data_7TPK # _entry.id 7TPK # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.366 _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 7TPK pdb_00007tpk 10.2210/pdb7tpk/pdb WWPDB D_1000262714 ? ? EMDB EMD-26058 ? ? # _pdbx_database_related.db_name EMDB _pdbx_database_related.details 'SARS-CoV-2 E406W mutant RBD - Local Refinement' _pdbx_database_related.db_id EMD-26058 _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 7TPK _pdbx_database_status.recvd_initial_deposition_date 2022-01-25 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Addetia, A.' 1 ? 'Veesler, D.' 2 ? # _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 'SARS-CoV-2 E406W mutant RBD - Local Refinement' _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 'Addetia, A.' 1 ? primary 'Veesler, D.' 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 7TPK _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 7TPK _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' 21833.477 1 ? E406W 'Receptor-binding domain' ? 2 non-polymer syn 2-acetamido-2-deoxy-beta-D-glucopyranose 221.208 1 ? ? ? ? # _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 ;TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDWVRQIAP GQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPL QSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCG ; _entity_poly.pdbx_seq_one_letter_code_can ;TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDWVRQIAP GQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPL QSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCG ; _entity_poly.pdbx_strand_id E _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 ASN n 1 3 LEU n 1 4 CYS n 1 5 PRO n 1 6 PHE n 1 7 GLY n 1 8 GLU n 1 9 VAL n 1 10 PHE n 1 11 ASN n 1 12 ALA n 1 13 THR n 1 14 ARG n 1 15 PHE n 1 16 ALA n 1 17 SER n 1 18 VAL n 1 19 TYR n 1 20 ALA n 1 21 TRP n 1 22 ASN n 1 23 ARG n 1 24 LYS n 1 25 ARG n 1 26 ILE n 1 27 SER n 1 28 ASN n 1 29 CYS n 1 30 VAL n 1 31 ALA n 1 32 ASP n 1 33 TYR n 1 34 SER n 1 35 VAL n 1 36 LEU n 1 37 TYR n 1 38 ASN n 1 39 SER n 1 40 ALA n 1 41 SER n 1 42 PHE n 1 43 SER n 1 44 THR n 1 45 PHE n 1 46 LYS n 1 47 CYS n 1 48 TYR n 1 49 GLY n 1 50 VAL n 1 51 SER n 1 52 PRO n 1 53 THR n 1 54 LYS n 1 55 LEU n 1 56 ASN n 1 57 ASP n 1 58 LEU n 1 59 CYS n 1 60 PHE n 1 61 THR n 1 62 ASN n 1 63 VAL n 1 64 TYR n 1 65 ALA n 1 66 ASP n 1 67 SER n 1 68 PHE n 1 69 VAL n 1 70 ILE n 1 71 ARG n 1 72 GLY n 1 73 ASP n 1 74 TRP n 1 75 VAL n 1 76 ARG n 1 77 GLN n 1 78 ILE n 1 79 ALA n 1 80 PRO n 1 81 GLY n 1 82 GLN n 1 83 THR n 1 84 GLY n 1 85 LYS n 1 86 ILE n 1 87 ALA n 1 88 ASP n 1 89 TYR n 1 90 ASN n 1 91 TYR n 1 92 LYS n 1 93 LEU n 1 94 PRO n 1 95 ASP n 1 96 ASP n 1 97 PHE n 1 98 THR n 1 99 GLY n 1 100 CYS n 1 101 VAL n 1 102 ILE n 1 103 ALA n 1 104 TRP n 1 105 ASN n 1 106 SER n 1 107 ASN n 1 108 ASN n 1 109 LEU n 1 110 ASP n 1 111 SER n 1 112 LYS n 1 113 VAL n 1 114 GLY n 1 115 GLY n 1 116 ASN n 1 117 TYR n 1 118 ASN n 1 119 TYR n 1 120 LEU n 1 121 TYR n 1 122 ARG n 1 123 LEU n 1 124 PHE n 1 125 ARG n 1 126 LYS n 1 127 SER n 1 128 ASN n 1 129 LEU n 1 130 LYS n 1 131 PRO n 1 132 PHE n 1 133 GLU n 1 134 ARG n 1 135 ASP n 1 136 ILE n 1 137 SER n 1 138 THR n 1 139 GLU n 1 140 ILE n 1 141 TYR n 1 142 GLN n 1 143 ALA n 1 144 GLY n 1 145 SER n 1 146 THR n 1 147 PRO n 1 148 CYS n 1 149 ASN n 1 150 GLY n 1 151 VAL n 1 152 GLU n 1 153 GLY n 1 154 PHE n 1 155 ASN n 1 156 CYS n 1 157 TYR n 1 158 PHE n 1 159 PRO n 1 160 LEU n 1 161 GLN n 1 162 SER n 1 163 TYR n 1 164 GLY n 1 165 PHE n 1 166 GLN n 1 167 PRO n 1 168 THR n 1 169 ASN n 1 170 GLY n 1 171 VAL n 1 172 GLY n 1 173 TYR n 1 174 GLN n 1 175 PRO n 1 176 TYR n 1 177 ARG n 1 178 VAL n 1 179 VAL n 1 180 VAL n 1 181 LEU n 1 182 SER n 1 183 PHE n 1 184 GLU n 1 185 LEU n 1 186 LEU n 1 187 HIS n 1 188 ALA n 1 189 PRO n 1 190 ALA n 1 191 THR n 1 192 VAL n 1 193 CYS n 1 194 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 194 _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 ? # _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 ;TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAP GQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPL QSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCG ; _struct_ref.pdbx_align_begin 333 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 7TPK _struct_ref_seq.pdbx_strand_id E _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 194 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P0DTC2 _struct_ref_seq.db_align_beg 333 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 526 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 333 _struct_ref_seq.pdbx_auth_seq_align_end 526 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 7TPK _struct_ref_seq_dif.mon_id TRP _struct_ref_seq_dif.pdbx_pdb_strand_id E _struct_ref_seq_dif.seq_num 74 _struct_ref_seq_dif.pdbx_pdb_ins_code ? _struct_ref_seq_dif.pdbx_seq_db_name UNP _struct_ref_seq_dif.pdbx_seq_db_accession_code P0DTC2 _struct_ref_seq_dif.db_mon_id GLU _struct_ref_seq_dif.pdbx_seq_db_seq_num 406 _struct_ref_seq_dif.details 'engineered mutation' _struct_ref_seq_dif.pdbx_auth_seq_num 406 _struct_ref_seq_dif.pdbx_ordinal 1 # 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 7TPK _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _struct.entry_id 7TPK _struct.title 'SARS-CoV-2 E406W mutant RBD - Local Refinement' _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 7TPK _struct_keywords.text 'viral entry protein, viral glycoprotein, 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 ? # 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 6 ? ASN A 11 ? PHE E 338 ASN E 343 1 ? 6 HELX_P HELX_P2 AA2 SER A 17 ? TRP A 21 ? SER E 349 TRP E 353 5 ? 5 HELX_P HELX_P3 AA3 TYR A 33 ? ASN A 38 ? TYR E 365 ASN E 370 1 ? 6 HELX_P HELX_P4 AA4 LYS A 54 ? ASP A 57 ? LYS E 386 ASP E 389 5 ? 4 HELX_P HELX_P5 AA5 ASP A 73 ? ILE A 78 ? ASP E 405 ILE E 410 5 ? 6 HELX_P HELX_P6 AA6 GLY A 84 ? ASN A 90 ? GLY E 416 ASN E 422 1 ? 7 # _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 4 SG ? ? ? 1_555 A CYS 29 SG ? ? E CYS 336 E CYS 361 1_555 ? ? ? ? ? ? ? 2.027 ? ? disulf2 disulf ? ? A CYS 47 SG ? ? ? 1_555 A CYS 100 SG ? ? E CYS 379 E CYS 432 1_555 ? ? ? ? ? ? ? 2.051 ? ? disulf3 disulf ? ? A CYS 59 SG ? ? ? 1_555 A CYS 193 SG ? ? E CYS 391 E CYS 525 1_555 ? ? ? ? ? ? ? 2.111 ? ? disulf4 disulf ? ? A CYS 148 SG ? ? ? 1_555 A CYS 156 SG ? ? E CYS 480 E CYS 488 1_555 ? ? ? ? ? ? ? 2.091 ? ? covale1 covale one ? A ASN 11 ND2 ? ? ? 1_555 B NAG . C1 ? ? E ASN 343 E NAG 601 1_555 ? ? ? ? ? ? ? 1.491 ? 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 ? 5 ? AA2 ? 3 ? AA3 ? 2 ? AA4 ? 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 AA1 4 5 ? anti-parallel AA2 1 2 ? parallel AA2 2 3 ? anti-parallel AA3 1 2 ? anti-parallel AA4 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 22 ? ILE A 26 ? ASN E 354 ILE E 358 AA1 2 ASN A 62 ? ARG A 71 ? ASN E 394 ARG E 403 AA1 3 PRO A 175 ? GLU A 184 ? PRO E 507 GLU E 516 AA1 4 GLY A 99 ? ASN A 105 ? GLY E 431 ASN E 437 AA1 5 THR A 44 ? TYR A 48 ? THR E 376 TYR E 380 AA2 1 CYS A 29 ? VAL A 30 ? CYS E 361 VAL E 362 AA2 2 VAL A 192 ? CYS A 193 ? VAL E 524 CYS E 525 AA2 3 CYS A 59 ? PHE A 60 ? CYS E 391 PHE E 392 AA3 1 LEU A 120 ? ARG A 122 ? LEU E 452 ARG E 454 AA3 2 LEU A 160 ? SER A 162 ? LEU E 492 SER E 494 AA4 1 TYR A 141 ? GLN A 142 ? TYR E 473 GLN E 474 AA4 2 CYS A 156 ? TYR A 157 ? CYS E 488 TYR E 489 # 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 26 ? N ILE E 358 O VAL A 63 ? O VAL E 395 AA1 2 3 N TYR A 64 ? N TYR E 396 O SER A 182 ? O SER E 514 AA1 3 4 O LEU A 181 ? O LEU E 513 N CYS A 100 ? N CYS E 432 AA1 4 5 O GLY A 99 ? O GLY E 431 N TYR A 48 ? N TYR E 380 AA2 1 2 N CYS A 29 ? N CYS E 361 O CYS A 193 ? O CYS E 525 AA2 2 3 O VAL A 192 ? O VAL E 524 N PHE A 60 ? N PHE E 392 AA3 1 2 N TYR A 121 ? N TYR E 453 O GLN A 161 ? O GLN E 493 AA4 1 2 N TYR A 141 ? N TYR E 473 O TYR A 157 ? O TYR E 489 # _atom_sites.entry_id 7TPK _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 1 333 333 THR THR E . n A 1 2 ASN 2 334 334 ASN ASN E . n A 1 3 LEU 3 335 335 LEU LEU E . n A 1 4 CYS 4 336 336 CYS CYS E . n A 1 5 PRO 5 337 337 PRO PRO E . n A 1 6 PHE 6 338 338 PHE PHE E . n A 1 7 GLY 7 339 339 GLY GLY E . n A 1 8 GLU 8 340 340 GLU GLU E . n A 1 9 VAL 9 341 341 VAL VAL E . n A 1 10 PHE 10 342 342 PHE PHE E . n A 1 11 ASN 11 343 343 ASN ASN E . n A 1 12 ALA 12 344 344 ALA ALA E . n A 1 13 THR 13 345 345 THR THR E . n A 1 14 ARG 14 346 346 ARG ARG E . n A 1 15 PHE 15 347 347 PHE PHE E . n A 1 16 ALA 16 348 348 ALA ALA E . n A 1 17 SER 17 349 349 SER SER E . n A 1 18 VAL 18 350 350 VAL VAL E . n A 1 19 TYR 19 351 351 TYR TYR E . n A 1 20 ALA 20 352 352 ALA ALA E . n A 1 21 TRP 21 353 353 TRP TRP E . n A 1 22 ASN 22 354 354 ASN ASN E . n A 1 23 ARG 23 355 355 ARG ARG E . n A 1 24 LYS 24 356 356 LYS LYS E . n A 1 25 ARG 25 357 357 ARG ARG E . n A 1 26 ILE 26 358 358 ILE ILE E . n A 1 27 SER 27 359 359 SER SER E . n A 1 28 ASN 28 360 360 ASN ASN E . n A 1 29 CYS 29 361 361 CYS CYS E . n A 1 30 VAL 30 362 362 VAL VAL E . n A 1 31 ALA 31 363 363 ALA ALA E . n A 1 32 ASP 32 364 364 ASP ASP E . n A 1 33 TYR 33 365 365 TYR TYR E . n A 1 34 SER 34 366 366 SER SER E . n A 1 35 VAL 35 367 367 VAL VAL E . n A 1 36 LEU 36 368 368 LEU LEU E . n A 1 37 TYR 37 369 369 TYR TYR E . n A 1 38 ASN 38 370 370 ASN ASN E . n A 1 39 SER 39 371 371 SER SER E . n A 1 40 ALA 40 372 372 ALA ALA E . n A 1 41 SER 41 373 373 SER SER E . n A 1 42 PHE 42 374 374 PHE PHE E . n A 1 43 SER 43 375 375 SER SER E . n A 1 44 THR 44 376 376 THR THR E . n A 1 45 PHE 45 377 377 PHE PHE E . n A 1 46 LYS 46 378 378 LYS LYS E . n A 1 47 CYS 47 379 379 CYS CYS E . n A 1 48 TYR 48 380 380 TYR TYR E . n A 1 49 GLY 49 381 381 GLY GLY E . n A 1 50 VAL 50 382 382 VAL VAL E . n A 1 51 SER 51 383 383 SER SER E . n A 1 52 PRO 52 384 384 PRO PRO E . n A 1 53 THR 53 385 385 THR THR E . n A 1 54 LYS 54 386 386 LYS LYS E . n A 1 55 LEU 55 387 387 LEU LEU E . n A 1 56 ASN 56 388 388 ASN ASN E . n A 1 57 ASP 57 389 389 ASP ASP E . n A 1 58 LEU 58 390 390 LEU LEU E . n A 1 59 CYS 59 391 391 CYS CYS E . n A 1 60 PHE 60 392 392 PHE PHE E . n A 1 61 THR 61 393 393 THR THR E . n A 1 62 ASN 62 394 394 ASN ASN E . n A 1 63 VAL 63 395 395 VAL VAL E . n A 1 64 TYR 64 396 396 TYR TYR E . n A 1 65 ALA 65 397 397 ALA ALA E . n A 1 66 ASP 66 398 398 ASP ASP E . n A 1 67 SER 67 399 399 SER SER E . n A 1 68 PHE 68 400 400 PHE PHE E . n A 1 69 VAL 69 401 401 VAL VAL E . n A 1 70 ILE 70 402 402 ILE ILE E . n A 1 71 ARG 71 403 403 ARG ARG E . n A 1 72 GLY 72 404 404 GLY GLY E . n A 1 73 ASP 73 405 405 ASP ASP E . n A 1 74 TRP 74 406 406 TRP TRP E . n A 1 75 VAL 75 407 407 VAL VAL E . n A 1 76 ARG 76 408 408 ARG ARG E . n A 1 77 GLN 77 409 409 GLN GLN E . n A 1 78 ILE 78 410 410 ILE ILE E . n A 1 79 ALA 79 411 411 ALA ALA E . n A 1 80 PRO 80 412 412 PRO PRO E . n A 1 81 GLY 81 413 413 GLY GLY E . n A 1 82 GLN 82 414 414 GLN GLN E . n A 1 83 THR 83 415 415 THR THR E . n A 1 84 GLY 84 416 416 GLY GLY E . n A 1 85 LYS 85 417 417 LYS LYS E . n A 1 86 ILE 86 418 418 ILE ILE E . n A 1 87 ALA 87 419 419 ALA ALA E . n A 1 88 ASP 88 420 420 ASP ASP E . n A 1 89 TYR 89 421 421 TYR TYR E . n A 1 90 ASN 90 422 422 ASN ASN E . n A 1 91 TYR 91 423 423 TYR TYR E . n A 1 92 LYS 92 424 424 LYS LYS E . n A 1 93 LEU 93 425 425 LEU LEU E . n A 1 94 PRO 94 426 426 PRO PRO E . n A 1 95 ASP 95 427 427 ASP ASP E . n A 1 96 ASP 96 428 428 ASP ASP E . n A 1 97 PHE 97 429 429 PHE PHE E . n A 1 98 THR 98 430 430 THR THR E . n A 1 99 GLY 99 431 431 GLY GLY E . n A 1 100 CYS 100 432 432 CYS CYS E . n A 1 101 VAL 101 433 433 VAL VAL E . n A 1 102 ILE 102 434 434 ILE ILE E . n A 1 103 ALA 103 435 435 ALA ALA E . n A 1 104 TRP 104 436 436 TRP TRP E . n A 1 105 ASN 105 437 437 ASN ASN E . n A 1 106 SER 106 438 438 SER SER E . n A 1 107 ASN 107 439 439 ASN ASN E . n A 1 108 ASN 108 440 440 ASN ASN E . n A 1 109 LEU 109 441 441 LEU LEU E . n A 1 110 ASP 110 442 442 ASP ASP E . n A 1 111 SER 111 443 443 SER SER E . n A 1 112 LYS 112 444 444 LYS LYS E . n A 1 113 VAL 113 445 445 VAL VAL E . n A 1 114 GLY 114 446 446 GLY GLY E . n A 1 115 GLY 115 447 447 GLY GLY E . n A 1 116 ASN 116 448 448 ASN ASN E . n A 1 117 TYR 117 449 449 TYR TYR E . n A 1 118 ASN 118 450 450 ASN ASN E . n A 1 119 TYR 119 451 451 TYR TYR E . n A 1 120 LEU 120 452 452 LEU LEU E . n A 1 121 TYR 121 453 453 TYR TYR E . n A 1 122 ARG 122 454 454 ARG ARG E . n A 1 123 LEU 123 455 455 LEU LEU E . n A 1 124 PHE 124 456 456 PHE PHE E . n A 1 125 ARG 125 457 457 ARG ARG E . n A 1 126 LYS 126 458 458 LYS LYS E . n A 1 127 SER 127 459 459 SER SER E . n A 1 128 ASN 128 460 460 ASN ASN E . n A 1 129 LEU 129 461 461 LEU LEU E . n A 1 130 LYS 130 462 462 LYS LYS E . n A 1 131 PRO 131 463 463 PRO PRO E . n A 1 132 PHE 132 464 464 PHE PHE E . n A 1 133 GLU 133 465 465 GLU GLU E . n A 1 134 ARG 134 466 466 ARG ARG E . n A 1 135 ASP 135 467 467 ASP ASP E . n A 1 136 ILE 136 468 468 ILE ILE E . n A 1 137 SER 137 469 469 SER SER E . n A 1 138 THR 138 470 470 THR THR E . n A 1 139 GLU 139 471 471 GLU GLU E . n A 1 140 ILE 140 472 472 ILE ILE E . n A 1 141 TYR 141 473 473 TYR TYR E . n A 1 142 GLN 142 474 474 GLN GLN E . n A 1 143 ALA 143 475 475 ALA ALA E . n A 1 144 GLY 144 476 476 GLY GLY E . n A 1 145 SER 145 477 477 SER SER E . n A 1 146 THR 146 478 478 THR THR E . n A 1 147 PRO 147 479 479 PRO PRO E . n A 1 148 CYS 148 480 480 CYS CYS E . n A 1 149 ASN 149 481 481 ASN ASN E . n A 1 150 GLY 150 482 482 GLY GLY E . n A 1 151 VAL 151 483 483 VAL VAL E . n A 1 152 GLU 152 484 484 GLU GLU E . n A 1 153 GLY 153 485 485 GLY GLY E . n A 1 154 PHE 154 486 486 PHE PHE E . n A 1 155 ASN 155 487 487 ASN ASN E . n A 1 156 CYS 156 488 488 CYS CYS E . n A 1 157 TYR 157 489 489 TYR TYR E . n A 1 158 PHE 158 490 490 PHE PHE E . n A 1 159 PRO 159 491 491 PRO PRO E . n A 1 160 LEU 160 492 492 LEU LEU E . n A 1 161 GLN 161 493 493 GLN GLN E . n A 1 162 SER 162 494 494 SER SER E . n A 1 163 TYR 163 495 495 TYR TYR E . n A 1 164 GLY 164 496 496 GLY GLY E . n A 1 165 PHE 165 497 497 PHE PHE E . n A 1 166 GLN 166 498 498 GLN GLN E . n A 1 167 PRO 167 499 499 PRO PRO E . n A 1 168 THR 168 500 500 THR THR E . n A 1 169 ASN 169 501 501 ASN ASN E . n A 1 170 GLY 170 502 502 GLY GLY E . n A 1 171 VAL 171 503 503 VAL VAL E . n A 1 172 GLY 172 504 504 GLY GLY E . n A 1 173 TYR 173 505 505 TYR TYR E . n A 1 174 GLN 174 506 506 GLN GLN E . n A 1 175 PRO 175 507 507 PRO PRO E . n A 1 176 TYR 176 508 508 TYR TYR E . n A 1 177 ARG 177 509 509 ARG ARG E . n A 1 178 VAL 178 510 510 VAL VAL E . n A 1 179 VAL 179 511 511 VAL VAL E . n A 1 180 VAL 180 512 512 VAL VAL E . n A 1 181 LEU 181 513 513 LEU LEU E . n A 1 182 SER 182 514 514 SER SER E . n A 1 183 PHE 183 515 515 PHE PHE E . n A 1 184 GLU 184 516 516 GLU GLU E . n A 1 185 LEU 185 517 517 LEU LEU E . n A 1 186 LEU 186 518 518 LEU LEU E . n A 1 187 HIS 187 519 519 HIS HIS E . n A 1 188 ALA 188 520 520 ALA ALA E . n A 1 189 PRO 189 521 521 PRO PRO E . n A 1 190 ALA 190 522 522 ALA ALA E . n A 1 191 THR 191 523 523 THR THR E . n A 1 192 VAL 192 524 524 VAL VAL E . n A 1 193 CYS 193 525 525 CYS CYS E . n A 1 194 GLY 194 526 526 GLY GLY E . n # _pdbx_contact_author.id 2 _pdbx_contact_author.email dveesler@uw.edu _pdbx_contact_author.name_first David _pdbx_contact_author.name_last Veesler _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0002-6019-8675 # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id NAG _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 601 _pdbx_nonpoly_scheme.auth_seq_num 601 _pdbx_nonpoly_scheme.pdb_mon_id NAG _pdbx_nonpoly_scheme.auth_mon_id NAG _pdbx_nonpoly_scheme.pdb_strand_id E _pdbx_nonpoly_scheme.pdb_ins_code . # _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 # _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 2023-02-08 # _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_entry_details.entry_id 7TPK _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 7TPK _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 7TPK _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 113154 _em_3d_reconstruction.resolution 3.4 _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 _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 'Receptor binding domain of the SARS-CoV-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 7TPK _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 2600 _em_imaging.nominal_defocus_min 0 _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 7TPK _em_vitrification.citation_id ? _em_vitrification.method ? _em_vitrification.temp ? _em_vitrification.time_resolved_state ? # _em_experiment.entry_id 7TPK _em_experiment.id 1 _em_experiment.aggregation_state PARTICLE _em_experiment.reconstruction_method 'SINGLE PARTICLE' _em_experiment.entity_assembly_id 1 # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 ND2 _pdbx_validate_close_contact.auth_asym_id_1 E _pdbx_validate_close_contact.auth_comp_id_1 ASN _pdbx_validate_close_contact.auth_seq_id_1 343 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 O5 _pdbx_validate_close_contact.auth_asym_id_2 E _pdbx_validate_close_contact.auth_comp_id_2 NAG _pdbx_validate_close_contact.auth_seq_id_2 601 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.17 # 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 GLN E 498 ? ? -34.87 114.97 2 1 THR E 500 ? ? 34.69 57.90 3 1 ASN E 501 ? ? 179.81 171.01 # 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 E SER 359 ? OG ? A SER 27 OG 2 1 Y 1 E SER 366 ? OG ? A SER 34 OG 3 1 Y 1 E THR 385 ? OG1 ? A THR 53 OG1 4 1 Y 1 E THR 385 ? CG2 ? A THR 53 CG2 5 1 Y 1 E THR 415 ? OG1 ? A THR 83 OG1 6 1 Y 1 E THR 415 ? CG2 ? A THR 83 CG2 7 1 Y 1 E ASP 420 ? CG ? A ASP 88 CG 8 1 Y 1 E ASP 420 ? OD1 ? A ASP 88 OD1 9 1 Y 1 E ASP 420 ? OD2 ? A ASP 88 OD2 10 1 Y 1 E ASP 427 ? CG ? A ASP 95 CG 11 1 Y 1 E ASP 427 ? OD1 ? A ASP 95 OD1 12 1 Y 1 E ASP 427 ? OD2 ? A ASP 95 OD2 13 1 Y 1 E ASP 428 ? CG ? A ASP 96 CG 14 1 Y 1 E ASP 428 ? OD1 ? A ASP 96 OD1 15 1 Y 1 E ASP 428 ? OD2 ? A ASP 96 OD2 16 1 Y 1 E ASN 439 ? CG ? A ASN 107 CG 17 1 Y 1 E ASN 439 ? OD1 ? A ASN 107 OD1 18 1 Y 1 E ASN 439 ? ND2 ? A ASN 107 ND2 19 1 Y 1 E ASN 440 ? CG ? A ASN 108 CG 20 1 Y 1 E ASN 440 ? OD1 ? A ASN 108 OD1 21 1 Y 1 E ASN 440 ? ND2 ? A ASN 108 ND2 22 1 Y 1 E ASP 442 ? CG ? A ASP 110 CG 23 1 Y 1 E ASP 442 ? OD1 ? A ASP 110 OD1 24 1 Y 1 E ASP 442 ? OD2 ? A ASP 110 OD2 25 1 Y 1 E SER 443 ? OG ? A SER 111 OG 26 1 Y 1 E LYS 444 ? CG ? A LYS 112 CG 27 1 Y 1 E LYS 444 ? CD ? A LYS 112 CD 28 1 Y 1 E LYS 444 ? CE ? A LYS 112 CE 29 1 Y 1 E LYS 444 ? NZ ? A LYS 112 NZ 30 1 Y 1 E VAL 445 ? CG1 ? A VAL 113 CG1 31 1 Y 1 E VAL 445 ? CG2 ? A VAL 113 CG2 32 1 Y 1 E ASN 448 ? CG ? A ASN 116 CG 33 1 Y 1 E ASN 448 ? OD1 ? A ASN 116 OD1 34 1 Y 1 E ASN 448 ? ND2 ? A ASN 116 ND2 35 1 Y 1 E ASN 450 ? CG ? A ASN 118 CG 36 1 Y 1 E ASN 450 ? OD1 ? A ASN 118 OD1 37 1 Y 1 E ASN 450 ? ND2 ? A ASN 118 ND2 38 1 Y 1 E SER 459 ? OG ? A SER 127 OG 39 1 Y 1 E SER 477 ? OG ? A SER 145 OG 40 1 Y 1 E THR 478 ? OG1 ? A THR 146 OG1 41 1 Y 1 E THR 478 ? CG2 ? A THR 146 CG2 42 1 Y 1 E ASN 481 ? CG ? A ASN 149 CG 43 1 Y 1 E ASN 481 ? OD1 ? A ASN 149 OD1 44 1 Y 1 E ASN 481 ? ND2 ? A ASN 149 ND2 45 1 Y 1 E VAL 483 ? CG1 ? A VAL 151 CG1 46 1 Y 1 E VAL 483 ? CG2 ? A VAL 151 CG2 47 1 Y 1 E ASN 487 ? CG ? A ASN 155 CG 48 1 Y 1 E ASN 487 ? OD1 ? A ASN 155 OD1 49 1 Y 1 E ASN 487 ? ND2 ? A ASN 155 ND2 50 1 Y 1 E GLN 498 ? CG ? A GLN 166 CG 51 1 Y 1 E GLN 498 ? CD ? A GLN 166 CD 52 1 Y 1 E GLN 498 ? OE1 ? A GLN 166 OE1 53 1 Y 1 E GLN 498 ? NE2 ? A GLN 166 NE2 54 1 Y 1 E THR 500 ? OG1 ? A THR 168 OG1 55 1 Y 1 E THR 500 ? CG2 ? A THR 168 CG2 56 1 Y 1 E ASN 501 ? CG ? A ASN 169 CG 57 1 Y 1 E ASN 501 ? OD1 ? A ASN 169 OD1 58 1 Y 1 E ASN 501 ? ND2 ? A ASN 169 ND2 59 1 Y 1 E VAL 503 ? CG1 ? A VAL 171 CG1 60 1 Y 1 E VAL 503 ? CG2 ? A VAL 171 CG2 61 1 Y 1 E GLU 516 ? CG ? A GLU 184 CG 62 1 Y 1 E GLU 516 ? CD ? A GLU 184 CD 63 1 Y 1 E GLU 516 ? OE1 ? A GLU 184 OE1 64 1 Y 1 E GLU 516 ? OE2 ? A GLU 184 OE2 65 1 Y 1 E HIS 519 ? CG ? A HIS 187 CG 66 1 Y 1 E HIS 519 ? ND1 ? A HIS 187 ND1 67 1 Y 1 E HIS 519 ? CD2 ? A HIS 187 CD2 68 1 Y 1 E HIS 519 ? CE1 ? A HIS 187 CE1 69 1 Y 1 E HIS 519 ? NE2 ? A HIS 187 NE2 70 1 Y 1 E THR 523 ? OG1 ? A THR 191 OG1 71 1 Y 1 E THR 523 ? CG2 ? A THR 191 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 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 63 _em_image_recording.average_exposure_time ? _em_image_recording.details ? _em_image_recording.detector_mode ? _em_image_recording.film_or_detector_model 'GATAN K3 (6k x 4k)' _em_image_recording.num_diffraction_images ? _em_image_recording.num_grids_imaged ? _em_image_recording.num_real_images ? _em_image_recording.avg_electron_dose_per_subtomogram ? # _em_particle_selection.id 1 _em_particle_selection.image_processing_id 1 _em_particle_selection.details ? _em_particle_selection.method ? _em_particle_selection.num_particles_selected 1281585 _em_particle_selection.reference_model ? # 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 'SYMMETRY DETERMINATION' ? ? ? 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 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' _pdbx_audit_support.country 'United States' _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 microscopy _pdbx_struct_assembly_auth_evidence.details ? #