data_6HYK # _entry.id 6HYK # _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 6HYK pdb_00006hyk 10.2210/pdb6hyk/pdb WWPDB D_1200012503 ? ? BMRB 34321 ? ? # _pdbx_database_related.db_name BMRB _pdbx_database_related.details 'NMR solution structure of the C/D box snoRNA U14' _pdbx_database_related.db_id 34321 _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 6HYK _pdbx_database_status.recvd_initial_deposition_date 2018-10-22 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _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 _audit_author.identifier_ORCID 'Chagot, M.E.' 1 ? 'Quinternet, M.' 2 ? 'Rothe, B.' 3 ? 'Charpentier, B.' 4 ? 'Coutant, J.' 5 ? 'Manival, X.' 6 ? 'Lebars, I.' 7 ? # _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 FR _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Biochimie _citation.journal_id_ASTM BICMBE _citation.journal_id_CSD 0466 _citation.journal_id_ISSN 0300-9084 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 164 _citation.language ? _citation.page_first 70 _citation.page_last 82 _citation.title ;The yeast C/D box snoRNA U14 adopts a "weak" K-turn like conformation recognized by the Snu13 core protein in solution. ; _citation.year 2019 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1016/j.biochi.2019.03.014 _citation.pdbx_database_id_PubMed 30914254 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Chagot, M.E.' 1 ? primary 'Quinternet, M.' 2 ? primary 'Rothe, B.' 3 ? primary 'Charpentier, B.' 4 ? primary 'Coutant, J.' 5 ? primary 'Manival, X.' 6 ? primary 'Lebars, I.' 7 ? # _entity.id 1 _entity.type polymer _entity.src_method man _entity.pdbx_description 'RNA (31-MER)' _entity.formula_weight 9998.949 _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 GGCACGGUGAUGACCUUCGGGUCUGAGUGCC _entity_poly.pdbx_seq_one_letter_code_can GGCACGGUGAUGACCUUCGGGUCUGAGUGCC _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 C n 1 4 A n 1 5 C n 1 6 G n 1 7 G n 1 8 U n 1 9 G n 1 10 A n 1 11 U n 1 12 G n 1 13 A n 1 14 C n 1 15 C n 1 16 U n 1 17 U n 1 18 C n 1 19 G n 1 20 G n 1 21 G n 1 22 U n 1 23 C n 1 24 U n 1 25 G n 1 26 A n 1 27 G n 1 28 U n 1 29 G n 1 30 C n 1 31 C n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type 'Biological sequence' _entity_src_gen.pdbx_beg_seq_num 1 _entity_src_gen.pdbx_end_seq_num 31 _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene ? _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'synthetic construct' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 32630 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'synthetic construct' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 32630 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 6HYK _struct_ref.pdbx_db_accession 6HYK _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 6HYK _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 31 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 6HYK _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 31 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 31 # 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-1H NOESY' 1 isotropic 2 2 1 '2D 1H-1H NOESY' 1 isotropic 3 4 1 '2D 1H-1H NOESY' 1 isotropic 4 1 1 '2D 1H-15N HSQC' 1 isotropic 5 2 1 '2D 1H-15N HSQC' 1 isotropic 6 4 1 '2D 1H-15N HSQC' 1 isotropic 7 4 1 '2D 1H-13C HSQC' 1 isotropic 8 6 1 '2D 1H-15N HSQC' 1 anisotropic 16 1 1 '2D HNN COSY' 1 isotropic 17 2 1 '2D HNN COSY' 1 isotropic 18 3 1 '2D HNN COSY' 1 isotropic 9 3 2 '2D 1H-1H NOESY' 1 isotropic 10 4 2 '2D 1H-1H NOESY' 1 isotropic 11 5 2 '2D 1H-1H NOESY' 1 isotropic 12 3 2 '2D MLEV' 1 isotropic 13 4 2 '2D MLEV' 1 isotropic 14 5 2 '2D MLEV' 1 isotropic 15 3 2 '2D 1H-13C HSQC' 1 isotropic 19 4 2 '2D 1H-13C HSQC' 1 isotropic 20 5 2 '2D 1H-13C HSQC' 1 isotropic 21 6 2 '2D 1H-13C HSQC' 1 anisotropic 22 4 2 '2D DQF-COSY' 1 isotropic 23 4 2 '2D HCN' 1 isotropic 24 4 2 '3D HCCH-TOCSY' 1 isotropic 25 4 2 '3D HCP' 2 isotropic 26 4 2 '2D HPCOSY' 2 isotropic 27 4 2 '2D HCC' 2 isotropic # loop_ _pdbx_nmr_exptl_sample_conditions.conditions_id _pdbx_nmr_exptl_sample_conditions.temperature _pdbx_nmr_exptl_sample_conditions.pressure_units _pdbx_nmr_exptl_sample_conditions.pressure _pdbx_nmr_exptl_sample_conditions.pH _pdbx_nmr_exptl_sample_conditions.ionic_strength _pdbx_nmr_exptl_sample_conditions.details _pdbx_nmr_exptl_sample_conditions.ionic_strength_err _pdbx_nmr_exptl_sample_conditions.ionic_strength_units _pdbx_nmr_exptl_sample_conditions.label _pdbx_nmr_exptl_sample_conditions.pH_err _pdbx_nmr_exptl_sample_conditions.pH_units _pdbx_nmr_exptl_sample_conditions.pressure_err _pdbx_nmr_exptl_sample_conditions.temperature_err _pdbx_nmr_exptl_sample_conditions.temperature_units 1 283 Pa atmospheric 6.4 '150 mM NaCl' ;50 mM sodium phosphate buffer pH6.4 150 mM NaCl ; ? 'Not defined' conditions_1 ? pH ? ? K 2 288 Pa ambient 6.4 '150 mM NaCl' ;50 mM sodium phosphate buffer pH6.4 150 mM NaCl ; ? 'Not defined' conditions_2 ? pH ? ? K 3 293 Pa ambient 6.4 '150 mM NaCl' ;50 mM sodium phosphate buffer pH6.4 150 mM NaCl ; ? 'Not defined' conditions_3 ? pH ? ? K 4 298 Pa ambient 6.4 '150 mM NaCl' ;50 mM sodium phosphate buffer pH6.4 150 mM NaCl ; ? M conditions_4 ? pH ? ? K 5 303 Pa ambient 6.4 '150 mM NaCl' ;50 mM sodium phosphate buffer pH6.4 150 mM NaCl ; ? 'Not defined' condition_5 ? pH ? ? K 6 298 Pa ambient 6.4 '150 mM NaCl' ;50 mM sodium phosphate buffer pH6.4 150 mM NaCl pf1 filamentous bacteriophage ; ? 'Not defined' conditions_6 ? pH ? ? 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 '500 uM RNA (31-MER), 500 uM [U-99% 13C; U-99% 15N] RNA (31-MER), 90% H2O/10% D2O' '90% H2O/10% D2O' U14_H2O solution ;50 mM sodium phosphate buffer pH6.4 150 mM NaCl ; 2 '500 uM RNA (31-MER), 500 uM [U-99% 13C; U-99% 15N] RNA (31-MER), 100% D2O' '100% D2O' U14_D2O solution ;50 mM sodium phosphate buffer pH6.4 150 mM NaCl ; # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.type _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.details 1 DRX ? Bruker 600 ? 2 'AVANCE NEO' ? Bruker 500 ? # _pdbx_nmr_refine.entry_id 6HYK _pdbx_nmr_refine.method 'torsion angle dynamics' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 2 # _pdbx_nmr_ensemble.entry_id 6HYK _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the least restraint violations' _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 6HYK _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'fewest violations' # loop_ _pdbx_nmr_software.ordinal _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors 1 refinement CNS ? 'Brunger A. T. et.al.' 2 'structure calculation' CNS ? 'Brunger, Adams, Clore, Gros, Nilges and Read' 3 processing TopSpin ? 'Bruker Biospin' 4 'chemical shift assignment' 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 6HYK _exptl.crystals_number ? _exptl.details ? _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 6HYK _struct.title 'NMR solution structure of the C/D box snoRNA U14' _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 6HYK _struct_keywords.text 'snoRNA, U14, K-turn, Snu13p, RNA' _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 31 N3 ? ? A G 1 A C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 31 O2 ? ? A G 1 A C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 31 N4 ? ? A G 1 A C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 30 N3 ? ? A G 2 A C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 30 O2 ? ? A G 2 A C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 30 N4 ? ? A G 2 A C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 3 N3 ? ? ? 1_555 A G 29 N1 ? ? A C 3 A G 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 3 N4 ? ? ? 1_555 A G 29 O6 ? ? A C 3 A G 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 3 O2 ? ? ? 1_555 A G 29 N2 ? ? A C 3 A G 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A A 4 N1 ? ? ? 1_555 A U 28 N3 ? ? A A 4 A U 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A A 4 N6 ? ? ? 1_555 A U 28 O4 ? ? A A 4 A U 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 5 N3 ? ? ? 1_555 A G 27 N1 ? ? A C 5 A G 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 5 N4 ? ? ? 1_555 A G 27 O6 ? ? A C 5 A G 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 5 O2 ? ? ? 1_555 A G 27 N2 ? ? A C 5 A G 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 9 N2 ? ? ? 1_555 A A 26 N7 ? ? A G 9 A A 26 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog16 hydrog ? ? A G 9 N3 ? ? ? 1_555 A A 26 N6 ? ? A G 9 A A 26 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog17 hydrog ? ? A A 10 N6 ? ? ? 1_555 A G 25 N3 ? ? A A 10 A G 25 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog18 hydrog ? ? A A 10 N7 ? ? ? 1_555 A G 25 N2 ? ? A A 10 A G 25 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog19 hydrog ? ? A U 11 N3 ? ? ? 1_555 A U 24 O2 ? ? A U 11 A U 24 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog20 hydrog ? ? A U 11 O4 ? ? ? 1_555 A U 24 N3 ? ? A U 11 A U 24 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog21 hydrog ? ? A G 12 N1 ? ? ? 1_555 A C 23 N3 ? ? A G 12 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 12 N2 ? ? ? 1_555 A C 23 O2 ? ? A G 12 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 12 O6 ? ? ? 1_555 A C 23 N4 ? ? A G 12 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A A 13 N1 ? ? ? 1_555 A U 22 N3 ? ? A A 13 A U 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A A 13 N6 ? ? ? 1_555 A U 22 O4 ? ? A A 13 A U 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 14 N3 ? ? ? 1_555 A G 21 N1 ? ? A C 14 A G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 14 N4 ? ? ? 1_555 A G 21 O6 ? ? A C 14 A G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 14 O2 ? ? ? 1_555 A G 21 N2 ? ? A C 14 A G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A C 15 N3 ? ? ? 1_555 A G 20 N1 ? ? A C 15 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A C 15 N4 ? ? ? 1_555 A G 20 O6 ? ? A C 15 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A C 15 O2 ? ? ? 1_555 A G 20 N2 ? ? A C 15 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A U 16 O2 ? ? ? 1_555 A G 19 N1 ? ? A U 16 A G 19 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 6HYK _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 1 1 G GUA A . n A 1 2 G 2 2 2 G GUA A . n A 1 3 C 3 3 3 C CYT A . n A 1 4 A 4 4 4 A ADE A . n A 1 5 C 5 5 5 C CYT A . n A 1 6 G 6 6 6 G GUA A . n A 1 7 G 7 7 7 G GUA A . n A 1 8 U 8 8 8 U URI A . n A 1 9 G 9 9 9 G GUA A . n A 1 10 A 10 10 10 A ADE A . n A 1 11 U 11 11 11 U URI A . n A 1 12 G 12 12 12 G GUA A . n A 1 13 A 13 13 13 A ADE A . n A 1 14 C 14 14 14 C CYT A . n A 1 15 C 15 15 15 C CYT A . n A 1 16 U 16 16 16 U URI A . n A 1 17 U 17 17 17 U URI A . n A 1 18 C 18 18 18 C CYT A . n A 1 19 G 19 19 19 G GUA A . n A 1 20 G 20 20 20 G GUA A . n A 1 21 G 21 21 21 G GUA A . n A 1 22 U 22 22 22 U URI A . n A 1 23 C 23 23 23 C CYT A . n A 1 24 U 24 24 24 U URI A . n A 1 25 G 25 25 25 G GUA A . n A 1 26 A 26 26 26 A ADE A . n A 1 27 G 27 27 27 G GUA A . n A 1 28 U 28 28 28 U URI A . n A 1 29 G 29 29 29 G GUA A . n A 1 30 C 30 30 30 C CYT A . n A 1 31 C 31 31 31 C CYT A . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _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 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 0 ? 1 MORE 0 ? 1 'SSA (A^2)' 6170 ? # _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 2019-04-24 2 'Structure model' 1 1 2019-05-08 3 'Structure model' 1 2 2019-08-21 4 'Structure model' 1 3 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' 'Data collection' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 4 'Structure model' 'Database references' 5 4 '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_nmr_software 2 3 'Structure model' citation 3 4 'Structure model' database_2 4 4 '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' '_pdbx_nmr_software.name' 2 3 'Structure model' '_citation.journal_volume' 3 3 'Structure model' '_citation.page_first' 4 3 'Structure model' '_citation.page_last' 5 4 'Structure model' '_database_2.pdbx_DOI' 6 4 'Structure model' '_database_2.pdbx_database_accession' 7 4 '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 'RNA (31-MER)_unlabel' 500 ? uM 'natural abundance' 1 'RNA (31-MER)_label' 500 ? uM '[U-99% 13C; U-99% 15N]' 2 'RNA (31-MER)_unlabel' 500 ? uM 'natural abundance' 2 'RNA (31-MER)_label' 500 ? uM '[U-99% 13C; U-99% 15N]' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 6HYK 'double helix' 6HYK 'a-form double helix' 6HYK tetraloop 6HYK 'bulge loop' 6HYK '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 31 1_555 -0.886 0.113 0.005 -0.214 -0.694 2.416 1 A_G1:C31_A A 1 ? A 31 ? 19 1 1 A G 2 1_555 A C 30 1_555 0.750 0.288 -0.006 -1.724 -0.157 3.996 2 A_G2:C30_A A 2 ? A 30 ? 19 1 1 A C 3 1_555 A G 29 1_555 -0.141 0.323 -0.074 -1.903 -3.859 3.245 3 A_C3:G29_A A 3 ? A 29 ? 19 1 1 A A 4 1_555 A U 28 1_555 -1.166 -0.040 0.062 3.864 -1.273 6.405 4 A_A4:U28_A A 4 ? A 28 ? 20 1 1 A C 5 1_555 A G 27 1_555 -0.331 0.214 -0.419 0.676 1.552 5.455 5 A_C5:G27_A A 5 ? A 27 ? 19 1 1 A G 9 1_555 A A 26 1_555 6.777 -3.689 0.379 5.412 -0.335 16.334 6 A_G9:A26_A A 9 ? A 26 ? 11 9 1 A A 10 1_555 A G 25 1_555 -6.826 -5.111 0.064 -9.860 2.547 -2.588 7 A_A10:G25_A A 10 ? A 25 ? 11 10 1 A U 11 1_555 A U 24 1_555 -0.936 -1.493 0.326 -3.188 -6.741 19.510 8 A_U11:U24_A A 11 ? A 24 ? 16 1 1 A G 12 1_555 A C 23 1_555 -1.503 -0.348 -0.136 -4.646 1.665 1.073 9 A_G12:C23_A A 12 ? A 23 ? 19 1 1 A A 13 1_555 A U 22 1_555 0.563 0.266 -0.084 -3.113 -2.803 4.821 10 A_A13:U22_A A 13 ? A 22 ? 20 1 1 A C 14 1_555 A G 21 1_555 -0.430 0.331 -0.243 -2.343 0.608 -4.174 11 A_C14:G21_A A 14 ? A 21 ? 19 1 1 A C 15 1_555 A G 20 1_555 0.754 -0.112 -0.122 2.202 3.119 -1.476 12 A_C15:G20_A A 15 ? A 20 ? 19 1 1 A U 16 1_555 A G 19 1_555 1.775 -4.152 -0.326 2.819 -17.166 -96.807 13 A_U16:G19_A A 16 ? A 19 ? ? 6 # 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 31 1_555 A G 2 1_555 A C 30 1_555 0.094 -0.365 3.796 -0.089 22.602 33.453 -3.462 -0.148 2.980 34.775 0.138 40.191 1 AA_G1G2:C30C31_AA A 1 ? A 31 ? A 2 ? A 30 ? 1 A G 2 1_555 A C 30 1_555 A C 3 1_555 A G 29 1_555 0.072 -0.953 3.783 0.542 13.155 23.745 -5.647 -0.006 2.867 29.265 -1.207 27.105 2 AA_G2C3:G29C30_AA A 2 ? A 30 ? A 3 ? A 29 ? 1 A C 3 1_555 A G 29 1_555 A A 4 1_555 A U 28 1_555 -0.087 -0.955 3.176 -3.854 15.727 26.088 -4.598 -0.520 2.243 31.296 7.670 30.631 3 AA_C3A4:U28G29_AA A 3 ? A 29 ? A 4 ? A 28 ? 1 A A 4 1_555 A U 28 1_555 A C 5 1_555 A G 27 1_555 0.051 -1.135 3.706 -1.878 17.406 29.038 -4.894 -0.404 2.621 31.375 3.385 33.810 4 AA_A4C5:G27U28_AA A 4 ? A 28 ? A 5 ? A 27 ? 1 A G 9 1_555 A A 26 1_555 A A 10 1_555 A G 25 1_555 -1.172 -2.442 3.913 -6.719 -3.868 -15.223 10.790 -8.402 2.484 13.516 -23.481 -17.073 5 AA_G9A10:G25A26_AA A 9 ? A 26 ? A 10 ? A 25 ? 1 A A 10 1_555 A G 25 1_555 A U 11 1_555 A U 24 1_555 0.943 1.414 4.032 -8.680 12.399 58.892 0.644 -1.464 4.067 12.388 8.673 60.636 6 AA_A10U11:U24G25_AA A 10 ? A 25 ? A 11 ? A 24 ? 1 A U 11 1_555 A U 24 1_555 A G 12 1_555 A C 23 1_555 -0.611 -0.875 3.495 -0.662 25.021 27.879 -4.630 0.870 2.069 42.642 1.129 37.300 7 AA_U11G12:C23U24_AA A 11 ? A 24 ? A 12 ? A 23 ? 1 A G 12 1_555 A C 23 1_555 A A 13 1_555 A U 22 1_555 0.477 -0.983 3.669 2.638 7.346 40.409 -2.277 -0.364 3.469 10.515 -3.777 41.125 8 AA_G12A13:U22C23_AA A 12 ? A 23 ? A 13 ? A 22 ? 1 A A 13 1_555 A U 22 1_555 A C 14 1_555 A G 21 1_555 -0.722 -1.424 3.637 -0.318 -0.114 25.059 -3.244 1.559 3.652 -0.262 0.734 25.062 9 AA_A13C14:G21U22_AA A 13 ? A 22 ? A 14 ? A 21 ? 1 A C 14 1_555 A G 21 1_555 A C 15 1_555 A G 20 1_555 -0.216 -1.199 3.807 -3.346 -0.129 30.260 -2.254 -0.371 3.813 -0.246 6.386 30.440 10 AA_C14C15:G20G21_AA A 14 ? A 21 ? A 15 ? A 20 ? 1 A C 15 1_555 A G 20 1_555 A U 16 1_555 A G 19 1_555 -0.973 -1.631 3.651 13.359 15.160 81.106 -1.621 1.079 3.201 11.499 -10.133 83.161 11 AA_C15U16:G19G20_AA A 15 ? A 20 ? A 16 ? A 19 ? # _pdbx_audit_support.funding_organization 'French National Research Agency' _pdbx_audit_support.country France _pdbx_audit_support.grant_number ANR-16-CE11-0032-02 _pdbx_audit_support.ordinal 1 # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? #