data_7JU1 # _entry.id 7JU1 # _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_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 7JU1 pdb_00007ju1 10.2210/pdb7ju1/pdb WWPDB D_1000251328 ? ? BMRB 30788 ? ? # _pdbx_database_related.db_name BMRB _pdbx_database_related.details 'FARFAR-NMR Ensemble of 29-mer HIV-1 Trans-activation response element RNA (N=20)' _pdbx_database_related.db_id 30788 _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.entry_id 7JU1 _pdbx_database_status.recvd_initial_deposition_date 2020-08-18 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs REL _pdbx_database_status.status_code_nmr_data REL _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 'Shi, H.' 1 0000-0003-3847-1652 'Rangadurai, A.' 2 ? 'Roy, R.' 3 ? 'Yesselman, J.D.' 4 ? 'Al-Hashimi, H.M.' 5 0000-0003-0681-1747 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Nat Commun' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 2041-1723 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 11 _citation.language ? _citation.page_first 5531 _citation.page_last ? _citation.title 'Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction' _citation.year 2020 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1038/s41467-020-19371-y _citation.pdbx_database_id_PubMed ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Shi, H.' 1 0000-0003-3847-1652 primary 'Rangadurai, A.' 2 ? primary 'Abou-Assi, H.' 3 ? primary 'Roy, R.' 4 ? primary 'Case, D.A.' 5 ? primary 'Herschlag, D.' 6 ? primary 'Yesselman, J.D.' 7 ? primary 'Al-Hashimi, H.M.' 8 0000-0003-0681-1747 # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'RNA (29-MER)' _entity.formula_weight 9307.555 _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 GGCAGAUCUGAGCCUGGGAGCUCUCUGCC _entity_poly.pdbx_seq_one_letter_code_can GGCAGAUCUGAGCCUGGGAGCUCUCUGCC _entity_poly.pdbx_strand_id X _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 C n 1 4 A n 1 5 G n 1 6 A n 1 7 U n 1 8 C n 1 9 U n 1 10 G n 1 11 A n 1 12 G n 1 13 C n 1 14 C n 1 15 U n 1 16 G n 1 17 G n 1 18 G n 1 19 A n 1 20 G n 1 21 C n 1 22 U n 1 23 C n 1 24 U n 1 25 C n 1 26 U n 1 27 G n 1 28 C n 1 29 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 1 _pdbx_entity_src_syn.pdbx_end_seq_num 29 _pdbx_entity_src_syn.organism_scientific 'Human immunodeficiency virus 1' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 11676 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 7JU1 _struct_ref.pdbx_db_accession 7JU1 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 7JU1 _struct_ref_seq.pdbx_strand_id X _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 29 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 7JU1 _struct_ref_seq.db_align_beg 17 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 45 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 17 _struct_ref_seq.pdbx_auth_seq_align_end 45 # 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.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.spectrometer_id _pdbx_nmr_exptl.sample_state 1 1 1 '2D 1H-13C HSQC' 1 isotropic 2 1 2 '2D 1H-13C HSQC' 1 isotropic 3 1 3 '2D 1H-13C HSQC' 1 isotropic 4 1 4 '2D 1H-13C HSQC' 1 isotropic 16 1 1 '2D 1H-15N HSQC' 1 isotropic 15 1 2 '2D 1H-15N HSQC' 1 isotropic 14 1 3 '2D 1H-15N HSQC' 1 isotropic 13 1 4 '2D 1H-15N HSQC' 1 isotropic 5 1 1 '2D 1H-13C TROSY' 1 anisotropic 8 1 2 '2D 1H-13C TROSY' 1 anisotropic 7 1 3 '2D 1H-13C TROSY' 1 anisotropic 6 1 4 '2D 1H-13C TROSY' 1 anisotropic 12 1 1 '2D 1H-13C S3CT HSQC' 1 anisotropic 11 1 2 '2D 1H-13C S3CT HSQC' 1 anisotropic 10 1 3 '2D 1H-13C S3CT HSQC' 1 anisotropic 9 1 4 '2D 1H-13C S3CT HSQC' 1 anisotropic 20 1 1 '2D 1H-15N HSQC without decoupling' 1 anisotropic 19 1 2 '2D 1H-15N HSQC without decoupling' 1 anisotropic 18 1 3 '2D 1H-15N HSQC without decoupling' 1 anisotropic 17 1 4 '2D 1H-15N HSQC without decoupling' 1 anisotropic # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.pressure 1 _pdbx_nmr_exptl_sample_conditions.pH 6.4 _pdbx_nmr_exptl_sample_conditions.ionic_strength 25 _pdbx_nmr_exptl_sample_conditions.details '25mM NaCl, 15mM Na3PO4, 0.1mM EDTA' _pdbx_nmr_exptl_sample_conditions.ionic_strength_err ? _pdbx_nmr_exptl_sample_conditions.ionic_strength_units mM _pdbx_nmr_exptl_sample_conditions.label conditions_1 _pdbx_nmr_exptl_sample_conditions.pH_err ? _pdbx_nmr_exptl_sample_conditions.pH_units pH _pdbx_nmr_exptl_sample_conditions.pressure_err ? _pdbx_nmr_exptl_sample_conditions.temperature_err ? _pdbx_nmr_exptl_sample_conditions.temperature_units K # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system _pdbx_nmr_sample_details.label _pdbx_nmr_sample_details.type _pdbx_nmr_sample_details.details 1 '1.0 mM 13C,15N mtTAR_E0, 90% H2O/10% D2O' '90% H2O/10% D2O' mtTAR_E0 solution 'UUCGTAR with no elongation' 2 '1.0 mM 13C,15N mtTAR_EI22, 90% H2O/10% D2O' '90% H2O/10% D2O' mtTAR_EI22 solution 'UUCGTAR with Helix I elongated 22 bps' 3 '1.0 mM 13C,15N mtTAR_EII22, 90% H2O/10% D2O' '90% H2O/10% D2O' mtTAR_EII22 solution 'UUCGTAR with Helix II elongated 22 bps' 4 '1.0 mM 13C,15N mtTAR_EI3, 90% H2O/10% D2O' '90% H2O/10% D2O' mtTAR_EI3 solution 'UUCGTAR with Helix I elongated 3 bps' # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model 'AVANCE III' _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.field_strength 600 _pdbx_nmr_spectrometer.details ? # _pdbx_nmr_refine.entry_id 7JU1 _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ;This is a thermodynamic ensemble in which each confomer is equally populated. The ensemble was generated by sample and select approach which utilize Monte-Carlo simulation annealing. ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 7JU1 _pdbx_nmr_ensemble.conformers_calculated_total_number 20 _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _pdbx_nmr_ensemble.conformer_selection_criteria 'target function' _pdbx_nmr_ensemble.representative_conformer ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.entry_id 7JU1 _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.ordinal _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors 1 refinement 'X-PLOR NIH' ? 'Schwieters, Kuszewski, Tjandra and Clore' 2 processing NMRPipe ? 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' 3 'chemical shift assignment' Sparky ? Goddard 4 'peak picking' Sparky ? Goddard # _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 7JU1 _exptl.crystals_number ? _exptl.details ? _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 7JU1 _struct.title 'The FARFAR-NMR Ensemble of 29-mer HIV-1 Trans-activation Response Element RNA (N=20)' _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 7JU1 _struct_keywords.text 'VIRUS RNA, HIV-1 RNA, RNA, FARFAR, FARFAR-NMR' _struct_keywords.pdbx_keywords 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 29 N3 ? ? X G 17 X C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 29 O2 ? ? X G 17 X C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 29 N4 ? ? X G 17 X C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 28 N3 ? ? X G 18 X C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 28 O2 ? ? X G 18 X C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 28 N4 ? ? X G 18 X C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 3 N3 ? ? ? 1_555 A G 27 N1 ? ? X C 19 X G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 3 N4 ? ? ? 1_555 A G 27 O6 ? ? X C 19 X G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 3 O2 ? ? ? 1_555 A G 27 N2 ? ? X C 19 X G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A A 4 N1 ? ? ? 1_555 A U 26 N3 ? ? X A 20 X U 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A A 4 N6 ? ? ? 1_555 A U 26 O4 ? ? X A 20 X U 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 5 N1 ? ? ? 1_555 A C 25 N3 ? ? X G 21 X C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 5 N2 ? ? ? 1_555 A C 25 O2 ? ? X G 21 X C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 5 O6 ? ? ? 1_555 A C 25 N4 ? ? X G 21 X C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A A 6 N1 ? ? ? 1_555 A U 24 N3 ? ? X A 22 X U 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A A 6 N6 ? ? ? 1_555 A U 24 O4 ? ? X A 22 X U 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 10 N1 ? ? ? 1_555 A C 23 N3 ? ? X G 26 X C 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 10 N2 ? ? ? 1_555 A C 23 O2 ? ? X G 26 X C 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 10 O6 ? ? ? 1_555 A C 23 N4 ? ? X G 26 X C 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A A 11 N1 ? ? ? 1_555 A U 22 N3 ? ? X A 27 X U 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A A 11 N6 ? ? ? 1_555 A U 22 O4 ? ? X A 27 X U 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 12 N1 ? ? ? 1_555 A C 21 N3 ? ? X G 28 X C 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 12 N2 ? ? ? 1_555 A C 21 O2 ? ? X G 28 X C 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 12 O6 ? ? ? 1_555 A C 21 N4 ? ? X G 28 X C 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 13 N3 ? ? ? 1_555 A G 20 N1 ? ? X C 29 X G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 13 N4 ? ? ? 1_555 A G 20 O6 ? ? X C 29 X G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 13 O2 ? ? ? 1_555 A G 20 N2 ? ? X C 29 X G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 14 O2 ? ? ? 1_555 A A 19 N6 ? ? X C 30 X A 35 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog29 hydrog ? ? A U 15 N3 ? ? ? 1_555 A G 18 N7 ? ? X U 31 X G 34 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 7JU1 _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 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 17 17 G G X . n A 1 2 G 2 18 18 G G X . n A 1 3 C 3 19 19 C C X . n A 1 4 A 4 20 20 A A X . n A 1 5 G 5 21 21 G G X . n A 1 6 A 6 22 22 A A X . n A 1 7 U 7 23 23 U U X . n A 1 8 C 8 24 24 C C X . n A 1 9 U 9 25 25 U U X . n A 1 10 G 10 26 26 G G X . n A 1 11 A 11 27 27 A A X . n A 1 12 G 12 28 28 G G X . n A 1 13 C 13 29 29 C C X . n A 1 14 C 14 30 30 C C X . n A 1 15 U 15 31 31 U U X . n A 1 16 G 16 32 32 G G X . n A 1 17 G 17 33 33 G G X . n A 1 18 G 18 34 34 G G X . n A 1 19 A 19 35 35 A A X . n A 1 20 G 20 36 36 G G X . n A 1 21 C 21 37 37 C C X . n A 1 22 U 22 38 38 U U X . n A 1 23 C 23 39 39 C C X . n A 1 24 U 24 40 40 U U X . n A 1 25 C 25 41 41 C C X . n A 1 26 U 26 42 42 U U X . n A 1 27 G 27 43 43 G G X . n A 1 28 C 28 44 44 C C X . n A 1 29 C 29 45 45 C C X . 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 ? _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 2020-10-07 2 'Structure model' 1 1 2020-11-11 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' 'Database references' 3 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' citation 2 3 'Structure model' database_2 3 3 'Structure model' pdbx_database_status # 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.pdbx_database_id_DOI' 4 3 'Structure model' '_database_2.pdbx_DOI' 5 3 'Structure model' '_database_2.pdbx_database_accession' 6 3 'Structure model' '_pdbx_database_status.status_code_nmr_data' # loop_ _pdbx_nmr_exptl_sample.solution_id _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 1 mtTAR_E0 1.0 ? mM 13C,15N 2 mtTAR_EI22 1.0 ? mM 13C,15N 3 mtTAR_EII22 1.0 ? mM 13C,15N 4 mtTAR_EI3 1.0 ? mM 13C,15N # 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 4 "O2'" X A 22 ? ? OP1 X U 23 ? ? 1.72 2 11 "O2'" X C 24 ? ? OP2 X U 25 ? ? 1.66 3 13 "O2'" X G 32 ? ? OP2 X G 33 ? ? 1.51 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 2 "O3'" X A 22 ? ? P X U 23 ? ? 1.533 1.607 -0.074 0.012 Y 2 4 "O3'" X A 22 ? ? P X U 23 ? ? 1.508 1.607 -0.099 0.012 Y 3 5 "O3'" X C 29 ? ? P X C 30 ? ? 1.458 1.607 -0.149 0.012 Y 4 13 "O3'" X G 32 ? ? P X G 33 ? ? 1.524 1.607 -0.083 0.012 Y # 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 2 "C3'" X U 31 ? ? "O3'" X U 31 ? ? P X G 32 ? ? 133.00 119.70 13.30 1.20 Y 2 7 "C5'" X C 30 ? ? "C4'" X C 30 ? ? "O4'" X C 30 ? ? 115.37 109.80 5.57 0.90 N # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 X G 17 ? "O5'" ? A G 1 "O5'" 2 2 Y 1 X G 17 ? "O5'" ? A G 1 "O5'" 3 3 Y 1 X G 17 ? "O5'" ? A G 1 "O5'" 4 4 Y 1 X G 17 ? "O5'" ? A G 1 "O5'" 5 5 Y 1 X G 17 ? "O5'" ? A G 1 "O5'" 6 6 Y 1 X G 17 ? "O5'" ? A G 1 "O5'" 7 7 Y 1 X G 17 ? "O5'" ? A G 1 "O5'" 8 8 Y 1 X G 17 ? "O5'" ? A G 1 "O5'" 9 9 Y 1 X G 17 ? "O5'" ? A G 1 "O5'" 10 10 Y 1 X G 17 ? "O5'" ? A G 1 "O5'" 11 11 Y 1 X G 17 ? "O5'" ? A G 1 "O5'" 12 12 Y 1 X G 17 ? "O5'" ? A G 1 "O5'" 13 13 Y 1 X G 17 ? "O5'" ? A G 1 "O5'" 14 14 Y 1 X G 17 ? "O5'" ? A G 1 "O5'" 15 15 Y 1 X G 17 ? "O5'" ? A G 1 "O5'" 16 16 Y 1 X G 17 ? "O5'" ? A G 1 "O5'" 17 17 Y 1 X G 17 ? "O5'" ? A G 1 "O5'" 18 18 Y 1 X G 17 ? "O5'" ? A G 1 "O5'" 19 19 Y 1 X G 17 ? "O5'" ? A G 1 "O5'" 20 20 Y 1 X G 17 ? "O5'" ? A G 1 "O5'" # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 7JU1 'double helix' 7JU1 'a-form double helix' 7JU1 'hairpin loop' 7JU1 'bulge loop' 7JU1 'mismatched base pair' # 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 29 1_555 -0.075 -0.155 -0.439 -6.961 -0.138 -3.908 1 X_G17:C45_X X 17 ? X 45 ? 19 1 1 A G 2 1_555 A C 28 1_555 -0.137 -0.136 -0.111 -4.986 -5.585 -1.081 2 X_G18:C44_X X 18 ? X 44 ? 19 1 1 A C 3 1_555 A G 27 1_555 0.155 -0.132 -0.030 -0.473 -1.866 -0.904 3 X_C19:G43_X X 19 ? X 43 ? 19 1 1 A A 4 1_555 A U 26 1_555 0.034 -0.076 -0.156 -3.865 -2.739 -3.764 4 X_A20:U42_X X 20 ? X 42 ? 20 1 1 A G 5 1_555 A C 25 1_555 -0.108 -0.121 -0.123 -5.434 -4.646 -1.660 5 X_G21:C41_X X 21 ? X 41 ? 19 1 1 A A 6 1_555 A U 24 1_555 -0.029 -0.149 -0.486 -6.036 -20.122 -2.361 6 X_A22:U40_X X 22 ? X 40 ? 20 1 1 A G 10 1_555 A C 23 1_555 -0.141 -0.139 -0.114 -4.805 -5.087 -0.965 7 X_G26:C39_X X 26 ? X 39 ? 19 1 1 A A 11 1_555 A U 22 1_555 0.013 -0.081 -0.148 -5.053 -2.492 -3.080 8 X_A27:U38_X X 27 ? X 38 ? 20 1 1 A G 12 1_555 A C 21 1_555 -0.109 -0.122 -0.112 -4.890 -4.230 -1.657 9 X_G28:C37_X X 28 ? X 37 ? 19 1 1 A C 13 1_555 A G 20 1_555 0.163 -0.129 -0.045 0.554 -2.728 -1.159 10 X_C29:G36_X X 29 ? X 36 ? 19 1 1 A C 14 1_555 A A 19 1_555 3.592 -1.283 -1.011 3.652 -0.209 -39.784 11 X_C30:A35_X X 30 ? X 35 ? ? 1 1 A U 15 1_555 A G 18 1_555 4.134 -2.634 0.741 27.801 14.118 -74.539 12 X_U31:G34_X X 31 ? X 34 ? ? 4 # 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 29 1_555 A G 2 1_555 A C 28 1_555 0.134 -1.979 3.190 -2.112 8.377 32.407 -4.674 -0.546 2.598 14.687 3.702 33.509 1 XX_G17G18:C44C45_XX X 17 ? X 45 ? X 18 ? X 44 ? 1 A G 2 1_555 A C 28 1_555 A C 3 1_555 A G 27 1_555 0.043 -1.748 3.112 -0.090 4.449 33.844 -3.625 -0.086 2.866 7.601 0.154 34.127 2 XX_G18C19:G43C44_XX X 18 ? X 44 ? X 19 ? X 43 ? 1 A C 3 1_555 A G 27 1_555 A A 4 1_555 A U 26 1_555 -0.052 -1.756 3.356 1.398 8.419 30.893 -4.636 0.336 2.788 15.438 -2.564 32.022 3 XX_C19A20:U42G43_XX X 19 ? X 43 ? X 20 ? X 42 ? 1 A A 4 1_555 A U 26 1_555 A G 5 1_555 A C 25 1_555 0.337 -1.715 3.347 -0.098 7.526 31.445 -4.366 -0.623 2.869 13.642 0.177 32.312 4 XX_A20G21:C41U42_XX X 20 ? X 42 ? X 21 ? X 41 ? 1 A G 5 1_555 A C 25 1_555 A A 6 1_555 A U 24 1_555 0.243 -1.423 3.394 4.628 13.052 32.858 -4.165 0.254 2.664 21.902 -7.766 35.583 5 XX_G21A22:U40C41_XX X 21 ? X 41 ? X 22 ? X 40 ? 1 A A 6 1_555 A U 24 1_555 A G 10 1_555 A C 23 1_555 1.021 -1.938 3.279 0.056 18.705 26.768 -6.155 -1.813 1.616 35.431 -0.106 32.558 6 XX_A22G26:C39U40_XX X 22 ? X 40 ? X 26 ? X 39 ? 1 A G 10 1_555 A C 23 1_555 A A 11 1_555 A U 22 1_555 -0.144 -1.741 3.234 -0.081 7.846 33.245 -4.122 0.233 2.763 13.481 0.139 34.133 7 XX_G26A27:U38C39_XX X 26 ? X 39 ? X 27 ? X 38 ? 1 A A 11 1_555 A U 22 1_555 A G 12 1_555 A C 21 1_555 0.244 -1.731 3.286 -0.085 6.748 31.072 -4.336 -0.461 2.855 12.413 0.157 31.779 8 XX_A27G28:C37U38_XX X 27 ? X 38 ? X 28 ? X 37 ? 1 A G 12 1_555 A C 21 1_555 A C 13 1_555 A G 20 1_555 0.217 -1.651 3.112 0.019 5.015 33.287 -3.600 -0.371 2.840 8.694 -0.034 33.653 9 XX_G28C29:G36C37_XX X 28 ? X 37 ? X 29 ? X 36 ? 1 A C 13 1_555 A G 20 1_555 A C 14 1_555 A A 19 1_555 -2.549 -1.881 3.483 8.350 11.819 45.548 -3.210 3.777 2.472 14.831 -10.477 47.675 10 XX_C29C30:A35G36_XX X 29 ? X 36 ? X 30 ? X 35 ? 1 A C 14 1_555 A A 19 1_555 A U 15 1_555 A G 18 1_555 -2.813 -2.007 3.370 1.217 15.802 35.437 -4.762 4.376 2.215 24.506 -1.888 38.715 11 XX_C30U31:G34A35_XX X 30 ? X 35 ? X 31 ? X 34 ? # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' 'United States' 1R01GM132899 1 'National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)' 'United States' 'U54 AI150470' 2 # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'gel filtration' _pdbx_struct_assembly_auth_evidence.details ? #