data_7B14 # _entry.id 7B14 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.362 _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 7B14 pdb_00007b14 10.2210/pdb7b14/pdb WWPDB D_1292112464 ? ? EMDB EMD-11978 ? ? # _pdbx_database_related.db_name EMDB _pdbx_database_related.details 'Nanobody E bound to Spike-RBD in a localized reconstruction.' _pdbx_database_related.db_id EMD-11978 _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 7B14 _pdbx_database_status.recvd_initial_deposition_date 2020-11-23 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _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 'Hallberg, B.M.' 1 0000-0002-6781-0345 'Das, H.' 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 US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Science _citation.journal_id_ASTM SCIEAS _citation.journal_id_CSD 0038 _citation.journal_id_ISSN 1095-9203 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 371 _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape' _citation.year 2021 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1126/science.abe6230 _citation.pdbx_database_id_PubMed 33436526 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Koenig, P.A.' 1 0000-0001-5995-2557 primary 'Das, H.' 2 0000-0001-7495-7065 primary 'Liu, H.' 3 0000-0002-2412-7853 primary 'Kummerer, B.M.' 4 ? primary 'Gohr, F.N.' 5 0000-0001-7167-8431 primary 'Jenster, L.M.' 6 0000-0001-8580-4590 primary 'Schiffelers, L.D.J.' 7 0000-0003-2301-1610 primary 'Tesfamariam, Y.M.' 8 0000-0003-0106-7277 primary 'Uchima, M.' 9 0000-0002-1570-8445 primary 'Wuerth, J.D.' 10 0000-0002-3391-9633 primary 'Gatterdam, K.' 11 0000-0003-0114-5730 primary 'Ruetalo, N.' 12 ? primary 'Christensen, M.H.' 13 0000-0003-4778-3009 primary 'Fandrey, C.I.' 14 0000-0001-6513-8877 primary 'Normann, S.' 15 ? primary 'Todtmann, J.M.P.' 16 0000-0002-9104-5858 primary 'Pritzl, S.' 17 ? primary 'Hanke, L.' 18 0000-0001-5514-2418 primary 'Boos, J.' 19 0000-0003-3675-6523 primary 'Yuan, M.' 20 0000-0001-9754-4503 primary 'Zhu, X.' 21 0000-0002-6021-3740 primary 'Schmid-Burgk, J.L.' 22 0000-0003-0988-2487 primary 'Kato, H.' 23 ? primary 'Schindler, M.' 24 0000-0001-8989-5813 primary 'Wilson, I.A.' 25 0000-0002-6469-2419 primary 'Geyer, M.' 26 0000-0002-7718-5002 primary 'Ludwig, K.U.' 27 0000-0002-8541-2519 primary 'Hallberg, B.M.' 28 0000-0002-6781-0345 primary 'Wu, N.C.' 29 0000-0002-9078-6697 primary 'Schmidt, F.I.' 30 0000-0002-9979-9769 # _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 7B14 _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 ? # _symmetry.entry_id 7B14 _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' 22002.676 1 ? ? ? ? 2 polymer man 'Nanobody against SARS-CoV-2' 14109.523 1 ? ? ? ? 3 non-polymer syn 2-acetamido-2-deoxy-beta-D-glucopyranose 221.208 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 ;TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAP GQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPL QSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPK ; ;TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAP GQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPL QSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPK ; A ? 2 'polypeptide(L)' no no ;QVQLVETGGGFVQPGGSLRLSCAASGVTLDYYAIGWFRQAPGKEREGVSCIGSSDGRTYYSDSVKGRFTISRDNAKNTVY LQMNSLKPEDTAVYYCALTVGTYYSGNYHYTCSDDMDYWGKGTQVTVSS ; ;QVQLVETGGGFVQPGGSLRLSCAASGVTLDYYAIGWFRQAPGKEREGVSCIGSSDGRTYYSDSVKGRFTISRDNAKNTVY LQMNSLKPEDTAVYYCALTVGTYYSGNYHYTCSDDMDYWGKGTQVTVSS ; D ? # 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 GLU 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 1 195 PRO n 1 196 LYS n 2 1 GLN n 2 2 VAL n 2 3 GLN n 2 4 LEU n 2 5 VAL n 2 6 GLU n 2 7 THR n 2 8 GLY n 2 9 GLY n 2 10 GLY n 2 11 PHE n 2 12 VAL n 2 13 GLN n 2 14 PRO n 2 15 GLY n 2 16 GLY n 2 17 SER n 2 18 LEU n 2 19 ARG n 2 20 LEU n 2 21 SER n 2 22 CYS n 2 23 ALA n 2 24 ALA n 2 25 SER n 2 26 GLY n 2 27 VAL n 2 28 THR n 2 29 LEU n 2 30 ASP n 2 31 TYR n 2 32 TYR n 2 33 ALA n 2 34 ILE n 2 35 GLY n 2 36 TRP n 2 37 PHE n 2 38 ARG n 2 39 GLN n 2 40 ALA n 2 41 PRO n 2 42 GLY n 2 43 LYS n 2 44 GLU n 2 45 ARG n 2 46 GLU n 2 47 GLY n 2 48 VAL n 2 49 SER n 2 50 CYS n 2 51 ILE n 2 52 GLY n 2 53 SER n 2 54 SER n 2 55 ASP n 2 56 GLY n 2 57 ARG n 2 58 THR n 2 59 TYR n 2 60 TYR n 2 61 SER n 2 62 ASP n 2 63 SER n 2 64 VAL n 2 65 LYS n 2 66 GLY n 2 67 ARG n 2 68 PHE n 2 69 THR n 2 70 ILE n 2 71 SER n 2 72 ARG n 2 73 ASP n 2 74 ASN n 2 75 ALA n 2 76 LYS n 2 77 ASN n 2 78 THR n 2 79 VAL n 2 80 TYR n 2 81 LEU n 2 82 GLN n 2 83 MET n 2 84 ASN n 2 85 SER n 2 86 LEU n 2 87 LYS n 2 88 PRO n 2 89 GLU n 2 90 ASP n 2 91 THR n 2 92 ALA n 2 93 VAL n 2 94 TYR n 2 95 TYR n 2 96 CYS n 2 97 ALA n 2 98 LEU n 2 99 THR n 2 100 VAL n 2 101 GLY n 2 102 THR n 2 103 TYR n 2 104 TYR n 2 105 SER n 2 106 GLY n 2 107 ASN n 2 108 TYR n 2 109 HIS n 2 110 TYR n 2 111 THR n 2 112 CYS n 2 113 SER n 2 114 ASP n 2 115 ASP n 2 116 MET n 2 117 ASP n 2 118 TYR n 2 119 TRP n 2 120 GLY n 2 121 LYS n 2 122 GLY n 2 123 THR n 2 124 GLN n 2 125 VAL n 2 126 THR n 2 127 VAL n 2 128 SER n 2 129 SER n # loop_ _entity_src_gen.entity_id _entity_src_gen.pdbx_src_id _entity_src_gen.pdbx_alt_source_flag _entity_src_gen.pdbx_seq_type _entity_src_gen.pdbx_beg_seq_num _entity_src_gen.pdbx_end_seq_num _entity_src_gen.gene_src_common_name _entity_src_gen.gene_src_genus _entity_src_gen.pdbx_gene_src_gene _entity_src_gen.gene_src_species _entity_src_gen.gene_src_strain _entity_src_gen.gene_src_tissue _entity_src_gen.gene_src_tissue_fraction _entity_src_gen.gene_src_details _entity_src_gen.pdbx_gene_src_fragment _entity_src_gen.pdbx_gene_src_scientific_name _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id _entity_src_gen.pdbx_gene_src_variant _entity_src_gen.pdbx_gene_src_cell_line _entity_src_gen.pdbx_gene_src_atcc _entity_src_gen.pdbx_gene_src_organ _entity_src_gen.pdbx_gene_src_organelle _entity_src_gen.pdbx_gene_src_cell _entity_src_gen.pdbx_gene_src_cellular_location _entity_src_gen.host_org_common_name _entity_src_gen.pdbx_host_org_scientific_name _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id _entity_src_gen.host_org_genus _entity_src_gen.pdbx_host_org_gene _entity_src_gen.pdbx_host_org_organ _entity_src_gen.host_org_species _entity_src_gen.pdbx_host_org_tissue _entity_src_gen.pdbx_host_org_tissue_fraction _entity_src_gen.pdbx_host_org_strain _entity_src_gen.pdbx_host_org_variant _entity_src_gen.pdbx_host_org_cell_line _entity_src_gen.pdbx_host_org_atcc _entity_src_gen.pdbx_host_org_culture_collection _entity_src_gen.pdbx_host_org_cell _entity_src_gen.pdbx_host_org_organelle _entity_src_gen.pdbx_host_org_cellular_location _entity_src_gen.pdbx_host_org_vector_type _entity_src_gen.pdbx_host_org_vector _entity_src_gen.host_org_details _entity_src_gen.expression_system_id _entity_src_gen.plasmid_name _entity_src_gen.plasmid_details _entity_src_gen.pdbx_description 1 1 sample 'Biological sequence' 1 196 '2019-nCoV, SARS-CoV-2' ? 'S, 2' ? ? ? ? ? ? 'Severe acute respiratory syndrome coronavirus 2' 2697049 ? ? ? ? ? ? ? ? 'Homo sapiens' 9606 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 2 1 sample 'Biological sequence' 1 129 ? ? ? ? ? ? ? ? ? 'Camelus bactrianus' 9837 ? ? ? ? ? ? ? ? 'Escherichia coli' 562 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? # 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 ;TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAP GQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPL QSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPK ; 333 2 PDB 7B14 7B14 ? 2 ? 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 7B14 A 1 ? 196 ? P0DTC2 333 ? 528 ? 333 528 2 2 7B14 D 1 ? 129 ? 7B14 1 ? 113 ? 1 113 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 NAG 'D-saccharide, beta linking' . 2-acetamido-2-deoxy-beta-D-glucopyranose ;N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE ; 'C8 H15 N O6' 221.208 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 7B14 _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _refine.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine.entry_id 7B14 _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' ? 0.001 ? 2592 ? f_bond_d ? ? 'ELECTRON MICROSCOPY' ? 0.425 ? 3526 ? f_angle_d ? ? 'ELECTRON MICROSCOPY' ? 3.323 ? 370 ? f_dihedral_angle_d ? ? 'ELECTRON MICROSCOPY' ? 0.042 ? 376 ? f_chiral_restr ? ? 'ELECTRON MICROSCOPY' ? 0.003 ? 458 ? f_plane_restr ? ? # _struct.entry_id 7B14 _struct.title 'Nanobody E bound to Spike-RBD in a localized reconstruction' _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 7B14 _struct_keywords.text 'spike glycoprotein, SARS-CoV-2, nanobody, 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 ASP A 32 ? ASN A 38 ? ASP A 364 ASN A 370 1 ? 7 HELX_P HELX_P2 AA2 SER A 51 ? LEU A 55 ? SER A 383 LEU A 387 5 ? 5 HELX_P HELX_P3 AA3 ARG A 71 ? ILE A 78 ? ARG A 403 ILE A 410 1 ? 8 HELX_P HELX_P4 AA4 GLY A 170 ? GLN A 174 ? GLY A 502 GLN A 506 5 ? 5 HELX_P HELX_P5 AA5 LYS B 87 ? THR B 91 ? LYS D 83 THR D 87 5 ? 5 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role disulf1 disulf ? ? A CYS 4 SG ? ? ? 1_555 A CYS 29 SG ? ? A CYS 336 A CYS 361 1_555 ? ? ? ? ? ? ? 2.032 ? ? disulf2 disulf ? ? A CYS 47 SG ? ? ? 1_555 A CYS 100 SG ? ? A CYS 379 A CYS 432 1_555 ? ? ? ? ? ? ? 2.029 ? ? disulf3 disulf ? ? A CYS 59 SG ? ? ? 1_555 A CYS 193 SG ? ? A CYS 391 A CYS 525 1_555 ? ? ? ? ? ? ? 2.031 ? ? disulf4 disulf ? ? A CYS 148 SG ? ? ? 1_555 A CYS 156 SG ? ? A CYS 480 A CYS 488 1_555 ? ? ? ? ? ? ? 2.028 ? ? disulf5 disulf ? ? B CYS 22 SG ? ? ? 1_555 B CYS 96 SG ? ? D CYS 22 D CYS 92 1_555 ? ? ? ? ? ? ? 2.030 ? ? disulf6 disulf ? ? B CYS 50 SG ? ? ? 1_555 B CYS 112 SG ? H D CYS 50 D CYS 100 1_555 ? ? ? ? ? ? ? 2.030 ? ? covale1 covale one ? A ASN 11 ND2 ? ? ? 1_555 C NAG . C1 ? ? A ASN 343 A NAG 1301 1_555 ? ? ? ? ? ? ? 1.446 ? N-Glycosylation # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference disulf ? ? covale ? ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA1 ? 4 ? AA2 ? 2 ? AA3 ? 4 ? AA4 ? 5 ? AA5 ? 2 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense AA1 1 2 ? anti-parallel AA1 2 3 ? anti-parallel AA1 3 4 ? anti-parallel AA2 1 2 ? anti-parallel AA3 1 2 ? anti-parallel AA3 2 3 ? anti-parallel AA3 3 4 ? anti-parallel AA4 1 2 ? anti-parallel AA4 2 3 ? anti-parallel AA4 3 4 ? anti-parallel AA4 4 5 ? anti-parallel AA5 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 A 354 ILE A 358 AA1 2 ASN A 62 ? ILE A 70 ? ASN A 394 ILE A 402 AA1 3 TYR A 176 ? GLU A 184 ? TYR A 508 GLU A 516 AA1 4 GLY A 99 ? ASN A 105 ? GLY A 431 ASN A 437 AA2 1 LEU A 120 ? ARG A 122 ? LEU A 452 ARG A 454 AA2 2 LEU A 160 ? SER A 162 ? LEU A 492 SER A 494 AA3 1 GLN B 3 ? THR B 7 ? GLN D 3 THR D 7 AA3 2 LEU B 18 ? SER B 25 ? LEU D 18 SER D 25 AA3 3 THR B 78 ? MET B 83 ? THR D 77 MET D 82 AA3 4 THR B 69 ? ASP B 73 ? THR D 68 ASP D 72 AA4 1 THR B 58 ? TYR B 60 ? THR D 57 TYR D 59 AA4 2 ARG B 45 ? GLY B 52 ? ARG D 45 GLY D 52 AA4 3 TYR B 32 ? GLN B 39 ? TYR D 32 GLN D 39 AA4 4 ALA B 92 ? VAL B 100 ? ALA D 88 VAL D 96 AA4 5 THR B 123 ? VAL B 125 ? THR D 107 VAL D 109 AA5 1 THR B 102 ? TYR B 104 ? THR D 98 TYR D 100 AA5 2 ASN B 107 C HIS B 109 E ASN D 100 HIS D 100 # 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 24 ? N LYS A 356 O ALA A 65 ? O ALA A 397 AA1 2 3 N ILE A 70 ? N ILE A 402 O TYR A 176 ? O TYR A 508 AA1 3 4 O LEU A 181 ? O LEU A 513 N CYS A 100 ? N CYS A 432 AA2 1 2 N TYR A 121 ? N TYR A 453 O GLN A 161 ? O GLN A 493 AA3 1 2 N THR B 7 ? N THR D 7 O SER B 21 ? O SER D 21 AA3 2 3 N LEU B 20 ? N LEU D 20 O LEU B 81 ? O LEU D 80 AA3 3 4 O GLN B 82 ? O GLN D 81 N THR B 69 ? N THR D 68 AA4 1 2 O TYR B 59 ? O TYR D 58 N CYS B 50 ? N CYS D 50 AA4 2 3 O ILE B 51 ? O ILE D 51 N ILE B 34 ? N ILE D 34 AA4 3 4 N GLN B 39 ? N GLN D 39 O VAL B 93 ? O VAL D 89 AA4 4 5 N TYR B 94 ? N TYR D 90 O THR B 123 ? O THR D 107 AA5 1 2 N TYR B 104 ? N TYR D 100 O ASN B 107 C O ASN D 100 # _atom_sites.entry_id 7B14 _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 A . n A 1 2 ASN 2 334 334 ASN ASN A . n A 1 3 LEU 3 335 335 LEU LEU A . n A 1 4 CYS 4 336 336 CYS CYS A . n A 1 5 PRO 5 337 337 PRO PRO A . n A 1 6 PHE 6 338 338 PHE PHE A . n A 1 7 GLY 7 339 339 GLY GLY A . n A 1 8 GLU 8 340 340 GLU GLU A . n A 1 9 VAL 9 341 341 VAL VAL A . n A 1 10 PHE 10 342 342 PHE PHE A . n A 1 11 ASN 11 343 343 ASN ASN A . n A 1 12 ALA 12 344 344 ALA ALA A . n A 1 13 THR 13 345 345 THR THR A . n A 1 14 ARG 14 346 346 ARG ARG A . n A 1 15 PHE 15 347 347 PHE PHE A . n A 1 16 ALA 16 348 348 ALA ALA A . n A 1 17 SER 17 349 349 SER SER A . n A 1 18 VAL 18 350 350 VAL VAL A . n A 1 19 TYR 19 351 351 TYR TYR A . n A 1 20 ALA 20 352 352 ALA ALA A . n A 1 21 TRP 21 353 353 TRP TRP A . n A 1 22 ASN 22 354 354 ASN ASN A . n A 1 23 ARG 23 355 355 ARG ARG A . n A 1 24 LYS 24 356 356 LYS LYS A . n A 1 25 ARG 25 357 357 ARG ARG A . n A 1 26 ILE 26 358 358 ILE ILE A . n A 1 27 SER 27 359 359 SER SER A . n A 1 28 ASN 28 360 360 ASN ASN A . n A 1 29 CYS 29 361 361 CYS CYS A . n A 1 30 VAL 30 362 362 VAL VAL A . n A 1 31 ALA 31 363 363 ALA ALA A . n A 1 32 ASP 32 364 364 ASP ASP A . n A 1 33 TYR 33 365 365 TYR TYR A . n A 1 34 SER 34 366 366 SER SER A . n A 1 35 VAL 35 367 367 VAL VAL A . n A 1 36 LEU 36 368 368 LEU LEU A . n A 1 37 TYR 37 369 369 TYR TYR A . n A 1 38 ASN 38 370 370 ASN ASN A . n A 1 39 SER 39 371 371 SER SER A . n A 1 40 ALA 40 372 372 ALA ALA A . n A 1 41 SER 41 373 373 SER SER A . n A 1 42 PHE 42 374 374 PHE PHE A . n A 1 43 SER 43 375 375 SER SER A . n A 1 44 THR 44 376 376 THR THR A . n A 1 45 PHE 45 377 377 PHE PHE A . n A 1 46 LYS 46 378 378 LYS LYS A . n A 1 47 CYS 47 379 379 CYS CYS A . n A 1 48 TYR 48 380 380 TYR TYR A . n A 1 49 GLY 49 381 381 GLY GLY A . n A 1 50 VAL 50 382 382 VAL VAL A . n A 1 51 SER 51 383 383 SER SER A . n A 1 52 PRO 52 384 384 PRO PRO A . n A 1 53 THR 53 385 385 THR THR A . n A 1 54 LYS 54 386 386 LYS LYS A . n A 1 55 LEU 55 387 387 LEU LEU A . n A 1 56 ASN 56 388 388 ASN ASN A . n A 1 57 ASP 57 389 389 ASP ASP A . n A 1 58 LEU 58 390 390 LEU LEU A . n A 1 59 CYS 59 391 391 CYS CYS A . n A 1 60 PHE 60 392 392 PHE PHE A . n A 1 61 THR 61 393 393 THR THR A . n A 1 62 ASN 62 394 394 ASN ASN A . n A 1 63 VAL 63 395 395 VAL VAL A . n A 1 64 TYR 64 396 396 TYR TYR A . n A 1 65 ALA 65 397 397 ALA ALA A . n A 1 66 ASP 66 398 398 ASP ASP A . n A 1 67 SER 67 399 399 SER SER A . n A 1 68 PHE 68 400 400 PHE PHE A . n A 1 69 VAL 69 401 401 VAL VAL A . n A 1 70 ILE 70 402 402 ILE ILE A . n A 1 71 ARG 71 403 403 ARG ARG A . n A 1 72 GLY 72 404 404 GLY GLY A . n A 1 73 ASP 73 405 405 ASP ASP A . n A 1 74 GLU 74 406 406 GLU GLU A . n A 1 75 VAL 75 407 407 VAL VAL A . n A 1 76 ARG 76 408 408 ARG ARG A . n A 1 77 GLN 77 409 409 GLN GLN A . n A 1 78 ILE 78 410 410 ILE ILE A . n A 1 79 ALA 79 411 411 ALA ALA A . n A 1 80 PRO 80 412 412 PRO PRO A . n A 1 81 GLY 81 413 413 GLY GLY A . n A 1 82 GLN 82 414 414 GLN GLN A . n A 1 83 THR 83 415 415 THR THR A . n A 1 84 GLY 84 416 416 GLY GLY A . n A 1 85 LYS 85 417 417 LYS LYS A . n A 1 86 ILE 86 418 418 ILE ILE A . n A 1 87 ALA 87 419 419 ALA ALA A . n A 1 88 ASP 88 420 420 ASP ASP A . n A 1 89 TYR 89 421 421 TYR TYR A . n A 1 90 ASN 90 422 422 ASN ASN A . n A 1 91 TYR 91 423 423 TYR TYR A . n A 1 92 LYS 92 424 424 LYS LYS A . n A 1 93 LEU 93 425 425 LEU LEU A . n A 1 94 PRO 94 426 426 PRO PRO A . n A 1 95 ASP 95 427 427 ASP ASP A . n A 1 96 ASP 96 428 428 ASP ASP A . n A 1 97 PHE 97 429 429 PHE PHE A . n A 1 98 THR 98 430 430 THR THR A . n A 1 99 GLY 99 431 431 GLY GLY A . n A 1 100 CYS 100 432 432 CYS CYS A . n A 1 101 VAL 101 433 433 VAL VAL A . n A 1 102 ILE 102 434 434 ILE ILE A . n A 1 103 ALA 103 435 435 ALA ALA A . n A 1 104 TRP 104 436 436 TRP TRP A . n A 1 105 ASN 105 437 437 ASN ASN A . n A 1 106 SER 106 438 438 SER SER A . n A 1 107 ASN 107 439 439 ASN ASN A . n A 1 108 ASN 108 440 440 ASN ASN A . n A 1 109 LEU 109 441 441 LEU LEU A . n A 1 110 ASP 110 442 442 ASP ASP A . n A 1 111 SER 111 443 443 SER SER A . n A 1 112 LYS 112 444 444 LYS LYS A . n A 1 113 VAL 113 445 445 VAL VAL A . n A 1 114 GLY 114 446 446 GLY GLY A . n A 1 115 GLY 115 447 447 GLY GLY A . n A 1 116 ASN 116 448 448 ASN ASN A . n A 1 117 TYR 117 449 449 TYR TYR A . n A 1 118 ASN 118 450 450 ASN ASN A . n A 1 119 TYR 119 451 451 TYR TYR A . n A 1 120 LEU 120 452 452 LEU LEU A . n A 1 121 TYR 121 453 453 TYR TYR A . n A 1 122 ARG 122 454 454 ARG ARG A . n A 1 123 LEU 123 455 455 LEU LEU A . n A 1 124 PHE 124 456 456 PHE PHE A . n A 1 125 ARG 125 457 457 ARG ARG A . n A 1 126 LYS 126 458 458 LYS LYS A . n A 1 127 SER 127 459 459 SER SER A . n A 1 128 ASN 128 460 460 ASN ASN A . n A 1 129 LEU 129 461 461 LEU LEU A . n A 1 130 LYS 130 462 462 LYS LYS A . n A 1 131 PRO 131 463 463 PRO PRO A . n A 1 132 PHE 132 464 464 PHE PHE A . n A 1 133 GLU 133 465 465 GLU GLU A . n A 1 134 ARG 134 466 466 ARG ARG A . n A 1 135 ASP 135 467 467 ASP ASP A . n A 1 136 ILE 136 468 468 ILE ILE A . n A 1 137 SER 137 469 469 SER SER A . n A 1 138 THR 138 470 470 THR THR A . n A 1 139 GLU 139 471 471 GLU GLU A . n A 1 140 ILE 140 472 472 ILE ILE A . n A 1 141 TYR 141 473 473 TYR TYR A . n A 1 142 GLN 142 474 474 GLN GLN A . n A 1 143 ALA 143 475 475 ALA ALA A . n A 1 144 GLY 144 476 476 GLY GLY A . n A 1 145 SER 145 477 477 SER SER A . n A 1 146 THR 146 478 478 THR THR A . n A 1 147 PRO 147 479 479 PRO PRO A . n A 1 148 CYS 148 480 480 CYS CYS A . n A 1 149 ASN 149 481 481 ASN ASN A . n A 1 150 GLY 150 482 482 GLY GLY A . n A 1 151 VAL 151 483 483 VAL VAL A . n A 1 152 GLU 152 484 484 GLU GLU A . n A 1 153 GLY 153 485 485 GLY GLY A . n A 1 154 PHE 154 486 486 PHE PHE A . n A 1 155 ASN 155 487 487 ASN ASN A . n A 1 156 CYS 156 488 488 CYS CYS A . n A 1 157 TYR 157 489 489 TYR TYR A . n A 1 158 PHE 158 490 490 PHE PHE A . n A 1 159 PRO 159 491 491 PRO PRO A . n A 1 160 LEU 160 492 492 LEU LEU A . n A 1 161 GLN 161 493 493 GLN GLN A . n A 1 162 SER 162 494 494 SER SER A . n A 1 163 TYR 163 495 495 TYR TYR A . n A 1 164 GLY 164 496 496 GLY GLY A . n A 1 165 PHE 165 497 497 PHE PHE A . n A 1 166 GLN 166 498 498 GLN GLN A . n A 1 167 PRO 167 499 499 PRO PRO A . n A 1 168 THR 168 500 500 THR THR A . n A 1 169 ASN 169 501 501 ASN ASN A . n A 1 170 GLY 170 502 502 GLY GLY A . n A 1 171 VAL 171 503 503 VAL VAL A . n A 1 172 GLY 172 504 504 GLY GLY A . n A 1 173 TYR 173 505 505 TYR TYR A . n A 1 174 GLN 174 506 506 GLN GLN A . n A 1 175 PRO 175 507 507 PRO PRO A . n A 1 176 TYR 176 508 508 TYR TYR A . n A 1 177 ARG 177 509 509 ARG ARG A . n A 1 178 VAL 178 510 510 VAL VAL A . n A 1 179 VAL 179 511 511 VAL VAL A . n A 1 180 VAL 180 512 512 VAL VAL A . n A 1 181 LEU 181 513 513 LEU LEU A . n A 1 182 SER 182 514 514 SER SER A . n A 1 183 PHE 183 515 515 PHE PHE A . n A 1 184 GLU 184 516 516 GLU GLU A . n A 1 185 LEU 185 517 517 LEU LEU A . n A 1 186 LEU 186 518 518 LEU LEU A . n A 1 187 HIS 187 519 519 HIS HIS A . n A 1 188 ALA 188 520 520 ALA ALA A . n A 1 189 PRO 189 521 521 PRO PRO A . n A 1 190 ALA 190 522 522 ALA ALA A . n A 1 191 THR 191 523 523 THR THR A . n A 1 192 VAL 192 524 524 VAL VAL A . n A 1 193 CYS 193 525 525 CYS CYS A . n A 1 194 GLY 194 526 526 GLY GLY A . n A 1 195 PRO 195 527 527 PRO PRO A . n A 1 196 LYS 196 528 ? ? ? A . n B 2 1 GLN 1 1 1 GLN GLN D . n B 2 2 VAL 2 2 2 VAL VAL D . n B 2 3 GLN 3 3 3 GLN GLN D . n B 2 4 LEU 4 4 4 LEU LEU D . n B 2 5 VAL 5 5 5 VAL VAL D . n B 2 6 GLU 6 6 6 GLU GLU D . n B 2 7 THR 7 7 7 THR THR D . n B 2 8 GLY 8 8 8 GLY GLY D . n B 2 9 GLY 9 9 9 GLY GLY D . n B 2 10 GLY 10 10 10 GLY GLY D . n B 2 11 PHE 11 11 11 PHE PHE D . n B 2 12 VAL 12 12 12 VAL VAL D . n B 2 13 GLN 13 13 13 GLN GLN D . n B 2 14 PRO 14 14 14 PRO PRO D . n B 2 15 GLY 15 15 15 GLY GLY D . n B 2 16 GLY 16 16 16 GLY GLY D . n B 2 17 SER 17 17 17 SER SER D . n B 2 18 LEU 18 18 18 LEU LEU D . n B 2 19 ARG 19 19 19 ARG ARG D . n B 2 20 LEU 20 20 20 LEU LEU D . n B 2 21 SER 21 21 21 SER SER D . n B 2 22 CYS 22 22 22 CYS CYS D . n B 2 23 ALA 23 23 23 ALA ALA D . n B 2 24 ALA 24 24 24 ALA ALA D . n B 2 25 SER 25 25 25 SER SER D . n B 2 26 GLY 26 26 26 GLY GLY D . n B 2 27 VAL 27 27 27 VAL VAL D . n B 2 28 THR 28 28 28 THR THR D . n B 2 29 LEU 29 29 29 LEU LEU D . n B 2 30 ASP 30 30 30 ASP ASP D . n B 2 31 TYR 31 31 31 TYR TYR D . n B 2 32 TYR 32 32 32 TYR TYR D . n B 2 33 ALA 33 33 33 ALA ALA D . n B 2 34 ILE 34 34 34 ILE ILE D . n B 2 35 GLY 35 35 35 GLY GLY D . n B 2 36 TRP 36 36 36 TRP TRP D . n B 2 37 PHE 37 37 37 PHE PHE D . n B 2 38 ARG 38 38 38 ARG ARG D . n B 2 39 GLN 39 39 39 GLN GLN D . n B 2 40 ALA 40 40 40 ALA ALA D . n B 2 41 PRO 41 41 41 PRO PRO D . n B 2 42 GLY 42 42 42 GLY GLY D . n B 2 43 LYS 43 43 43 LYS LYS D . n B 2 44 GLU 44 44 44 GLU GLU D . n B 2 45 ARG 45 45 45 ARG ARG D . n B 2 46 GLU 46 46 46 GLU GLU D . n B 2 47 GLY 47 47 47 GLY GLY D . n B 2 48 VAL 48 48 48 VAL VAL D . n B 2 49 SER 49 49 49 SER SER D . n B 2 50 CYS 50 50 50 CYS CYS D . n B 2 51 ILE 51 51 51 ILE ILE D . n B 2 52 GLY 52 52 52 GLY GLY D . n B 2 53 SER 53 52 52 SER SER D A n B 2 54 SER 54 53 53 SER SER D . n B 2 55 ASP 55 54 54 ASP ASP D . n B 2 56 GLY 56 55 55 GLY GLY D . n B 2 57 ARG 57 56 56 ARG ARG D . n B 2 58 THR 58 57 57 THR THR D . n B 2 59 TYR 59 58 58 TYR TYR D . n B 2 60 TYR 60 59 59 TYR TYR D . n B 2 61 SER 61 60 60 SER SER D . n B 2 62 ASP 62 61 61 ASP ASP D . n B 2 63 SER 63 62 62 SER SER D . n B 2 64 VAL 64 63 63 VAL VAL D . n B 2 65 LYS 65 64 64 LYS LYS D . n B 2 66 GLY 66 65 65 GLY GLY D . n B 2 67 ARG 67 66 66 ARG ARG D . n B 2 68 PHE 68 67 67 PHE PHE D . n B 2 69 THR 69 68 68 THR THR D . n B 2 70 ILE 70 69 69 ILE ILE D . n B 2 71 SER 71 70 70 SER SER D . n B 2 72 ARG 72 71 71 ARG ARG D . n B 2 73 ASP 73 72 72 ASP ASP D . n B 2 74 ASN 74 73 73 ASN ASN D . n B 2 75 ALA 75 74 74 ALA ALA D . n B 2 76 LYS 76 75 75 LYS LYS D . n B 2 77 ASN 77 76 76 ASN ASN D . n B 2 78 THR 78 77 77 THR THR D . n B 2 79 VAL 79 78 78 VAL VAL D . n B 2 80 TYR 80 79 79 TYR TYR D . n B 2 81 LEU 81 80 80 LEU LEU D . n B 2 82 GLN 82 81 81 GLN GLN D . n B 2 83 MET 83 82 82 MET MET D . n B 2 84 ASN 84 82 82 ASN ASN D A n B 2 85 SER 85 82 82 SER SER D B n B 2 86 LEU 86 82 82 LEU LEU D C n B 2 87 LYS 87 83 83 LYS LYS D . n B 2 88 PRO 88 84 84 PRO PRO D . n B 2 89 GLU 89 85 85 GLU GLU D . n B 2 90 ASP 90 86 86 ASP ASP D . n B 2 91 THR 91 87 87 THR THR D . n B 2 92 ALA 92 88 88 ALA ALA D . n B 2 93 VAL 93 89 89 VAL VAL D . n B 2 94 TYR 94 90 90 TYR TYR D . n B 2 95 TYR 95 91 91 TYR TYR D . n B 2 96 CYS 96 92 92 CYS CYS D . n B 2 97 ALA 97 93 93 ALA ALA D . n B 2 98 LEU 98 94 94 LEU LEU D . n B 2 99 THR 99 95 95 THR THR D . n B 2 100 VAL 100 96 96 VAL VAL D . n B 2 101 GLY 101 97 97 GLY GLY D . n B 2 102 THR 102 98 98 THR THR D . n B 2 103 TYR 103 99 99 TYR TYR D . n B 2 104 TYR 104 100 100 TYR TYR D . n B 2 105 SER 105 100 100 SER SER D A n B 2 106 GLY 106 100 100 GLY GLY D B n B 2 107 ASN 107 100 100 ASN ASN D C n B 2 108 TYR 108 100 100 TYR TYR D D n B 2 109 HIS 109 100 100 HIS HIS D E n B 2 110 TYR 110 100 100 TYR TYR D F n B 2 111 THR 111 100 100 THR THR D G n B 2 112 CYS 112 100 100 CYS CYS D H n B 2 113 SER 113 100 100 SER SER D I n B 2 114 ASP 114 100 100 ASP ASP D J n B 2 115 ASP 115 100 100 ASP ASP D K n B 2 116 MET 116 100 100 MET MET D L n B 2 117 ASP 117 101 101 ASP ASP D . n B 2 118 TYR 118 102 102 TYR TYR D . n B 2 119 TRP 119 103 103 TRP TRP D . n B 2 120 GLY 120 104 104 GLY GLY D . n B 2 121 LYS 121 105 105 LYS LYS D . n B 2 122 GLY 122 106 106 GLY GLY D . n B 2 123 THR 123 107 107 THR THR D . n B 2 124 GLN 124 108 108 GLN GLN D . n B 2 125 VAL 125 109 109 VAL VAL D . n B 2 126 THR 126 110 110 THR THR D . n B 2 127 VAL 127 111 111 VAL VAL D . n B 2 128 SER 128 112 112 SER SER D . n B 2 129 SER 129 113 113 SER SER D . n # _pdbx_nonpoly_scheme.asym_id C _pdbx_nonpoly_scheme.entity_id 3 _pdbx_nonpoly_scheme.mon_id NAG _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 1301 _pdbx_nonpoly_scheme.auth_seq_num 528 _pdbx_nonpoly_scheme.pdb_mon_id NAG _pdbx_nonpoly_scheme.auth_mon_id NAG _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.pdb_ins_code . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 1760 ? 1 MORE -8 ? 1 'SSA (A^2)' 17610 ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation ? _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2021-04-28 2 'Structure model' 1 1 2021-05-26 3 'Structure model' 2 0 2021-06-02 4 'Structure model' 2 1 2022-12-21 # _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 ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Structure summary' 2 3 'Structure model' Advisory 3 3 'Structure model' 'Atomic model' 4 3 'Structure model' 'Database references' 5 3 'Structure model' 'Derived calculations' 6 3 'Structure model' 'Polymer sequence' 7 3 'Structure model' 'Source and taxonomy' 8 3 'Structure model' 'Structure summary' 9 4 'Structure model' 'Database references' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' struct 2 3 'Structure model' atom_site 3 3 'Structure model' entity 4 3 'Structure model' entity_name_com 5 3 'Structure model' entity_poly 6 3 'Structure model' entity_poly_seq 7 3 'Structure model' entity_src_gen 8 3 'Structure model' pdbx_poly_seq_scheme 9 3 'Structure model' pdbx_struct_sheet_hbond 10 3 'Structure model' pdbx_unobs_or_zero_occ_atoms 11 3 'Structure model' pdbx_unobs_or_zero_occ_residues 12 3 'Structure model' struct_conf 13 3 'Structure model' struct_conn 14 3 'Structure model' struct_ref 15 3 'Structure model' struct_ref_seq 16 3 'Structure model' struct_ref_seq_dif 17 3 'Structure model' struct_sheet_range 18 4 'Structure model' citation 19 4 'Structure model' database_2 # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_struct.title' 2 3 'Structure model' '_atom_site.label_seq_id' 3 3 'Structure model' '_entity.formula_weight' 4 3 'Structure model' '_entity.pdbx_description' 5 3 'Structure model' '_entity_poly.pdbx_seq_one_letter_code' 6 3 'Structure model' '_entity_poly.pdbx_seq_one_letter_code_can' 7 3 'Structure model' '_entity_src_gen.gene_src_common_name' 8 3 'Structure model' '_entity_src_gen.pdbx_end_seq_num' 9 3 'Structure model' '_pdbx_struct_sheet_hbond.range_1_label_seq_id' 10 3 'Structure model' '_pdbx_struct_sheet_hbond.range_2_label_seq_id' 11 3 'Structure model' '_pdbx_unobs_or_zero_occ_atoms.label_seq_id' 12 3 'Structure model' '_struct_conf.beg_label_seq_id' 13 3 'Structure model' '_struct_conf.end_label_seq_id' 14 3 'Structure model' '_struct_conn.ptnr1_label_seq_id' 15 3 'Structure model' '_struct_conn.ptnr2_label_seq_id' 16 3 'Structure model' '_struct_ref.pdbx_align_begin' 17 3 'Structure model' '_struct_ref.pdbx_seq_one_letter_code' 18 3 'Structure model' '_struct_ref_seq.db_align_beg' 19 3 'Structure model' '_struct_ref_seq.db_align_end' 20 3 'Structure model' '_struct_ref_seq.pdbx_auth_seq_align_beg' 21 3 'Structure model' '_struct_ref_seq.pdbx_auth_seq_align_end' 22 3 'Structure model' '_struct_ref_seq.seq_align_end' 23 3 'Structure model' '_struct_sheet_range.beg_label_seq_id' 24 3 'Structure model' '_struct_sheet_range.end_label_seq_id' 25 4 'Structure model' '_citation.title' 26 4 'Structure model' '_database_2.pdbx_DOI' 27 4 'Structure model' '_database_2.pdbx_database_accession' # _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 1.18.2_3874: _software.pdbx_ordinal 1 # _pdbx_entry_details.entry_id 7B14 _pdbx_entry_details.has_ligand_of_interest N _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? # _em_3d_fitting.entry_id 7B14 _em_3d_fitting.id 1 _em_3d_fitting.details ? _em_3d_fitting.overall_b_value ? _em_3d_fitting.ref_protocol 'FLEXIBLE FIT' _em_3d_fitting.ref_space REAL _em_3d_fitting.target_criteria ? _em_3d_fitting.method ? # _em_3d_reconstruction.entry_id 7B14 _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 38308 _em_3d_reconstruction.resolution 3.79 _em_3d_reconstruction.resolution_method 'FSC 0.143 CUT-OFF' _em_3d_reconstruction.symmetry_type POINT _em_3d_reconstruction.method ? _em_3d_reconstruction.nominal_pixel_size ? _em_3d_reconstruction.actual_pixel_size ? _em_3d_reconstruction.magnification_calibration ? # _em_buffer.id 1 _em_buffer.details ? _em_buffer.pH 7.3 _em_buffer.specimen_id 1 _em_buffer.name ? # loop_ _em_entity_assembly.id _em_entity_assembly.parent_id _em_entity_assembly.details _em_entity_assembly.name _em_entity_assembly.source _em_entity_assembly.type _em_entity_assembly.entity_id_list _em_entity_assembly.synonym _em_entity_assembly.oligomeric_details 1 0 ? 'SARS-CoV-2 glycoprotein in complex with a nanobody named V' 'MULTIPLE SOURCES' COMPLEX '1, 2' ? ? 2 1 ? 'Spike glycoprotein' RECOMBINANT COMPLEX 1 ? ? 3 1 ? 'Nanobody against SARS-CoV-2' RECOMBINANT COMPLEX 2 ? ? # _em_imaging.id 1 _em_imaging.entry_id 7B14 _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 ? _em_imaging.nominal_defocus_min ? _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 7B14 _em_vitrification.citation_id ? _em_vitrification.method ? _em_vitrification.temp ? _em_vitrification.time_resolved_state ? # _em_experiment.entry_id 7B14 _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 OG _pdbx_validate_close_contact.auth_asym_id_1 D _pdbx_validate_close_contact.auth_comp_id_1 SER _pdbx_validate_close_contact.auth_seq_id_1 100 _pdbx_validate_close_contact.PDB_ins_code_1 I _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 OD1 _pdbx_validate_close_contact.auth_asym_id_2 D _pdbx_validate_close_contact.auth_comp_id_2 ASP _pdbx_validate_close_contact.auth_seq_id_2 100 _pdbx_validate_close_contact.PDB_ins_code_2 K _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.19 # 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 CYS A 432 ? ? -173.97 -179.40 2 1 LYS D 64 ? ? 57.75 15.11 # 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 A LEU 518 ? CG ? A LEU 186 CG 2 1 Y 1 A LEU 518 ? CD1 ? A LEU 186 CD1 3 1 Y 1 A LEU 518 ? CD2 ? A LEU 186 CD2 4 1 Y 1 D GLN 1 ? OE1 ? B GLN 1 OE1 5 1 Y 1 D GLN 1 ? NE2 ? B GLN 1 NE2 6 1 Y 1 D GLN 13 ? CG ? B GLN 13 CG 7 1 Y 1 D GLN 13 ? CD ? B GLN 13 CD 8 1 Y 1 D GLN 13 ? OE1 ? B GLN 13 OE1 9 1 Y 1 D GLN 13 ? NE2 ? B GLN 13 NE2 10 1 Y 1 D LYS 64 ? CE ? B LYS 65 CE 11 1 Y 1 D LYS 64 ? NZ ? B LYS 65 NZ 12 1 Y 1 D ASN 73 ? OD1 ? B ASN 74 OD1 13 1 Y 1 D ASN 73 ? ND2 ? B ASN 74 ND2 14 1 Y 1 D LYS 75 ? CE ? B LYS 76 CE 15 1 Y 1 D LYS 75 ? NZ ? B LYS 76 NZ 16 1 Y 1 D GLU 85 ? CD ? B GLU 89 CD 17 1 Y 1 D GLU 85 ? OE1 ? B GLU 89 OE1 18 1 Y 1 D GLU 85 ? OE2 ? B GLU 89 OE2 19 1 Y 1 D LYS 105 ? CD ? B LYS 121 CD 20 1 Y 1 D LYS 105 ? CE ? B LYS 121 CE 21 1 Y 1 D LYS 105 ? NZ ? B LYS 121 NZ # _pdbx_unobs_or_zero_occ_residues.id 1 _pdbx_unobs_or_zero_occ_residues.PDB_model_num 1 _pdbx_unobs_or_zero_occ_residues.polymer_flag Y _pdbx_unobs_or_zero_occ_residues.occupancy_flag 1 _pdbx_unobs_or_zero_occ_residues.auth_asym_id A _pdbx_unobs_or_zero_occ_residues.auth_comp_id LYS _pdbx_unobs_or_zero_occ_residues.auth_seq_id 528 _pdbx_unobs_or_zero_occ_residues.PDB_ins_code ? _pdbx_unobs_or_zero_occ_residues.label_asym_id A _pdbx_unobs_or_zero_occ_residues.label_comp_id LYS _pdbx_unobs_or_zero_occ_residues.label_seq_id 196 # _em_ctf_correction.id 1 _em_ctf_correction.em_image_processing_id 1 _em_ctf_correction.type 'PHASE FLIPPING AND AMPLITUDE CORRECTION' _em_ctf_correction.details ? # _em_entity_assembly_molwt.entity_assembly_id 1 _em_entity_assembly_molwt.id 1 _em_entity_assembly_molwt.experimental_flag NO _em_entity_assembly_molwt.units MEGADALTONS _em_entity_assembly_molwt.value 0.51 # loop_ _em_entity_assembly_naturalsource.id _em_entity_assembly_naturalsource.entity_assembly_id _em_entity_assembly_naturalsource.cell _em_entity_assembly_naturalsource.cellular_location _em_entity_assembly_naturalsource.ncbi_tax_id _em_entity_assembly_naturalsource.organ _em_entity_assembly_naturalsource.organelle _em_entity_assembly_naturalsource.organism _em_entity_assembly_naturalsource.strain _em_entity_assembly_naturalsource.tissue 2 2 ? ? 2697049 ? ? 'Severe acute respiratory syndrome coronavirus 2' ? ? 3 3 ? ? 9837 ? ? 'Camelus bactrianus' ? ? # 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 2 ? 9606 'Homo sapiens' ? ? 3 3 ? 562 'Escherichia coli' ? ? # _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 49 _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 ? # 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 'PARTICLE SELECTION' ? ? ? 1 ? ? 2 'IMAGE ACQUISITION' ? ? ? ? ? 1 3 MASKING ? ? ? ? ? ? 4 'CTF CORRECTION' ? ? ? 1 ? ? 5 'LAYERLINE INDEXING' ? ? ? ? ? ? 6 'DIFFRACTION INDEXING' ? ? ? ? ? ? 7 'MODEL FITTING' ? ? ? ? 1 ? 8 OTHER ? ? ? ? ? ? 9 'MODEL REFINEMENT' ? ? ? ? 1 ? 10 'INITIAL EULER ASSIGNMENT' ? ? ? 1 ? ? 11 'FINAL EULER ASSIGNMENT' ? cryoSPARC 2.15 1 ? ? 12 CLASSIFICATION ? cryoSPARC 2.15 1 ? ? 13 RECONSTRUCTION ? cryoSPARC 2.15 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 # 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_nonpoly.entity_id 3 _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 none _pdbx_struct_assembly_auth_evidence.details ? #