1 195 CYS 195 525 525 CYS CYS C . n A 1 196 GLY 196 526 526 GLY GLY C . n A 1 197 PRO 197 527 527 PRO PRO C . n A 1 198 LYS 198 528 528 LYS LYS C . n B 2 1 GLN 1 1 1 GLN GLN A . n B 2 2 VAL 2 2 2 VAL VAL A . n B 2 3 THR 3 3 3 THR THR A . n B 2 4 LEU 4 4 4 LEU LEU A . n B 2 5 ARG 5 5 5 ARG ARG A . n B 2 6 GLU 6 6 6 GLU GLU A . n B 2 7 SER 7 7 7 SER SER A . n B 2 8 GLY 8 8 8 GLY GLY A . n B 2 9 PRO 9 9 9 PRO PRO A . n B 2 10 THR 10 10 10 THR THR A . n B 2 11 LEU 11 11 11 LEU LEU A . n B 2 12 VAL 12 12 12 VAL VAL A . n B 2 13 LYS 13 13 13 LYS LYS A . n B 2 14 PRO 14 14 14 PRO PRO A . n B 2 15 LYS 15 15 15 LYS LYS A . n B 2 16 GLN 16 16 16 GLN GLN A . n B 2 17 THR 17 17 17 THR THR A . n B 2 18 LEU 18 18 18 LEU LEU A . n B 2 19 THR 19 19 19 THR THR A . n B 2 20 LEU 20 20 20 LEU LEU A . n B 2 21 THR 21 21 21 THR THR A . n B 2 22 CYS 22 22 22 CYS CYS A . n B 2 23 THR 23 23 23 THR THR A . n B 2 24 PHE 24 24 24 PHE PHE A . n B 2 25 SER 25 25 25 SER SER A . n B 2 26 GLY 26 26 26 GLY GLY A . n B 2 27 PHE 27 27 27 PHE PHE A . n B 2 28 SER 28 28 28 SER SER A . n B 2 29 LEU 29 29 29 LEU LEU A . n B 2 30 SER 30 30 30 SER SER A . n B 2 31 THR 31 31 31 THR THR A . n B 2 32 PRO 32 32 32 PRO PRO A . n B 2 33 GLY 33 33 33 GLY GLY A . n B 2 34 GLY 34 34 34 GLY GLY A . n B 2 35 GLY 35 35 35 GLY GLY A . n B 2 36 VAL 36 36 36 VAL VAL A . n B 2 37 GLY 37 37 37 GLY GLY A . n B 2 38 TRP 38 38 38 TRP TRP A . n B 2 39 ILE 39 39 39 ILE ILE A . n B 2 40 ARG 40 40 40 ARG ARG A . n B 2 41 GLN 41 41 41 GLN GLN A . n B 2 42 PRO 42 42 42 PRO PRO A . n B 2 43 PRO 43 43 43 PRO PRO A . n B 2 44 GLY 44 44 44 GLY GLY A . n B 2 45 LYS 45 45 45 LYS LYS A . n B 2 46 ALA 46 46 46 ALA ALA A . n B 2 47 LEU 47 47 47 LEU LEU A . n B 2 48 GLU 48 48 48 GLU GLU A . n B 2 49 TRP 49 49 49 TRP TRP A . n B 2 50 LEU 50 50 50 LEU LEU A . n B 2 51 ALA 51 51 51 ALA ALA A . n B 2 52 LEU 52 52 52 LEU LEU A . n B 2 53 ILE 53 53 53 ILE ILE A . n B 2 54 TYR 54 54 54 TYR TYR A . n B 2 55 TRP 55 55 55 TRP TRP A . n B 2 56 ASP 56 56 56 ASP ASP A . n B 2 57 ASP 57 57 57 ASP ASP A . n B 2 58 ASP 58 58 58 ASP ASP A . n B 2 59 LYS 59 59 59 LYS LYS A . n B 2 60 ARG 60 60 60 ARG ARG A . n B 2 61 TYR 61 61 61 TYR TYR A . n B 2 62 SER 62 62 62 SER SER A . n B 2 63 PRO 63 63 63 PRO PRO A . n B 2 64 SER 64 64 64 SER SER A . n B 2 65 LEU 65 65 65 LEU LEU A . n B 2 66 LYS 66 66 66 LYS LYS A . n B 2 67 SER 67 67 67 SER SER A . n B 2 68 SER 68 68 68 SER SER A . n B 2 69 LEU 69 69 69 LEU LEU A . n B 2 70 THR 70 70 70 THR THR A . n B 2 71 ILE 71 71 71 ILE ILE A . n B 2 72 THR 72 72 72 THR THR A . n B 2 73 LYS 73 73 73 LYS LYS A . n B 2 74 ASP 74 74 74 ASP ASP A . n B 2 75 THR 75 75 75 THR THR A . n B 2 76 SER 76 76 76 SER SER A . n B 2 77 LYS 77 77 77 LYS LYS A . n B 2 78 ASN 78 78 78 ASN ASN A . n B 2 79 GLN 79 79 79 GLN GLN A . n B 2 80 VAL 80 80 80 VAL VAL A . n B 2 81 VAL 81 81 81 VAL VAL A . n B 2 82 LEU 82 82 82 LEU LEU A . n B 2 83 THR 83 83 83 THR THR A . n B 2 84 MET 84 84 84 MET MET A . n B 2 85 THR 85 85 85 THR THR A . n B 2 86 ASN 86 86 86 ASN ASN A . n B 2 87 MET 87 87 87 MET MET A . n B 2 88 ASP 88 88 88 ASP ASP A . n B 2 89 PRO 89 89 89 PRO PRO A . n B 2 90 VAL 90 90 90 VAL VAL A . n B 2 91 ASP 91 91 91 ASP ASP A . n B 2 92 THR 92 92 92 THR THR A . n B 2 93 ALA 93 93 93 ALA ALA A . n B 2 94 THR 94 94 94 THR THR A . n B 2 95 TYR 95 95 95 TYR TYR A . n B 2 96 TYR 96 96 96 TYR TYR A . n B 2 97 CYS 97 97 97 CYS CYS A . n B 2 98 ALA 98 98 98 ALA ALA A . n B 2 99 ARG 99 99 99 ARG ARG A . n B 2 100 LEU 100 100 100 LEU LEU A . n B 2 101 THR 101 101 101 THR THR A . n B 2 102 ALA 102 102 102 ALA ALA A . n B 2 103 ALA 103 103 103 ALA ALA A . n B 2 104 ASP 104 104 104 ASP ASP A . n B 2 105 THR 105 105 105 THR THR A . n B 2 106 ILE 106 106 106 ILE ILE A . n B 2 107 PHE 107 107 107 PHE PHE A . n B 2 108 ASP 108 108 108 ASP ASP A . n B 2 109 CYS 109 109 109 CYS CYS A . n B 2 110 TRP 110 110 110 TRP TRP A . n B 2 111 GLY 111 111 111 GLY GLY A . n B 2 112 GLN 112 112 112 GLN GLN A . n B 2 113 GLY 113 113 113 GLY GLY A . n B 2 114 THR 114 114 114 THR THR A . n B 2 115 LEU 115 115 115 LEU LEU A . n B 2 116 VAL 116 116 116 VAL VAL A . n B 2 117 THR 117 117 117 THR THR A . n B 2 118 VAL 118 118 118 VAL VAL A . n B 2 119 SER 119 119 119 SER SER A . n B 2 120 SER 120 120 120 SER SER A . n B 2 121 ALA 121 121 121 ALA ALA A . n B 2 122 SER 122 122 122 SER SER A . n C 3 1 ALA 1 3 3 ALA ALA B . n C 3 2 LEU 2 4 4 LEU LEU B . n C 3 3 THR 3 5 5 THR THR B . n C 3 4 GLN 4 6 6 GLN GLN B . n C 3 5 PRO 5 7 7 PRO PRO B . n C 3 6 ALA 6 8 8 ALA ALA B . n C 3 7 SER 7 9 9 SER SER B . n C 3 8 VAL 8 10 10 VAL VAL B . n C 3 9 SER 9 11 11 SER SER B . n C 3 10 GLY 10 12 12 GLY GLY B . n C 3 11 SER 11 13 13 SER SER B . n C 3 12 PRO 12 14 14 PRO PRO B . n C 3 13 GLY 13 15 15 GLY GLY B . n C 3 14 LEU 14 16 16 LEU LEU B . n C 3 15 SER 15 17 17 SER SER B . n C 3 16 ILE 16 18 18 ILE ILE B . n C 3 17 THR 17 19 19 THR THR B . n C 3 18 ILE 18 20 20 ILE ILE B . n C 3 19 SER 19 21 21 SER SER B . n C 3 20 CYS 20 22 22 CYS CYS B . n C 3 21 THR 21 23 23 THR THR B . n C 3 22 ALA 22 24 24 ALA ALA B . n C 3 23 THR 23 25 25 THR THR B . n C 3 24 SER 24 26 26 SER SER B . n C 3 25 SER 25 27 27 SER SER B . n C 3 26 ASP 26 28 28 ASP ASP B . n C 3 27 VAL 27 29 29 VAL VAL B . n C 3 28 GLY 28 30 30 GLY GLY B . n C 3 29 ALA 29 31 31 ALA ALA B . n C 3 30 TYR 30 32 32 TYR TYR B . n C 3 31 ASN 31 33 33 ASN ASN B . n C 3 32 TYR 32 34 34 TYR TYR B . n C 3 33 VAL 33 35 35 VAL VAL B . n C 3 34 SER 34 36 36 SER SER B . n C 3 35 TRP 35 37 37 TRP TRP B . n C 3 36 TYR 36 38 38 TYR TYR B . n C 3 37 GLN 37 39 39 GLN GLN B . n C 3 38 GLN 38 40 40 GLN GLN B . n C 3 39 HIS 39 41 41 HIS HIS B . n C 3 40 PRO 40 42 42 PRO PRO B . n C 3 41 GLY 41 43 43 GLY GLY B . n C 3 42 GLN 42 44 44 GLN GLN B . n C 3 43 ALA 43 45 45 ALA ALA B . n C 3 44 PRO 44 46 46 PRO PRO B . n C 3 45 LYS 45 47 47 LYS LYS B . n C 3 46 LEU 46 48 48 LEU LEU B . n C 3 47 MET 47 49 49 MET MET B . n C 3 48 ILE 48 50 50 ILE ILE B . n C 3 49 TYR 49 51 51 TYR TYR B . n C 3 50 ASP 50 52 52 ASP ASP B . n C 3 51 VAL 51 53 53 VAL VAL B . n C 3 52 SER 52 54 54 SER SER B . n C 3 53 LYS 53 55 55 LYS LYS B . n C 3 54 ARG 54 56 56 ARG ARG B . n C 3 55 PRO 55 57 57 PRO PRO B . n C 3 56 SER 56 58 58 SER SER B . n C 3 57 GLY 57 59 59 GLY GLY B . n C 3 58 VAL 58 60 60 VAL VAL B . n C 3 59 SER 59 61 61 SER SER B . n C 3 60 ASN 60 62 62 ASN ASN B . n C 3 61 ARG 61 63 63 ARG ARG B . n C 3 62 PHE 62 64 64 PHE PHE B . n C 3 63 SER 63 65 65 SER SER B . n C 3 64 GLY 64 66 66 GLY GLY B . n C 3 65 SER 65 67 67 SER SER B . n C 3 66 LYS 66 68 68 LYS LYS B . n C 3 67 SER 67 69 69 SER SER B . n C 3 68 ALA 68 70 70 ALA ALA B . n C 3 69 ASN 69 71 71 ASN ASN B . n C 3 70 THR 70 72 72 THR THR B . n C 3 71 ALA 71 73 73 ALA ALA B . n C 3 72 SER 72 74 74 SER SER B . n C 3 73 LEU 73 75 75 LEU LEU B . n C 3 74 THR 74 76 76 THR THR B . n C 3 75 ILE 75 77 77 ILE ILE B . n C 3 76 SER 76 78 78 SER SER B . n C 3 77 GLY 77 79 79 GLY GLY B . n C 3 78 LEU 78 80 80 LEU LEU B . n C 3 79 GLN 79 81 81 GLN GLN B . n C 3 80 ALA 80 82 82 ALA ALA B . n C 3 81 GLU 81 83 83 GLU GLU B . n C 3 82 ASP 82 84 84 ASP ASP B . n C 3 83 GLU 83 85 85 GLU GLU B . n C 3 84 ALA 84 86 86 ALA ALA B . n C 3 85 ASP 85 87 87 ASP ASP B . n C 3 86 TYR 86 88 88 TYR TYR B . n C 3 87 TYR 87 89 89 TYR TYR B . n C 3 88 CYS 88 90 90 CYS CYS B . n C 3 89 SER 89 91 91 SER SER B . n C 3 90 SER 90 92 92 SER SER B . n C 3 91 TYR 91 93 93 TYR TYR B . n C 3 92 THR 92 94 94 THR THR B . n C 3 93 THR 93 95 95 THR THR B . n C 3 94 THR 94 96 96 THR THR B . n C 3 95 SER 95 97 97 SER SER B . n C 3 96 VAL 96 98 98 VAL VAL B . n C 3 97 VAL 97 99 99 VAL VAL B . n C 3 98 PHE 98 100 100 PHE PHE B . n C 3 99 GLY 99 101 101 GLY GLY B . n C 3 100 GLY 100 102 102 GLY GLY B . n C 3 101 GLY 101 103 103 GLY GLY B . n C 3 102 THR 102 104 104 THR THR B . n C 3 103 LYS 103 105 105 LYS LYS B . n C 3 104 LEU 104 106 106 LEU LEU B . n C 3 105 THR 105 107 107 THR THR B . n C 3 106 VAL 106 108 108 VAL VAL B . n C 3 107 LEU 107 109 109 LEU LEU B . n C 3 108 GLY 108 110 110 GLY GLY B . n # loop_ _pdbx_contact_author.id _pdbx_contact_author.email _pdbx_contact_author.name_first _pdbx_contact_author.name_last _pdbx_contact_author.name_mi _pdbx_contact_author.role _pdbx_contact_author.identifier_ORCID 3 ZhenguoChen@fudan.edu.cn Zhenguo Chen ? 'principal investigator/group leader' 0000-0003-4748-9299 4 llsun@fudan.edu.cn Lei Sun ? 'principal investigator/group leader' 0000-0001-8741-0202 # _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 # _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 2023-07-12 # _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 1.17.1_3660: _software.pdbx_ordinal 1 # _em_3d_fitting.entry_id 7YD1 _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 7YD1 _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 313560 _em_3d_reconstruction.resolution 2.99 _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 'Omicron RBD with XG005' _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 7YD1 _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 'BRIGHT FIELD' _em_imaging.nominal_cs ? _em_imaging.nominal_defocus_max 2500 _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 7YD1 _em_vitrification.citation_id ? _em_vitrification.method ? _em_vitrification.temp ? _em_vitrification.time_resolved_state ? # _em_experiment.entry_id 7YD1 _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 ILE C 332 ? ? -125.69 -50.78 2 1 ALA C 348 ? ? -178.85 -179.71 3 1 SER C 383 ? ? 54.23 75.78 4 1 LEU C 390 ? ? -160.99 119.36 5 1 GLN C 414 ? ? -171.05 148.31 6 1 ASP C 427 ? ? -88.66 44.85 7 1 ASP C 428 ? ? -142.03 17.05 8 1 PRO A 89 ? ? -76.06 45.00 9 1 ASP B 52 ? ? -35.50 137.45 10 1 ALA B 70 ? ? -121.55 -57.26 11 1 ASN B 71 ? ? -142.23 18.81 12 1 GLU B 83 ? ? -91.12 53.49 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 C THR 333 ? OG1 ? A THR 3 OG1 2 1 Y 1 C THR 333 ? CG2 ? A THR 3 CG2 # _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_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 ? # loop_ _em_entity_assembly_recombinant.id _em_entity_assembly_recombinant.entity_assembly_id _em_entity_assembly_recombinant.cell _em_entity_assembly_recombinant.ncbi_tax_id _em_entity_assembly_recombinant.organism _em_entity_assembly_recombinant.plasmid _em_entity_assembly_recombinant.strain 2 1 ? 9606 'Homo sapiens' ? ? 3 1 ? 9606 'Homo sapiens' ? ? # _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 61 _em_image_recording.average_exposure_time ? _em_image_recording.details ? _em_image_recording.detector_mode ? _em_image_recording.film_or_detector_model 'GATAN K3 BIOQUANTUM (6k 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 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 'Ministry of Science and Technology (MoST, China)' _pdbx_audit_support.country China _pdbx_audit_support.grant_number 2021YFC2302500 _pdbx_audit_support.ordinal 1 # _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 ? #