data_7ZSD # _entry.id 7ZSD # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.370 _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 7ZSD pdb_00007zsd 10.2210/pdb7zsd/pdb WWPDB D_1292122855 ? ? EMDB EMD-14930 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.details _pdbx_database_related.db_id _pdbx_database_related.content_type EMDB . EMD-14922 'other EM volume' EMDB 'cryo-EM structure of omicron spike in complex with de novo designed binder, local' EMD-14930 '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 7ZSD _pdbx_database_status.recvd_initial_deposition_date 2022-05-06 _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 'Pablo, G.' 1 ? 'Sarah, W.' 2 ? 'Alexandra, V.H.' 3 ? 'Anthony, M.' 4 ? 'Andreas, S.' 5 ? 'Zander, H.' 6 ? 'Dongchun, N.' 7 ? 'Shuguang, T.' 8 ? 'Freyr, S.' 9 ? 'Casper, G.' 10 ? 'Priscilla, T.' 11 ? 'Alexandra, T.' 12 ? 'Stephane, R.' 13 ? 'Sandrine, G.' 14 ? 'Jane, M.' 15 ? 'Aaron, P.' 16 ? 'Zepeng, X.' 17 ? 'Yan, C.' 18 ? 'Pu, H.' 19 ? 'George, G.' 20 ? 'Elisa, O.' 21 ? 'Beat, F.' 22 ? 'Didier, T.' 23 ? 'Henning, S.' 24 ? 'Michael, B.' 25 ? 'Bruno, E.C.' 26 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Nature _citation.journal_id_ASTM NATUAS _citation.journal_id_CSD 0006 _citation.journal_id_ISSN 1476-4687 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 617 _citation.language ? _citation.page_first 176 _citation.page_last 184 _citation.title 'De novo design of protein interactions with learned surface fingerprints.' _citation.year 2023 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1038/s41586-023-05993-x _citation.pdbx_database_id_PubMed 37100904 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Gainza, P.' 1 ? primary 'Wehrle, S.' 2 ? primary 'Van Hall-Beauvais, A.' 3 ? primary 'Marchand, A.' 4 ? primary 'Scheck, A.' 5 ? primary 'Harteveld, Z.' 6 ? primary 'Buckley, S.' 7 ? primary 'Ni, D.' 8 ? primary 'Tan, S.' 9 ? primary 'Sverrisson, F.' 10 ? primary 'Goverde, C.' 11 ? primary 'Turelli, P.' 12 ? primary 'Raclot, C.' 13 ? primary 'Teslenko, A.' 14 ? primary 'Pacesa, M.' 15 ? primary 'Rosset, S.' 16 ? primary 'Georgeon, S.' 17 ? primary 'Marsden, J.' 18 ? primary 'Petruzzella, A.' 19 ? primary 'Liu, K.' 20 ? primary 'Xu, Z.' 21 ? primary 'Chai, Y.' 22 ? primary 'Han, P.' 23 ? primary 'Gao, G.F.' 24 ? primary 'Oricchio, E.' 25 ? primary 'Fierz, B.' 26 ? primary 'Trono, D.' 27 ? primary 'Stahlberg, H.' 28 ? primary 'Bronstein, M.' 29 ? primary 'Correia, B.E.' 30 ? # _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 7ZSD _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 7ZSD _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 glycoprotein' 22280.193 1 ? ? ? ? 2 polymer man 'de novo designed binder' 8829.904 1 ? ? ? ? 3 branched man '2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose' 424.401 1 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'S glycoprotein,E2,Peplomer protein' # 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 ;ITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIA PGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFP LRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGP ; ;ITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIA PGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFP LRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGP ; M ? 2 'polypeptide(L)' no no ETGASSTNMLEALQQRLQFYHGQVARAALENNSGKARRFGRIVKQYEDAIKLYKAGKPVPYDELPVPPGFGGSENLYFQ ETGASSTNMLEALQQRLQFYHGQVARAALENNSGKARRFGRIVKQYEDAIKLYKAGKPVPYDELPVPPGFGGSENLYFQ P ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 ILE n 1 2 THR n 1 3 ASN n 1 4 LEU n 1 5 CYS n 1 6 PRO n 1 7 PHE n 1 8 ASP n 1 9 GLU n 1 10 VAL n 1 11 PHE n 1 12 ASN n 1 13 ALA n 1 14 THR n 1 15 ARG n 1 16 PHE n 1 17 ALA n 1 18 SER n 1 19 VAL n 1 20 TYR n 1 21 ALA n 1 22 TRP n 1 23 ASN n 1 24 ARG n 1 25 LYS n 1 26 ARG n 1 27 ILE n 1 28 SER n 1 29 ASN n 1 30 CYS n 1 31 VAL n 1 32 ALA n 1 33 ASP n 1 34 TYR n 1 35 SER n 1 36 VAL n 1 37 LEU n 1 38 TYR n 1 39 ASN n 1 40 LEU n 1 41 ALA n 1 42 PRO n 1 43 PHE n 1 44 PHE n 1 45 THR n 1 46 PHE n 1 47 LYS n 1 48 CYS n 1 49 TYR n 1 50 GLY n 1 51 VAL n 1 52 SER n 1 53 PRO n 1 54 THR n 1 55 LYS n 1 56 LEU n 1 57 ASN n 1 58 ASP n 1 59 LEU n 1 60 CYS n 1 61 PHE n 1 62 THR n 1 63 ASN n 1 64 VAL n 1 65 TYR n 1 66 ALA n 1 67 ASP n 1 68 SER n 1 69 PHE n 1 70 VAL n 1 71 ILE n 1 72 ARG n 1 73 GLY n 1 74 ASP n 1 75 GLU n 1 76 VAL n 1 77 ARG n 1 78 GLN n 1 79 ILE n 1 80 ALA n 1 81 PRO n 1 82 GLY n 1 83 GLN n 1 84 THR n 1 85 GLY n 1 86 ASN n 1 87 ILE n 1 88 ALA n 1 89 ASP n 1 90 TYR n 1 91 ASN n 1 92 TYR n 1 93 LYS n 1 94 LEU n 1 95 PRO n 1 96 ASP n 1 97 ASP n 1 98 PHE n 1 99 THR n 1 100 GLY n 1 101 CYS n 1 102 VAL n 1 103 ILE n 1 104 ALA n 1 105 TRP n 1 106 ASN n 1 107 SER n 1 108 ASN n 1 109 LYS n 1 110 LEU n 1 111 ASP n 1 112 SER n 1 113 LYS n 1 114 VAL n 1 115 SER n 1 116 GLY n 1 117 ASN n 1 118 TYR n 1 119 ASN n 1 120 TYR n 1 121 LEU n 1 122 TYR n 1 123 ARG n 1 124 LEU n 1 125 PHE n 1 126 ARG n 1 127 LYS n 1 128 SER n 1 129 ASN n 1 130 LEU n 1 131 LYS n 1 132 PRO n 1 133 PHE n 1 134 GLU n 1 135 ARG n 1 136 ASP n 1 137 ILE n 1 138 SER n 1 139 THR n 1 140 GLU n 1 141 ILE n 1 142 TYR n 1 143 GLN n 1 144 ALA n 1 145 GLY n 1 146 ASN n 1 147 LYS n 1 148 PRO n 1 149 CYS n 1 150 ASN n 1 151 GLY n 1 152 VAL n 1 153 ALA n 1 154 GLY n 1 155 PHE n 1 156 ASN n 1 157 CYS n 1 158 TYR n 1 159 PHE n 1 160 PRO n 1 161 LEU n 1 162 ARG n 1 163 SER n 1 164 TYR n 1 165 SER n 1 166 PHE n 1 167 ARG n 1 168 PRO n 1 169 THR n 1 170 TYR n 1 171 GLY n 1 172 VAL n 1 173 GLY n 1 174 HIS n 1 175 GLN n 1 176 PRO n 1 177 TYR n 1 178 ARG n 1 179 VAL n 1 180 VAL n 1 181 VAL n 1 182 LEU n 1 183 SER n 1 184 PHE n 1 185 GLU n 1 186 LEU n 1 187 LEU n 1 188 HIS n 1 189 ALA n 1 190 PRO n 1 191 ALA n 1 192 THR n 1 193 VAL n 1 194 CYS n 1 195 GLY n 1 196 PRO n 2 1 GLU n 2 2 THR n 2 3 GLY n 2 4 ALA n 2 5 SER n 2 6 SER n 2 7 THR n 2 8 ASN n 2 9 MET n 2 10 LEU n 2 11 GLU n 2 12 ALA n 2 13 LEU n 2 14 GLN n 2 15 GLN n 2 16 ARG n 2 17 LEU n 2 18 GLN n 2 19 PHE n 2 20 TYR n 2 21 HIS n 2 22 GLY n 2 23 GLN n 2 24 VAL n 2 25 ALA n 2 26 ARG n 2 27 ALA n 2 28 ALA n 2 29 LEU n 2 30 GLU n 2 31 ASN n 2 32 ASN n 2 33 SER n 2 34 GLY n 2 35 LYS n 2 36 ALA n 2 37 ARG n 2 38 ARG n 2 39 PHE n 2 40 GLY n 2 41 ARG n 2 42 ILE n 2 43 VAL n 2 44 LYS n 2 45 GLN n 2 46 TYR n 2 47 GLU n 2 48 ASP n 2 49 ALA n 2 50 ILE n 2 51 LYS n 2 52 LEU n 2 53 TYR n 2 54 LYS n 2 55 ALA n 2 56 GLY n 2 57 LYS n 2 58 PRO n 2 59 VAL n 2 60 PRO n 2 61 TYR n 2 62 ASP n 2 63 GLU n 2 64 LEU n 2 65 PRO n 2 66 VAL n 2 67 PRO n 2 68 PRO n 2 69 GLY n 2 70 PHE n 2 71 GLY n 2 72 GLY n 2 73 SER n 2 74 GLU n 2 75 ASN n 2 76 LEU n 2 77 TYR n 2 78 PHE n 2 79 GLN 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 ? ? 'S, 2' ? ? ? ? ? ? 'Severe acute respiratory syndrome coronavirus 2' 2697049 ? ? ? ? ? ? ? ? 'Homo sapiens' 9606 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 2 1 sample 'Biological sequence' 1 79 'fruit fly' ? 'l(2)gd1, lgd, CG4713' ? ? ? ? ? ? 'Drosophila melanogaster' 7227 ? ? ? ? ? ? ? ? '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 ;ITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIA PGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFP LQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGP ; 332 2 UNP C2D1_DROME Q9VKJ9 ? 2 TNMLEALQQRLEKYQSVEAAAKAENNSGKARRFGRIVKQYEDAIKLYKAGKPVPYDELPVPPGFG 359 # 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 7ZSD M 1 ? 196 ? P0DTC2 332 ? 527 ? 332 527 2 2 7ZSD P 7 ? 71 ? Q9VKJ9 359 ? 423 ? 1 65 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 7ZSD ASP M 8 ? UNP P0DTC2 GLY 339 variant 339 1 1 7ZSD LEU M 40 ? UNP P0DTC2 SER 371 variant 371 2 1 7ZSD PRO M 42 ? UNP P0DTC2 SER 373 variant 373 3 1 7ZSD PHE M 44 ? UNP P0DTC2 SER 375 variant 375 4 1 7ZSD ASN M 86 ? UNP P0DTC2 LYS 417 variant 417 5 1 7ZSD LYS M 109 ? UNP P0DTC2 ASN 440 variant 440 6 1 7ZSD SER M 115 ? UNP P0DTC2 GLY 446 variant 446 7 1 7ZSD ASN M 146 ? UNP P0DTC2 SER 477 variant 477 8 1 7ZSD LYS M 147 ? UNP P0DTC2 THR 478 variant 478 9 1 7ZSD ALA M 153 ? UNP P0DTC2 GLU 484 variant 484 10 1 7ZSD ARG M 162 ? UNP P0DTC2 GLN 493 'engineered mutation' 493 11 1 7ZSD SER M 165 ? UNP P0DTC2 GLY 496 variant 496 12 1 7ZSD ARG M 167 ? UNP P0DTC2 GLN 498 variant 498 13 1 7ZSD TYR M 170 ? UNP P0DTC2 ASN 501 variant 501 14 1 7ZSD HIS M 174 ? UNP P0DTC2 TYR 505 variant 505 15 2 7ZSD GLU P 1 ? UNP Q9VKJ9 ? ? 'expression tag' -5 16 2 7ZSD THR P 2 ? UNP Q9VKJ9 ? ? 'expression tag' -4 17 2 7ZSD GLY P 3 ? UNP Q9VKJ9 ? ? 'expression tag' -3 18 2 7ZSD ALA P 4 ? UNP Q9VKJ9 ? ? 'expression tag' -2 19 2 7ZSD SER P 5 ? UNP Q9VKJ9 ? ? 'expression tag' -1 20 2 7ZSD SER P 6 ? UNP Q9VKJ9 ? ? 'expression tag' 0 21 2 7ZSD GLN P 18 ? UNP Q9VKJ9 GLU 370 'engineered mutation' 12 22 2 7ZSD PHE P 19 ? UNP Q9VKJ9 LYS 371 'engineered mutation' 13 23 2 7ZSD HIS P 21 ? UNP Q9VKJ9 GLN 373 'engineered mutation' 15 24 2 7ZSD GLY P 22 ? UNP Q9VKJ9 SER 374 'engineered mutation' 16 25 2 7ZSD GLN P 23 ? UNP Q9VKJ9 VAL 375 'engineered mutation' 17 26 2 7ZSD VAL P 24 ? UNP Q9VKJ9 GLU 376 'engineered mutation' 18 27 2 7ZSD ARG P 26 ? UNP Q9VKJ9 ALA 378 'engineered mutation' 20 28 2 7ZSD ALA P 28 ? UNP Q9VKJ9 LYS 380 'engineered mutation' 22 29 2 7ZSD LEU P 29 ? UNP Q9VKJ9 ALA 381 'engineered mutation' 23 30 2 7ZSD GLY P 72 ? UNP Q9VKJ9 ? ? 'expression tag' 66 31 2 7ZSD SER P 73 ? UNP Q9VKJ9 ? ? 'expression tag' 67 32 2 7ZSD GLU P 74 ? UNP Q9VKJ9 ? ? 'expression tag' 68 33 2 7ZSD ASN P 75 ? UNP Q9VKJ9 ? ? 'expression tag' 69 34 2 7ZSD LEU P 76 ? UNP Q9VKJ9 ? ? 'expression tag' 70 35 2 7ZSD TYR P 77 ? UNP Q9VKJ9 ? ? 'expression tag' 71 36 2 7ZSD PHE P 78 ? UNP Q9VKJ9 ? ? 'expression tag' 72 37 2 7ZSD GLN P 79 ? UNP Q9VKJ9 ? ? 'expression tag' 73 38 # 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 7ZSD _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _refine.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine.entry_id 7ZSD _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' ? 0.003 ? 2180 ? f_bond_d ? ? 'ELECTRON MICROSCOPY' ? 0.565 ? 2961 ? f_angle_d ? ? 'ELECTRON MICROSCOPY' ? 9.638 ? 307 ? f_dihedral_angle_d ? ? 'ELECTRON MICROSCOPY' ? 0.046 ? 314 ? f_chiral_restr ? ? 'ELECTRON MICROSCOPY' ? 0.003 ? 387 ? f_plane_restr ? ? # _struct.entry_id 7ZSD _struct.title 'cryo-EM structure of omicron spike in complex with de novo designed binder, local' _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 7ZSD _struct_keywords.text 'SARS-COV2, de novo, design binder, spike, RBD, receptor binding domain, ANTIVIRAL PROTEIN' _struct_keywords.pdbx_keywords 'ANTIVIRAL 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 PRO A 6 ? ASN A 12 ? PRO M 337 ASN M 343 1 ? 7 HELX_P HELX_P2 AA2 SER A 18 ? TRP A 22 ? SER M 349 TRP M 353 5 ? 5 HELX_P HELX_P3 AA3 TYR A 34 ? LEU A 40 ? TYR M 365 LEU M 371 1 ? 7 HELX_P HELX_P4 AA4 SER A 52 ? LEU A 59 ? SER M 383 LEU M 390 1 ? 8 HELX_P HELX_P5 AA5 ASP A 74 ? ILE A 79 ? ASP M 405 ILE M 410 5 ? 6 HELX_P HELX_P6 AA6 GLY A 85 ? ASN A 91 ? GLY M 416 ASN M 422 1 ? 7 HELX_P HELX_P7 AA7 MET B 9 ? GLU B 30 ? MET P 3 GLU P 24 1 ? 22 HELX_P HELX_P8 AA8 ASN B 32 ? ALA B 55 ? ASN P 26 ALA P 49 1 ? 24 # _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 5 SG ? ? ? 1_555 A CYS 30 SG ? ? M CYS 336 M CYS 361 1_555 ? ? ? ? ? ? ? 2.033 ? ? disulf2 disulf ? ? A CYS 48 SG ? ? ? 1_555 A CYS 101 SG ? ? M CYS 379 M CYS 432 1_555 ? ? ? ? ? ? ? 2.028 ? ? disulf3 disulf ? ? A CYS 60 SG ? ? ? 1_555 A CYS 194 SG ? ? M CYS 391 M CYS 525 1_555 ? ? ? ? ? ? ? 2.028 ? ? disulf4 disulf ? ? A CYS 149 SG ? ? ? 1_555 A CYS 157 SG ? ? M CYS 480 M CYS 488 1_555 ? ? ? ? ? ? ? 2.034 ? ? covale1 covale one ? A ASN 12 ND2 ? ? ? 1_555 C NAG . C1 ? ? M ASN 343 A NAG 1 1_555 ? ? ? ? ? ? ? 1.444 ? N-Glycosylation covale2 covale both ? C NAG . O4 ? ? ? 1_555 C NAG . C1 ? ? A NAG 1 A NAG 2 1_555 ? ? ? ? ? ? ? 1.449 ? ? # 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 ? 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 ? 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 23 ? ILE A 27 ? ASN M 354 ILE M 358 AA1 2 VAL A 64 ? ARG A 72 ? VAL M 395 ARG M 403 AA1 3 PRO A 176 ? SER A 183 ? PRO M 507 SER M 514 AA1 4 GLY A 100 ? ASN A 106 ? GLY M 431 ASN M 437 AA1 5 CYS A 48 ? TYR A 49 ? CYS M 379 TYR M 380 AA2 1 LEU A 121 ? ARG A 123 ? LEU M 452 ARG M 454 AA2 2 LEU A 161 ? SER A 163 ? LEU M 492 SER M 494 # 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 27 ? N ILE M 358 O VAL A 64 ? O VAL M 395 AA1 2 3 N ASP A 67 ? N ASP M 398 O VAL A 181 ? O VAL M 512 AA1 3 4 O VAL A 180 ? O VAL M 511 N ILE A 103 ? N ILE M 434 AA1 4 5 O GLY A 100 ? O GLY M 431 N TYR A 49 ? N TYR M 380 AA2 1 2 N TYR A 122 ? N TYR M 453 O ARG A 162 ? O ARG M 493 # _atom_sites.entry_id 7ZSD _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 ILE 1 332 332 ILE ILE M . n A 1 2 THR 2 333 333 THR THR M . n A 1 3 ASN 3 334 334 ASN ASN M . n A 1 4 LEU 4 335 335 LEU LEU M . n A 1 5 CYS 5 336 336 CYS CYS M . n A 1 6 PRO 6 337 337 PRO PRO M . n A 1 7 PHE 7 338 338 PHE PHE M . n A 1 8 ASP 8 339 339 ASP ASP M . n A 1 9 GLU 9 340 340 GLU GLU M . n A 1 10 VAL 10 341 341 VAL VAL M . n A 1 11 PHE 11 342 342 PHE PHE M . n A 1 12 ASN 12 343 343 ASN ASN M . n A 1 13 ALA 13 344 344 ALA ALA M . n A 1 14 THR 14 345 345 THR THR M . n A 1 15 ARG 15 346 346 ARG ARG M . n A 1 16 PHE 16 347 347 PHE PHE M . n A 1 17 ALA 17 348 348 ALA ALA M . n A 1 18 SER 18 349 349 SER SER M . n A 1 19 VAL 19 350 350 VAL VAL M . n A 1 20 TYR 20 351 351 TYR TYR M . n A 1 21 ALA 21 352 352 ALA ALA M . n A 1 22 TRP 22 353 353 TRP TRP M . n A 1 23 ASN 23 354 354 ASN ASN M . n A 1 24 ARG 24 355 355 ARG ARG M . n A 1 25 LYS 25 356 356 LYS LYS M . n A 1 26 ARG 26 357 357 ARG ARG M . n A 1 27 ILE 27 358 358 ILE ILE M . n A 1 28 SER 28 359 359 SER SER M . n A 1 29 ASN 29 360 360 ASN ASN M . n A 1 30 CYS 30 361 361 CYS CYS M . n A 1 31 VAL 31 362 362 VAL VAL M . n A 1 32 ALA 32 363 363 ALA ALA M . n A 1 33 ASP 33 364 364 ASP ASP M . n A 1 34 TYR 34 365 365 TYR TYR M . n A 1 35 SER 35 366 366 SER SER M . n A 1 36 VAL 36 367 367 VAL VAL M . n A 1 37 LEU 37 368 368 LEU LEU M . n A 1 38 TYR 38 369 369 TYR TYR M . n A 1 39 ASN 39 370 370 ASN ASN M . n A 1 40 LEU 40 371 371 LEU LEU M . n A 1 41 ALA 41 372 372 ALA ALA M . n A 1 42 PRO 42 373 373 PRO PRO M . n A 1 43 PHE 43 374 374 PHE PHE M . n A 1 44 PHE 44 375 375 PHE PHE M . n A 1 45 THR 45 376 376 THR THR M . n A 1 46 PHE 46 377 377 PHE PHE M . n A 1 47 LYS 47 378 378 LYS LYS M . n A 1 48 CYS 48 379 379 CYS CYS M . n A 1 49 TYR 49 380 380 TYR TYR M . n A 1 50 GLY 50 381 381 GLY GLY M . n A 1 51 VAL 51 382 382 VAL VAL M . n A 1 52 SER 52 383 383 SER SER M . n A 1 53 PRO 53 384 384 PRO PRO M . n A 1 54 THR 54 385 385 THR THR M . n A 1 55 LYS 55 386 386 LYS LYS M . n A 1 56 LEU 56 387 387 LEU LEU M . n A 1 57 ASN 57 388 388 ASN ASN M . n A 1 58 ASP 58 389 389 ASP ASP M . n A 1 59 LEU 59 390 390 LEU LEU M . n A 1 60 CYS 60 391 391 CYS CYS M . n A 1 61 PHE 61 392 392 PHE PHE M . n A 1 62 THR 62 393 393 THR THR M . n A 1 63 ASN 63 394 394 ASN ASN M . n A 1 64 VAL 64 395 395 VAL VAL M . n A 1 65 TYR 65 396 396 TYR TYR M . n A 1 66 ALA 66 397 397 ALA ALA M . n A 1 67 ASP 67 398 398 ASP ASP M . n A 1 68 SER 68 399 399 SER SER M . n A 1 69 PHE 69 400 400 PHE PHE M . n A 1 70 VAL 70 401 401 VAL VAL M . n A 1 71 ILE 71 402 402 ILE ILE M . n A 1 72 ARG 72 403 403 ARG ARG M . n A 1 73 GLY 73 404 404 GLY GLY M . n A 1 74 ASP 74 405 405 ASP ASP M . n A 1 75 GLU 75 406 406 GLU GLU M . n A 1 76 VAL 76 407 407 VAL VAL M . n A 1 77 ARG 77 408 408 ARG ARG M . n A 1 78 GLN 78 409 409 GLN GLN M . n A 1 79 ILE 79 410 410 ILE ILE M . n A 1 80 ALA 80 411 411 ALA ALA M . n A 1 81 PRO 81 412 412 PRO PRO M . n A 1 82 GLY 82 413 413 GLY GLY M . n A 1 83 GLN 83 414 414 GLN GLN M . n A 1 84 THR 84 415 415 THR THR M . n A 1 85 GLY 85 416 416 GLY GLY M . n A 1 86 ASN 86 417 417 ASN ASN M . n A 1 87 ILE 87 418 418 ILE ILE M . n A 1 88 ALA 88 419 419 ALA ALA M . n A 1 89 ASP 89 420 420 ASP ASP M . n A 1 90 TYR 90 421 421 TYR TYR M . n A 1 91 ASN 91 422 422 ASN ASN M . n A 1 92 TYR 92 423 423 TYR TYR M . n A 1 93 LYS 93 424 424 LYS LYS M . n A 1 94 LEU 94 425 425 LEU LEU M . n A 1 95 PRO 95 426 426 PRO PRO M . n A 1 96 ASP 96 427 427 ASP ASP M . n A 1 97 ASP 97 428 428 ASP ASP M . n A 1 98 PHE 98 429 429 PHE PHE M . n A 1 99 THR 99 430 430 THR THR M . n A 1 100 GLY 100 431 431 GLY GLY M . n A 1 101 CYS 101 432 432 CYS CYS M . n A 1 102 VAL 102 433 433 VAL VAL M . n A 1 103 ILE 103 434 434 ILE ILE M . n A 1 104 ALA 104 435 435 ALA ALA M . n A 1 105 TRP 105 436 436 TRP TRP M . n A 1 106 ASN 106 437 437 ASN ASN M . n A 1 107 SER 107 438 438 SER SER M . n A 1 108 ASN 108 439 439 ASN ASN M . n A 1 109 LYS 109 440 440 LYS LYS M . n A 1 110 LEU 110 441 441 LEU LEU M . n A 1 111 ASP 111 442 442 ASP ASP M . n A 1 112 SER 112 443 443 SER SER M . n A 1 113 LYS 113 444 444 LYS LYS M . n A 1 114 VAL 114 445 445 VAL VAL M . n A 1 115 SER 115 446 446 SER SER M . n A 1 116 GLY 116 447 447 GLY GLY M . n A 1 117 ASN 117 448 448 ASN ASN M . n A 1 118 TYR 118 449 449 TYR TYR M . n A 1 119 ASN 119 450 450 ASN ASN M . n A 1 120 TYR 120 451 451 TYR TYR M . n A 1 121 LEU 121 452 452 LEU LEU M . n A 1 122 TYR 122 453 453 TYR TYR M . n A 1 123 ARG 123 454 454 ARG ARG M . n A 1 124 LEU 124 455 455 LEU LEU M . n A 1 125 PHE 125 456 456 PHE PHE M . n A 1 126 ARG 126 457 457 ARG ARG M . n A 1 127 LYS 127 458 458 LYS LYS M . n A 1 128 SER 128 459 459 SER SER M . n A 1 129 ASN 129 460 460 ASN ASN M . n A 1 130 LEU 130 461 461 LEU LEU M . n A 1 131 LYS 131 462 462 LYS LYS M . n A 1 132 PRO 132 463 463 PRO PRO M . n A 1 133 PHE 133 464 464 PHE PHE M . n A 1 134 GLU 134 465 465 GLU GLU M . n A 1 135 ARG 135 466 466 ARG ARG M . n A 1 136 ASP 136 467 467 ASP ASP M . n A 1 137 ILE 137 468 468 ILE ILE M . n A 1 138 SER 138 469 469 SER SER M . n A 1 139 THR 139 470 470 THR THR M . n A 1 140 GLU 140 471 471 GLU GLU M . n A 1 141 ILE 141 472 472 ILE ILE M . n A 1 142 TYR 142 473 473 TYR TYR M . n A 1 143 GLN 143 474 474 GLN GLN M . n A 1 144 ALA 144 475 475 ALA ALA M . n A 1 145 GLY 145 476 476 GLY GLY M . n A 1 146 ASN 146 477 477 ASN ASN M . n A 1 147 LYS 147 478 478 LYS LYS M . n A 1 148 PRO 148 479 479 PRO PRO M . n A 1 149 CYS 149 480 480 CYS CYS M . n A 1 150 ASN 150 481 481 ASN ASN M . n A 1 151 GLY 151 482 482 GLY GLY M . n A 1 152 VAL 152 483 483 VAL VAL M . n A 1 153 ALA 153 484 484 ALA ALA M . n A 1 154 GLY 154 485 485 GLY GLY M . n A 1 155 PHE 155 486 486 PHE PHE M . n A 1 156 ASN 156 487 487 ASN ASN M . n A 1 157 CYS 157 488 488 CYS CYS M . n A 1 158 TYR 158 489 489 TYR TYR M . n A 1 159 PHE 159 490 490 PHE PHE M . n A 1 160 PRO 160 491 491 PRO PRO M . n A 1 161 LEU 161 492 492 LEU LEU M . n A 1 162 ARG 162 493 493 ARG ARG M . n A 1 163 SER 163 494 494 SER SER M . n A 1 164 TYR 164 495 495 TYR TYR M . n A 1 165 SER 165 496 496 SER SER M . n A 1 166 PHE 166 497 497 PHE PHE M . n A 1 167 ARG 167 498 498 ARG ARG M . n A 1 168 PRO 168 499 499 PRO PRO M . n A 1 169 THR 169 500 500 THR THR M . n A 1 170 TYR 170 501 501 TYR TYR M . n A 1 171 GLY 171 502 502 GLY GLY M . n A 1 172 VAL 172 503 503 VAL VAL M . n A 1 173 GLY 173 504 504 GLY GLY M . n A 1 174 HIS 174 505 505 HIS HIS M . n A 1 175 GLN 175 506 506 GLN GLN M . n A 1 176 PRO 176 507 507 PRO PRO M . n A 1 177 TYR 177 508 508 TYR TYR M . n A 1 178 ARG 178 509 509 ARG ARG M . n A 1 179 VAL 179 510 510 VAL VAL M . n A 1 180 VAL 180 511 511 VAL VAL M . n A 1 181 VAL 181 512 512 VAL VAL M . n A 1 182 LEU 182 513 513 LEU LEU M . n A 1 183 SER 183 514 514 SER SER M . n A 1 184 PHE 184 515 515 PHE PHE M . n A 1 185 GLU 185 516 516 GLU GLU M . n A 1 186 LEU 186 517 517 LEU LEU M . n A 1 187 LEU 187 518 518 LEU LEU M . n A 1 188 HIS 188 519 519 HIS HIS M . n A 1 189 ALA 189 520 520 ALA ALA M . n A 1 190 PRO 190 521 521 PRO PRO M . n A 1 191 ALA 191 522 522 ALA ALA M . n A 1 192 THR 192 523 523 THR THR M . n A 1 193 VAL 193 524 524 VAL VAL M . n A 1 194 CYS 194 525 525 CYS CYS M . n A 1 195 GLY 195 526 526 GLY GLY M . n A 1 196 PRO 196 527 527 PRO PRO M . n B 2 1 GLU 1 -5 ? ? ? P . n B 2 2 THR 2 -4 ? ? ? P . n B 2 3 GLY 3 -3 ? ? ? P . n B 2 4 ALA 4 -2 ? ? ? P . n B 2 5 SER 5 -1 ? ? ? P . n B 2 6 SER 6 0 ? ? ? P . n B 2 7 THR 7 1 1 THR THR P . n B 2 8 ASN 8 2 2 ASN ASN P . n B 2 9 MET 9 3 3 MET MET P . n B 2 10 LEU 10 4 4 LEU LEU P . n B 2 11 GLU 11 5 5 GLU GLU P . n B 2 12 ALA 12 6 6 ALA ALA P . n B 2 13 LEU 13 7 7 LEU LEU P . n B 2 14 GLN 14 8 8 GLN GLN P . n B 2 15 GLN 15 9 9 GLN GLN P . n B 2 16 ARG 16 10 10 ARG ARG P . n B 2 17 LEU 17 11 11 LEU LEU P . n B 2 18 GLN 18 12 12 GLN GLN P . n B 2 19 PHE 19 13 13 PHE PHE P . n B 2 20 TYR 20 14 14 TYR TYR P . n B 2 21 HIS 21 15 15 HIS HIS P . n B 2 22 GLY 22 16 16 GLY GLY P . n B 2 23 GLN 23 17 17 GLN GLN P . n B 2 24 VAL 24 18 18 VAL VAL P . n B 2 25 ALA 25 19 19 ALA ALA P . n B 2 26 ARG 26 20 20 ARG ARG P . n B 2 27 ALA 27 21 21 ALA ALA P . n B 2 28 ALA 28 22 22 ALA ALA P . n B 2 29 LEU 29 23 23 LEU LEU P . n B 2 30 GLU 30 24 24 GLU GLU P . n B 2 31 ASN 31 25 25 ASN ASN P . n B 2 32 ASN 32 26 26 ASN ASN P . n B 2 33 SER 33 27 27 SER SER P . n B 2 34 GLY 34 28 28 GLY GLY P . n B 2 35 LYS 35 29 29 LYS LYS P . n B 2 36 ALA 36 30 30 ALA ALA P . n B 2 37 ARG 37 31 31 ARG ARG P . n B 2 38 ARG 38 32 32 ARG ARG P . n B 2 39 PHE 39 33 33 PHE PHE P . n B 2 40 GLY 40 34 34 GLY GLY P . n B 2 41 ARG 41 35 35 ARG ARG P . n B 2 42 ILE 42 36 36 ILE ILE P . n B 2 43 VAL 43 37 37 VAL VAL P . n B 2 44 LYS 44 38 38 LYS LYS P . n B 2 45 GLN 45 39 39 GLN GLN P . n B 2 46 TYR 46 40 40 TYR TYR P . n B 2 47 GLU 47 41 41 GLU GLU P . n B 2 48 ASP 48 42 42 ASP ASP P . n B 2 49 ALA 49 43 43 ALA ALA P . n B 2 50 ILE 50 44 44 ILE ILE P . n B 2 51 LYS 51 45 45 LYS LYS P . n B 2 52 LEU 52 46 46 LEU LEU P . n B 2 53 TYR 53 47 47 TYR TYR P . n B 2 54 LYS 54 48 48 LYS LYS P . n B 2 55 ALA 55 49 49 ALA ALA P . n B 2 56 GLY 56 50 50 GLY GLY P . n B 2 57 LYS 57 51 51 LYS LYS P . n B 2 58 PRO 58 52 52 PRO PRO P . n B 2 59 VAL 59 53 53 VAL VAL P . n B 2 60 PRO 60 54 54 PRO PRO P . n B 2 61 TYR 61 55 55 TYR TYR P . n B 2 62 ASP 62 56 56 ASP ASP P . n B 2 63 GLU 63 57 57 GLU GLU P . n B 2 64 LEU 64 58 58 LEU LEU P . n B 2 65 PRO 65 59 59 PRO PRO P . n B 2 66 VAL 66 60 60 VAL VAL P . n B 2 67 PRO 67 61 61 PRO PRO P . n B 2 68 PRO 68 62 62 PRO PRO P . n B 2 69 GLY 69 63 63 GLY GLY P . n B 2 70 PHE 70 64 64 PHE PHE P . n B 2 71 GLY 71 65 65 GLY GLY P . n B 2 72 GLY 72 66 ? ? ? P . n B 2 73 SER 73 67 ? ? ? P . n B 2 74 GLU 74 68 ? ? ? P . n B 2 75 ASN 75 69 ? ? ? P . n B 2 76 LEU 76 70 ? ? ? P . n B 2 77 TYR 77 71 ? ? ? P . n B 2 78 PHE 78 72 ? ? ? P . n B 2 79 GLN 79 73 ? ? ? P . n # loop_ _pdbx_contact_author.id _pdbx_contact_author.email _pdbx_contact_author.name_first _pdbx_contact_author.name_last _pdbx_contact_author.name_mi _pdbx_contact_author.role _pdbx_contact_author.identifier_ORCID 3 henning.stahlberg@epfl.ch Henning Stahlberg ? 'principal investigator/group leader' 0000-0002-1185-4592 4 bruno.correia@epfl.ch Bruno Correia ? 'principal investigator/group leader' 0000-0002-7377-8636 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _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)' 2140 ? 1 MORE -3 ? 1 'SSA (A^2)' 13950 ? # _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 2023-03-01 2 'Structure model' 1 1 2023-04-26 3 'Structure model' 1 2 2023-05-10 4 'Structure model' 1 3 2023-05-17 5 'Structure model' 1 4 2023-05-24 # _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' 'Database references' 2 3 'Structure model' 'Database references' 3 4 'Structure model' 'Database references' 4 5 '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' citation 2 3 'Structure model' citation 3 3 'Structure model' citation_author 4 4 'Structure model' citation 5 5 'Structure model' citation # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_citation.country' 2 2 'Structure model' '_citation.journal_abbrev' 3 2 'Structure model' '_citation.journal_id_ASTM' 4 2 'Structure model' '_citation.journal_id_CSD' 5 2 'Structure model' '_citation.journal_id_ISSN' 6 2 'Structure model' '_citation.pdbx_database_id_DOI' 7 2 'Structure model' '_citation.year' 8 3 'Structure model' '_citation.page_first' 9 3 'Structure model' '_citation.page_last' 10 3 'Structure model' '_citation.pdbx_database_id_PubMed' 11 3 'Structure model' '_citation.title' 12 4 'Structure model' '_citation.journal_volume' 13 4 'Structure model' '_citation.page_first' 14 4 'Structure model' '_citation.page_last' 15 4 'Structure model' '_citation.pdbx_database_id_PubMed' 16 4 'Structure model' '_citation.title' 17 5 'Structure model' '_citation.page_first' 18 5 'Structure model' '_citation.page_last' 19 5 'Structure model' '_citation.pdbx_database_id_PubMed' 20 5 'Structure model' '_citation.title' # _software.citation_id ? _software.classification refinement _software.compiler_name ? _software.compiler_version ? _software.contact_author ? _software.contact_author_email ? _software.date ? _software.description ? _software.dependencies ? _software.hardware ? _software.language ? _software.location ? _software.mods ? _software.name PHENIX _software.os ? _software.os_version ? _software.type ? _software.version 1.19.2_4158: _software.pdbx_ordinal 1 # _pdbx_entry_details.entry_id 7ZSD _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 7ZSD _em_3d_fitting.id 1 _em_3d_fitting.details ? _em_3d_fitting.overall_b_value 33.8 _em_3d_fitting.ref_protocol 'AB INITIO MODEL' _em_3d_fitting.ref_space REAL _em_3d_fitting.target_criteria ? _em_3d_fitting.method ? # _em_3d_fitting_list.3d_fitting_id 1 _em_3d_fitting_list.id 1 _em_3d_fitting_list.details ? _em_3d_fitting_list.pdb_chain_id ? _em_3d_fitting_list.pdb_chain_residue_range ? _em_3d_fitting_list.pdb_entry_id 7QO7 # _em_3d_reconstruction.entry_id 7ZSD _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 50758 _em_3d_reconstruction.resolution 3.29 _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 7.5 _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 ? 'omicron spike in complex with de novo designed binder' 'MULTIPLE SOURCES' COMPLEX '1, 2' ? ? 2 1 ? 'omicron spike' RECOMBINANT COMPLEX 1 ? ? 3 1 ? 'de novo designed binder' RECOMBINANT COMPLEX 2 ? ? # _em_imaging.id 1 _em_imaging.entry_id 7ZSD _em_imaging.accelerating_voltage 300 _em_imaging.alignment_procedure 'COMA FREE' _em_imaging.c2_aperture_diameter ? _em_imaging.calibrated_defocus_max ? _em_imaging.calibrated_defocus_min ? _em_imaging.calibrated_magnification ? _em_imaging.cryogen NITROGEN _em_imaging.details ? _em_imaging.electron_source 'FIELD EMISSION GUN' _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.microscope_model 'FEI TITAN KRIOS' _em_imaging.mode 'BRIGHT FIELD' _em_imaging.nominal_cs 2.7 _em_imaging.nominal_defocus_max 2000 _em_imaging.nominal_defocus_min 800 _em_imaging.nominal_magnification 165000 _em_imaging.recording_temperature_maximum ? _em_imaging.recording_temperature_minimum ? _em_imaging.residual_tilt ? _em_imaging.specimen_holder_model 'FEI TITAN KRIOS AUTOGRID HOLDER' _em_imaging.specimen_id 1 _em_imaging.citation_id ? _em_imaging.date ? _em_imaging.temperature ? _em_imaging.tilt_angle_min ? _em_imaging.tilt_angle_max ? _em_imaging.astigmatism ? _em_imaging.detector_distance ? _em_imaging.electron_beam_tilt_params ? _em_imaging.specimen_holder_type ? # _em_sample_support.id 1 _em_sample_support.specimen_id 1 _em_sample_support.details ? _em_sample_support.grid_material ? _em_sample_support.grid_mesh_size ? _em_sample_support.grid_type 'Quantifoil R2/1' _em_sample_support.method ? _em_sample_support.film_material ? # _em_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.chamber_temperature 298 _em_vitrification.cryogen_name ETHANE _em_vitrification.details ? _em_vitrification.humidity 90 _em_vitrification.instrument 'FEI VITROBOT MARK IV' _em_vitrification.entry_id 7ZSD _em_vitrification.citation_id ? _em_vitrification.method ? _em_vitrification.temp ? _em_vitrification.time_resolved_state ? # _em_experiment.entry_id 7ZSD _em_experiment.id 1 _em_experiment.aggregation_state PARTICLE _em_experiment.reconstruction_method 'SINGLE PARTICLE' _em_experiment.entity_assembly_id 1 # _em_single_particle_entity.entry_id 7ZSD _em_single_particle_entity.id 1 _em_single_particle_entity.image_processing_id 1 _em_single_particle_entity.point_symmetry C1 # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 PRO M 337 ? ? -81.23 49.11 2 1 ALA M 372 ? ? 53.52 75.22 3 1 ALA M 411 ? ? -171.17 149.15 4 1 PHE M 486 ? ? -67.57 -175.57 5 1 ASN M 487 ? ? -69.67 65.36 6 1 TYR M 489 ? ? 65.41 163.96 7 1 ASN P 2 ? ? 39.61 -135.80 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 P GLU -5 ? B GLU 1 2 1 Y 1 P THR -4 ? B THR 2 3 1 Y 1 P GLY -3 ? B GLY 3 4 1 Y 1 P ALA -2 ? B ALA 4 5 1 Y 1 P SER -1 ? B SER 5 6 1 Y 1 P SER 0 ? B SER 6 7 1 Y 1 P GLY 66 ? B GLY 72 8 1 Y 1 P SER 67 ? B SER 73 9 1 Y 1 P GLU 68 ? B GLU 74 10 1 Y 1 P ASN 69 ? B ASN 75 11 1 Y 1 P LEU 70 ? B LEU 76 12 1 Y 1 P TYR 71 ? B TYR 77 13 1 Y 1 P PHE 72 ? B PHE 78 14 1 Y 1 P GLN 73 ? B GLN 79 # _em_ctf_correction.id 1 _em_ctf_correction.em_image_processing_id 1 _em_ctf_correction.type NONE _em_ctf_correction.details ? # _em_entity_assembly_molwt.entity_assembly_id 1 _em_entity_assembly_molwt.id 1 _em_entity_assembly_molwt.experimental_flag YES _em_entity_assembly_molwt.units MEGADALTONS _em_entity_assembly_molwt.value 0.45 # 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 ? ? 7227 ? ? 'Drosophila melanogaster' ? ? # 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 60 _em_image_recording.average_exposure_time 5.82 _em_image_recording.details ? _em_image_recording.detector_mode ? _em_image_recording.film_or_detector_model 'FEI FALCON IV (4k x 4k)' _em_image_recording.num_diffraction_images ? _em_image_recording.num_grids_imaged ? _em_image_recording.num_real_images ? _em_image_recording.avg_electron_dose_per_subtomogram ? # _em_imaging_optics.id 1 _em_imaging_optics.imaging_id 1 _em_imaging_optics.chr_aberration_corrector ? _em_imaging_optics.energyfilter_lower ? _em_imaging_optics.energyfilter_name 'TFS Selectris X' _em_imaging_optics.energyfilter_upper ? _em_imaging_optics.energyfilter_slit_width ? _em_imaging_optics.phase_plate ? _em_imaging_optics.sph_aberration_corrector ? _em_imaging_optics.details ? # _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 1820333 _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 'PARTICLE SELECTION' ? cryoSPARC ? 1 ? ? 2 'IMAGE ACQUISITION' ? EPU ? ? ? 1 3 MASKING ? ? ? ? ? ? 4 'CTF CORRECTION' ? cryoSPARC ? 1 ? ? 5 'LAYERLINE INDEXING' ? ? ? ? ? ? 6 'DIFFRACTION INDEXING' ? ? ? ? ? ? 7 'MODEL FITTING' ? 'UCSF Chimera' ? ? 1 ? 8 'MODEL FITTING' ? Coot ? ? 1 ? 9 OTHER ? ? ? ? ? ? 10 'MODEL REFINEMENT' ? PHENIX ? ? 1 ? 11 'INITIAL EULER ASSIGNMENT' ? cryoSPARC ? 1 ? ? 12 'FINAL EULER ASSIGNMENT' ? cryoSPARC ? 1 ? ? 13 CLASSIFICATION ? cryoSPARC ? 1 ? ? 14 RECONSTRUCTION ? cryoSPARC ? 1 ? ? # _em_specimen.id 1 _em_specimen.experiment_id 1 _em_specimen.concentration 1.0 _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_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'European Research Council (ERC)' 'European Union' 'European Research Council (starting grant no. 716058)' 1 'Swiss National Science Foundation' Switzerland 'NCCR transcure 185544' 2 'Swiss National Science Foundation' Switzerland 310030_188744 3 'Swiss National Science Foundation' Switzerland 'NCCR Molecular Systems Engineering' 4 'Swiss National Science Foundation' Switzerland 'NCCR Chemical Biology' 5 # loop_ _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_mon_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.hetero C 3 NAG 1 A NAG 1 M NAG 528 n C 3 NAG 2 A NAG 2 M NAG 529 n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier NAG 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DGlcpNAcb NAG 'COMMON NAME' GMML 1.0 N-acetyl-b-D-glucopyranosamine NAG 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 b-D-GlcpNAc NAG 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 GlcNAc # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_descriptor.ordinal _pdbx_entity_branch_descriptor.entity_id _pdbx_entity_branch_descriptor.descriptor _pdbx_entity_branch_descriptor.type _pdbx_entity_branch_descriptor.program _pdbx_entity_branch_descriptor.program_version 1 3 DGlcpNAcb1-4DGlcpNAcb1- 'Glycam Condensed Sequence' GMML 1.0 2 3 'WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1' WURCS PDB2Glycan 1.1.0 3 3 '[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}' LINUCS PDB-CARE ? # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.entity_id 3 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.value_order sing _pdbx_entity_branch_link.details ? # loop_ _pdbx_entity_branch_list.entity_id _pdbx_entity_branch_list.comp_id _pdbx_entity_branch_list.num _pdbx_entity_branch_list.hetero 3 NAG 1 n 3 NAG 2 n # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 7QO7 # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'electron microscopy' _pdbx_struct_assembly_auth_evidence.details ? #