data_9N2L # _entry.id 9N2L # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.402 _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 9N2L pdb_00009n2l 10.2210/pdb9n2l/pdb WWPDB D_1000292268 ? ? EMDB EMD-48839 ? ? # 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 _pdbx_audit_revision_history.part_number 1 'Structure model' 1 0 2025-03-05 ? 2 'EM metadata' 1 0 2025-03-05 ? 3 FSC 1 0 2025-03-05 ? 4 'Half map' 1 0 2025-03-05 1 5 'Half map' 1 0 2025-03-05 2 6 Image 1 0 2025-03-05 ? 7 'Primary map' 1 0 2025-03-05 ? 8 'Structure model' 1 1 2025-03-19 ? # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description _pdbx_audit_revision_details.details 1 1 'Structure model' repository 'Initial release' ? ? 2 2 'EM metadata' repository 'Initial release' ? ? 3 3 FSC repository 'Initial release' ? ? 4 4 'Half map' repository 'Initial release' ? ? 5 5 'Half map' repository 'Initial release' ? ? 6 6 Image repository 'Initial release' ? ? 7 7 'Primary map' repository 'Initial release' ? ? # 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 8 'Structure model' 'Data collection' 2 8 '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 8 'Structure model' citation 2 8 'Structure model' em_admin # 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 8 'Structure model' '_citation.page_last' 2 8 'Structure model' '_citation.pdbx_database_id_PubMed' 3 8 'Structure model' '_citation.title' 4 8 'Structure model' '_em_admin.last_update' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 9N2L _pdbx_database_status.recvd_initial_deposition_date 2025-01-29 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # _pdbx_database_related.db_name EMDB _pdbx_database_related.details 'Cryo-EM structure of locally refined up conformation of SARS-CoV-2 spike protein Receptor Binding Domain' _pdbx_database_related.db_id EMD-48839 _pdbx_database_related.content_type 'associated EM volume' # _pdbx_contact_author.id 2 _pdbx_contact_author.email sshasan@som.umaryland.edu _pdbx_contact_author.name_first S.Saif _pdbx_contact_author.name_last Hasan _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0002-4306-9345 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Singh, S.' 1 ? 'Hasan, S.S.' 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 NE _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'J Struct Biol X' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 2590-1524 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 11 _citation.language ? _citation.page_first 100123 _citation.page_last 100123 _citation.title 'Production and cryo-electron microscopy structure of an internally tagged SARS-CoV-2 spike ecto-domain construct.' _citation.year 2025 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1016/j.yjsbx.2025.100123 _citation.pdbx_database_id_PubMed 40046771 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Singh, S.' 1 ? primary 'Liu, Y.' 2 ? primary 'Burke, M.' 3 ? primary 'Rayaprolu, V.' 4 ? primary 'Stein, S.E.' 5 ? primary 'Hasan, S.S.' 6 ? # _entity.id 1 _entity.type polymer _entity.src_method man _entity.pdbx_description 'Spike protein S1' _entity.formula_weight 25122.336 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code ;RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYAD SFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGST PCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNF ; _entity_poly.pdbx_seq_one_letter_code_can ;RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYAD SFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGST PCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNF ; _entity_poly.pdbx_strand_id F _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 ARG n 1 2 VAL n 1 3 GLN n 1 4 PRO n 1 5 THR n 1 6 GLU n 1 7 SER n 1 8 ILE n 1 9 VAL n 1 10 ARG n 1 11 PHE n 1 12 PRO n 1 13 ASN n 1 14 ILE n 1 15 THR n 1 16 ASN n 1 17 LEU n 1 18 CYS n 1 19 PRO n 1 20 PHE n 1 21 GLY n 1 22 GLU n 1 23 VAL n 1 24 PHE n 1 25 ASN n 1 26 ALA n 1 27 THR n 1 28 ARG n 1 29 PHE n 1 30 ALA n 1 31 SER n 1 32 VAL n 1 33 TYR n 1 34 ALA n 1 35 TRP n 1 36 ASN n 1 37 ARG n 1 38 LYS n 1 39 ARG n 1 40 ILE n 1 41 SER n 1 42 ASN n 1 43 CYS n 1 44 VAL n 1 45 ALA n 1 46 ASP n 1 47 TYR n 1 48 SER n 1 49 VAL n 1 50 LEU n 1 51 TYR n 1 52 ASN n 1 53 SER n 1 54 ALA n 1 55 SER n 1 56 PHE n 1 57 SER n 1 58 THR n 1 59 PHE n 1 60 LYS n 1 61 CYS n 1 62 TYR n 1 63 GLY n 1 64 VAL n 1 65 SER n 1 66 PRO n 1 67 THR n 1 68 LYS n 1 69 LEU n 1 70 ASN n 1 71 ASP n 1 72 LEU n 1 73 CYS n 1 74 PHE n 1 75 THR n 1 76 ASN n 1 77 VAL n 1 78 TYR n 1 79 ALA n 1 80 ASP n 1 81 SER n 1 82 PHE n 1 83 VAL n 1 84 ILE n 1 85 ARG n 1 86 GLY n 1 87 ASP n 1 88 GLU n 1 89 VAL n 1 90 ARG n 1 91 GLN n 1 92 ILE n 1 93 ALA n 1 94 PRO n 1 95 GLY n 1 96 GLN n 1 97 THR n 1 98 GLY n 1 99 LYS n 1 100 ILE n 1 101 ALA n 1 102 ASP n 1 103 TYR n 1 104 ASN n 1 105 TYR n 1 106 LYS n 1 107 LEU n 1 108 PRO n 1 109 ASP n 1 110 ASP n 1 111 PHE n 1 112 THR n 1 113 GLY n 1 114 CYS n 1 115 VAL n 1 116 ILE n 1 117 ALA n 1 118 TRP n 1 119 ASN n 1 120 SER n 1 121 ASN n 1 122 ASN n 1 123 LEU n 1 124 ASP n 1 125 SER n 1 126 LYS n 1 127 VAL n 1 128 GLY n 1 129 GLY n 1 130 ASN n 1 131 TYR n 1 132 ASN n 1 133 TYR n 1 134 LEU n 1 135 TYR n 1 136 ARG n 1 137 LEU n 1 138 PHE n 1 139 ARG n 1 140 LYS n 1 141 SER n 1 142 ASN n 1 143 LEU n 1 144 LYS n 1 145 PRO n 1 146 PHE n 1 147 GLU n 1 148 ARG n 1 149 ASP n 1 150 ILE n 1 151 SER n 1 152 THR n 1 153 GLU n 1 154 ILE n 1 155 TYR n 1 156 GLN n 1 157 ALA n 1 158 GLY n 1 159 SER n 1 160 THR n 1 161 PRO n 1 162 CYS n 1 163 ASN n 1 164 GLY n 1 165 VAL n 1 166 GLU n 1 167 GLY n 1 168 PHE n 1 169 ASN n 1 170 CYS n 1 171 TYR n 1 172 PHE n 1 173 PRO n 1 174 LEU n 1 175 GLN n 1 176 SER n 1 177 TYR n 1 178 GLY n 1 179 PHE n 1 180 GLN n 1 181 PRO n 1 182 THR n 1 183 ASN n 1 184 GLY n 1 185 VAL n 1 186 GLY n 1 187 TYR n 1 188 GLN n 1 189 PRO n 1 190 TYR n 1 191 ARG n 1 192 VAL n 1 193 VAL n 1 194 VAL n 1 195 LEU n 1 196 SER n 1 197 PHE n 1 198 GLU n 1 199 LEU n 1 200 LEU n 1 201 HIS n 1 202 ALA n 1 203 PRO n 1 204 ALA n 1 205 THR n 1 206 VAL n 1 207 CYS n 1 208 GLY n 1 209 PRO n 1 210 LYS n 1 211 LYS n 1 212 SER n 1 213 THR n 1 214 ASN n 1 215 LEU n 1 216 VAL n 1 217 LYS n 1 218 ASN n 1 219 LYS n 1 220 CYS n 1 221 VAL n 1 222 ASN n 1 223 PHE n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type 'Biological sequence' _entity_src_gen.pdbx_beg_seq_num 1 _entity_src_gen.pdbx_end_seq_num 223 _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'S, 2' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Severe acute respiratory syndrome coronavirus' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 2901879 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Homo sapiens' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 9606 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # loop_ _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 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 # 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 ARG 1 319 ? ? ? F . n A 1 2 VAL 2 320 ? ? ? F . n A 1 3 GLN 3 321 ? ? ? F . n A 1 4 PRO 4 322 ? ? ? F . n A 1 5 THR 5 323 ? ? ? F . n A 1 6 GLU 6 324 ? ? ? F . n A 1 7 SER 7 325 ? ? ? F . n A 1 8 ILE 8 326 ? ? ? F . n A 1 9 VAL 9 327 ? ? ? F . n A 1 10 ARG 10 328 ? ? ? F . n A 1 11 PHE 11 329 ? ? ? F . n A 1 12 PRO 12 330 ? ? ? F . n A 1 13 ASN 13 331 ? ? ? F . n A 1 14 ILE 14 332 ? ? ? F . n A 1 15 THR 15 333 333 THR THR F . n A 1 16 ASN 16 334 334 ASN ASN F . n A 1 17 LEU 17 335 335 LEU LEU F . n A 1 18 CYS 18 336 336 CYS CYS F . n A 1 19 PRO 19 337 337 PRO PRO F . n A 1 20 PHE 20 338 338 PHE PHE F . n A 1 21 GLY 21 339 339 GLY GLY F . n A 1 22 GLU 22 340 340 GLU GLU F . n A 1 23 VAL 23 341 341 VAL VAL F . n A 1 24 PHE 24 342 342 PHE PHE F . n A 1 25 ASN 25 343 343 ASN ASN F . n A 1 26 ALA 26 344 344 ALA ALA F . n A 1 27 THR 27 345 345 THR THR F . n A 1 28 ARG 28 346 346 ARG ARG F . n A 1 29 PHE 29 347 347 PHE PHE F . n A 1 30 ALA 30 348 348 ALA ALA F . n A 1 31 SER 31 349 349 SER SER F . n A 1 32 VAL 32 350 350 VAL VAL F . n A 1 33 TYR 33 351 351 TYR TYR F . n A 1 34 ALA 34 352 352 ALA ALA F . n A 1 35 TRP 35 353 353 TRP TRP F . n A 1 36 ASN 36 354 354 ASN ASN F . n A 1 37 ARG 37 355 355 ARG ARG F . n A 1 38 LYS 38 356 356 LYS LYS F . n A 1 39 ARG 39 357 357 ARG ARG F . n A 1 40 ILE 40 358 358 ILE ILE F . n A 1 41 SER 41 359 359 SER SER F . n A 1 42 ASN 42 360 360 ASN ASN F . n A 1 43 CYS 43 361 361 CYS CYS F . n A 1 44 VAL 44 362 362 VAL VAL F . n A 1 45 ALA 45 363 363 ALA ALA F . n A 1 46 ASP 46 364 364 ASP ASP F . n A 1 47 TYR 47 365 365 TYR TYR F . n A 1 48 SER 48 366 366 SER SER F . n A 1 49 VAL 49 367 367 VAL VAL F . n A 1 50 LEU 50 368 368 LEU LEU F . n A 1 51 TYR 51 369 369 TYR TYR F . n A 1 52 ASN 52 370 370 ASN ASN F . n A 1 53 SER 53 371 371 SER SER F . n A 1 54 ALA 54 372 372 ALA ALA F . n A 1 55 SER 55 373 373 SER SER F . n A 1 56 PHE 56 374 374 PHE PHE F . n A 1 57 SER 57 375 375 SER SER F . n A 1 58 THR 58 376 376 THR THR F . n A 1 59 PHE 59 377 377 PHE PHE F . n A 1 60 LYS 60 378 378 LYS LYS F . n A 1 61 CYS 61 379 379 CYS CYS F . n A 1 62 TYR 62 380 380 TYR TYR F . n A 1 63 GLY 63 381 381 GLY GLY F . n A 1 64 VAL 64 382 382 VAL VAL F . n A 1 65 SER 65 383 383 SER SER F . n A 1 66 PRO 66 384 384 PRO PRO F . n A 1 67 THR 67 385 385 THR THR F . n A 1 68 LYS 68 386 386 LYS LYS F . n A 1 69 LEU 69 387 387 LEU LEU F . n A 1 70 ASN 70 388 388 ASN ASN F . n A 1 71 ASP 71 389 389 ASP ASP F . n A 1 72 LEU 72 390 390 LEU LEU F . n A 1 73 CYS 73 391 391 CYS CYS F . n A 1 74 PHE 74 392 392 PHE PHE F . n A 1 75 THR 75 393 393 THR THR F . n A 1 76 ASN 76 394 394 ASN ASN F . n A 1 77 VAL 77 395 395 VAL VAL F . n A 1 78 TYR 78 396 396 TYR TYR F . n A 1 79 ALA 79 397 397 ALA ALA F . n A 1 80 ASP 80 398 398 ASP ASP F . n A 1 81 SER 81 399 399 SER SER F . n A 1 82 PHE 82 400 400 PHE PHE F . n A 1 83 VAL 83 401 401 VAL VAL F . n A 1 84 ILE 84 402 402 ILE ILE F . n A 1 85 ARG 85 403 403 ARG ARG F . n A 1 86 GLY 86 404 404 GLY GLY F . n A 1 87 ASP 87 405 405 ASP ASP F . n A 1 88 GLU 88 406 406 GLU GLU F . n A 1 89 VAL 89 407 407 VAL VAL F . n A 1 90 ARG 90 408 408 ARG ARG F . n A 1 91 GLN 91 409 409 GLN GLN F . n A 1 92 ILE 92 410 410 ILE ILE F . n A 1 93 ALA 93 411 411 ALA ALA F . n A 1 94 PRO 94 412 412 PRO PRO F . n A 1 95 GLY 95 413 413 GLY GLY F . n A 1 96 GLN 96 414 414 GLN GLN F . n A 1 97 THR 97 415 415 THR THR F . n A 1 98 GLY 98 416 416 GLY GLY F . n A 1 99 LYS 99 417 417 LYS LYS F . n A 1 100 ILE 100 418 418 ILE ILE F . n A 1 101 ALA 101 419 419 ALA ALA F . n A 1 102 ASP 102 420 420 ASP ASP F . n A 1 103 TYR 103 421 421 TYR TYR F . n A 1 104 ASN 104 422 422 ASN ASN F . n A 1 105 TYR 105 423 423 TYR TYR F . n A 1 106 LYS 106 424 424 LYS LYS F . n A 1 107 LEU 107 425 425 LEU LEU F . n A 1 108 PRO 108 426 426 PRO PRO F . n A 1 109 ASP 109 427 427 ASP ASP F . n A 1 110 ASP 110 428 428 ASP ASP F . n A 1 111 PHE 111 429 429 PHE PHE F . n A 1 112 THR 112 430 430 THR THR F . n A 1 113 GLY 113 431 431 GLY GLY F . n A 1 114 CYS 114 432 432 CYS CYS F . n A 1 115 VAL 115 433 433 VAL VAL F . n A 1 116 ILE 116 434 434 ILE ILE F . n A 1 117 ALA 117 435 435 ALA ALA F . n A 1 118 TRP 118 436 436 TRP TRP F . n A 1 119 ASN 119 437 437 ASN ASN F . n A 1 120 SER 120 438 438 SER SER F . n A 1 121 ASN 121 439 439 ASN ASN F . n A 1 122 ASN 122 440 440 ASN ASN F . n A 1 123 LEU 123 441 441 LEU LEU F . n A 1 124 ASP 124 442 442 ASP ASP F . n A 1 125 SER 125 443 443 SER SER F . n A 1 126 LYS 126 444 444 LYS LYS F . n A 1 127 VAL 127 445 445 VAL VAL F . n A 1 128 GLY 128 446 446 GLY GLY F . n A 1 129 GLY 129 447 447 GLY GLY F . n A 1 130 ASN 130 448 448 ASN ASN F . n A 1 131 TYR 131 449 449 TYR TYR F . n A 1 132 ASN 132 450 450 ASN ASN F . n A 1 133 TYR 133 451 451 TYR TYR F . n A 1 134 LEU 134 452 452 LEU LEU F . n A 1 135 TYR 135 453 453 TYR TYR F . n A 1 136 ARG 136 454 454 ARG ARG F . n A 1 137 LEU 137 455 455 LEU LEU F . n A 1 138 PHE 138 456 456 PHE PHE F . n A 1 139 ARG 139 457 ? ? ? F . n A 1 140 LYS 140 458 ? ? ? F . n A 1 141 SER 141 459 ? ? ? F . n A 1 142 ASN 142 460 ? ? ? F . n A 1 143 LEU 143 461 461 LEU LEU F . n A 1 144 LYS 144 462 462 LYS LYS F . n A 1 145 PRO 145 463 463 PRO PRO F . n A 1 146 PHE 146 464 464 PHE PHE F . n A 1 147 GLU 147 465 465 GLU GLU F . n A 1 148 ARG 148 466 466 ARG ARG F . n A 1 149 ASP 149 467 467 ASP ASP F . n A 1 150 ILE 150 468 468 ILE ILE F . n A 1 151 SER 151 469 469 SER SER F . n A 1 152 THR 152 470 ? ? ? F . n A 1 153 GLU 153 471 ? ? ? F . n A 1 154 ILE 154 472 ? ? ? F . n A 1 155 TYR 155 473 ? ? ? F . n A 1 156 GLN 156 474 ? ? ? F . n A 1 157 ALA 157 475 ? ? ? F . n A 1 158 GLY 158 476 ? ? ? F . n A 1 159 SER 159 477 ? ? ? F . n A 1 160 THR 160 478 ? ? ? F . n A 1 161 PRO 161 479 ? ? ? F . n A 1 162 CYS 162 480 ? ? ? F . n A 1 163 ASN 163 481 ? ? ? F . n A 1 164 GLY 164 482 ? ? ? F . n A 1 165 VAL 165 483 ? ? ? F . n A 1 166 GLU 166 484 ? ? ? F . n A 1 167 GLY 167 485 ? ? ? F . n A 1 168 PHE 168 486 ? ? ? F . n A 1 169 ASN 169 487 ? ? ? F . n A 1 170 CYS 170 488 488 CYS CYS F . n A 1 171 TYR 171 489 489 TYR TYR F . n A 1 172 PHE 172 490 490 PHE PHE F . n A 1 173 PRO 173 491 491 PRO PRO F . n A 1 174 LEU 174 492 492 LEU LEU F . n A 1 175 GLN 175 493 493 GLN GLN F . n A 1 176 SER 176 494 494 SER SER F . n A 1 177 TYR 177 495 495 TYR TYR F . n A 1 178 GLY 178 496 496 GLY GLY F . n A 1 179 PHE 179 497 497 PHE PHE F . n A 1 180 GLN 180 498 498 GLN GLN F . n A 1 181 PRO 181 499 499 PRO PRO F . n A 1 182 THR 182 500 500 THR THR F . n A 1 183 ASN 183 501 501 ASN ASN F . n A 1 184 GLY 184 502 502 GLY GLY F . n A 1 185 VAL 185 503 503 VAL VAL F . n A 1 186 GLY 186 504 504 GLY GLY F . n A 1 187 TYR 187 505 505 TYR TYR F . n A 1 188 GLN 188 506 506 GLN GLN F . n A 1 189 PRO 189 507 507 PRO PRO F . n A 1 190 TYR 190 508 508 TYR TYR F . n A 1 191 ARG 191 509 509 ARG ARG F . n A 1 192 VAL 192 510 510 VAL VAL F . n A 1 193 VAL 193 511 511 VAL VAL F . n A 1 194 VAL 194 512 512 VAL VAL F . n A 1 195 LEU 195 513 513 LEU LEU F . n A 1 196 SER 196 514 514 SER SER F . n A 1 197 PHE 197 515 515 PHE PHE F . n A 1 198 GLU 198 516 516 GLU GLU F . n A 1 199 LEU 199 517 517 LEU LEU F . n A 1 200 LEU 200 518 518 LEU LEU F . n A 1 201 HIS 201 519 519 HIS HIS F . n A 1 202 ALA 202 520 520 ALA ALA F . n A 1 203 PRO 203 521 521 PRO PRO F . n A 1 204 ALA 204 522 522 ALA ALA F . n A 1 205 THR 205 523 523 THR THR F . n A 1 206 VAL 206 524 524 VAL VAL F . n A 1 207 CYS 207 525 525 CYS CYS F . n A 1 208 GLY 208 526 526 GLY GLY F . n A 1 209 PRO 209 527 ? ? ? F . n A 1 210 LYS 210 528 ? ? ? F . n A 1 211 LYS 211 529 ? ? ? F . n A 1 212 SER 212 530 ? ? ? F . n A 1 213 THR 213 531 ? ? ? F . n A 1 214 ASN 214 532 ? ? ? F . n A 1 215 LEU 215 533 ? ? ? F . n A 1 216 VAL 216 534 ? ? ? F . n A 1 217 LYS 217 535 ? ? ? F . n A 1 218 ASN 218 536 ? ? ? F . n A 1 219 LYS 219 537 ? ? ? F . n A 1 220 CYS 220 538 ? ? ? F . n A 1 221 VAL 221 539 ? ? ? F . n A 1 222 ASN 222 540 ? ? ? F . n A 1 223 PHE 223 541 ? ? ? F . n # _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 9N2L _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 9N2L _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 ? # _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 9N2L _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max ? _refine.B_iso_mean 266.95 _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 9N2L _refine.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high . _refine.ls_d_res_low ? _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs ? _refine.ls_number_reflns_R_free ? _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs ? _refine.ls_percent_reflns_R_free ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work ? _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method NONE _refine.pdbx_method_to_determine_struct ? _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values 'GeoStd + Monomer Library + CDL v1.2' _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id ? _refine.overall_SU_B ? _refine.overall_SU_ML ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # 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' ? 0.0077 ? 1416 ? f_bond_d ? ? 'ELECTRON MICROSCOPY' ? 1.3575 ? 1927 ? f_angle_d ? ? 'ELECTRON MICROSCOPY' ? 0.0735 ? 204 ? f_chiral_restr ? ? 'ELECTRON MICROSCOPY' ? 0.0092 ? 250 ? f_plane_restr ? ? 'ELECTRON MICROSCOPY' ? 7.3113 ? 193 ? f_dihedral_angle_d ? ? # _struct.entry_id 9N2L _struct.title 'Cryo-EM structure of locally refined up conformation of SARS-CoV-2 spike protein Receptor Binding Domain' _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 9N2L _struct_keywords.text 'SARS-CoV-2 Spike protein, Receptor Binding Domain, VIRAL PROTEIN' _struct_keywords.pdbx_keywords 'VIRAL PROTEIN' # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code SPIKE_SARS2 _struct_ref.pdbx_db_accession P0DTC2 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYAD SFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGST PCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNF ; _struct_ref.pdbx_align_begin 319 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 9N2L _struct_ref_seq.pdbx_strand_id F _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 223 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P0DTC2 _struct_ref_seq.db_align_beg 319 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 541 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 319 _struct_ref_seq.pdbx_auth_seq_align_end 541 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A # _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 'not applicable' # _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 x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0 _pdbx_struct_oper_list.matrix[1][2] 0.0 _pdbx_struct_oper_list.matrix[1][3] 0.0 _pdbx_struct_oper_list.vector[1] 0.0 _pdbx_struct_oper_list.matrix[2][1] 0.0 _pdbx_struct_oper_list.matrix[2][2] 1.0 _pdbx_struct_oper_list.matrix[2][3] 0.0 _pdbx_struct_oper_list.vector[2] 0.0 _pdbx_struct_oper_list.matrix[3][1] 0.0 _pdbx_struct_oper_list.matrix[3][2] 0.0 _pdbx_struct_oper_list.matrix[3][3] 1.0 _pdbx_struct_oper_list.vector[3] 0.0 # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 AA1 PHE A 20 ? ASN A 25 ? PHE F 338 ASN F 343 1 ? 6 HELX_P HELX_P2 AA2 SER A 31 ? TRP A 35 ? SER F 349 TRP F 353 5 ? 5 HELX_P HELX_P3 AA3 TYR A 47 ? ASN A 52 ? TYR F 365 ASN F 370 1 ? 6 HELX_P HELX_P4 AA4 THR A 67 ? LEU A 72 ? THR F 385 LEU F 390 5 ? 6 HELX_P HELX_P5 AA5 GLY A 86 ? ILE A 92 ? GLY F 404 ILE F 410 5 ? 7 HELX_P HELX_P6 AA6 GLY A 98 ? ASN A 104 ? GLY F 416 ASN F 422 1 ? 7 HELX_P HELX_P7 AA7 SER A 120 ? SER A 125 ? SER F 438 SER F 443 1 ? 6 # _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 18 SG ? ? ? 1_555 A CYS 43 SG ? ? F CYS 336 F CYS 361 1_555 ? ? ? ? ? ? ? 2.020 ? ? disulf2 disulf ? ? A CYS 61 SG ? ? ? 1_555 A CYS 114 SG ? ? F CYS 379 F CYS 432 1_555 ? ? ? ? ? ? ? 2.032 ? ? disulf3 disulf ? ? A CYS 73 SG ? ? ? 1_555 A CYS 207 SG ? ? F CYS 391 F CYS 525 1_555 ? ? ? ? ? ? ? 2.033 ? ? # _struct_conn_type.id disulf _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _pdbx_modification_feature.ordinal _pdbx_modification_feature.label_comp_id _pdbx_modification_feature.label_asym_id _pdbx_modification_feature.label_seq_id _pdbx_modification_feature.label_alt_id _pdbx_modification_feature.modified_residue_label_comp_id _pdbx_modification_feature.modified_residue_label_asym_id _pdbx_modification_feature.modified_residue_label_seq_id _pdbx_modification_feature.modified_residue_label_alt_id _pdbx_modification_feature.auth_comp_id _pdbx_modification_feature.auth_asym_id _pdbx_modification_feature.auth_seq_id _pdbx_modification_feature.PDB_ins_code _pdbx_modification_feature.symmetry _pdbx_modification_feature.modified_residue_auth_comp_id _pdbx_modification_feature.modified_residue_auth_asym_id _pdbx_modification_feature.modified_residue_auth_seq_id _pdbx_modification_feature.modified_residue_PDB_ins_code _pdbx_modification_feature.modified_residue_symmetry _pdbx_modification_feature.comp_id_linking_atom _pdbx_modification_feature.modified_residue_id_linking_atom _pdbx_modification_feature.modified_residue_id _pdbx_modification_feature.ref_pcm_id _pdbx_modification_feature.ref_comp_id _pdbx_modification_feature.type _pdbx_modification_feature.category 1 CYS A 18 ? CYS A 43 ? CYS F 336 ? 1_555 CYS F 361 ? 1_555 SG SG . . . None 'Disulfide bridge' 2 CYS A 61 ? CYS A 114 ? CYS F 379 ? 1_555 CYS F 432 ? 1_555 SG SG . . . None 'Disulfide bridge' 3 CYS A 73 ? CYS A 207 ? CYS F 391 ? 1_555 CYS F 525 ? 1_555 SG SG . . . None 'Disulfide bridge' # 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 36 ? ILE A 40 ? ASN F 354 ILE F 358 AA1 2 ASN A 76 ? ILE A 84 ? ASN F 394 ILE F 402 AA1 3 TYR A 190 ? GLU A 198 ? TYR F 508 GLU F 516 AA1 4 CYS A 114 ? ASN A 119 ? CYS F 432 ASN F 437 AA1 5 THR A 58 ? CYS A 61 ? THR F 376 CYS F 379 AA2 1 LEU A 134 ? ARG A 136 ? LEU F 452 ARG F 454 AA2 2 LEU A 174 ? SER A 176 ? LEU F 492 SER F 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 LYS A 38 ? N LYS F 356 O ALA A 79 ? O ALA F 397 AA1 2 3 N ILE A 84 ? N ILE F 402 O TYR A 190 ? O TYR F 508 AA1 3 4 O LEU A 195 ? O LEU F 513 N CYS A 114 ? N CYS F 432 AA1 4 5 O VAL A 115 ? O VAL F 433 N LYS A 60 ? N LYS F 378 AA2 1 2 N TYR A 135 ? N TYR F 453 O GLN A 175 ? O GLN F 493 # _pdbx_entry_details.entry_id 9N2L _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest ? _pdbx_entry_details.has_protein_modification Y # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 C _pdbx_validate_rmsd_angle.auth_asym_id_1 F _pdbx_validate_rmsd_angle.auth_comp_id_1 PHE _pdbx_validate_rmsd_angle.auth_seq_id_1 497 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 N _pdbx_validate_rmsd_angle.auth_asym_id_2 F _pdbx_validate_rmsd_angle.auth_comp_id_2 GLN _pdbx_validate_rmsd_angle.auth_seq_id_2 498 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 CA _pdbx_validate_rmsd_angle.auth_asym_id_3 F _pdbx_validate_rmsd_angle.auth_comp_id_3 GLN _pdbx_validate_rmsd_angle.auth_seq_id_3 498 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 139.43 _pdbx_validate_rmsd_angle.angle_target_value 121.70 _pdbx_validate_rmsd_angle.angle_deviation 17.73 _pdbx_validate_rmsd_angle.angle_standard_deviation 2.50 _pdbx_validate_rmsd_angle.linker_flag Y # 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 ASN F 343 ? ? -94.68 37.96 2 1 ASN F 360 ? ? 39.62 52.09 3 1 ASP F 389 ? ? -96.51 46.75 4 1 ASP F 428 ? ? -86.36 47.36 5 1 SER F 438 ? ? -141.14 44.63 6 1 LEU F 518 ? ? -125.42 -169.04 # _space_group_symop.id 1 _space_group_symop.operation_xyz x,y,z # loop_ _em_3d_fitting.id _em_3d_fitting.entry_id _em_3d_fitting.method _em_3d_fitting.target_criteria _em_3d_fitting.details _em_3d_fitting.overall_b_value _em_3d_fitting.ref_space _em_3d_fitting.ref_protocol 1 9N2L ? ? ? ? REAL 'FLEXIBLE FIT' 2 9N2L ? ? ? ? ? ? # loop_ _em_3d_fitting_list.id _em_3d_fitting_list.3d_fitting_id _em_3d_fitting_list.pdb_entry_id _em_3d_fitting_list.pdb_chain_id _em_3d_fitting_list.pdb_chain_residue_range _em_3d_fitting_list.details _em_3d_fitting_list.chain_id _em_3d_fitting_list.chain_residue_range _em_3d_fitting_list.source_name _em_3d_fitting_list.type _em_3d_fitting_list.accession_code _em_3d_fitting_list.initial_refinement_model_id 1 1 9CSS F 319-541 ? F 319-541 PDB 'experimental model' 9CSS 1 2 2 . . . ? ? ? ? ? ? ? # _em_3d_reconstruction.entry_id 9N2L _em_3d_reconstruction.id 1 _em_3d_reconstruction.method ? _em_3d_reconstruction.algorithm ? _em_3d_reconstruction.citation_id ? _em_3d_reconstruction.details ? _em_3d_reconstruction.resolution 2.99 _em_3d_reconstruction.resolution_method 'FSC 0.143 CUT-OFF' _em_3d_reconstruction.magnification_calibration ? _em_3d_reconstruction.nominal_pixel_size ? _em_3d_reconstruction.actual_pixel_size ? _em_3d_reconstruction.num_particles 326639 _em_3d_reconstruction.euler_angles_details ? _em_3d_reconstruction.num_class_averages ? _em_3d_reconstruction.refinement_type ? _em_3d_reconstruction.image_processing_id 1 _em_3d_reconstruction.symmetry_type POINT # _em_buffer.id 1 _em_buffer.specimen_id 1 _em_buffer.name ? _em_buffer.details ? _em_buffer.pH 7.5 # _em_entity_assembly.id 1 _em_entity_assembly.parent_id 0 _em_entity_assembly.source RECOMBINANT _em_entity_assembly.type COMPLEX _em_entity_assembly.name 'SARS-CoV-2 Spike protein Ectodomain with Internal tag' _em_entity_assembly.details ? _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? _em_entity_assembly.entity_id_list 1 # _em_imaging.entry_id 9N2L _em_imaging.id 1 _em_imaging.astigmatism ? _em_imaging.electron_beam_tilt_params ? _em_imaging.residual_tilt ? _em_imaging.microscope_model 'TFS KRIOS' _em_imaging.specimen_holder_type ? _em_imaging.specimen_holder_model ? _em_imaging.details ? _em_imaging.date ? _em_imaging.accelerating_voltage 300 _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.mode 'BRIGHT FIELD' _em_imaging.nominal_cs ? _em_imaging.nominal_defocus_min 800 _em_imaging.nominal_defocus_max 2500 _em_imaging.calibrated_defocus_min ? _em_imaging.calibrated_defocus_max ? _em_imaging.tilt_angle_min ? _em_imaging.tilt_angle_max ? _em_imaging.nominal_magnification 16500 _em_imaging.calibrated_magnification 191780 _em_imaging.electron_source 'FIELD EMISSION GUN' _em_imaging.citation_id ? _em_imaging.temperature ? _em_imaging.detector_distance ? _em_imaging.recording_temperature_minimum ? _em_imaging.recording_temperature_maximum ? _em_imaging.alignment_procedure ? _em_imaging.c2_aperture_diameter ? _em_imaging.specimen_id 1 _em_imaging.cryogen ? # _em_vitrification.entry_id 9N2L _em_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.cryogen_name ETHANE _em_vitrification.humidity 100 _em_vitrification.temp ? _em_vitrification.chamber_temperature 298 _em_vitrification.instrument ? _em_vitrification.method ? _em_vitrification.time_resolved_state ? _em_vitrification.citation_id ? _em_vitrification.details ? # _em_experiment.entry_id 9N2L _em_experiment.id 1 _em_experiment.reconstruction_method 'SINGLE PARTICLE' _em_experiment.aggregation_state PARTICLE _em_experiment.entity_assembly_id 1 # 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 F ARG 319 ? A ARG 1 2 1 Y 1 F VAL 320 ? A VAL 2 3 1 Y 1 F GLN 321 ? A GLN 3 4 1 Y 1 F PRO 322 ? A PRO 4 5 1 Y 1 F THR 323 ? A THR 5 6 1 Y 1 F GLU 324 ? A GLU 6 7 1 Y 1 F SER 325 ? A SER 7 8 1 Y 1 F ILE 326 ? A ILE 8 9 1 Y 1 F VAL 327 ? A VAL 9 10 1 Y 1 F ARG 328 ? A ARG 10 11 1 Y 1 F PHE 329 ? A PHE 11 12 1 Y 1 F PRO 330 ? A PRO 12 13 1 Y 1 F ASN 331 ? A ASN 13 14 1 Y 1 F ILE 332 ? A ILE 14 15 1 Y 1 F ARG 457 ? A ARG 139 16 1 Y 1 F LYS 458 ? A LYS 140 17 1 Y 1 F SER 459 ? A SER 141 18 1 Y 1 F ASN 460 ? A ASN 142 19 1 Y 1 F THR 470 ? A THR 152 20 1 Y 1 F GLU 471 ? A GLU 153 21 1 Y 1 F ILE 472 ? A ILE 154 22 1 Y 1 F TYR 473 ? A TYR 155 23 1 Y 1 F GLN 474 ? A GLN 156 24 1 Y 1 F ALA 475 ? A ALA 157 25 1 Y 1 F GLY 476 ? A GLY 158 26 1 Y 1 F SER 477 ? A SER 159 27 1 Y 1 F THR 478 ? A THR 160 28 1 Y 1 F PRO 479 ? A PRO 161 29 1 Y 1 F CYS 480 ? A CYS 162 30 1 Y 1 F ASN 481 ? A ASN 163 31 1 Y 1 F GLY 482 ? A GLY 164 32 1 Y 1 F VAL 483 ? A VAL 165 33 1 Y 1 F GLU 484 ? A GLU 166 34 1 Y 1 F GLY 485 ? A GLY 167 35 1 Y 1 F PHE 486 ? A PHE 168 36 1 Y 1 F ASN 487 ? A ASN 169 37 1 Y 1 F PRO 527 ? A PRO 209 38 1 Y 1 F LYS 528 ? A LYS 210 39 1 Y 1 F LYS 529 ? A LYS 211 40 1 Y 1 F SER 530 ? A SER 212 41 1 Y 1 F THR 531 ? A THR 213 42 1 Y 1 F ASN 532 ? A ASN 214 43 1 Y 1 F LEU 533 ? A LEU 215 44 1 Y 1 F VAL 534 ? A VAL 216 45 1 Y 1 F LYS 535 ? A LYS 217 46 1 Y 1 F ASN 536 ? A ASN 218 47 1 Y 1 F LYS 537 ? A LYS 219 48 1 Y 1 F CYS 538 ? A CYS 220 49 1 Y 1 F VAL 539 ? A VAL 221 50 1 Y 1 F ASN 540 ? A ASN 222 51 1 Y 1 F PHE 541 ? A PHE 223 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal ALA N N N N 1 ALA CA C N S 2 ALA C C N N 3 ALA O O N N 4 ALA CB C N N 5 ALA OXT O N N 6 ALA H H N N 7 ALA H2 H N N 8 ALA HA H N N 9 ALA HB1 H N N 10 ALA HB2 H N N 11 ALA HB3 H N N 12 ALA HXT H N N 13 ARG N N N N 14 ARG CA C N S 15 ARG C C N N 16 ARG O O N N 17 ARG CB C N N 18 ARG CG C N N 19 ARG CD C N N 20 ARG NE N N N 21 ARG CZ C N N 22 ARG NH1 N N N 23 ARG NH2 N N N 24 ARG OXT O N N 25 ARG H H N N 26 ARG H2 H N N 27 ARG HA H N N 28 ARG HB2 H N N 29 ARG HB3 H N N 30 ARG HG2 H N N 31 ARG HG3 H N N 32 ARG HD2 H N N 33 ARG HD3 H N N 34 ARG HE H N N 35 ARG HH11 H N N 36 ARG HH12 H N N 37 ARG HH21 H N N 38 ARG HH22 H N N 39 ARG HXT H N N 40 ASN N N N N 41 ASN CA C N S 42 ASN C C N N 43 ASN O O N N 44 ASN CB C N N 45 ASN CG C N N 46 ASN OD1 O N N 47 ASN ND2 N N N 48 ASN OXT O N N 49 ASN H H N N 50 ASN H2 H N N 51 ASN HA H N N 52 ASN HB2 H N N 53 ASN HB3 H N N 54 ASN HD21 H N N 55 ASN HD22 H N N 56 ASN HXT H N N 57 ASP N N N N 58 ASP CA C N S 59 ASP C C N N 60 ASP O O N N 61 ASP CB C N N 62 ASP CG C N N 63 ASP OD1 O N N 64 ASP OD2 O N N 65 ASP OXT O N N 66 ASP H H N N 67 ASP H2 H N N 68 ASP HA H N N 69 ASP HB2 H N N 70 ASP HB3 H N N 71 ASP HD2 H N N 72 ASP HXT H N N 73 CYS N N N N 74 CYS CA C N R 75 CYS C C N N 76 CYS O O N N 77 CYS CB C N N 78 CYS SG S N N 79 CYS OXT O N N 80 CYS H H N N 81 CYS H2 H N N 82 CYS HA H N N 83 CYS HB2 H N N 84 CYS HB3 H N N 85 CYS HG H N N 86 CYS HXT H N N 87 GLN N N N N 88 GLN CA C N S 89 GLN C C N N 90 GLN O O N N 91 GLN CB C N N 92 GLN CG C N N 93 GLN CD C N N 94 GLN OE1 O N N 95 GLN NE2 N N N 96 GLN OXT O N N 97 GLN H H N N 98 GLN H2 H N N 99 GLN HA H N N 100 GLN HB2 H N N 101 GLN HB3 H N N 102 GLN HG2 H N N 103 GLN HG3 H N N 104 GLN HE21 H N N 105 GLN HE22 H N N 106 GLN HXT H N N 107 GLU N N N N 108 GLU CA C N S 109 GLU C C N N 110 GLU O O N N 111 GLU CB C N N 112 GLU CG C N N 113 GLU CD C N N 114 GLU OE1 O N N 115 GLU OE2 O N N 116 GLU OXT O N N 117 GLU H H N N 118 GLU H2 H N N 119 GLU HA H N N 120 GLU HB2 H N N 121 GLU HB3 H N N 122 GLU HG2 H N N 123 GLU HG3 H N N 124 GLU HE2 H N N 125 GLU HXT H N N 126 GLY N N N N 127 GLY CA C N N 128 GLY C C N N 129 GLY O O N N 130 GLY OXT O N N 131 GLY H H N N 132 GLY H2 H N N 133 GLY HA2 H N N 134 GLY HA3 H N N 135 GLY HXT H N N 136 HIS N N N N 137 HIS CA C N S 138 HIS C C N N 139 HIS O O N N 140 HIS CB C N N 141 HIS CG C Y N 142 HIS ND1 N Y N 143 HIS CD2 C Y N 144 HIS CE1 C Y N 145 HIS NE2 N Y N 146 HIS OXT O N N 147 HIS H H N N 148 HIS H2 H N N 149 HIS HA H N N 150 HIS HB2 H N N 151 HIS HB3 H N N 152 HIS HD1 H N N 153 HIS HD2 H N N 154 HIS HE1 H N N 155 HIS HE2 H N N 156 HIS HXT H N N 157 ILE N N N N 158 ILE CA C N S 159 ILE C C N N 160 ILE O O N N 161 ILE CB C N S 162 ILE CG1 C N N 163 ILE CG2 C N N 164 ILE CD1 C N N 165 ILE OXT O N N 166 ILE H H N N 167 ILE H2 H N N 168 ILE HA H N N 169 ILE HB H N N 170 ILE HG12 H N N 171 ILE HG13 H N N 172 ILE HG21 H N N 173 ILE HG22 H N N 174 ILE HG23 H N N 175 ILE HD11 H N N 176 ILE HD12 H N N 177 ILE HD13 H N N 178 ILE HXT H N N 179 LEU N N N N 180 LEU CA C N S 181 LEU C C N N 182 LEU O O N N 183 LEU CB C N N 184 LEU CG C N N 185 LEU CD1 C N N 186 LEU CD2 C N N 187 LEU OXT O N N 188 LEU H H N N 189 LEU H2 H N N 190 LEU HA H N N 191 LEU HB2 H N N 192 LEU HB3 H N N 193 LEU HG H N N 194 LEU HD11 H N N 195 LEU HD12 H N N 196 LEU HD13 H N N 197 LEU HD21 H N N 198 LEU HD22 H N N 199 LEU HD23 H N N 200 LEU HXT H N N 201 LYS N N N N 202 LYS CA C N S 203 LYS C C N N 204 LYS O O N N 205 LYS CB C N N 206 LYS CG C N N 207 LYS CD C N N 208 LYS CE C N N 209 LYS NZ N N N 210 LYS OXT O N N 211 LYS H H N N 212 LYS H2 H N N 213 LYS HA H N N 214 LYS HB2 H N N 215 LYS HB3 H N N 216 LYS HG2 H N N 217 LYS HG3 H N N 218 LYS HD2 H N N 219 LYS HD3 H N N 220 LYS HE2 H N N 221 LYS HE3 H N N 222 LYS HZ1 H N N 223 LYS HZ2 H N N 224 LYS HZ3 H N N 225 LYS HXT H N N 226 PHE N N N N 227 PHE CA C N S 228 PHE C C N N 229 PHE O O N N 230 PHE CB C N N 231 PHE CG C Y N 232 PHE CD1 C Y N 233 PHE CD2 C Y N 234 PHE CE1 C Y N 235 PHE CE2 C Y N 236 PHE CZ C Y N 237 PHE OXT O N N 238 PHE H H N N 239 PHE H2 H N N 240 PHE HA H N N 241 PHE HB2 H N N 242 PHE HB3 H N N 243 PHE HD1 H N N 244 PHE HD2 H N N 245 PHE HE1 H N N 246 PHE HE2 H N N 247 PHE HZ H N N 248 PHE HXT H N N 249 PRO N N N N 250 PRO CA C N S 251 PRO C C N N 252 PRO O O N N 253 PRO CB C N N 254 PRO CG C N N 255 PRO CD C N N 256 PRO OXT O N N 257 PRO H H N N 258 PRO HA H N N 259 PRO HB2 H N N 260 PRO HB3 H N N 261 PRO HG2 H N N 262 PRO HG3 H N N 263 PRO HD2 H N N 264 PRO HD3 H N N 265 PRO HXT H N N 266 SER N N N N 267 SER CA C N S 268 SER C C N N 269 SER O O N N 270 SER CB C N N 271 SER OG O N N 272 SER OXT O N N 273 SER H H N N 274 SER H2 H N N 275 SER HA H N N 276 SER HB2 H N N 277 SER HB3 H N N 278 SER HG H N N 279 SER HXT H N N 280 THR N N N N 281 THR CA C N S 282 THR C C N N 283 THR O O N N 284 THR CB C N R 285 THR OG1 O N N 286 THR CG2 C N N 287 THR OXT O N N 288 THR H H N N 289 THR H2 H N N 290 THR HA H N N 291 THR HB H N N 292 THR HG1 H N N 293 THR HG21 H N N 294 THR HG22 H N N 295 THR HG23 H N N 296 THR HXT H N N 297 TRP N N N N 298 TRP CA C N S 299 TRP C C N N 300 TRP O O N N 301 TRP CB C N N 302 TRP CG C Y N 303 TRP CD1 C Y N 304 TRP CD2 C Y N 305 TRP NE1 N Y N 306 TRP CE2 C Y N 307 TRP CE3 C Y N 308 TRP CZ2 C Y N 309 TRP CZ3 C Y N 310 TRP CH2 C Y N 311 TRP OXT O N N 312 TRP H H N N 313 TRP H2 H N N 314 TRP HA H N N 315 TRP HB2 H N N 316 TRP HB3 H N N 317 TRP HD1 H N N 318 TRP HE1 H N N 319 TRP HE3 H N N 320 TRP HZ2 H N N 321 TRP HZ3 H N N 322 TRP HH2 H N N 323 TRP HXT H N N 324 TYR N N N N 325 TYR CA C N S 326 TYR C C N N 327 TYR O O N N 328 TYR CB C N N 329 TYR CG C Y N 330 TYR CD1 C Y N 331 TYR CD2 C Y N 332 TYR CE1 C Y N 333 TYR CE2 C Y N 334 TYR CZ C Y N 335 TYR OH O N N 336 TYR OXT O N N 337 TYR H H N N 338 TYR H2 H N N 339 TYR HA H N N 340 TYR HB2 H N N 341 TYR HB3 H N N 342 TYR HD1 H N N 343 TYR HD2 H N N 344 TYR HE1 H N N 345 TYR HE2 H N N 346 TYR HH H N N 347 TYR HXT H N N 348 VAL N N N N 349 VAL CA C N S 350 VAL C C N N 351 VAL O O N N 352 VAL CB C N N 353 VAL CG1 C N N 354 VAL CG2 C N N 355 VAL OXT O N N 356 VAL H H N N 357 VAL H2 H N N 358 VAL HA H N N 359 VAL HB H N N 360 VAL HG11 H N N 361 VAL HG12 H N N 362 VAL HG13 H N N 363 VAL HG21 H N N 364 VAL HG22 H N N 365 VAL HG23 H N N 366 VAL HXT H N N 367 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal ALA N CA sing N N 1 ALA N H sing N N 2 ALA N H2 sing N N 3 ALA CA C sing N N 4 ALA CA CB sing N N 5 ALA CA HA sing N N 6 ALA C O doub N N 7 ALA C OXT sing N N 8 ALA CB HB1 sing N N 9 ALA CB HB2 sing N N 10 ALA CB HB3 sing N N 11 ALA OXT HXT sing N N 12 ARG N CA sing N N 13 ARG N H sing N N 14 ARG N H2 sing N N 15 ARG CA C sing N N 16 ARG CA CB sing N N 17 ARG CA HA sing N N 18 ARG C O doub N N 19 ARG C OXT sing N N 20 ARG CB CG sing N N 21 ARG CB HB2 sing N N 22 ARG CB HB3 sing N N 23 ARG CG CD sing N N 24 ARG CG HG2 sing N N 25 ARG CG HG3 sing N N 26 ARG CD NE sing N N 27 ARG CD HD2 sing N N 28 ARG CD HD3 sing N N 29 ARG NE CZ sing N N 30 ARG NE HE sing N N 31 ARG CZ NH1 sing N N 32 ARG CZ NH2 doub N N 33 ARG NH1 HH11 sing N N 34 ARG NH1 HH12 sing N N 35 ARG NH2 HH21 sing N N 36 ARG NH2 HH22 sing N N 37 ARG OXT HXT sing N N 38 ASN N CA sing N N 39 ASN N H sing N N 40 ASN N H2 sing N N 41 ASN CA C sing N N 42 ASN CA CB sing N N 43 ASN CA HA sing N N 44 ASN C O doub N N 45 ASN C OXT sing N N 46 ASN CB CG sing N N 47 ASN CB HB2 sing N N 48 ASN CB HB3 sing N N 49 ASN CG OD1 doub N N 50 ASN CG ND2 sing N N 51 ASN ND2 HD21 sing N N 52 ASN ND2 HD22 sing N N 53 ASN OXT HXT sing N N 54 ASP N CA sing N N 55 ASP N H sing N N 56 ASP N H2 sing N N 57 ASP CA C sing N N 58 ASP CA CB sing N N 59 ASP CA HA sing N N 60 ASP C O doub N N 61 ASP C OXT sing N N 62 ASP CB CG sing N N 63 ASP CB HB2 sing N N 64 ASP CB HB3 sing N N 65 ASP CG OD1 doub N N 66 ASP CG OD2 sing N N 67 ASP OD2 HD2 sing N N 68 ASP OXT HXT sing N N 69 CYS N CA sing N N 70 CYS N H sing N N 71 CYS N H2 sing N N 72 CYS CA C sing N N 73 CYS CA CB sing N N 74 CYS CA HA sing N N 75 CYS C O doub N N 76 CYS C OXT sing N N 77 CYS CB SG sing N N 78 CYS CB HB2 sing N N 79 CYS CB HB3 sing N N 80 CYS SG HG sing N N 81 CYS OXT HXT sing N N 82 GLN N CA sing N N 83 GLN N H sing N N 84 GLN N H2 sing N N 85 GLN CA C sing N N 86 GLN CA CB sing N N 87 GLN CA HA sing N N 88 GLN C O doub N N 89 GLN C OXT sing N N 90 GLN CB CG sing N N 91 GLN CB HB2 sing N N 92 GLN CB HB3 sing N N 93 GLN CG CD sing N N 94 GLN CG HG2 sing N N 95 GLN CG HG3 sing N N 96 GLN CD OE1 doub N N 97 GLN CD NE2 sing N N 98 GLN NE2 HE21 sing N N 99 GLN NE2 HE22 sing N N 100 GLN OXT HXT sing N N 101 GLU N CA sing N N 102 GLU N H sing N N 103 GLU N H2 sing N N 104 GLU CA C sing N N 105 GLU CA CB sing N N 106 GLU CA HA sing N N 107 GLU C O doub N N 108 GLU C OXT sing N N 109 GLU CB CG sing N N 110 GLU CB HB2 sing N N 111 GLU CB HB3 sing N N 112 GLU CG CD sing N N 113 GLU CG HG2 sing N N 114 GLU CG HG3 sing N N 115 GLU CD OE1 doub N N 116 GLU CD OE2 sing N N 117 GLU OE2 HE2 sing N N 118 GLU OXT HXT sing N N 119 GLY N CA sing N N 120 GLY N H sing N N 121 GLY N H2 sing N N 122 GLY CA C sing N N 123 GLY CA HA2 sing N N 124 GLY CA HA3 sing N N 125 GLY C O doub N N 126 GLY C OXT sing N N 127 GLY OXT HXT sing N N 128 HIS N CA sing N N 129 HIS N H sing N N 130 HIS N H2 sing N N 131 HIS CA C sing N N 132 HIS CA CB sing N N 133 HIS CA HA sing N N 134 HIS C O doub N N 135 HIS C OXT sing N N 136 HIS CB CG sing N N 137 HIS CB HB2 sing N N 138 HIS CB HB3 sing N N 139 HIS CG ND1 sing Y N 140 HIS CG CD2 doub Y N 141 HIS ND1 CE1 doub Y N 142 HIS ND1 HD1 sing N N 143 HIS CD2 NE2 sing Y N 144 HIS CD2 HD2 sing N N 145 HIS CE1 NE2 sing Y N 146 HIS CE1 HE1 sing N N 147 HIS NE2 HE2 sing N N 148 HIS OXT HXT sing N N 149 ILE N CA sing N N 150 ILE N H sing N N 151 ILE N H2 sing N N 152 ILE CA C sing N N 153 ILE CA CB sing N N 154 ILE CA HA sing N N 155 ILE C O doub N N 156 ILE C OXT sing N N 157 ILE CB CG1 sing N N 158 ILE CB CG2 sing N N 159 ILE CB HB sing N N 160 ILE CG1 CD1 sing N N 161 ILE CG1 HG12 sing N N 162 ILE CG1 HG13 sing N N 163 ILE CG2 HG21 sing N N 164 ILE CG2 HG22 sing N N 165 ILE CG2 HG23 sing N N 166 ILE CD1 HD11 sing N N 167 ILE CD1 HD12 sing N N 168 ILE CD1 HD13 sing N N 169 ILE OXT HXT sing N N 170 LEU N CA sing N N 171 LEU N H sing N N 172 LEU N H2 sing N N 173 LEU CA C sing N N 174 LEU CA CB sing N N 175 LEU CA HA sing N N 176 LEU C O doub N N 177 LEU C OXT sing N N 178 LEU CB CG sing N N 179 LEU CB HB2 sing N N 180 LEU CB HB3 sing N N 181 LEU CG CD1 sing N N 182 LEU CG CD2 sing N N 183 LEU CG HG sing N N 184 LEU CD1 HD11 sing N N 185 LEU CD1 HD12 sing N N 186 LEU CD1 HD13 sing N N 187 LEU CD2 HD21 sing N N 188 LEU CD2 HD22 sing N N 189 LEU CD2 HD23 sing N N 190 LEU OXT HXT sing N N 191 LYS N CA sing N N 192 LYS N H sing N N 193 LYS N H2 sing N N 194 LYS CA C sing N N 195 LYS CA CB sing N N 196 LYS CA HA sing N N 197 LYS C O doub N N 198 LYS C OXT sing N N 199 LYS CB CG sing N N 200 LYS CB HB2 sing N N 201 LYS CB HB3 sing N N 202 LYS CG CD sing N N 203 LYS CG HG2 sing N N 204 LYS CG HG3 sing N N 205 LYS CD CE sing N N 206 LYS CD HD2 sing N N 207 LYS CD HD3 sing N N 208 LYS CE NZ sing N N 209 LYS CE HE2 sing N N 210 LYS CE HE3 sing N N 211 LYS NZ HZ1 sing N N 212 LYS NZ HZ2 sing N N 213 LYS NZ HZ3 sing N N 214 LYS OXT HXT sing N N 215 PHE N CA sing N N 216 PHE N H sing N N 217 PHE N H2 sing N N 218 PHE CA C sing N N 219 PHE CA CB sing N N 220 PHE CA HA sing N N 221 PHE C O doub N N 222 PHE C OXT sing N N 223 PHE CB CG sing N N 224 PHE CB HB2 sing N N 225 PHE CB HB3 sing N N 226 PHE CG CD1 doub Y N 227 PHE CG CD2 sing Y N 228 PHE CD1 CE1 sing Y N 229 PHE CD1 HD1 sing N N 230 PHE CD2 CE2 doub Y N 231 PHE CD2 HD2 sing N N 232 PHE CE1 CZ doub Y N 233 PHE CE1 HE1 sing N N 234 PHE CE2 CZ sing Y N 235 PHE CE2 HE2 sing N N 236 PHE CZ HZ sing N N 237 PHE OXT HXT sing N N 238 PRO N CA sing N N 239 PRO N CD sing N N 240 PRO N H sing N N 241 PRO CA C sing N N 242 PRO CA CB sing N N 243 PRO CA HA sing N N 244 PRO C O doub N N 245 PRO C OXT sing N N 246 PRO CB CG sing N N 247 PRO CB HB2 sing N N 248 PRO CB HB3 sing N N 249 PRO CG CD sing N N 250 PRO CG HG2 sing N N 251 PRO CG HG3 sing N N 252 PRO CD HD2 sing N N 253 PRO CD HD3 sing N N 254 PRO OXT HXT sing N N 255 SER N CA sing N N 256 SER N H sing N N 257 SER N H2 sing N N 258 SER CA C sing N N 259 SER CA CB sing N N 260 SER CA HA sing N N 261 SER C O doub N N 262 SER C OXT sing N N 263 SER CB OG sing N N 264 SER CB HB2 sing N N 265 SER CB HB3 sing N N 266 SER OG HG sing N N 267 SER OXT HXT sing N N 268 THR N CA sing N N 269 THR N H sing N N 270 THR N H2 sing N N 271 THR CA C sing N N 272 THR CA CB sing N N 273 THR CA HA sing N N 274 THR C O doub N N 275 THR C OXT sing N N 276 THR CB OG1 sing N N 277 THR CB CG2 sing N N 278 THR CB HB sing N N 279 THR OG1 HG1 sing N N 280 THR CG2 HG21 sing N N 281 THR CG2 HG22 sing N N 282 THR CG2 HG23 sing N N 283 THR OXT HXT sing N N 284 TRP N CA sing N N 285 TRP N H sing N N 286 TRP N H2 sing N N 287 TRP CA C sing N N 288 TRP CA CB sing N N 289 TRP CA HA sing N N 290 TRP C O doub N N 291 TRP C OXT sing N N 292 TRP CB CG sing N N 293 TRP CB HB2 sing N N 294 TRP CB HB3 sing N N 295 TRP CG CD1 doub Y N 296 TRP CG CD2 sing Y N 297 TRP CD1 NE1 sing Y N 298 TRP CD1 HD1 sing N N 299 TRP CD2 CE2 doub Y N 300 TRP CD2 CE3 sing Y N 301 TRP NE1 CE2 sing Y N 302 TRP NE1 HE1 sing N N 303 TRP CE2 CZ2 sing Y N 304 TRP CE3 CZ3 doub Y N 305 TRP CE3 HE3 sing N N 306 TRP CZ2 CH2 doub Y N 307 TRP CZ2 HZ2 sing N N 308 TRP CZ3 CH2 sing Y N 309 TRP CZ3 HZ3 sing N N 310 TRP CH2 HH2 sing N N 311 TRP OXT HXT sing N N 312 TYR N CA sing N N 313 TYR N H sing N N 314 TYR N H2 sing N N 315 TYR CA C sing N N 316 TYR CA CB sing N N 317 TYR CA HA sing N N 318 TYR C O doub N N 319 TYR C OXT sing N N 320 TYR CB CG sing N N 321 TYR CB HB2 sing N N 322 TYR CB HB3 sing N N 323 TYR CG CD1 doub Y N 324 TYR CG CD2 sing Y N 325 TYR CD1 CE1 sing Y N 326 TYR CD1 HD1 sing N N 327 TYR CD2 CE2 doub Y N 328 TYR CD2 HD2 sing N N 329 TYR CE1 CZ doub Y N 330 TYR CE1 HE1 sing N N 331 TYR CE2 CZ sing Y N 332 TYR CE2 HE2 sing N N 333 TYR CZ OH sing N N 334 TYR OH HH sing N N 335 TYR OXT HXT sing N N 336 VAL N CA sing N N 337 VAL N H sing N N 338 VAL N H2 sing N N 339 VAL CA C sing N N 340 VAL CA CB sing N N 341 VAL CA HA sing N N 342 VAL C O doub N N 343 VAL C OXT sing N N 344 VAL CB CG1 sing N N 345 VAL CB CG2 sing N N 346 VAL CB HB sing N N 347 VAL CG1 HG11 sing N N 348 VAL CG1 HG12 sing N N 349 VAL CG1 HG13 sing N N 350 VAL CG2 HG21 sing N N 351 VAL CG2 HG22 sing N N 352 VAL CG2 HG23 sing N N 353 VAL OXT HXT sing N N 354 # _em_admin.current_status REL _em_admin.deposition_date 2025-01-29 _em_admin.deposition_site RCSB _em_admin.entry_id 9N2L _em_admin.last_update 2025-03-19 _em_admin.map_release_date 2025-03-05 _em_admin.title 'Cryo-EM structure of locally refined up conformation of SARS-CoV-2 spike protein Receptor Binding Domain' # _em_ctf_correction.details ? _em_ctf_correction.em_image_processing_id 1 _em_ctf_correction.id 1 _em_ctf_correction.type 'PHASE FLIPPING AND AMPLITUDE CORRECTION' # _em_entity_assembly_molwt.entity_assembly_id 1 _em_entity_assembly_molwt.experimental_flag YES _em_entity_assembly_molwt.id 1 _em_entity_assembly_molwt.units KILODALTONS/NANOMETER _em_entity_assembly_molwt.value 585 # _em_entity_assembly_naturalsource.cell ? _em_entity_assembly_naturalsource.cellular_location ? _em_entity_assembly_naturalsource.entity_assembly_id 1 _em_entity_assembly_naturalsource.id 2 _em_entity_assembly_naturalsource.ncbi_tax_id 2697049 _em_entity_assembly_naturalsource.organism 'Severe acute respiratory syndrome coronavirus 2' _em_entity_assembly_naturalsource.organelle ? _em_entity_assembly_naturalsource.organ ? _em_entity_assembly_naturalsource.strain ? _em_entity_assembly_naturalsource.tissue ? _em_entity_assembly_naturalsource.details ? # _em_entity_assembly_recombinant.cell ? _em_entity_assembly_recombinant.entity_assembly_id 1 _em_entity_assembly_recombinant.id 2 _em_entity_assembly_recombinant.ncbi_tax_id 9606 _em_entity_assembly_recombinant.organism 'Homo sapiens' _em_entity_assembly_recombinant.plasmid ? _em_entity_assembly_recombinant.strain ? # _em_image_processing.details ? _em_image_processing.id 1 _em_image_processing.image_recording_id 1 # _em_image_recording.average_exposure_time ? _em_image_recording.avg_electron_dose_per_subtomogram ? _em_image_recording.avg_electron_dose_per_image 43.97 _em_image_recording.details ? _em_image_recording.detector_mode ? _em_image_recording.film_or_detector_model 'TFS FALCON 4i (4k x 4k)' _em_image_recording.id 1 _em_image_recording.imaging_id 1 _em_image_recording.num_diffraction_images ? _em_image_recording.num_grids_imaged ? _em_image_recording.num_real_images ? # loop_ _em_software.category _em_software.details _em_software.id _em_software.image_processing_id _em_software.fitting_id _em_software.imaging_id _em_software.name _em_software.version 'PARTICLE SELECTION' ? 1 1 ? ? ? ? 'IMAGE ACQUISITION' ? 2 ? ? 1 ? ? MASKING ? 3 ? ? ? ? ? 'CTF CORRECTION' ? 4 1 ? ? cryoSPARC ? 'LAYERLINE INDEXING' ? 5 ? ? ? ? ? 'DIFFRACTION INDEXING' ? 6 ? ? ? ? ? 'MODEL FITTING' ? 7 ? 1 ? 'UCSF Chimera' ? OTHER ? 8 ? ? ? ? ? 'IMAGE ACQUISITION' ? 9 ? ? ? ? ? 'CTF CORRECTION' ? 10 1 ? ? ? ? 'INITIAL EULER ASSIGNMENT' ? 11 1 ? ? ? ? 'FINAL EULER ASSIGNMENT' ? 12 1 ? ? ? ? CLASSIFICATION ? 13 1 ? ? ? ? RECONSTRUCTION ? 14 1 ? ? ? ? 'MODEL REFINEMENT' ? 15 ? 1 ? PHENIX ? 'MODEL REFINEMENT' ? 16 ? 1 ? Coot ? 'MODEL FITTING' ? 17 ? 2 ? ? ? 'MODEL REFINEMENT' ? 18 ? 2 ? ? ? 'VOLUME SELECTION' ? 19 1 1 1 ? ? 'SERIES ALIGNMENT' ? 20 1 1 1 ? ? 'MOLECULAR REPLACEMENT' ? 21 1 1 1 ? ? 'LATTICE DISTORTION CORRECTION' ? 22 1 1 1 ? ? 'SYMMETRY DETERMINATION' ? 23 1 1 1 ? ? 'CRYSTALLOGRAPHY MERGING' ? 24 1 1 1 ? ? # _em_specimen.concentration 2.5 _em_specimen.details ? _em_specimen.embedding_applied NO _em_specimen.experiment_id 1 _em_specimen.id 1 _em_specimen.shadowing_applied NO _em_specimen.staining_applied NO _em_specimen.vitrification_applied YES # _pdbx_audit_support.funding_organization 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' _pdbx_audit_support.country 'United States' _pdbx_audit_support.grant_number GM150187 _pdbx_audit_support.ordinal 1 # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 9CSS _pdbx_initial_refinement_model.details ? # _space_group.crystal_system triclinic _space_group.name_H-M_alt 'P 1' _space_group.IT_number 1 _space_group.name_Hall 'P 1' _space_group.id 1 # _atom_sites.entry_id 9N2L _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.Cartn_transform_axes ? _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_