data_9EOQ # _entry.id 9EOQ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.392 _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 9EOQ pdb_00009eoq 10.2210/pdb9eoq/pdb WWPDB D_1292136989 ? ? EMDB EMD-19867 ? ? # 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 2024-04-24 2 'Structure model' 1 1 2024-05-08 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # _pdbx_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' # _pdbx_audit_revision_category.ordinal 1 _pdbx_audit_revision_category.revision_ordinal 2 _pdbx_audit_revision_category.data_content_type 'Structure model' _pdbx_audit_revision_category.category citation # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_citation.journal_volume' 2 2 'Structure model' '_citation.page_first' 3 2 'Structure model' '_citation.page_last' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 9EOQ _pdbx_database_status.recvd_initial_deposition_date 2024-03-15 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _pdbx_database_related.db_name _pdbx_database_related.details _pdbx_database_related.db_id _pdbx_database_related.content_type EMDB 'Cryo-EM Structure of a 1033 Scaffold Base DNA Origami Nanostructure V4 and TBA' EMD-19867 'associated EM volume' EMDB 'Refinement Focused on the 3rd Body of a 1033 Scaffold-Based DNA Origami Nanostructure V4 with TBA' EMD-19876 'focused EM volume' EMDB 'Refinement Focused on the 2nd Body of a 1033 Scaffold-Based DNA Origami Nanostructure V4 with TBA' EMD-19875 'focused EM volume' EMDB 'Refinement Focused on the 1st Body of a 1033 Scaffold-Based DNA Origami Nanostructure V4 with TBA' EMD-19874 'focused EM volume' # _pdbx_contact_author.id 3 _pdbx_contact_author.email dietz@tum.de _pdbx_contact_author.name_first Hendrik _pdbx_contact_author.name_last Dietz _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0003-1270-3662 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Ali, K.' 1 ? 'Georg, K.' 2 ? 'Volodymyr, M.' 3 ? 'Johanna, G.' 4 ? 'Maximilian, N.H.' 5 ? 'Lukas, K.' 6 ? 'Simone, C.' 7 ? 'Hendrik, D.' 8 ? # _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 'Nano Lett.' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 1530-6992 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 24 _citation.language ? _citation.page_first 5031 _citation.page_last 5038 _citation.title 'Designing Rigid DNA Origami Templates for Molecular Visualization Using Cryo-EM.' _citation.year 2024 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1021/acs.nanolett.4c00915 _citation.pdbx_database_id_PubMed 38602296 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Khoshouei, A.' 1 0000-0003-1735-8423 primary 'Kempf, G.' 2 0000-0002-0228-6730 primary 'Mykhailiuk, V.' 3 0000-0001-9928-3845 primary 'Griessing, J.M.' 4 0009-0003-0828-4749 primary 'Honemann, M.N.' 5 0000-0001-7805-906X primary 'Kater, L.' 6 ? primary 'Cavadini, S.' 7 0000-0003-2777-7584 primary 'Dietz, H.' 8 0000-0003-1270-3662 # 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 syn 'DNA (42-MER)' 13034.333 1 ? ? ? ? 2 polymer syn ;DNA (5'-D(P*AP*TP*AP*TP*AP*GP*CP*GP*TP*GP*GP*AP*AP*GP*T)-3') ; 4673.059 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 polydeoxyribonucleotide no no ;(DA)(DC)(DT)(DT)(DC)(DC)(DA)(DG)(DT)(DC)(DC)(DG)(DT)(DG)(DG)(DT)(DA)(DG)(DG)(DG) (DC)(DA)(DG)(DG)(DT)(DT)(DG)(DG)(DG)(DG)(DT)(DG)(DA)(DC)(DC)(DG)(DC)(DT)(DA)(DT) (DA)(DT) ; ACTTCCAGTCCGTGGTAGGGCAGGTTGGGGTGACCGCTATAT A ? 2 polydeoxyribonucleotide no no '(DA)(DT)(DA)(DT)(DA)(DG)(DC)(DG)(DT)(DG)(DG)(DA)(DA)(DG)(DT)' ATATAGCGTGGAAGT B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DA n 1 2 DC n 1 3 DT n 1 4 DT n 1 5 DC n 1 6 DC n 1 7 DA n 1 8 DG n 1 9 DT n 1 10 DC n 1 11 DC n 1 12 DG n 1 13 DT n 1 14 DG n 1 15 DG n 1 16 DT n 1 17 DA n 1 18 DG n 1 19 DG n 1 20 DG n 1 21 DC n 1 22 DA n 1 23 DG n 1 24 DG n 1 25 DT n 1 26 DT n 1 27 DG n 1 28 DG n 1 29 DG n 1 30 DG n 1 31 DT n 1 32 DG n 1 33 DA n 1 34 DC n 1 35 DC n 1 36 DG n 1 37 DC n 1 38 DT n 1 39 DA n 1 40 DT n 1 41 DA n 1 42 DT n 2 1 DA n 2 2 DT n 2 3 DA n 2 4 DT n 2 5 DA n 2 6 DG n 2 7 DC n 2 8 DG n 2 9 DT n 2 10 DG n 2 11 DG n 2 12 DA n 2 13 DA n 2 14 DG n 2 15 DT n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample 1 42 'synthetic construct' ? 32630 ? 2 1 sample 1 15 'synthetic construct' ? 32630 ? # 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 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 # 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 DA 1 2 2 DA DA A . n A 1 2 DC 2 3 3 DC DC A . n A 1 3 DT 3 4 4 DT DT A . n A 1 4 DT 4 5 5 DT DT A . n A 1 5 DC 5 6 6 DC DC A . n A 1 6 DC 6 7 7 DC DC A . n A 1 7 DA 7 8 8 DA DA A . n A 1 8 DG 8 9 9 DG DG A . n A 1 9 DT 9 10 10 DT DT A . n A 1 10 DC 10 11 11 DC DC A . n A 1 11 DC 11 12 12 DC DC A . n A 1 12 DG 12 13 13 DG DG A . n A 1 13 DT 13 14 14 DT DT A . n A 1 14 DG 14 15 15 DG DG A . n A 1 15 DG 15 16 16 DG DG A . n A 1 16 DT 16 17 17 DT DT A . n A 1 17 DA 17 18 18 DA DA A . n A 1 18 DG 18 19 19 DG DG A . n A 1 19 DG 19 20 20 DG DG A . n A 1 20 DG 20 21 21 DG DG A . n A 1 21 DC 21 22 22 DC DC A . n A 1 22 DA 22 23 23 DA DA A . n A 1 23 DG 23 24 24 DG DG A . n A 1 24 DG 24 25 25 DG DG A . n A 1 25 DT 25 26 26 DT DT A . n A 1 26 DT 26 27 27 DT DT A . n A 1 27 DG 27 28 28 DG DG A . n A 1 28 DG 28 29 29 DG DG A . n A 1 29 DG 29 30 30 DG DG A . n A 1 30 DG 30 31 31 DG DG A . n A 1 31 DT 31 32 32 DT DT A . n A 1 32 DG 32 33 33 DG DG A . n A 1 33 DA 33 34 34 DA DA A . n A 1 34 DC 34 35 35 DC DC A . n A 1 35 DC 35 36 36 DC DC A . n A 1 36 DG 36 37 37 DG DG A . n A 1 37 DC 37 38 38 DC DC A . n A 1 38 DT 38 39 39 DT DT A . n A 1 39 DA 39 40 40 DA DA A . n A 1 40 DT 40 41 41 DT DT A . n A 1 41 DA 41 42 42 DA DA A . n A 1 42 DT 42 43 43 DT DT A . n B 2 1 DA 1 1 1 DA DA B . n B 2 2 DT 2 2 2 DT DT B . n B 2 3 DA 3 3 3 DA DA B . n B 2 4 DT 4 4 4 DT DT B . n B 2 5 DA 5 5 5 DA DA B . n B 2 6 DG 6 6 6 DG DG B . n B 2 7 DC 7 7 7 DC DC B . n B 2 8 DG 8 8 8 DG DG B . n B 2 9 DT 9 9 9 DT DT B . n B 2 10 DG 10 10 10 DG DG B . n B 2 11 DG 11 11 11 DG DG B . n B 2 12 DA 12 12 12 DA DA B . n B 2 13 DA 13 13 13 DA DA B . n B 2 14 DG 14 14 14 DG DG B . n B 2 15 DT 15 15 15 DT DT B . 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 9EOQ _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 9EOQ _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 9EOQ _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _struct.entry_id 9EOQ _struct.title 'Cryo-EM Structure of a 1033 Scaffold Base DNA Origami Nanostructure V4 and TBA' _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 9EOQ _struct_keywords.text 'DNA Origami, Multilayer, Square lattice, 1033 scaffold, DNA, TBA' _struct_keywords.pdbx_keywords DNA # 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_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 9EOQ 9EOQ ? 1 ? 1 2 PDB 9EOQ 9EOQ ? 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 9EOQ A 1 ? 42 ? 9EOQ 2 ? 43 ? 2 43 2 2 9EOQ B 1 ? 15 ? 9EOQ 1 ? 15 ? 1 15 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # _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 ? # _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_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 hydrog1 hydrog ? ? A DA 1 N1 ? ? ? 1_555 B DT 15 N3 ? ? A DA 2 B DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DA 1 N6 ? ? ? 1_555 B DT 15 O4 ? ? A DA 2 B DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 14 N1 ? ? A DC 3 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 14 O6 ? ? A DC 3 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 14 N2 ? ? A DC 3 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DT 3 N3 ? ? ? 1_555 B DA 13 N1 ? ? A DT 4 B DA 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DT 3 O4 ? ? ? 1_555 B DA 13 N6 ? ? A DT 4 B DA 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DT 4 N3 ? ? ? 1_555 B DA 12 N1 ? ? A DT 5 B DA 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DT 4 O4 ? ? ? 1_555 B DA 12 N6 ? ? A DT 5 B DA 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B DG 11 N1 ? ? A DC 6 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B DG 11 O6 ? ? A DC 6 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DG 11 N2 ? ? A DC 6 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 6 N3 ? ? ? 1_555 B DG 10 N1 ? ? A DC 7 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 6 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 7 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 6 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 7 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 7 N1 ? ? ? 1_555 B DT 9 N3 ? ? A DA 8 B DT 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DA 7 N6 ? ? ? 1_555 B DT 9 O4 ? ? A DA 8 B DT 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DT 9 N3 ? ? ? 1_555 A DA 33 N1 ? ? A DT 10 A DA 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DT 9 O4 ? ? ? 1_555 A DA 33 N6 ? ? A DT 10 A DA 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 10 N3 ? ? ? 1_555 A DG 32 N1 ? ? A DC 11 A DG 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 10 N4 ? ? ? 1_555 A DG 32 O6 ? ? A DC 11 A DG 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 10 O2 ? ? ? 1_555 A DG 32 N2 ? ? A DC 11 A DG 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DC 11 O2 ? ? ? 1_555 A DG 30 N2 ? ? A DC 12 A DG 31 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog24 hydrog ? ? A DG 12 N2 ? ? ? 1_555 A DG 14 O6 ? ? A DG 13 A DG 15 1_555 ? ? ? ? ? ? 'DG-DG MISPAIR' ? ? ? hydrog25 hydrog ? ? A DG 12 N1 ? ? ? 1_555 A DG 23 N7 ? ? A DG 13 A DG 24 1_555 ? ? ? ? ? ? TYPE_7_PAIR ? ? ? hydrog26 hydrog ? ? A DG 12 N2 ? ? ? 1_555 A DG 23 O6 ? ? A DG 13 A DG 24 1_555 ? ? ? ? ? ? TYPE_7_PAIR ? ? ? hydrog27 hydrog ? ? A DT 13 N3 ? ? ? 1_555 A DA 22 N7 ? ? A DT 14 A DA 23 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog28 hydrog ? ? A DT 13 O2 ? ? ? 1_555 A DA 22 N6 ? ? A DT 14 A DA 23 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog29 hydrog ? ? A DG 15 N7 ? ? ? 1_555 A DG 18 N2 ? ? A DG 16 A DG 19 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog30 hydrog ? ? A DG 15 O6 ? ? ? 1_555 A DG 18 N1 ? ? A DG 16 A DG 19 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog31 hydrog ? ? A DG 15 N1 ? ? ? 1_555 A DG 27 O6 ? ? A DG 16 A DG 28 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog32 hydrog ? ? A DG 15 N2 ? ? ? 1_555 A DG 27 N7 ? ? A DG 16 A DG 28 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog33 hydrog ? ? A DA 17 N1 ? ? ? 1_555 A DT 26 N3 ? ? A DA 18 A DT 27 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog34 hydrog ? ? A DA 17 N6 ? ? ? 1_555 A DT 26 O2 ? ? A DA 18 A DT 27 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog35 hydrog ? ? A DG 18 N7 ? ? ? 1_555 A DG 24 N2 ? ? A DG 19 A DG 25 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog36 hydrog ? ? A DG 18 O6 ? ? ? 1_555 A DG 24 N1 ? ? A DG 19 A DG 25 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog37 hydrog ? ? A DG 24 N7 ? ? ? 1_555 A DG 27 N2 ? ? A DG 25 A DG 28 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog38 hydrog ? ? A DG 24 O6 ? ? ? 1_555 A DG 27 N1 ? ? A DG 25 A DG 28 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog39 hydrog ? ? A DC 35 N3 ? ? ? 1_555 B DG 8 N1 ? ? A DC 36 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A DC 35 N4 ? ? ? 1_555 B DG 8 O6 ? ? A DC 36 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A DC 35 O2 ? ? ? 1_555 B DG 8 N2 ? ? A DC 36 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A DG 36 N1 ? ? ? 1_555 B DC 7 N3 ? ? A DG 37 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A DG 36 N2 ? ? ? 1_555 B DC 7 O2 ? ? A DG 37 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A DG 36 O6 ? ? ? 1_555 B DC 7 N4 ? ? A DG 37 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A DC 37 N3 ? ? ? 1_555 B DG 6 N1 ? ? A DC 38 B DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A DC 37 N4 ? ? ? 1_555 B DG 6 O6 ? ? A DC 38 B DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A DC 37 O2 ? ? ? 1_555 B DG 6 N2 ? ? A DC 38 B DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A DT 38 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 39 B DA 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A DT 38 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 39 B DA 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A DA 39 N1 ? ? ? 1_555 B DT 4 N3 ? ? A DA 40 B DT 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? A DA 39 N6 ? ? ? 1_555 B DT 4 O4 ? ? A DA 40 B DT 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? A DT 40 N3 ? ? ? 1_555 B DA 3 N1 ? ? A DT 41 B DA 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? A DT 40 O4 ? ? ? 1_555 B DA 3 N6 ? ? A DT 41 B DA 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? A DA 41 N1 ? ? ? 1_555 B DT 2 N3 ? ? A DA 42 B DT 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? A DA 41 N6 ? ? ? 1_555 B DT 2 O4 ? ? A DA 42 B DT 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? A DT 42 N3 ? ? ? 1_555 B DA 1 N1 ? ? A DT 43 B DA 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? A DT 42 O4 ? ? ? 1_555 B DA 1 N6 ? ? A DT 43 B DA 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # 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 "O4'" A DG 16 ? ? "C1'" A DG 16 ? ? N9 A DG 16 ? ? 110.74 108.30 2.44 0.30 N 2 1 "O4'" A DG 20 ? ? "C1'" A DG 20 ? ? N9 A DG 20 ? ? 110.39 108.30 2.09 0.30 N 3 1 "O4'" A DC 22 ? ? "C1'" A DC 22 ? ? N1 A DC 22 ? ? 111.08 108.30 2.78 0.30 N 4 1 "O4'" A DC 36 ? ? "C4'" A DC 36 ? ? "C3'" A DC 36 ? ? 102.09 104.50 -2.41 0.40 N # _em_3d_fitting.id 1 _em_3d_fitting.entry_id 9EOQ _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 ? # _em_3d_reconstruction.entry_id 9EOQ _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 7.5 _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 966383 _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 8 # _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 'Cryo-EM Structure of a 1033 Scaffold Base DNA Origami Nanostructure V4 and TBA' _em_entity_assembly.details ? _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? _em_entity_assembly.entity_id_list '1, 2' # _em_imaging.entry_id 9EOQ _em_imaging.id 1 _em_imaging.astigmatism ? _em_imaging.electron_beam_tilt_params ? _em_imaging.residual_tilt ? _em_imaging.microscope_model 'FEI TITAN 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 0.01 _em_imaging.nominal_defocus_min 500 _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 75000 _em_imaging.calibrated_magnification ? _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 50.0 _em_imaging.specimen_id 1 _em_imaging.cryogen NITROGEN # _em_vitrification.entry_id 9EOQ _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 277 _em_vitrification.instrument 'FEI VITROBOT MARK IV' _em_vitrification.method ? _em_vitrification.time_resolved_state ? _em_vitrification.citation_id ? _em_vitrification.details ? # _em_experiment.entry_id 9EOQ _em_experiment.id 1 _em_experiment.reconstruction_method 'SINGLE PARTICLE' _em_experiment.aggregation_state PARTICLE _em_experiment.entity_assembly_id 1 # 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 DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 # 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 DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 # _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_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 32630 _em_entity_assembly_naturalsource.organism 'synthetic construct' _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 32630 _em_entity_assembly_recombinant.organism 'synthetic construct' _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 50 _em_image_recording.details ? _em_image_recording.detector_mode COUNTING _em_image_recording.film_or_detector_model 'FEI FALCON III (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 EPU ? MASKING ? 3 ? ? ? ? ? 'CTF CORRECTION' ? 4 1 ? ? CTFFIND ? 'LAYERLINE INDEXING' ? 5 ? ? ? ? ? 'DIFFRACTION INDEXING' ? 6 ? ? ? ? ? 'MODEL FITTING' ? 7 ? ? ? ? ? 'MODEL REFINEMENT' ? 8 ? ? ? ? ? OTHER ? 9 ? ? ? ? ? 'INITIAL EULER ASSIGNMENT' ? 10 1 ? ? RELION ? 'FINAL EULER ASSIGNMENT' ? 11 1 ? ? RELION ? CLASSIFICATION ? 12 1 ? ? ? ? RECONSTRUCTION ? 13 1 ? ? ? ? # _em_specimen.concentration ? _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 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 9EOQ 'double helix' 9EOQ 'b-form double helix' 9EOQ 'hairpin loop' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DA 1 1_555 B DT 15 1_555 -0.040 -0.150 -0.228 -13.688 -1.010 -0.249 1 A_DA2:DT15_B A 2 ? B 15 ? 20 1 1 A DC 2 1_555 B DG 14 1_555 0.095 -0.187 0.078 -4.928 0.554 -2.822 2 A_DC3:DG14_B A 3 ? B 14 ? 19 1 1 A DT 3 1_555 B DA 13 1_555 -0.092 -0.140 -0.102 -0.778 -7.600 -6.712 3 A_DT4:DA13_B A 4 ? B 13 ? 20 1 1 A DT 4 1_555 B DA 12 1_555 -0.065 -0.162 -0.165 0.890 -7.979 -6.968 4 A_DT5:DA12_B A 5 ? B 12 ? 20 1 1 A DC 5 1_555 B DG 11 1_555 0.059 -0.199 0.017 2.432 -7.046 -2.775 5 A_DC6:DG11_B A 6 ? B 11 ? 19 1 1 A DC 6 1_555 B DG 10 1_555 0.007 -0.205 0.004 4.040 -8.114 -4.068 6 A_DC7:DG10_B A 7 ? B 10 ? 19 1 1 A DA 7 1_555 B DT 9 1_555 0.035 -0.173 -0.028 -7.032 -0.963 -5.751 7 A_DA8:DT9_B A 8 ? B 9 ? 20 1 1 A DC 35 1_555 B DG 8 1_555 0.068 -0.186 0.050 6.128 -9.654 -0.904 8 A_DC36:DG8_B A 36 ? B 8 ? 19 1 1 A DG 36 1_555 B DC 7 1_555 0.019 -0.183 0.015 0.566 -6.822 -2.795 9 A_DG37:DC7_B A 37 ? B 7 ? 19 1 1 A DC 37 1_555 B DG 6 1_555 0.061 -0.165 -0.057 2.711 -4.178 -1.453 10 A_DC38:DG6_B A 38 ? B 6 ? 19 1 1 A DT 38 1_555 B DA 5 1_555 -0.118 -0.136 -0.146 0.515 -7.293 -6.391 11 A_DT39:DA5_B A 39 ? B 5 ? 20 1 1 A DA 39 1_555 B DT 4 1_555 0.174 -0.120 -0.161 -1.485 -6.972 -5.326 12 A_DA40:DT4_B A 40 ? B 4 ? 20 1 1 A DT 40 1_555 B DA 3 1_555 -0.131 -0.141 -0.181 2.099 -7.945 -6.032 13 A_DT41:DA3_B A 41 ? B 3 ? 20 1 1 A DA 41 1_555 B DT 2 1_555 0.114 -0.115 -0.092 -1.034 -3.053 -7.391 14 A_DA42:DT2_B A 42 ? B 2 ? 20 1 1 A DT 42 1_555 B DA 1 1_555 -0.203 -0.070 -0.060 5.322 1.242 -4.625 15 A_DT43:DA1_B A 43 ? B 1 ? 20 1 1 A DT 9 1_555 A DA 33 1_555 -0.059 -0.131 0.110 -17.265 4.739 -6.533 16 A_DT10:DA34_A A 10 ? A 34 ? 20 1 1 A DC 10 1_555 A DG 32 1_555 0.090 -0.214 0.092 -4.644 0.126 -2.901 17 A_DC11:DG33_A A 11 ? A 33 ? 19 1 1 A DC 11 1_555 A DG 30 1_555 3.419 1.371 0.428 -5.038 -7.672 58.813 18 A_DC12:DG31_A A 12 ? A 31 ? ? 1 1 A DA 22 1_555 A DT 13 1_555 -4.116 -2.009 -0.151 -3.253 -7.097 -96.841 19 A_DA23:DT14_A A 23 ? A 14 ? 24 4 1 A DG 23 1_555 A DG 12 1_555 -5.598 -0.462 -0.058 -6.635 -4.367 -107.395 20 A_DG24:DG13_A A 24 ? A 13 ? 7 4 1 A DG 24 1_555 A DG 27 1_555 -1.713 -3.277 0.011 -0.539 8.248 89.491 21 A_DG25:DG28_A A 25 ? A 28 ? 6 3 1 A DA 17 1_555 A DT 26 1_555 0.094 1.142 -0.198 1.227 -15.813 164.804 22 A_DA18:DT27_A A 18 ? A 27 ? 21 2 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DA 1 1_555 B DT 15 1_555 A DC 2 1_555 B DG 14 1_555 -0.334 0.337 3.570 -0.292 0.500 34.105 0.488 0.519 3.577 0.853 0.497 34.110 1 AA_DA2DC3:DG14DT15_BB A 2 ? B 15 ? A 3 ? B 14 ? 1 A DC 2 1_555 B DG 14 1_555 A DT 3 1_555 B DA 13 1_555 -0.257 0.373 3.498 2.285 1.445 35.254 0.386 0.784 3.487 2.381 -3.766 35.354 2 AA_DC3DT4:DA13DG14_BB A 3 ? B 14 ? A 4 ? B 13 ? 1 A DT 3 1_555 B DA 13 1_555 A DT 4 1_555 B DA 12 1_555 -0.068 0.406 3.471 -0.156 1.386 36.764 0.443 0.086 3.484 2.196 0.248 36.789 3 AA_DT4DT5:DA12DA13_BB A 4 ? B 13 ? A 5 ? B 12 ? 1 A DT 4 1_555 B DA 12 1_555 A DC 5 1_555 B DG 11 1_555 0.066 0.563 3.417 -1.282 0.745 38.404 0.759 -0.267 3.423 1.133 1.948 38.431 4 AA_DT5DC6:DG11DA12_BB A 5 ? B 12 ? A 6 ? B 11 ? 1 A DC 5 1_555 B DG 11 1_555 A DC 6 1_555 B DG 10 1_555 -0.302 0.626 3.550 -2.056 -0.683 37.687 1.063 0.178 3.550 -1.056 3.179 37.747 5 AA_DC6DC7:DG10DG11_BB A 6 ? B 11 ? A 7 ? B 10 ? 1 A DC 6 1_555 B DG 10 1_555 A DA 7 1_555 B DT 9 1_555 -0.210 0.050 3.807 -3.339 -1.371 41.591 0.238 -0.114 3.808 -1.927 4.692 41.741 6 AA_DC7DA8:DT9DG10_BB A 7 ? B 10 ? A 8 ? B 9 ? 1 A DA 7 1_555 B DT 9 1_555 A DC 35 1_555 B DG 8 1_555 -1.459 1.682 3.444 -2.251 -12.469 43.550 3.294 1.696 2.948 -16.397 2.960 45.270 7 AA_DA8DC36:DG8DT9_BB A 8 ? B 9 ? A 36 ? B 8 ? 1 A DC 35 1_555 B DG 8 1_555 A DG 36 1_555 B DC 7 1_555 -0.177 0.152 3.854 0.623 25.281 26.418 -4.025 0.388 2.919 44.459 -1.096 36.415 8 AA_DC36DG37:DC7DG8_BB A 36 ? B 8 ? A 37 ? B 7 ? 1 A DG 36 1_555 B DC 7 1_555 A DC 37 1_555 B DG 6 1_555 0.363 0.301 3.375 0.321 3.195 38.517 0.047 -0.507 3.391 4.833 -0.486 38.646 9 AA_DG37DC38:DG6DC7_BB A 37 ? B 7 ? A 38 ? B 6 ? 1 A DC 37 1_555 B DG 6 1_555 A DT 38 1_555 B DA 5 1_555 -0.312 0.234 3.608 0.979 4.101 34.817 -0.292 0.681 3.601 6.823 -1.628 35.063 10 AA_DC38DT39:DA5DG6_BB A 38 ? B 6 ? A 39 ? B 5 ? 1 A DT 38 1_555 B DA 5 1_555 A DA 39 1_555 B DT 4 1_555 0.076 0.288 3.538 -1.294 7.466 36.285 -0.640 -0.310 3.522 11.830 2.051 37.042 11 AA_DT39DA40:DT4DA5_BB A 39 ? B 5 ? A 40 ? B 4 ? 1 A DA 39 1_555 B DT 4 1_555 A DT 40 1_555 B DA 3 1_555 -0.126 -0.078 3.253 -0.098 6.013 32.785 -1.130 0.203 3.189 10.542 0.172 33.317 12 AA_DA40DT41:DA3DT4_BB A 40 ? B 4 ? A 41 ? B 3 ? 1 A DT 40 1_555 B DA 3 1_555 A DA 41 1_555 B DT 2 1_555 -0.030 0.285 3.553 0.015 8.235 36.094 -0.766 0.049 3.531 13.081 -0.024 36.991 13 AA_DT41DA42:DT2DA3_BB A 41 ? B 3 ? A 42 ? B 2 ? 1 A DA 41 1_555 B DT 2 1_555 A DT 42 1_555 B DA 1 1_555 0.301 0.038 3.466 -0.276 5.100 32.223 -0.873 -0.588 3.429 9.117 0.494 32.615 14 AA_DA42DT43:DA1DT2_BB A 42 ? B 2 ? A 43 ? B 1 ? 1 A DT 9 1_555 A DA 33 1_555 A DC 10 1_555 A DG 32 1_555 -0.519 -0.458 3.255 -3.880 9.229 30.592 -2.456 0.252 3.034 16.932 7.119 32.151 15 AA_DT10DC11:DG33DA34_AA A 10 ? A 34 ? A 11 ? A 33 ? 1 A DC 10 1_555 A DG 32 1_555 A DC 11 1_555 A DG 30 1_555 1.982 -0.182 3.413 0.954 12.124 23.802 -3.698 -4.034 3.038 27.235 -2.142 26.689 16 AA_DC11DC12:DG31DG33_AA A 11 ? A 33 ? A 12 ? A 31 ? 1 A DA 22 1_555 A DT 13 1_555 A DG 23 1_555 A DG 12 1_555 0.750 1.086 3.327 9.841 -9.142 21.046 5.264 1.221 2.715 -22.333 -24.040 24.927 17 AA_DA23DG24:DG13DT14_AA A 23 ? A 14 ? A 24 ? A 13 ? 1 A DG 23 1_555 A DG 12 1_555 A DG 24 1_555 A DG 27 1_555 -0.920 -0.570 3.434 1.028 -4.512 -72.994 0.631 -0.737 3.410 3.790 0.864 -73.120 18 AA_DG24DG25:DG28DG13_AA A 24 ? A 13 ? A 25 ? A 28 ? 1 A DG 24 1_555 A DG 27 1_555 A DA 17 1_555 A DT 26 1_555 -4.099 -1.374 -0.433 56.239 166.400 105.839 -0.314 1.924 -1.921 83.617 -28.260 177.376 19 AA_DG25DA18:DT27DG28_AA A 25 ? A 28 ? A 18 ? A 27 ? # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'European Research Council (ERC)' 'European Union' 101018465 1 'German Research Foundation (DFG)' Germany ? 2 'Germanys Excellence Strategy' Germany ? 3 # _atom_sites.entry_id 9EOQ _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 H N O P # loop_