data_2NBY # _entry.id 2NBY # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.371 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_code _database_2.database_id _database_2.pdbx_database_accession _database_2.pdbx_DOI RCSB104675 RCSB ? ? 2NBY PDB pdb_00002nby 10.2210/pdb2nby/pdb 25997 BMRB ? ? D_1000104675 WWPDB ? ? # loop_ _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.content_type _pdbx_database_related.details 25997 BMRB unspecified . 2NBX PDB unspecified . 2NBZ PDB unspecified . 2NC0 PDB unspecified . 2NC1 PDB unspecified . # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2NBY _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2016-03-16 _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code REL _pdbx_database_status.status_code_mr REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs REL _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data REL # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Imai, S.' 1 ;D'Souza, V. ; 2 'Wagner, G.' 3 # _citation.id primary _citation.title 'An accurately preorganized IRES RNA structure enables eIF4G capture for initiation of viral translation.' _citation.journal_abbrev 'Nat. Struct. Mol. Biol.' _citation.journal_volume 23 _citation.page_first 859 _citation.page_last 864 _citation.year 2016 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 1545-9985 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 27525590 _citation.pdbx_database_id_DOI 10.1038/nsmb.3280 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Imai, S.' 1 ? primary 'Kumar, P.' 2 ? primary 'Hellen, C.U.' 3 ? primary ;D'Souza, V.M. ; 4 ? primary 'Wagner, G.' 5 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'IRES RNA (39-MER)' _entity.formula_weight 12538.468 _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 polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code GGGCAGAAGGUACCCCAUUGUAUGGGAUCUGAUCUGCCC _entity_poly.pdbx_seq_one_letter_code_can GGGCAGAAGGUACCCCAUUGUAUGGGAUCUGAUCUGCCC _entity_poly.pdbx_strand_id A _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 G n 1 2 G n 1 3 G n 1 4 C n 1 5 A n 1 6 G n 1 7 A n 1 8 A n 1 9 G n 1 10 G n 1 11 U n 1 12 A n 1 13 C n 1 14 C n 1 15 C n 1 16 C n 1 17 A n 1 18 U n 1 19 U n 1 20 G n 1 21 U n 1 22 A n 1 23 U n 1 24 G n 1 25 G n 1 26 G n 1 27 A n 1 28 U n 1 29 C n 1 30 U n 1 31 G n 1 32 A n 1 33 U n 1 34 C n 1 35 U n 1 36 G n 1 37 C n 1 38 C n 1 39 C n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 2NBY _struct_ref.pdbx_db_accession 2NBY _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2NBY _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 39 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2NBY _struct_ref_seq.db_align_beg 693 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 731 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 693 _struct_ref_seq.pdbx_auth_seq_align_end 731 # 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 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type 1 1 1 '2D 1H-1H NOESY' 2 2 2 '2D 1H-1H NOESY' 3 3 2 '2D 1H-1H NOESY' 1 4 3 '2D 1H-13C HSQC' 1 5 3 '3D 1H-13C NOESY' 1 6 4 '2D 1H-13C HSQC' 1 7 4 '3D 1H-13C NOESY' 2 8 5 '2D 1H-15N HSQC' 3 9 5 '2D 1H-15N HSQC' 2 10 6 '2D 1H-15N HSQC' 3 11 6 '2D 1H-15N HSQC' # loop_ _pdbx_nmr_exptl_sample_conditions.conditions_id _pdbx_nmr_exptl_sample_conditions.ionic_strength _pdbx_nmr_exptl_sample_conditions.pH _pdbx_nmr_exptl_sample_conditions.pressure _pdbx_nmr_exptl_sample_conditions.pressure_units _pdbx_nmr_exptl_sample_conditions.temperature _pdbx_nmr_exptl_sample_conditions.temperature_units 1 20 6.5 ambient ? 308 K 2 20 6.5 ambient ? 283 K 3 20 5.5 ambient ? 283 K # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system '0.5 mM RNA (39-MER), 10 mM potassium phosphate, 10 mM sodium chloride, 100% D2O' 1 '100% D2O' '0.5 mM RNA (39-MER), 10 mM potassium phosphate, 10 mM sodium chloride, 90% H2O/10% D2O' 2 '90% H2O/10% D2O' '0.5 mM [U-13C; U-15N]-Ade, [U-13C; U-15N]-Cyt RNA (39-MER), 10 mM potassium phosphate, 10 mM sodium chloride, 100% D2O' 3 '100% D2O' '0.5 mM [U-13C; U-15N]-Gua, [U-13C; U-15N]-Ura RNA (39-MER), 10 mM potassium phosphate, 10 mM sodium chloride, 100% D2O' 4 '100% D2O' '0.5 mM [U-13C; U-15N]-Ade, [U-13C; U-15N]-Cyt RNA (39-MER), 10 mM potassium phosphate, 10 mM sodium chloride, 90% H2O/10% D2O' 5 '90% H2O/10% D2O' '0.5 mM [U-13C; U-15N]-Gua, [U-13C; U-15N]-Ura RNA (39-MER), 10 mM potassium phosphate, 10 mM sodium chloride, 90% H2O/10% D2O' 6 '90% H2O/10% D2O' # loop_ _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type 800 Bruker AVANCE 1 'Bruker Avance' 700 Bruker AVANCE 2 'Bruker Avance' # _pdbx_nmr_refine.entry_id 2NBY _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _pdbx_nmr_ensemble.conformers_calculated_total_number 1000 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2NBY _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.entry_id 2NBY _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'Keller and Wuthrich' 'chemical shift assignment' CARA ? 1 'Guntert, Mumenthaler and Wuthrich' 'structure solution' CYANA ? 2 'Schwieters, Kuszewski, Tjandra and Clore' refinement 'X-PLOR NIH' ? 3 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.crystals_number ? _exptl.details ? _exptl.entry_id 2NBY _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2NBY _struct.title 'Solution structure of the J domain of EMCV IRES' _struct.pdbx_model_details 'lowest energy, model1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2NBY _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'IRES, translation initiation, Viral RNA, RNA' # _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 ? # 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 G 1 N1 ? ? ? 1_555 A C 39 N3 ? ? A G 693 A C 731 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 39 O2 ? ? A G 693 A C 731 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 39 N4 ? ? A G 693 A C 731 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 38 N3 ? ? A G 694 A C 730 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 38 O2 ? ? A G 694 A C 730 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 38 N4 ? ? A G 694 A C 730 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 3 N1 ? ? ? 1_555 A C 37 N3 ? ? A G 695 A C 729 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 3 N2 ? ? ? 1_555 A C 37 O2 ? ? A G 695 A C 729 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 3 O6 ? ? ? 1_555 A C 37 N4 ? ? A G 695 A C 729 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 4 N3 ? ? ? 1_555 A G 36 N1 ? ? A C 696 A G 728 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 4 N4 ? ? ? 1_555 A G 36 O6 ? ? A C 696 A G 728 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 4 O2 ? ? ? 1_555 A G 36 N2 ? ? A C 696 A G 728 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A A 5 N1 ? ? ? 1_555 A U 35 N3 ? ? A A 697 A U 727 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A A 5 N6 ? ? ? 1_555 A U 35 O4 ? ? A A 697 A U 727 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 6 N1 ? ? ? 1_555 A C 34 N3 ? ? A G 698 A C 726 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 6 N2 ? ? ? 1_555 A C 34 O2 ? ? A G 698 A C 726 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 6 O6 ? ? ? 1_555 A C 34 N4 ? ? A G 698 A C 726 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A A 7 N6 ? ? ? 1_555 A A 32 N1 ? ? A A 699 A A 724 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog19 hydrog ? ? A A 7 N1 ? ? ? 1_555 A U 33 N3 ? ? A A 699 A U 725 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A A 7 N6 ? ? ? 1_555 A U 33 O4 ? ? A A 699 A U 725 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A A 8 N1 ? ? ? 1_555 A G 31 N1 ? ? A A 700 A G 723 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog22 hydrog ? ? A A 8 N6 ? ? ? 1_555 A G 31 O6 ? ? A A 700 A G 723 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog23 hydrog ? ? A A 8 N1 ? ? ? 1_555 A A 32 N6 ? ? A A 700 A A 724 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog24 hydrog ? ? A G 9 N1 ? ? ? 1_555 A U 30 O2 ? ? A G 701 A U 722 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog25 hydrog ? ? A G 9 O6 ? ? ? 1_555 A U 30 N3 ? ? A G 701 A U 722 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog26 hydrog ? ? A G 10 N1 ? ? ? 1_555 A C 29 N3 ? ? A G 702 A C 721 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 10 N2 ? ? ? 1_555 A C 29 O2 ? ? A G 702 A C 721 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 10 O6 ? ? ? 1_555 A C 29 N4 ? ? A G 702 A C 721 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A A 12 N1 ? ? ? 1_555 A U 28 N3 ? ? A A 704 A U 720 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A A 12 N6 ? ? ? 1_555 A U 28 O4 ? ? A A 704 A U 720 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A C 13 N3 ? ? ? 1_555 A A 27 N6 ? ? A C 705 A A 719 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog32 hydrog ? ? A C 14 N3 ? ? ? 1_555 A G 26 N1 ? ? A C 706 A G 718 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A C 14 N4 ? ? ? 1_555 A G 26 O6 ? ? A C 706 A G 718 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A C 14 O2 ? ? ? 1_555 A G 26 N2 ? ? A C 706 A G 718 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A C 15 N3 ? ? ? 1_555 A G 25 N1 ? ? A C 707 A G 717 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A C 15 N4 ? ? ? 1_555 A G 25 O6 ? ? A C 707 A G 717 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A C 15 O2 ? ? ? 1_555 A G 25 N2 ? ? A C 707 A G 717 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A C 16 N3 ? ? ? 1_555 A G 24 N1 ? ? A C 708 A G 716 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A C 16 N4 ? ? ? 1_555 A G 24 O6 ? ? A C 708 A G 716 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A C 16 O2 ? ? ? 1_555 A G 24 N2 ? ? A C 708 A G 716 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A A 17 N1 ? ? ? 1_555 A U 23 N3 ? ? A A 709 A U 715 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A A 17 N6 ? ? ? 1_555 A U 23 O4 ? ? A A 709 A U 715 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A U 18 N3 ? ? ? 1_555 A A 22 N1 ? ? A U 710 A A 714 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A U 18 O4 ? ? ? 1_555 A A 22 N6 ? ? A U 710 A A 714 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 2NBY _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 # loop_ _atom_type.symbol C H N O P # 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 G 1 693 693 G G A . n A 1 2 G 2 694 694 G G A . n A 1 3 G 3 695 695 G G A . n A 1 4 C 4 696 696 C C A . n A 1 5 A 5 697 697 A A A . n A 1 6 G 6 698 698 G G A . n A 1 7 A 7 699 699 A A A . n A 1 8 A 8 700 700 A A A . n A 1 9 G 9 701 701 G G A . n A 1 10 G 10 702 702 G G A . n A 1 11 U 11 703 703 U U A . n A 1 12 A 12 704 704 A A A . n A 1 13 C 13 705 705 C C A . n A 1 14 C 14 706 706 C C A . n A 1 15 C 15 707 707 C C A . n A 1 16 C 16 708 708 C C A . n A 1 17 A 17 709 709 A A A . n A 1 18 U 18 710 710 U U A . n A 1 19 U 19 711 711 U U A . n A 1 20 G 20 712 712 G G A . n A 1 21 U 21 713 713 U U A . n A 1 22 A 22 714 714 A A A . n A 1 23 U 23 715 715 U U A . n A 1 24 G 24 716 716 G G A . n A 1 25 G 25 717 717 G G A . n A 1 26 G 26 718 718 G G A . n A 1 27 A 27 719 719 A A A . n A 1 28 U 28 720 720 U U A . n A 1 29 C 29 721 721 C C A . n A 1 30 U 30 722 722 U U A . n A 1 31 G 31 723 723 G G A . n A 1 32 A 32 724 724 A A A . n A 1 33 U 33 725 725 U U A . n A 1 34 C 34 726 726 C C A . n A 1 35 U 35 727 727 U U A . n A 1 36 G 36 728 728 G G A . n A 1 37 C 37 729 729 C C A . n A 1 38 C 38 730 730 C C A . n A 1 39 C 39 731 731 C C A . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_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_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] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2016-08-10 2 'Structure model' 1 1 2017-11-15 3 'Structure model' 1 2 2023-06-14 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' Other # 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' pdbx_database_related 2 3 'Structure model' database_2 3 3 'Structure model' pdbx_database_status 4 3 'Structure model' pdbx_nmr_software 5 3 'Structure model' pdbx_nmr_spectrometer # 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' '_pdbx_database_related.db_id' 2 2 'Structure model' '_pdbx_database_related.db_name' 3 3 'Structure model' '_database_2.pdbx_DOI' 4 3 'Structure model' '_database_2.pdbx_database_accession' 5 3 'Structure model' '_pdbx_database_status.status_code_nmr_data' 6 3 'Structure model' '_pdbx_nmr_software.name' 7 3 'Structure model' '_pdbx_nmr_spectrometer.model' # loop_ _pdbx_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_range _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling _pdbx_nmr_exptl_sample.solution_id 'RNA (39-MER)-1' 0.5 ? mM ? 1 'potassium phosphate-2' 10 ? mM ? 1 'sodium chloride-3' 10 ? mM ? 1 'RNA (39-MER)-4' 0.5 ? mM ? 2 'potassium phosphate-5' 10 ? mM ? 2 'sodium chloride-6' 10 ? mM ? 2 'RNA (39-MER)-7' 0.5 ? mM '[U-13C; U-15N]-Ade, [U-13C; U-15N]-Cyt' 3 'potassium phosphate-8' 10 ? mM ? 3 'sodium chloride-9' 10 ? mM ? 3 'RNA (39-MER)-10' 0.5 ? mM '[U-13C; U-15N]-Gua, [U-13C; U-15N]-Ura' 4 'potassium phosphate-11' 10 ? mM ? 4 'sodium chloride-12' 10 ? mM ? 4 'RNA (39-MER)-13' 0.5 ? mM '[U-13C; U-15N]-Ade, [U-13C; U-15N]-Cyt' 5 'potassium phosphate-14' 10 ? mM ? 5 'sodium chloride-15' 10 ? mM ? 5 'RNA (39-MER)-16' 0.5 ? mM '[U-13C; U-15N]-Gua, [U-13C; U-15N]-Ura' 6 'potassium phosphate-17' 10 ? mM ? 6 'sodium chloride-18' 10 ? mM ? 6 # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 3 "H4'" A U 703 ? ? H8 A A 704 ? ? 1.29 2 3 N1 A A 700 ? ? H1 A G 723 ? ? 1.55 3 4 N1 A A 700 ? ? H1 A G 723 ? ? 1.56 4 4 "HO2'" A G 712 ? ? "O5'" A U 713 ? ? 1.58 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2NBY 'double helix' 2NBY 'a-form double helix' 2NBY 'hairpin loop' 2NBY 'mismatched base pair' 2NBY 'triple helix' # 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 G 1 1_555 A C 39 1_555 -0.218 -0.079 -0.098 -0.160 -2.273 -2.271 1 A_G693:C731_A A 693 ? A 731 ? 19 1 1 A G 2 1_555 A C 38 1_555 -0.071 -0.149 -0.200 -0.751 -8.040 0.136 2 A_G694:C730_A A 694 ? A 730 ? 19 1 1 A G 3 1_555 A C 37 1_555 -0.180 -0.258 -0.179 -2.352 -7.671 1.212 3 A_G695:C729_A A 695 ? A 729 ? 19 1 1 A C 4 1_555 A G 36 1_555 0.062 -0.221 -0.149 0.805 -6.228 1.633 4 A_C696:G728_A A 696 ? A 728 ? 19 1 1 A A 5 1_555 A U 35 1_555 0.045 -0.175 -0.044 -0.098 -4.136 0.942 5 A_A697:U727_A A 697 ? A 727 ? 20 1 1 A G 6 1_555 A C 34 1_555 -0.098 -0.137 -0.102 -2.794 -0.677 2.642 6 A_G698:C726_A A 698 ? A 726 ? 19 1 1 A A 7 1_555 A U 33 1_555 -0.034 -0.266 0.008 3.399 -0.744 -0.899 7 A_A699:U725_A A 699 ? A 725 ? 20 1 1 A A 8 1_555 A G 31 1_555 0.887 0.480 -1.260 0.764 -8.979 -10.665 8 A_A700:G723_A A 700 ? A 723 ? 8 1 1 A G 9 1_555 A U 30 1_555 -1.910 -0.268 0.314 -4.185 -16.971 -4.516 9 A_G701:U722_A A 701 ? A 722 ? 28 1 1 A G 10 1_555 A C 29 1_555 0.133 -0.160 0.145 -7.760 -13.756 -5.965 10 A_G702:C721_A A 702 ? A 721 ? 19 1 1 A A 12 1_555 A U 28 1_555 0.060 -0.279 -0.055 1.562 -12.319 -0.363 11 A_A704:U720_A A 704 ? A 720 ? 20 1 1 A C 13 1_555 A A 27 1_555 2.077 -0.289 0.200 -1.946 -14.978 7.016 12 A_C705:A719_A A 705 ? A 719 ? ? 1 1 A C 14 1_555 A G 26 1_555 0.372 -0.295 -0.377 -2.576 -6.309 2.820 13 A_C706:G718_A A 706 ? A 718 ? 19 1 1 A C 15 1_555 A G 25 1_555 0.183 -0.228 -0.266 -0.669 -2.244 1.311 14 A_C707:G717_A A 707 ? A 717 ? 19 1 1 A C 16 1_555 A G 24 1_555 -0.024 -0.128 -0.250 0.431 0.358 -0.858 15 A_C708:G716_A A 708 ? A 716 ? 19 1 1 A A 17 1_555 A U 23 1_555 -0.045 -0.022 -0.262 6.919 4.807 -2.815 16 A_A709:U715_A A 709 ? A 715 ? 20 1 1 A U 18 1_555 A A 22 1_555 0.011 -0.351 -0.990 14.637 2.039 -2.344 17 A_U710:A714_A A 710 ? A 714 ? 20 1 # 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 G 1 1_555 A C 39 1_555 A G 2 1_555 A C 38 1_555 0.158 -1.718 3.251 -0.061 8.630 30.911 -4.547 -0.297 2.685 15.808 0.112 32.064 1 AA_G693G694:C730C731_AA A 693 ? A 731 ? A 694 ? A 730 ? 1 A G 2 1_555 A C 38 1_555 A G 3 1_555 A C 37 1_555 0.064 -1.668 3.296 -1.137 5.094 30.836 -4.029 -0.328 2.985 9.494 2.119 31.264 2 AA_G694G695:C729C730_AA A 694 ? A 730 ? A 695 ? A 729 ? 1 A G 3 1_555 A C 37 1_555 A C 4 1_555 A G 36 1_555 -0.002 -1.459 3.212 -0.358 2.381 32.797 -2.970 -0.056 3.101 4.209 0.632 32.883 3 AA_G695C696:G728C729_AA A 695 ? A 729 ? A 696 ? A 728 ? 1 A C 4 1_555 A G 36 1_555 A A 5 1_555 A U 35 1_555 -0.012 -1.587 3.216 0.098 7.993 31.702 -4.103 0.037 2.745 14.348 -0.176 32.669 4 AA_C696A697:U727G728_AA A 696 ? A 728 ? A 697 ? A 727 ? 1 A A 5 1_555 A U 35 1_555 A G 6 1_555 A C 34 1_555 0.009 -1.559 3.261 0.521 12.950 30.569 -4.707 0.064 2.419 23.292 -0.937 33.142 5 AA_A697G698:C726U727_AA A 697 ? A 727 ? A 698 ? A 726 ? 1 A G 6 1_555 A C 34 1_555 A A 7 1_555 A U 33 1_555 -0.172 -1.420 3.105 0.357 11.256 29.666 -4.412 0.373 2.416 21.053 -0.668 31.687 6 AA_G698A699:U725C726_AA A 698 ? A 726 ? A 699 ? A 725 ? 1 A A 7 1_555 A U 33 1_555 A A 8 1_555 A G 31 1_555 0.910 -1.840 5.248 -11.917 16.662 49.225 -3.663 -2.166 4.160 19.077 13.644 53.072 7 AA_A699A700:G723U725_AA A 699 ? A 725 ? A 700 ? A 723 ? 1 A A 8 1_555 A G 31 1_555 A G 9 1_555 A U 30 1_555 0.668 -1.719 3.217 -7.313 7.806 24.773 -5.444 -3.076 2.292 17.207 16.121 26.951 8 AA_A700G701:U722G723_AA A 700 ? A 723 ? A 701 ? A 722 ? 1 A G 9 1_555 A U 30 1_555 A G 10 1_555 A C 29 1_555 -0.078 -1.642 3.337 2.480 6.630 39.599 -3.127 0.389 3.025 9.692 -3.625 40.202 9 AA_G701G702:C721U722_AA A 701 ? A 722 ? A 702 ? A 721 ? 1 A G 10 1_555 A C 29 1_555 A A 12 1_555 A U 28 1_555 0.065 -1.719 3.013 5.966 9.567 38.175 -3.488 0.502 2.509 14.252 -8.887 39.746 10 AA_G702A704:U720C721_AA A 702 ? A 721 ? A 704 ? A 720 ? 1 A A 12 1_555 A U 28 1_555 A C 13 1_555 A A 27 1_555 0.131 -1.127 3.255 2.584 0.456 47.695 -1.428 0.043 3.247 0.564 -3.193 47.763 11 AA_A704C705:A719U720_AA A 704 ? A 720 ? A 705 ? A 719 ? 1 A C 13 1_555 A A 27 1_555 A C 14 1_555 A G 26 1_555 -0.206 -1.545 3.207 4.810 0.751 24.160 -3.843 1.909 3.060 1.771 -11.344 24.638 12 AA_C705C706:G718A719_AA A 705 ? A 719 ? A 706 ? A 718 ? 1 A C 14 1_555 A G 26 1_555 A C 15 1_555 A G 25 1_555 0.088 -1.546 3.220 1.249 5.065 29.699 -3.951 0.071 2.923 9.787 -2.412 30.144 13 AA_C706C707:G717G718_AA A 706 ? A 718 ? A 707 ? A 717 ? 1 A C 15 1_555 A G 25 1_555 A C 16 1_555 A G 24 1_555 0.046 -1.670 3.184 1.153 10.114 30.244 -4.689 0.104 2.509 18.729 -2.136 31.873 14 AA_C707C708:G716G717_AA A 707 ? A 717 ? A 708 ? A 716 ? 1 A C 16 1_555 A G 24 1_555 A A 17 1_555 A U 23 1_555 -0.079 -1.526 3.053 0.481 8.845 29.559 -4.367 0.229 2.501 16.864 -0.918 30.829 15 AA_C708A709:U715G716_AA A 708 ? A 716 ? A 709 ? A 715 ? 1 A A 17 1_555 A U 23 1_555 A U 18 1_555 A A 22 1_555 -0.193 -1.254 3.116 3.195 7.598 28.242 -3.940 0.997 2.658 15.168 -6.378 29.397 16 AA_A709U710:A714U715_AA A 709 ? A 715 ? A 710 ? A 714 ? #