data_6VFI # _entry.id 6VFI # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.331 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 6VFI WWPDB D_1000246115 EMDB EMD-21173 # _pdbx_database_related.db_name EMDB _pdbx_database_related.details 'De novo designed octahedral nanoparticle O43_dn18' _pdbx_database_related.db_id EMD-21173 _pdbx_database_related.content_type 'associated EM volume' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 6VFI _pdbx_database_status.recvd_initial_deposition_date 2020-01-05 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Antanasijevic, A.' 1 0000-0001-9452-8954 'Ward, A.B.' 2 0000-0001-7153-3769 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Elife _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 2050-084X _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 9 _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'Tailored design of protein nanoparticle scaffolds for multivalent presentation of viral glycoprotein antigens.' _citation.year 2020 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.7554/eLife.57659 _citation.pdbx_database_id_PubMed 32748788 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Ueda, G.' 1 0000-0002-9792-7149 primary 'Antanasijevic, A.' 2 0000-0001-9452-8954 primary 'Fallas, J.A.' 3 ? primary 'Sheffler, W.' 4 ? primary 'Copps, J.' 5 ? primary 'Ellis, D.' 6 ? primary 'Hutchinson, G.B.' 7 ? primary 'Moyer, A.' 8 ? primary 'Yasmeen, A.' 9 ? primary 'Tsybovsky, Y.' 10 ? primary 'Park, Y.J.' 11 ? primary 'Bick, M.J.' 12 0000-0002-9585-859X primary 'Sankaran, B.' 13 ? primary 'Gillespie, R.A.' 14 ? primary 'Brouwer, P.J.' 15 0000-0002-2902-7739 primary 'Zwart, P.H.' 16 ? primary 'Veesler, D.' 17 0000-0002-6019-8675 primary 'Kanekiyo, M.' 18 ? primary 'Graham, B.S.' 19 0000-0001-8112-0853 primary 'Sanders, R.W.' 20 ? primary 'Moore, J.P.' 21 ? primary 'Klasse, P.J.' 22 0000-0001-8222-278X primary 'Ward, A.B.' 23 0000-0001-7153-3769 primary 'King, N.P.' 24 ? primary 'Baker, D.' 25 0000-0001-7896-6217 # 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 O43_dn18B 13828.147 1 ? ? ? ? 2 polymer man O43_dn18A 22722.627 1 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 'polypeptide(L)' no no ;MGEEAELAYLLGELAYKLGEYRIAIRAYRIALKRDPNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLG NAYYKQGDYDEAIEYYQKALELDPSNLDAAVNLGAATMLTS ; ;MGEEAELAYLLGELAYKLGEYRIAIRAYRIALKRDPNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLG NAYYKQGDYDEAIEYYQKALELDPSNLDAAVNLGAATMLTS ; B ? 2 'polypeptide(L)' no no ;MDRCEELARRIAEVVERAKRAGTSEDEIAESVARVISLVIRALKLSGSSYEVICECVARIVAEIVEALKRSGTSAVEIAK IVARVISEVIRTLKESGSSYEVICECVARIVAEIVEALKRSGTSAAIIALIVALVISEVIRTLKESGSSFEVILECVIRI VLEIIEALKRSGTSEQDVMLIVMAVLLVVLATLQLSGSGGWLEHHHHHH ; ;MDRCEELARRIAEVVERAKRAGTSEDEIAESVARVISLVIRALKLSGSSYEVICECVARIVAEIVEALKRSGTSAVEIAK IVARVISEVIRTLKESGSSYEVICECVARIVAEIVEALKRSGTSAAIIALIVALVISEVIRTLKESGSSFEVILECVIRI VLEIIEALKRSGTSEQDVMLIVMAVLLVVLATLQLSGSGGWLEHHHHHH ; A ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 MET n 1 2 GLY n 1 3 GLU n 1 4 GLU n 1 5 ALA n 1 6 GLU n 1 7 LEU n 1 8 ALA n 1 9 TYR n 1 10 LEU n 1 11 LEU n 1 12 GLY n 1 13 GLU n 1 14 LEU n 1 15 ALA n 1 16 TYR n 1 17 LYS n 1 18 LEU n 1 19 GLY n 1 20 GLU n 1 21 TYR n 1 22 ARG n 1 23 ILE n 1 24 ALA n 1 25 ILE n 1 26 ARG n 1 27 ALA n 1 28 TYR n 1 29 ARG n 1 30 ILE n 1 31 ALA n 1 32 LEU n 1 33 LYS n 1 34 ARG n 1 35 ASP n 1 36 PRO n 1 37 ASN n 1 38 ASN n 1 39 ALA n 1 40 GLU n 1 41 ALA n 1 42 TRP n 1 43 TYR n 1 44 ASN n 1 45 LEU n 1 46 GLY n 1 47 ASN n 1 48 ALA n 1 49 TYR n 1 50 TYR n 1 51 LYS n 1 52 GLN n 1 53 GLY n 1 54 ASP n 1 55 TYR n 1 56 ASP n 1 57 GLU n 1 58 ALA n 1 59 ILE n 1 60 GLU n 1 61 TYR n 1 62 TYR n 1 63 GLN n 1 64 LYS n 1 65 ALA n 1 66 LEU n 1 67 GLU n 1 68 LEU n 1 69 ASP n 1 70 PRO n 1 71 ASN n 1 72 ASN n 1 73 ALA n 1 74 GLU n 1 75 ALA n 1 76 TRP n 1 77 TYR n 1 78 ASN n 1 79 LEU n 1 80 GLY n 1 81 ASN n 1 82 ALA n 1 83 TYR n 1 84 TYR n 1 85 LYS n 1 86 GLN n 1 87 GLY n 1 88 ASP n 1 89 TYR n 1 90 ASP n 1 91 GLU n 1 92 ALA n 1 93 ILE n 1 94 GLU n 1 95 TYR n 1 96 TYR n 1 97 GLN n 1 98 LYS n 1 99 ALA n 1 100 LEU n 1 101 GLU n 1 102 LEU n 1 103 ASP n 1 104 PRO n 1 105 SER n 1 106 ASN n 1 107 LEU n 1 108 ASP n 1 109 ALA n 1 110 ALA n 1 111 VAL n 1 112 ASN n 1 113 LEU n 1 114 GLY n 1 115 ALA n 1 116 ALA n 1 117 THR n 1 118 MET n 1 119 LEU n 1 120 THR n 1 121 SER n 2 1 MET n 2 2 ASP n 2 3 ARG n 2 4 CYS n 2 5 GLU n 2 6 GLU n 2 7 LEU n 2 8 ALA n 2 9 ARG n 2 10 ARG n 2 11 ILE n 2 12 ALA n 2 13 GLU n 2 14 VAL n 2 15 VAL n 2 16 GLU n 2 17 ARG n 2 18 ALA n 2 19 LYS n 2 20 ARG n 2 21 ALA n 2 22 GLY n 2 23 THR n 2 24 SER n 2 25 GLU n 2 26 ASP n 2 27 GLU n 2 28 ILE n 2 29 ALA n 2 30 GLU n 2 31 SER n 2 32 VAL n 2 33 ALA n 2 34 ARG n 2 35 VAL n 2 36 ILE n 2 37 SER n 2 38 LEU n 2 39 VAL n 2 40 ILE n 2 41 ARG n 2 42 ALA n 2 43 LEU n 2 44 LYS n 2 45 LEU n 2 46 SER n 2 47 GLY n 2 48 SER n 2 49 SER n 2 50 TYR n 2 51 GLU n 2 52 VAL n 2 53 ILE n 2 54 CYS n 2 55 GLU n 2 56 CYS n 2 57 VAL n 2 58 ALA n 2 59 ARG n 2 60 ILE n 2 61 VAL n 2 62 ALA n 2 63 GLU n 2 64 ILE n 2 65 VAL n 2 66 GLU n 2 67 ALA n 2 68 LEU n 2 69 LYS n 2 70 ARG n 2 71 SER n 2 72 GLY n 2 73 THR n 2 74 SER n 2 75 ALA n 2 76 VAL n 2 77 GLU n 2 78 ILE n 2 79 ALA n 2 80 LYS n 2 81 ILE n 2 82 VAL n 2 83 ALA n 2 84 ARG n 2 85 VAL n 2 86 ILE n 2 87 SER n 2 88 GLU n 2 89 VAL n 2 90 ILE n 2 91 ARG n 2 92 THR n 2 93 LEU n 2 94 LYS n 2 95 GLU n 2 96 SER n 2 97 GLY n 2 98 SER n 2 99 SER n 2 100 TYR n 2 101 GLU n 2 102 VAL n 2 103 ILE n 2 104 CYS n 2 105 GLU n 2 106 CYS n 2 107 VAL n 2 108 ALA n 2 109 ARG n 2 110 ILE n 2 111 VAL n 2 112 ALA n 2 113 GLU n 2 114 ILE n 2 115 VAL n 2 116 GLU n 2 117 ALA n 2 118 LEU n 2 119 LYS n 2 120 ARG n 2 121 SER n 2 122 GLY n 2 123 THR n 2 124 SER n 2 125 ALA n 2 126 ALA n 2 127 ILE n 2 128 ILE n 2 129 ALA n 2 130 LEU n 2 131 ILE n 2 132 VAL n 2 133 ALA n 2 134 LEU n 2 135 VAL n 2 136 ILE n 2 137 SER n 2 138 GLU n 2 139 VAL n 2 140 ILE n 2 141 ARG n 2 142 THR n 2 143 LEU n 2 144 LYS n 2 145 GLU n 2 146 SER n 2 147 GLY n 2 148 SER n 2 149 SER n 2 150 PHE n 2 151 GLU n 2 152 VAL n 2 153 ILE n 2 154 LEU n 2 155 GLU n 2 156 CYS n 2 157 VAL n 2 158 ILE n 2 159 ARG n 2 160 ILE n 2 161 VAL n 2 162 LEU n 2 163 GLU n 2 164 ILE n 2 165 ILE n 2 166 GLU n 2 167 ALA n 2 168 LEU n 2 169 LYS n 2 170 ARG n 2 171 SER n 2 172 GLY n 2 173 THR n 2 174 SER n 2 175 GLU n 2 176 GLN n 2 177 ASP n 2 178 VAL n 2 179 MET n 2 180 LEU n 2 181 ILE n 2 182 VAL n 2 183 MET n 2 184 ALA n 2 185 VAL n 2 186 LEU n 2 187 LEU n 2 188 VAL n 2 189 VAL n 2 190 LEU n 2 191 ALA n 2 192 THR n 2 193 LEU n 2 194 GLN n 2 195 LEU n 2 196 SER n 2 197 GLY n 2 198 SER n 2 199 GLY n 2 200 GLY n 2 201 TRP n 2 202 LEU n 2 203 GLU n 2 204 HIS n 2 205 HIS n 2 206 HIS n 2 207 HIS n 2 208 HIS n 2 209 HIS 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' 1 121 ? ? ? ? ? ? ? ? ? 'synthetic construct' 32630 ? ? ? ? ? ? ? ? 'Escherichia coli BL21(DE3)' 469008 ? ? ? ? ? ? ? ? ? ? ? ? ? ? plasmid ? ? ? pET28b ? ? 2 1 sample 'Biological sequence' 1 209 ? ? ? ? ? ? ? ? ? 'synthetic construct' 32630 ? ? ? ? ? ? ? ? 'Escherichia coli BL21(DE3)' 469008 ? ? ? ? ? ? ? ? ? ? ? ? ? ? plasmid ? ? ? pET28b ? ? # 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 PDB 6VFI 6VFI ? 1 ? 1 2 PDB 6VFI 6VFI ? 2 ? 1 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 6VFI B 1 ? 121 ? 6VFI -1 ? 119 ? -1 119 2 2 6VFI A 1 ? 209 ? 6VFI 0 ? 208 ? 0 208 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 6VFI _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _struct.entry_id 6VFI _struct.title 'De novo designed octahedral nanoparticle O43_dn18' _struct.pdbx_descriptor 'O43_dn18B, O43_dn18A' _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 6VFI _struct_keywords.text 'De novo, Nanoparticle, DE NOVO PROTEIN' _struct_keywords.pdbx_keywords 'DE NOVO PROTEIN' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 AA1 GLU A 3 ? LEU A 18 ? GLU B 1 LEU B 16 1 ? 16 HELX_P HELX_P2 AA2 GLU A 20 ? ASP A 35 ? GLU B 18 ASP B 33 1 ? 16 HELX_P HELX_P3 AA3 ASN A 38 ? GLN A 52 ? ASN B 36 GLN B 50 1 ? 15 HELX_P HELX_P4 AA4 ASP A 54 ? ASP A 69 ? ASP B 52 ASP B 67 1 ? 16 HELX_P HELX_P5 AA5 ALA A 73 ? GLN A 86 ? ALA B 71 GLN B 84 1 ? 14 HELX_P HELX_P6 AA6 ASP A 88 ? ASP A 103 ? ASP B 86 ASP B 101 1 ? 16 HELX_P HELX_P7 AA7 ASN A 106 ? LEU A 119 ? ASN B 104 LEU B 117 1 ? 14 HELX_P HELX_P8 AA8 ARG B 3 ? GLY B 22 ? ARG A 2 GLY A 21 1 ? 20 HELX_P HELX_P9 AA9 SER B 24 ? SER B 46 ? SER A 23 SER A 45 1 ? 23 HELX_P HELX_P10 AB1 SER B 49 ? SER B 71 ? SER A 48 SER A 70 1 ? 23 HELX_P HELX_P11 AB2 ALA B 75 ? GLY B 97 ? ALA A 74 GLY A 96 1 ? 23 HELX_P HELX_P12 AB3 VAL B 102 ? SER B 121 ? VAL A 101 SER A 120 1 ? 20 HELX_P HELX_P13 AB4 SER B 124 ? GLY B 147 ? SER A 123 GLY A 146 1 ? 24 HELX_P HELX_P14 AB5 SER B 149 ? SER B 171 ? SER A 148 SER A 170 1 ? 23 HELX_P HELX_P15 AB6 SER B 174 ? LEU B 195 ? SER A 173 LEU A 194 1 ? 22 # _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 ? ? B CYS 4 SG ? ? ? 1_555 B CYS 56 SG ? ? A CYS 3 A CYS 55 1_555 ? ? ? ? ? ? ? 2.038 ? ? disulf2 disulf ? ? B CYS 104 SG ? ? ? 1_555 B CYS 156 SG ? ? A CYS 103 A CYS 155 1_555 ? ? ? ? ? ? ? 2.023 ? ? # _struct_conn_type.id disulf _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 6VFI _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 MET 1 -1 ? ? ? B . n A 1 2 GLY 2 0 ? ? ? B . n A 1 3 GLU 3 1 1 GLU GLU B . n A 1 4 GLU 4 2 2 GLU GLU B . n A 1 5 ALA 5 3 3 ALA ALA B . n A 1 6 GLU 6 4 4 GLU GLU B . n A 1 7 LEU 7 5 5 LEU LEU B . n A 1 8 ALA 8 6 6 ALA ALA B . n A 1 9 TYR 9 7 7 TYR TYR B . n A 1 10 LEU 10 8 8 LEU LEU B . n A 1 11 LEU 11 9 9 LEU LEU B . n A 1 12 GLY 12 10 10 GLY GLY B . n A 1 13 GLU 13 11 11 GLU GLU B . n A 1 14 LEU 14 12 12 LEU LEU B . n A 1 15 ALA 15 13 13 ALA ALA B . n A 1 16 TYR 16 14 14 TYR TYR B . n A 1 17 LYS 17 15 15 LYS LYS B . n A 1 18 LEU 18 16 16 LEU LEU B . n A 1 19 GLY 19 17 17 GLY GLY B . n A 1 20 GLU 20 18 18 GLU GLU B . n A 1 21 TYR 21 19 19 TYR TYR B . n A 1 22 ARG 22 20 20 ARG ARG B . n A 1 23 ILE 23 21 21 ILE ILE B . n A 1 24 ALA 24 22 22 ALA ALA B . n A 1 25 ILE 25 23 23 ILE ILE B . n A 1 26 ARG 26 24 24 ARG ARG B . n A 1 27 ALA 27 25 25 ALA ALA B . n A 1 28 TYR 28 26 26 TYR TYR B . n A 1 29 ARG 29 27 27 ARG ARG B . n A 1 30 ILE 30 28 28 ILE ILE B . n A 1 31 ALA 31 29 29 ALA ALA B . n A 1 32 LEU 32 30 30 LEU LEU B . n A 1 33 LYS 33 31 31 LYS LYS B . n A 1 34 ARG 34 32 32 ARG ARG B . n A 1 35 ASP 35 33 33 ASP ASP B . n A 1 36 PRO 36 34 34 PRO PRO B . n A 1 37 ASN 37 35 35 ASN ASN B . n A 1 38 ASN 38 36 36 ASN ASN B . n A 1 39 ALA 39 37 37 ALA ALA B . n A 1 40 GLU 40 38 38 GLU GLU B . n A 1 41 ALA 41 39 39 ALA ALA B . n A 1 42 TRP 42 40 40 TRP TRP B . n A 1 43 TYR 43 41 41 TYR TYR B . n A 1 44 ASN 44 42 42 ASN ASN B . n A 1 45 LEU 45 43 43 LEU LEU B . n A 1 46 GLY 46 44 44 GLY GLY B . n A 1 47 ASN 47 45 45 ASN ASN B . n A 1 48 ALA 48 46 46 ALA ALA B . n A 1 49 TYR 49 47 47 TYR TYR B . n A 1 50 TYR 50 48 48 TYR TYR B . n A 1 51 LYS 51 49 49 LYS LYS B . n A 1 52 GLN 52 50 50 GLN GLN B . n A 1 53 GLY 53 51 51 GLY GLY B . n A 1 54 ASP 54 52 52 ASP ASP B . n A 1 55 TYR 55 53 53 TYR TYR B . n A 1 56 ASP 56 54 54 ASP ASP B . n A 1 57 GLU 57 55 55 GLU GLU B . n A 1 58 ALA 58 56 56 ALA ALA B . n A 1 59 ILE 59 57 57 ILE ILE B . n A 1 60 GLU 60 58 58 GLU GLU B . n A 1 61 TYR 61 59 59 TYR TYR B . n A 1 62 TYR 62 60 60 TYR TYR B . n A 1 63 GLN 63 61 61 GLN GLN B . n A 1 64 LYS 64 62 62 LYS LYS B . n A 1 65 ALA 65 63 63 ALA ALA B . n A 1 66 LEU 66 64 64 LEU LEU B . n A 1 67 GLU 67 65 65 GLU GLU B . n A 1 68 LEU 68 66 66 LEU LEU B . n A 1 69 ASP 69 67 67 ASP ASP B . n A 1 70 PRO 70 68 68 PRO PRO B . n A 1 71 ASN 71 69 69 ASN ASN B . n A 1 72 ASN 72 70 70 ASN ASN B . n A 1 73 ALA 73 71 71 ALA ALA B . n A 1 74 GLU 74 72 72 GLU GLU B . n A 1 75 ALA 75 73 73 ALA ALA B . n A 1 76 TRP 76 74 74 TRP TRP B . n A 1 77 TYR 77 75 75 TYR TYR B . n A 1 78 ASN 78 76 76 ASN ASN B . n A 1 79 LEU 79 77 77 LEU LEU B . n A 1 80 GLY 80 78 78 GLY GLY B . n A 1 81 ASN 81 79 79 ASN ASN B . n A 1 82 ALA 82 80 80 ALA ALA B . n A 1 83 TYR 83 81 81 TYR TYR B . n A 1 84 TYR 84 82 82 TYR TYR B . n A 1 85 LYS 85 83 83 LYS LYS B . n A 1 86 GLN 86 84 84 GLN GLN B . n A 1 87 GLY 87 85 85 GLY GLY B . n A 1 88 ASP 88 86 86 ASP ASP B . n A 1 89 TYR 89 87 87 TYR TYR B . n A 1 90 ASP 90 88 88 ASP ASP B . n A 1 91 GLU 91 89 89 GLU GLU B . n A 1 92 ALA 92 90 90 ALA ALA B . n A 1 93 ILE 93 91 91 ILE ILE B . n A 1 94 GLU 94 92 92 GLU GLU B . n A 1 95 TYR 95 93 93 TYR TYR B . n A 1 96 TYR 96 94 94 TYR TYR B . n A 1 97 GLN 97 95 95 GLN GLN B . n A 1 98 LYS 98 96 96 LYS LYS B . n A 1 99 ALA 99 97 97 ALA ALA B . n A 1 100 LEU 100 98 98 LEU LEU B . n A 1 101 GLU 101 99 99 GLU GLU B . n A 1 102 LEU 102 100 100 LEU LEU B . n A 1 103 ASP 103 101 101 ASP ASP B . n A 1 104 PRO 104 102 102 PRO PRO B . n A 1 105 SER 105 103 103 SER SER B . n A 1 106 ASN 106 104 104 ASN ASN B . n A 1 107 LEU 107 105 105 LEU LEU B . n A 1 108 ASP 108 106 106 ASP ASP B . n A 1 109 ALA 109 107 107 ALA ALA B . n A 1 110 ALA 110 108 108 ALA ALA B . n A 1 111 VAL 111 109 109 VAL VAL B . n A 1 112 ASN 112 110 110 ASN ASN B . n A 1 113 LEU 113 111 111 LEU LEU B . n A 1 114 GLY 114 112 112 GLY GLY B . n A 1 115 ALA 115 113 113 ALA ALA B . n A 1 116 ALA 116 114 114 ALA ALA B . n A 1 117 THR 117 115 115 THR THR B . n A 1 118 MET 118 116 116 MET MET B . n A 1 119 LEU 119 117 117 LEU LEU B . n A 1 120 THR 120 118 118 THR THR B . n A 1 121 SER 121 119 ? ? ? B . n B 2 1 MET 1 0 ? ? ? A . n B 2 2 ASP 2 1 1 ASP ASP A . n B 2 3 ARG 3 2 2 ARG ARG A . n B 2 4 CYS 4 3 3 CYS CYS A . n B 2 5 GLU 5 4 4 GLU GLU A . n B 2 6 GLU 6 5 5 GLU GLU A . n B 2 7 LEU 7 6 6 LEU LEU A . n B 2 8 ALA 8 7 7 ALA ALA A . n B 2 9 ARG 9 8 8 ARG ARG A . n B 2 10 ARG 10 9 9 ARG ARG A . n B 2 11 ILE 11 10 10 ILE ILE A . n B 2 12 ALA 12 11 11 ALA ALA A . n B 2 13 GLU 13 12 12 GLU GLU A . n B 2 14 VAL 14 13 13 VAL VAL A . n B 2 15 VAL 15 14 14 VAL VAL A . n B 2 16 GLU 16 15 15 GLU GLU A . n B 2 17 ARG 17 16 16 ARG ARG A . n B 2 18 ALA 18 17 17 ALA ALA A . n B 2 19 LYS 19 18 18 LYS LYS A . n B 2 20 ARG 20 19 19 ARG ARG A . n B 2 21 ALA 21 20 20 ALA ALA A . n B 2 22 GLY 22 21 21 GLY GLY A . n B 2 23 THR 23 22 22 THR THR A . n B 2 24 SER 24 23 23 SER SER A . n B 2 25 GLU 25 24 24 GLU GLU A . n B 2 26 ASP 26 25 25 ASP ASP A . n B 2 27 GLU 27 26 26 GLU GLU A . n B 2 28 ILE 28 27 27 ILE ILE A . n B 2 29 ALA 29 28 28 ALA ALA A . n B 2 30 GLU 30 29 29 GLU GLU A . n B 2 31 SER 31 30 30 SER SER A . n B 2 32 VAL 32 31 31 VAL VAL A . n B 2 33 ALA 33 32 32 ALA ALA A . n B 2 34 ARG 34 33 33 ARG ARG A . n B 2 35 VAL 35 34 34 VAL VAL A . n B 2 36 ILE 36 35 35 ILE ILE A . n B 2 37 SER 37 36 36 SER SER A . n B 2 38 LEU 38 37 37 LEU LEU A . n B 2 39 VAL 39 38 38 VAL VAL A . n B 2 40 ILE 40 39 39 ILE ILE A . n B 2 41 ARG 41 40 40 ARG ARG A . n B 2 42 ALA 42 41 41 ALA ALA A . n B 2 43 LEU 43 42 42 LEU LEU A . n B 2 44 LYS 44 43 43 LYS LYS A . n B 2 45 LEU 45 44 44 LEU LEU A . n B 2 46 SER 46 45 45 SER SER A . n B 2 47 GLY 47 46 46 GLY GLY A . n B 2 48 SER 48 47 47 SER SER A . n B 2 49 SER 49 48 48 SER SER A . n B 2 50 TYR 50 49 49 TYR TYR A . n B 2 51 GLU 51 50 50 GLU GLU A . n B 2 52 VAL 52 51 51 VAL VAL A . n B 2 53 ILE 53 52 52 ILE ILE A . n B 2 54 CYS 54 53 53 CYS CYS A . n B 2 55 GLU 55 54 54 GLU GLU A . n B 2 56 CYS 56 55 55 CYS CYS A . n B 2 57 VAL 57 56 56 VAL VAL A . n B 2 58 ALA 58 57 57 ALA ALA A . n B 2 59 ARG 59 58 58 ARG ARG A . n B 2 60 ILE 60 59 59 ILE ILE A . n B 2 61 VAL 61 60 60 VAL VAL A . n B 2 62 ALA 62 61 61 ALA ALA A . n B 2 63 GLU 63 62 62 GLU GLU A . n B 2 64 ILE 64 63 63 ILE ILE A . n B 2 65 VAL 65 64 64 VAL VAL A . n B 2 66 GLU 66 65 65 GLU GLU A . n B 2 67 ALA 67 66 66 ALA ALA A . n B 2 68 LEU 68 67 67 LEU LEU A . n B 2 69 LYS 69 68 68 LYS LYS A . n B 2 70 ARG 70 69 69 ARG ARG A . n B 2 71 SER 71 70 70 SER SER A . n B 2 72 GLY 72 71 71 GLY GLY A . n B 2 73 THR 73 72 72 THR THR A . n B 2 74 SER 74 73 73 SER SER A . n B 2 75 ALA 75 74 74 ALA ALA A . n B 2 76 VAL 76 75 75 VAL VAL A . n B 2 77 GLU 77 76 76 GLU GLU A . n B 2 78 ILE 78 77 77 ILE ILE A . n B 2 79 ALA 79 78 78 ALA ALA A . n B 2 80 LYS 80 79 79 LYS LYS A . n B 2 81 ILE 81 80 80 ILE ILE A . n B 2 82 VAL 82 81 81 VAL VAL A . n B 2 83 ALA 83 82 82 ALA ALA A . n B 2 84 ARG 84 83 83 ARG ARG A . n B 2 85 VAL 85 84 84 VAL VAL A . n B 2 86 ILE 86 85 85 ILE ILE A . n B 2 87 SER 87 86 86 SER SER A . n B 2 88 GLU 88 87 87 GLU GLU A . n B 2 89 VAL 89 88 88 VAL VAL A . n B 2 90 ILE 90 89 89 ILE ILE A . n B 2 91 ARG 91 90 90 ARG ARG A . n B 2 92 THR 92 91 91 THR THR A . n B 2 93 LEU 93 92 92 LEU LEU A . n B 2 94 LYS 94 93 93 LYS LYS A . n B 2 95 GLU 95 94 94 GLU GLU A . n B 2 96 SER 96 95 95 SER SER A . n B 2 97 GLY 97 96 96 GLY GLY A . n B 2 98 SER 98 97 97 SER SER A . n B 2 99 SER 99 98 98 SER SER A . n B 2 100 TYR 100 99 99 TYR TYR A . n B 2 101 GLU 101 100 100 GLU GLU A . n B 2 102 VAL 102 101 101 VAL VAL A . n B 2 103 ILE 103 102 102 ILE ILE A . n B 2 104 CYS 104 103 103 CYS CYS A . n B 2 105 GLU 105 104 104 GLU GLU A . n B 2 106 CYS 106 105 105 CYS CYS A . n B 2 107 VAL 107 106 106 VAL VAL A . n B 2 108 ALA 108 107 107 ALA ALA A . n B 2 109 ARG 109 108 108 ARG ARG A . n B 2 110 ILE 110 109 109 ILE ILE A . n B 2 111 VAL 111 110 110 VAL VAL A . n B 2 112 ALA 112 111 111 ALA ALA A . n B 2 113 GLU 113 112 112 GLU GLU A . n B 2 114 ILE 114 113 113 ILE ILE A . n B 2 115 VAL 115 114 114 VAL VAL A . n B 2 116 GLU 116 115 115 GLU GLU A . n B 2 117 ALA 117 116 116 ALA ALA A . n B 2 118 LEU 118 117 117 LEU LEU A . n B 2 119 LYS 119 118 118 LYS LYS A . n B 2 120 ARG 120 119 119 ARG ARG A . n B 2 121 SER 121 120 120 SER SER A . n B 2 122 GLY 122 121 121 GLY GLY A . n B 2 123 THR 123 122 122 THR THR A . n B 2 124 SER 124 123 123 SER SER A . n B 2 125 ALA 125 124 124 ALA ALA A . n B 2 126 ALA 126 125 125 ALA ALA A . n B 2 127 ILE 127 126 126 ILE ILE A . n B 2 128 ILE 128 127 127 ILE ILE A . n B 2 129 ALA 129 128 128 ALA ALA A . n B 2 130 LEU 130 129 129 LEU LEU A . n B 2 131 ILE 131 130 130 ILE ILE A . n B 2 132 VAL 132 131 131 VAL VAL A . n B 2 133 ALA 133 132 132 ALA ALA A . n B 2 134 LEU 134 133 133 LEU LEU A . n B 2 135 VAL 135 134 134 VAL VAL A . n B 2 136 ILE 136 135 135 ILE ILE A . n B 2 137 SER 137 136 136 SER SER A . n B 2 138 GLU 138 137 137 GLU GLU A . n B 2 139 VAL 139 138 138 VAL VAL A . n B 2 140 ILE 140 139 139 ILE ILE A . n B 2 141 ARG 141 140 140 ARG ARG A . n B 2 142 THR 142 141 141 THR THR A . n B 2 143 LEU 143 142 142 LEU LEU A . n B 2 144 LYS 144 143 143 LYS LYS A . n B 2 145 GLU 145 144 144 GLU GLU A . n B 2 146 SER 146 145 145 SER SER A . n B 2 147 GLY 147 146 146 GLY GLY A . n B 2 148 SER 148 147 147 SER SER A . n B 2 149 SER 149 148 148 SER SER A . n B 2 150 PHE 150 149 149 PHE PHE A . n B 2 151 GLU 151 150 150 GLU GLU A . n B 2 152 VAL 152 151 151 VAL VAL A . n B 2 153 ILE 153 152 152 ILE ILE A . n B 2 154 LEU 154 153 153 LEU LEU A . n B 2 155 GLU 155 154 154 GLU GLU A . n B 2 156 CYS 156 155 155 CYS CYS A . n B 2 157 VAL 157 156 156 VAL VAL A . n B 2 158 ILE 158 157 157 ILE ILE A . n B 2 159 ARG 159 158 158 ARG ARG A . n B 2 160 ILE 160 159 159 ILE ILE A . n B 2 161 VAL 161 160 160 VAL VAL A . n B 2 162 LEU 162 161 161 LEU LEU A . n B 2 163 GLU 163 162 162 GLU GLU A . n B 2 164 ILE 164 163 163 ILE ILE A . n B 2 165 ILE 165 164 164 ILE ILE A . n B 2 166 GLU 166 165 165 GLU GLU A . n B 2 167 ALA 167 166 166 ALA ALA A . n B 2 168 LEU 168 167 167 LEU LEU A . n B 2 169 LYS 169 168 168 LYS LYS A . n B 2 170 ARG 170 169 169 ARG ARG A . n B 2 171 SER 171 170 170 SER SER A . n B 2 172 GLY 172 171 171 GLY GLY A . n B 2 173 THR 173 172 172 THR THR A . n B 2 174 SER 174 173 173 SER SER A . n B 2 175 GLU 175 174 174 GLU GLU A . n B 2 176 GLN 176 175 175 GLN GLN A . n B 2 177 ASP 177 176 176 ASP ASP A . n B 2 178 VAL 178 177 177 VAL VAL A . n B 2 179 MET 179 178 178 MET MET A . n B 2 180 LEU 180 179 179 LEU LEU A . n B 2 181 ILE 181 180 180 ILE ILE A . n B 2 182 VAL 182 181 181 VAL VAL A . n B 2 183 MET 183 182 182 MET MET A . n B 2 184 ALA 184 183 183 ALA ALA A . n B 2 185 VAL 185 184 184 VAL VAL A . n B 2 186 LEU 186 185 185 LEU LEU A . n B 2 187 LEU 187 186 186 LEU LEU A . n B 2 188 VAL 188 187 187 VAL VAL A . n B 2 189 VAL 189 188 188 VAL VAL A . n B 2 190 LEU 190 189 189 LEU LEU A . n B 2 191 ALA 191 190 190 ALA ALA A . n B 2 192 THR 192 191 191 THR THR A . n B 2 193 LEU 193 192 192 LEU LEU A . n B 2 194 GLN 194 193 193 GLN GLN A . n B 2 195 LEU 195 194 194 LEU LEU A . n B 2 196 SER 196 195 195 SER SER A . n B 2 197 GLY 197 196 196 GLY GLY A . n B 2 198 SER 198 197 197 SER SER A . n B 2 199 GLY 199 198 ? ? ? A . n B 2 200 GLY 200 199 ? ? ? A . n B 2 201 TRP 201 200 ? ? ? A . n B 2 202 LEU 202 201 ? ? ? A . n B 2 203 GLU 203 202 ? ? ? A . n B 2 204 HIS 204 203 ? ? ? A . n B 2 205 HIS 205 204 ? ? ? A . n B 2 206 HIS 206 205 ? ? ? A . n B 2 207 HIS 207 206 ? ? ? A . n B 2 208 HIS 208 207 ? ? ? A . n B 2 209 HIS 209 208 ? ? ? A . n # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 'complete point assembly' ? 48-meric 48 2 'point asymmetric unit' ? dimeric 2 3 'point asymmetric unit, std point frame' ? dimeric 2 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 '(1-24)' A,B 2 1 A,B 3 P A,B # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] P 'transform to point frame' ? ? 1.00000000 0.00000000 0.00000000 -154.50000 0.00000000 1.00000000 0.00000000 -154.50000 0.00000000 0.00000000 1.00000000 -154.50000 1 'point symmetry operation' ? ? 1.00000000 0.00000000 0.00000000 0.00000 0.00000000 1.00000000 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 2 'point symmetry operation' ? ? -1.00000000 0.00000000 0.00000000 309.00000 0.00000000 -1.00000000 0.00000000 309.00000 0.00000000 0.00000000 1.00000000 0.00000 3 'point symmetry operation' ? ? -1.00000000 0.00000000 0.00000000 309.00000 0.00000000 1.00000000 0.00000000 0.00000 0.00000000 0.00000000 -1.00000000 309.00000 4 'point symmetry operation' ? ? 1.00000000 0.00000000 0.00000000 0.00000 0.00000000 -1.00000000 0.00000000 309.00000 0.00000000 0.00000000 -1.00000000 309.00000 5 'point symmetry operation' ? ? 0.00000000 0.00000000 1.00000000 0.00000 1.00000000 0.00000000 0.00000000 0.00000 0.00000000 1.00000000 0.00000000 0.00000 6 'point symmetry operation' ? ? 0.00000000 0.00000000 1.00000000 0.00000 -1.00000000 0.00000000 0.00000000 309.00000 0.00000000 -1.00000000 0.00000000 309.00000 7 'point symmetry operation' ? ? 0.00000000 0.00000000 -1.00000000 309.00000 -1.00000000 0.00000000 0.00000000 309.00000 0.00000000 1.00000000 0.00000000 0.00000 8 'point symmetry operation' ? ? 0.00000000 0.00000000 -1.00000000 309.00000 1.00000000 0.00000000 0.00000000 0.00000 0.00000000 -1.00000000 0.00000000 309.00000 9 'point symmetry operation' ? ? 0.00000000 1.00000000 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 1.00000000 0.00000000 0.00000000 0.00000 10 'point symmetry operation' ? ? 0.00000000 -1.00000000 0.00000000 309.00000 0.00000000 0.00000000 1.00000000 0.00000 -1.00000000 0.00000000 0.00000000 309.00000 11 'point symmetry operation' ? ? 0.00000000 1.00000000 0.00000000 0.00000 0.00000000 0.00000000 -1.00000000 309.00000 -1.00000000 0.00000000 0.00000000 309.00000 12 'point symmetry operation' ? ? 0.00000000 -1.00000000 0.00000000 309.00000 0.00000000 0.00000000 -1.00000000 309.00000 1.00000000 0.00000000 0.00000000 0.00000 13 'point symmetry operation' ? ? 0.00000000 1.00000000 0.00000000 0.00000 1.00000000 0.00000000 0.00000000 0.00000 0.00000000 0.00000000 -1.00000000 309.00000 14 'point symmetry operation' ? ? 0.00000000 -1.00000000 0.00000000 309.00000 -1.00000000 0.00000000 0.00000000 309.00000 0.00000000 0.00000000 -1.00000000 309.00000 15 'point symmetry operation' ? ? 0.00000000 1.00000000 0.00000000 0.00000 -1.00000000 0.00000000 0.00000000 309.00000 0.00000000 0.00000000 1.00000000 0.00000 16 'point symmetry operation' ? ? 0.00000000 -1.00000000 0.00000000 309.00000 1.00000000 0.00000000 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 17 'point symmetry operation' ? ? 1.00000000 0.00000000 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 0.00000000 -1.00000000 0.00000000 309.00000 18 'point symmetry operation' ? ? -1.00000000 0.00000000 0.00000000 309.00000 0.00000000 0.00000000 1.00000000 0.00000 0.00000000 1.00000000 0.00000000 0.00000 19 'point symmetry operation' ? ? -1.00000000 0.00000000 0.00000000 309.00000 0.00000000 0.00000000 -1.00000000 309.00000 0.00000000 -1.00000000 0.00000000 309.00000 20 'point symmetry operation' ? ? 1.00000000 0.00000000 0.00000000 0.00000 0.00000000 0.00000000 -1.00000000 309.00000 0.00000000 1.00000000 0.00000000 0.00000 21 'point symmetry operation' ? ? 0.00000000 0.00000000 1.00000000 0.00000 0.00000000 1.00000000 0.00000000 0.00000 -1.00000000 0.00000000 0.00000000 309.00000 22 'point symmetry operation' ? ? 0.00000000 0.00000000 1.00000000 0.00000 0.00000000 -1.00000000 0.00000000 309.00000 1.00000000 0.00000000 0.00000000 0.00000 23 'point symmetry operation' ? ? 0.00000000 0.00000000 -1.00000000 309.00000 0.00000000 1.00000000 0.00000000 0.00000 1.00000000 0.00000000 0.00000000 0.00000 24 'point symmetry operation' ? ? 0.00000000 0.00000000 -1.00000000 309.00000 0.00000000 -1.00000000 0.00000000 309.00000 -1.00000000 0.00000000 0.00000000 309.00000 # _pdbx_point_symmetry.entry_id 6VFI _pdbx_point_symmetry.Schoenflies_symbol O # 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 2020-08-12 2 'Structure model' 1 1 2020-08-19 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # _pdbx_audit_revision_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group '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 2 'Structure model' citation_author # 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.journal_volume' 2 2 'Structure model' '_citation.pdbx_database_id_DOI' 3 2 'Structure model' '_citation.pdbx_database_id_PubMed' 4 2 'Structure model' '_citation.title' # _em_3d_fitting.entry_id 6VFI _em_3d_fitting.id 1 _em_3d_fitting.details ;Octahedral nanoparticle O43_dn18 model was fit into the map using UCSF Chimera. A combination of Rosetta relaxed refinement and manual refinement in Coot was used to relax the model into the map. ; _em_3d_fitting.overall_b_value ? _em_3d_fitting.ref_protocol OTHER _em_3d_fitting.ref_space REAL _em_3d_fitting.target_criteria ? _em_3d_fitting.method ? # _em_3d_reconstruction.entry_id 6VFI _em_3d_reconstruction.id 1 _em_3d_reconstruction.algorithm 'BACK PROJECTION' _em_3d_reconstruction.details ? _em_3d_reconstruction.refinement_type ? _em_3d_reconstruction.image_processing_id 1 _em_3d_reconstruction.num_class_averages 1 _em_3d_reconstruction.num_particles 5050 _em_3d_reconstruction.resolution 4.54 _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 'TBS buffer, 0.2um filtered, 0.06mM DDM detergent added immediately before freezing' _em_buffer.pH 7.4 _em_buffer.specimen_id 1 _em_buffer.name ? # _em_entity_assembly.id 1 _em_entity_assembly.parent_id 0 _em_entity_assembly.details 'Self-assembling nanoparticle of octahedral symmetry' _em_entity_assembly.name 'De novo designed nanoparticle of octahedral symmetry O43_dn18_NP' _em_entity_assembly.source RECOMBINANT _em_entity_assembly.type COMPLEX _em_entity_assembly.entity_id_list '1, 2' _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? # _em_imaging.id 1 _em_imaging.entry_id 6VFI _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 1500 _em_imaging.nominal_defocus_min 600 _em_imaging.nominal_magnification 29000 _em_imaging.recording_temperature_maximum 90 _em_imaging.recording_temperature_minimum 70 _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 unspecified _em_sample_support.grid_material ? _em_sample_support.grid_mesh_size ? _em_sample_support.grid_type ? _em_sample_support.method ? _em_sample_support.film_material ? # _em_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.chamber_temperature 283 _em_vitrification.cryogen_name ETHANE _em_vitrification.details '0.06mM DDM detergent (from an 8X stock) added immediately before freezing' _em_vitrification.humidity 100 _em_vitrification.instrument 'FEI VITROBOT MARK IV' _em_vitrification.entry_id 6VFI _em_vitrification.citation_id ? _em_vitrification.method ? _em_vitrification.temp ? _em_vitrification.time_resolved_state ? # _em_experiment.entry_id 6VFI _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 6VFI _em_single_particle_entity.id 1 _em_single_particle_entity.image_processing_id 1 _em_single_particle_entity.point_symmetry O # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 NE B ARG 32 ? ? CZ B ARG 32 ? ? NH2 B ARG 32 ? ? 117.01 120.30 -3.29 0.50 N 2 1 CB B TYR 75 ? ? CG B TYR 75 ? ? CD2 B TYR 75 ? ? 117.29 121.00 -3.71 0.60 N 3 1 NE A ARG 16 ? ? CZ A ARG 16 ? ? NH2 A ARG 16 ? ? 117.05 120.30 -3.25 0.50 N 4 1 NE A ARG 58 ? ? CZ A ARG 58 ? ? NH2 A ARG 58 ? ? 116.30 120.30 -4.00 0.50 N # 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 ALA B 71 ? ? 58.40 16.21 2 1 SER A 47 ? ? -129.17 -147.60 3 1 ALA A 74 ? ? 47.26 -109.10 # 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 B MET -1 ? A MET 1 2 1 Y 1 B GLY 0 ? A GLY 2 3 1 Y 1 B SER 119 ? A SER 121 4 1 Y 1 A MET 0 ? B MET 1 5 1 Y 1 A GLY 198 ? B GLY 199 6 1 Y 1 A GLY 199 ? B GLY 200 7 1 Y 1 A TRP 200 ? B TRP 201 8 1 Y 1 A LEU 201 ? B LEU 202 9 1 Y 1 A GLU 202 ? B GLU 203 10 1 Y 1 A HIS 203 ? B HIS 204 11 1 Y 1 A HIS 204 ? B HIS 205 12 1 Y 1 A HIS 205 ? B HIS 206 13 1 Y 1 A HIS 206 ? B HIS 207 14 1 Y 1 A HIS 207 ? B HIS 208 15 1 Y 1 A HIS 208 ? B HIS 209 # loop_ _em_buffer_component.buffer_id _em_buffer_component.id _em_buffer_component.concentration _em_buffer_component.concentration_units _em_buffer_component.formula _em_buffer_component.name 1 1 25 mM ? Tris-HCl 1 2 150 mM NaCl 'Sodium Chloride' # _em_ctf_correction.id 1 _em_ctf_correction.em_image_processing_id 1 _em_ctf_correction.type 'PHASE FLIPPING ONLY' _em_ctf_correction.details ? # _em_entity_assembly_molwt.entity_assembly_id 1 _em_entity_assembly_molwt.id 1 _em_entity_assembly_molwt.experimental_flag NO _em_entity_assembly_molwt.units MEGADALTONS _em_entity_assembly_molwt.value 0.81 # _em_entity_assembly_naturalsource.id 1 _em_entity_assembly_naturalsource.entity_assembly_id 1 _em_entity_assembly_naturalsource.cell ? _em_entity_assembly_naturalsource.cellular_location ? _em_entity_assembly_naturalsource.ncbi_tax_id 32630 _em_entity_assembly_naturalsource.organ ? _em_entity_assembly_naturalsource.organelle ? _em_entity_assembly_naturalsource.organism 'synthetic construct' _em_entity_assembly_naturalsource.strain ? _em_entity_assembly_naturalsource.tissue ? # _em_entity_assembly_recombinant.id 1 _em_entity_assembly_recombinant.entity_assembly_id 1 _em_entity_assembly_recombinant.cell ? _em_entity_assembly_recombinant.ncbi_tax_id 469008 _em_entity_assembly_recombinant.organism 'Escherichia coli BL21(DE3)' _em_entity_assembly_recombinant.plasmid ? _em_entity_assembly_recombinant.strain ? # _em_image_processing.id 1 _em_image_processing.image_recording_id 1 _em_image_processing.details ? # _em_image_recording.id 1 _em_image_recording.imaging_id 1 _em_image_recording.avg_electron_dose_per_image 50.4 _em_image_recording.average_exposure_time ? _em_image_recording.details ? _em_image_recording.detector_mode COUNTING _em_image_recording.film_or_detector_model 'GATAN K2 SUMMIT (4k x 4k)' _em_image_recording.num_diffraction_images ? _em_image_recording.num_grids_imaged 1 _em_image_recording.num_real_images 1336 # _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 330095 _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 2.9.0 1 ? ? 2 'IMAGE ACQUISITION' ? Leginon ? ? ? 1 3 MASKING ? ? ? ? ? ? 4 'CTF CORRECTION' ? RELION 3.0 1 ? ? 5 'LAYERLINE INDEXING' ? ? ? ? ? ? 6 'DIFFRACTION INDEXING' ? ? ? ? ? ? 7 'MODEL FITTING' ? 'UCSF Chimera' ? ? 1 ? 8 OTHER ? ? ? ? ? ? 9 'INITIAL EULER ASSIGNMENT' ? RELION 3.0 1 ? ? 10 'FINAL EULER ASSIGNMENT' ? RELION 3.0 1 ? ? 11 CLASSIFICATION ? RELION 3.0 1 ? ? 12 RECONSTRUCTION ? RELION 3.0 1 ? ? 13 'VOLUME SELECTION' ? ? ? 1 1 1 14 'SERIES ALIGNMENT' ? ? ? 1 1 1 15 'MOLECULAR REPLACEMENT' ? ? ? 1 1 1 16 'LATTICE DISTORTION CORRECTION' ? ? ? 1 1 1 17 'SYMMETRY DETERMINATION' ? ? ? 1 1 1 18 'CRYSTALLOGRAPHY MERGING' ? ? ? 1 1 1 19 'MODEL REFINEMENT' ? Rosetta ? ? 1 ? # _em_specimen.id 1 _em_specimen.experiment_id 1 _em_specimen.concentration 3.0 _em_specimen.details ;Nanoparticles were generated by co-expression of the two components (A and B) in E coli. Assembled particles are purified by a combination of Ni-affinity and gel filtration chromatography. ; _em_specimen.embedding_applied NO _em_specimen.shadowing_applied NO _em_specimen.staining_applied NO _em_specimen.vitrification_applied YES # _pdbx_audit_support.funding_organization 'Bill & Melinda Gates Foundation' _pdbx_audit_support.country 'United States' _pdbx_audit_support.grant_number OPP1115782 _pdbx_audit_support.ordinal 1 # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support SAXS _pdbx_struct_assembly_auth_evidence.details ? #