data_8CQ1 # _entry.id 8CQ1 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.381 _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 8CQ1 pdb_00008cq1 10.2210/pdb8cq1/pdb WWPDB D_1292127949 ? ? BMRB 50347 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.details _pdbx_database_related.db_id _pdbx_database_related.content_type BMRB . 50760 unspecified BMRB . 50347 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 8CQ1 _pdbx_database_status.recvd_initial_deposition_date 2023-03-03 _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.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Duchardt-Ferner, E.' 1 0000-0001-7521-8264 'Voegele, J.' 2 0000-0001-8615-7524 # _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 'Nucleic Acids Res.' _citation.journal_id_ASTM NARHAD _citation.journal_id_CSD 0389 _citation.journal_id_ISSN 1362-4962 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 51 _citation.language ? _citation.page_first 11318 _citation.page_last 11331 _citation.title ;High-resolution structure of stem-loop 4 from the 5'-UTR of SARS-CoV-2 solved by solution state NMR. ; _citation.year 2023 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1093/nar/gkad762 _citation.pdbx_database_id_PubMed 37791874 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Vogele, J.' 1 ? primary 'Hymon, D.' 2 ? primary 'Martins, J.' 3 ? primary 'Ferner, J.' 4 ? primary 'Jonker, H.R.A.' 5 ? primary 'Hargrove, A.E.' 6 ? primary 'Weigand, J.E.' 7 ? primary 'Wacker, A.' 8 ? primary 'Schwalbe, H.' 9 ? primary 'Wohnert, J.' 10 ? primary 'Duchardt-Ferner, E.' 11 ? # _entity.id 1 _entity.type polymer _entity.src_method man _entity.pdbx_description 5_SL4 _entity.formula_weight 14074.320 _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 GGGUGUGGCUGUCACUCGGCUGCAUGCUUAGUGCACUCACGCCC _entity_poly.pdbx_seq_one_letter_code_can GGGUGUGGCUGUCACUCGGCUGCAUGCUUAGUGCACUCACGCCC _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 U n 1 5 G n 1 6 U n 1 7 G n 1 8 G n 1 9 C n 1 10 U n 1 11 G n 1 12 U n 1 13 C n 1 14 A n 1 15 C n 1 16 U n 1 17 C n 1 18 G n 1 19 G n 1 20 C n 1 21 U n 1 22 G n 1 23 C n 1 24 A n 1 25 U n 1 26 G n 1 27 C n 1 28 U n 1 29 U n 1 30 A n 1 31 G n 1 32 U n 1 33 G n 1 34 C n 1 35 A n 1 36 C n 1 37 U n 1 38 C n 1 39 A n 1 40 C n 1 41 G n 1 42 C n 1 43 C n 1 44 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 44 _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 'Severe acute respiratory syndrome coronavirus 2' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 2697049 _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 'Escherichia coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _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 8CQ1 _struct_ref.pdbx_db_accession 8CQ1 _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 8CQ1 _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 44 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 8CQ1 _struct_ref_seq.db_align_beg 84 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 127 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 84 _struct_ref_seq.pdbx_auth_seq_align_end 127 # 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' 2 isotropic 8 1 1 'NOESY[15N]-CPMG' 3 isotropic 10 1 4 'NOESY[15N]-CPMG' 2 isotropic 2 2 2 '3D 1H-13C NOESY aliphatic' 7 isotropic 4 2 2 '3D 13C,15N-filtered 1H-13C NOESY aromatic' 2 isotropic 3 1 2 '3D 1H-13C NOESY aromatic' 4 isotropic 5 2 3 '3D 1H-13C NOESY aliphatic' 3 isotropic 6 2 3 '3D 1H-13C NOESY aromatic' 3 isotropic 7 2 2 '3D 13C,15N-filtered 1H-13C NOESY aliphatic' 2 isotropic 20 1 9 '2D 1H-1H NOESY' 7 isotropic 11 2 4 '3D 1H-13C NOESY aromatic' 2 isotropic 12 2 4 '3D 1H-13C NOESY aliphatic' 6 isotropic 13 1 8 1H,15N-IPAP-sofast-HMQC 3 isotropic 14 1 7 1H,15N-IPAP-sofast-HMQC 3 anisotropic 15 1 8 1H,13C-IPAP-HSQC 3 isotropic 16 1 7 1H,13C-IPAP-HSQC 3 anisotropic 17 1 6 1H,13C-IPAP-HSQC 3 isotropic 18 1 5 1H,13C-IPAP-HSQC 3 anisotropic 21 1 1 'lr HNN-COSY' 7 isotropic 22 1 1 HNN-COSY 3 isotropic 23 2 3 '3D HCCH-TOCSY' 2 isotropic 24 2 2 '3D HCCH-TOCSY' 2 isotropic 25 2 2 '3D HCCH-TOCSY' 6 isotropic 26 2 3 '3D HCCH-COSY' 6 isotropic 27 2 2 '3D HCCH-COSY' 6 isotropic 28 1 3 '3D (H)CNC' 3 isotropic 29 1 2 '3D (H)CNC' 3 isotropic 30 1 2 '2D Best-TROSY H(N)CO' 3 isotropic 31 2 2 '2D H5(C5)C4' 8 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 bar 1 6.2 100 ;25 mM potassium phosphate buffer 50 mM potassium chloride ; ? mM conditions_1 0.05 pH ? ? K 2 298 bar 1 6.2 100 ;25 mM potassium phosphate buffer 50 mM potassium chloride ; ? mM conditions_1 0.05 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 [U-100% 15N] 5_SL4 RNA, 95% H2O/5% D2O' '95% H2O/5% D2O' 15N_sample solution ? 2 '500 uM [U-13C; U-15N]-Ura,Gua 5_SL4 RNA, 95% H2O/5% D2O' '95% H2O/5% D2O' G,U-13C,15N_sample solution ? 3 '500 uM [U-13C; U-15N]-Ade,Cyt 5_SL4 RNA, 95% H2O/5% D2O' '95% H2O/5% D2O' A,C-13C,15N_sample solution ? 4 '350 uM [U-13C; U-15N] 5_SL4sh RNA, 95% H2O/5% D2O' '95% H2O/5% D2O' '5_SL4sh 13C,15N_sample' solution 'sequence GGCACUCGGCUGCAUGCUUAGUGCC' 9 '1.8 mM 5_SL4sh RNA, 95% H2O/5% D2O' '95% H2O/5% D2O' '5_SL4sh unlabeled_sample' solution 'sequence GGCACUCGGCUGCAUGCUUAGUGCC' 5 '200 uM [U-13C; U-15N]-Ade,Cyt 5_SL4 RNA, 11.6 mg/mL unlabeled Pf1 phage, 95% H2O/5% D2O' '95% H2O/5% D2O' '5_SL4 A,C 13C,15N RDC' solution ? 7 '200 uM [U-13C; U-15N]-Gua,Ury 5_SL4 RNA, 11.6 uM unlabeled Pf1 phage, 95% H2O/5% D2O' '95% H2O/5% D2O' '5_SL4 G,U 13C,15N RDC' solution ? 6 '200 uM [U-13C; U-15N]-Ade,Cyt 5_SL4 RNA, 95% H2O/5% D2O' '95% H2O/5% D2O' '5_SL4 A,C 13C,15N RDC reference' solution ? 8 '200 uM [U-13C; U-15N]-Gua,Ura 5_SL4 RNA, 95% H2O/5% D2O' '95% H2O/5% D2O' '5_SL4 G,U 13C,15N RDC reference' solution ? # 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 'AVANCE NEO' ? Bruker 600 'TCI-N cryogenic probe' 2 'AVANCE III HD' ? Bruker 800 'TCI-N cryogenic probe' 3 'AVANCE II' ? Bruker 800 'TXO cryogenic probe' 4 AVANCE ? Bruker 600 'TCI-N cryogenic probe' 5 'AVANCE III HD' ? Bruker 700 'QCI-P cryogenic probe' 6 'AVANCE III HD' ? Bruker 600 'TCI-N cryoprobe prodigy' 7 'AVANCE III' ? Bruker 950 'TCI-N cryogenic probe' 8 'AVANCE NEO' ? Bruker 900 'TCI-N cryogenic Probe' # loop_ _pdbx_nmr_refine.entry_id _pdbx_nmr_refine.method _pdbx_nmr_refine.details _pdbx_nmr_refine.software_ordinal 8CQ1 na ? 1 8CQ1 na ? 3 8CQ1 'torsion angle dynamics' ? 2 8CQ1 'molecular dynamics' 'refinement in water' 4 # _pdbx_nmr_ensemble.entry_id 8CQ1 _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _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 8CQ1 _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'target function' # loop_ _pdbx_nmr_software.ordinal _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors 1 collection TopSpin ? 'Bruker Biospin' 2 'structure calculation' CYANA ? 'Guntert, Mumenthaler and Wuthrich' 3 'chemical shift assignment' CARA ? 'Keller and Wuthrich' 4 refinement ARIA ? ;Linge, O'Donoghue and Nilges ; # _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 8CQ1 _exptl.crystals_number ? _exptl.details ? _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 8CQ1 _struct.title ;Stem-Loop 4 of the 5'-UTR of the SARS-CoV2 genomic RNA ; _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 8CQ1 _struct_keywords.text 'SARS-CoV2, Stem-Loop, 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 44 N3 ? ? A G 84 A C 127 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 44 O2 ? ? A G 84 A C 127 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 44 N4 ? ? A G 84 A C 127 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 43 N3 ? ? A G 85 A C 126 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 43 O2 ? ? A G 85 A C 126 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 43 N4 ? ? A G 85 A C 126 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 3 N1 ? ? ? 1_555 A C 42 N3 ? ? A G 86 A C 125 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 3 N2 ? ? ? 1_555 A C 42 O2 ? ? A G 86 A C 125 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 3 O6 ? ? ? 1_555 A C 42 N4 ? ? A G 86 A C 125 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A U 4 N3 ? ? ? 1_555 A G 41 O6 ? ? A U 87 A G 124 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog11 hydrog ? ? A U 4 O2 ? ? ? 1_555 A G 41 N1 ? ? A U 87 A G 124 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog12 hydrog ? ? A G 5 N1 ? ? ? 1_555 A C 40 N3 ? ? A G 88 A C 123 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 5 N2 ? ? ? 1_555 A C 40 O2 ? ? A G 88 A C 123 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 5 O6 ? ? ? 1_555 A C 40 N4 ? ? A G 88 A C 123 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A U 6 N3 ? ? ? 1_555 A A 39 N1 ? ? A U 89 A A 122 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A U 6 O4 ? ? ? 1_555 A A 39 N6 ? ? A U 89 A A 122 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 7 N1 ? ? ? 1_555 A C 38 N3 ? ? A G 90 A C 121 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 7 N2 ? ? ? 1_555 A C 38 O2 ? ? A G 90 A C 121 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 7 O6 ? ? ? 1_555 A C 38 N4 ? ? A G 90 A C 121 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 8 N1 ? ? ? 1_555 A U 37 O2 ? ? A G 91 A U 120 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog21 hydrog ? ? A G 8 O6 ? ? ? 1_555 A U 37 N3 ? ? A G 91 A U 120 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog22 hydrog ? ? A U 10 N3 ? ? ? 1_555 A A 35 N1 ? ? A U 93 A A 118 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A U 10 O4 ? ? ? 1_555 A A 35 N6 ? ? A U 93 A A 118 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 11 N1 ? ? ? 1_555 A C 34 N3 ? ? A G 94 A C 117 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 11 N2 ? ? ? 1_555 A C 34 O2 ? ? A G 94 A C 117 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 11 O6 ? ? ? 1_555 A C 34 N4 ? ? A G 94 A C 117 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 13 N3 ? ? ? 1_555 A G 33 N1 ? ? A C 96 A G 116 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 13 N4 ? ? ? 1_555 A G 33 O6 ? ? A C 96 A G 116 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A C 13 O2 ? ? ? 1_555 A G 33 N2 ? ? A C 96 A G 116 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A A 14 N1 ? ? ? 1_555 A U 32 N3 ? ? A A 97 A U 115 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A A 14 N6 ? ? ? 1_555 A U 32 O4 ? ? A A 97 A U 115 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A C 15 N3 ? ? ? 1_555 A G 31 N1 ? ? A C 98 A G 114 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A C 15 N4 ? ? ? 1_555 A G 31 O6 ? ? A C 98 A G 114 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A C 15 O2 ? ? ? 1_555 A G 31 N2 ? ? A C 98 A G 114 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A U 16 N3 ? ? ? 1_555 A A 30 N1 ? ? A U 99 A A 113 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A U 16 O4 ? ? ? 1_555 A A 30 N6 ? ? A U 99 A A 113 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A C 17 N4 ? ? ? 1_555 A U 29 O4 ? ? A C 100 A U 112 1_555 ? ? ? ? ? ? 'C-U MISPAIR' ? ? ? hydrog38 hydrog ? ? A G 18 N1 ? ? ? 1_555 A U 28 O2 ? ? A G 101 A U 111 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog39 hydrog ? ? A G 18 O6 ? ? ? 1_555 A U 28 N3 ? ? A G 101 A U 111 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog40 hydrog ? ? A G 19 N1 ? ? ? 1_555 A C 27 N3 ? ? A G 102 A C 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A G 19 N2 ? ? ? 1_555 A C 27 O2 ? ? A G 102 A C 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A G 19 O6 ? ? ? 1_555 A C 27 N4 ? ? A G 102 A C 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A C 20 N3 ? ? ? 1_555 A G 26 N1 ? ? A C 103 A G 109 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A C 20 N4 ? ? ? 1_555 A G 26 O6 ? ? A C 103 A G 109 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A C 20 O2 ? ? ? 1_555 A G 26 N2 ? ? A C 103 A G 109 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 8CQ1 _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 84 84 G G A . n A 1 2 G 2 85 85 G G A . n A 1 3 G 3 86 86 G G A . n A 1 4 U 4 87 87 U U A . n A 1 5 G 5 88 88 G G A . n A 1 6 U 6 89 89 U U A . n A 1 7 G 7 90 90 G G A . n A 1 8 G 8 91 91 G G A . n A 1 9 C 9 92 92 C C A . n A 1 10 U 10 93 93 U U A . n A 1 11 G 11 94 94 G G A . n A 1 12 U 12 95 95 U U A . n A 1 13 C 13 96 96 C C A . n A 1 14 A 14 97 97 A A A . n A 1 15 C 15 98 98 C C A . n A 1 16 U 16 99 99 U U A . n A 1 17 C 17 100 100 C C A . n A 1 18 G 18 101 101 G G A . n A 1 19 G 19 102 102 G G A . n A 1 20 C 20 103 103 C C A . n A 1 21 U 21 104 104 U U A . n A 1 22 G 22 105 105 G G A . n A 1 23 C 23 106 106 C C A . n A 1 24 A 24 107 107 A A A . n A 1 25 U 25 108 108 U U A . n A 1 26 G 26 109 109 G G A . n A 1 27 C 27 110 110 C C A . n A 1 28 U 28 111 111 U U A . n A 1 29 U 29 112 112 U U A . n A 1 30 A 30 113 113 A A A . n A 1 31 G 31 114 114 G G A . n A 1 32 U 32 115 115 U U A . n A 1 33 G 33 116 116 G G A . n A 1 34 C 34 117 117 C C A . n A 1 35 A 35 118 118 A A A . n A 1 36 C 36 119 119 C C A . n A 1 37 U 37 120 120 U U A . n A 1 38 C 38 121 121 C C A . n A 1 39 A 39 122 122 A A A . n A 1 40 C 40 123 123 C C A . n A 1 41 G 41 124 124 G G A . n A 1 42 C 42 125 125 C C A . n A 1 43 C 43 126 126 C C A . n A 1 44 C 44 127 127 C C A . n # _pdbx_contact_author.id 2 _pdbx_contact_author.email Woehnert@bio.uni-frankfurt.de _pdbx_contact_author.name_first Jens _pdbx_contact_author.name_last Wohnert _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0001-7193-401X # _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 2023-09-20 2 'Structure model' 1 1 2023-10-18 3 'Structure model' 1 2 2023-11-22 # _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' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' citation 2 2 'Structure model' citation_author 3 3 'Structure model' 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.pdbx_database_id_PubMed' 2 2 'Structure model' '_citation.title' 3 2 'Structure model' '_citation_author.identifier_ORCID' 4 2 'Structure model' '_citation_author.name' 5 3 'Structure model' '_citation.journal_volume' 6 3 'Structure model' '_citation.page_first' 7 3 'Structure model' '_citation.page_last' # 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 '5_SL4 RNA' 500 ? uM '[U-100% 15N]' 2 '5_SL4 RNA' 500 ? uM '[U-13C; U-15N]-Ura,Gua' 3 '5_SL4 RNA' 500 ? uM '[U-13C; U-15N]-Ade,Cyt' 4 '5_SL4sh RNA' 350 ? uM '[U-13C; U-15N]' 9 '5_SL4sh RNA' 1.8 ? mM 'natural abundance' 5 '5_SL4 RNA' 200 ? uM '[U-13C; U-15N]-Ade,Cyt' 5 'Pf1 phage' 11.6 ? mg/mL unlabeled 7 '5_SL4 RNA' 200 ? uM '[U-13C; U-15N]-Gua,Ury' 7 'Pf1 phage' 11.6 ? uM unlabeled 6 '5_SL4 RNA' 200 ? uM '[U-13C; U-15N]-Ade,Cyt' 8 '5_SL4 RNA' 200 ? uM '[U-13C; U-15N]-Gua,Ura' # 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 6 "HO2'" A A 107 ? ? "O5'" A U 108 ? ? 1.60 2 7 "HO2'" A G 105 ? ? OP2 A C 106 ? ? 1.56 3 8 "HO2'" A A 107 ? ? "O5'" A U 108 ? ? 1.56 4 9 "HO2'" A A 107 ? ? "O5'" A U 108 ? ? 1.54 # 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 "C1'" A C 106 ? ? "O4'" A C 106 ? ? "C4'" A C 106 ? ? 104.36 109.70 -5.34 0.70 N 2 3 "C1'" A C 106 ? ? "O4'" A C 106 ? ? "C4'" A C 106 ? ? 103.84 109.70 -5.86 0.70 N 3 3 "C3'" A A 107 ? ? "C2'" A A 107 ? ? "C1'" A A 107 ? ? 97.05 101.30 -4.25 0.70 N 4 6 "C1'" A C 106 ? ? "O4'" A C 106 ? ? "C4'" A C 106 ? ? 105.00 109.70 -4.70 0.70 N 5 6 "C3'" A A 107 ? ? "C2'" A A 107 ? ? "C1'" A A 107 ? ? 96.76 101.30 -4.54 0.70 N 6 7 "C1'" A C 106 ? ? "O4'" A C 106 ? ? "C4'" A C 106 ? ? 105.46 109.70 -4.24 0.70 N 7 7 "C3'" A A 107 ? ? "O3'" A A 107 ? ? P A U 108 ? ? 127.08 119.70 7.38 1.20 Y 8 8 "C1'" A C 106 ? ? "O4'" A C 106 ? ? "C4'" A C 106 ? ? 105.47 109.70 -4.23 0.70 N 9 9 "C3'" A A 107 ? ? "O3'" A A 107 ? ? P A U 108 ? ? 127.16 119.70 7.46 1.20 Y 10 10 "C1'" A C 106 ? ? "O4'" A C 106 ? ? "C4'" A C 106 ? ? 104.33 109.70 -5.37 0.70 N # 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 A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 U OP3 O N N 111 U P P N N 112 U OP1 O N N 113 U OP2 O N N 114 U "O5'" O N N 115 U "C5'" C N N 116 U "C4'" C N R 117 U "O4'" O N N 118 U "C3'" C N S 119 U "O3'" O N N 120 U "C2'" C N R 121 U "O2'" O N N 122 U "C1'" C N R 123 U N1 N N N 124 U C2 C N N 125 U O2 O N N 126 U N3 N N N 127 U C4 C N N 128 U O4 O N N 129 U C5 C N N 130 U C6 C N N 131 U HOP3 H N N 132 U HOP2 H N N 133 U "H5'" H N N 134 U "H5''" H N N 135 U "H4'" H N N 136 U "H3'" H N N 137 U "HO3'" H N N 138 U "H2'" H N N 139 U "HO2'" H N N 140 U "H1'" H N N 141 U H3 H N N 142 U H5 H N N 143 U H6 H N N 144 # 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 A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 U OP3 P sing N N 116 U OP3 HOP3 sing N N 117 U P OP1 doub N N 118 U P OP2 sing N N 119 U P "O5'" sing N N 120 U OP2 HOP2 sing N N 121 U "O5'" "C5'" sing N N 122 U "C5'" "C4'" sing N N 123 U "C5'" "H5'" sing N N 124 U "C5'" "H5''" sing N N 125 U "C4'" "O4'" sing N N 126 U "C4'" "C3'" sing N N 127 U "C4'" "H4'" sing N N 128 U "O4'" "C1'" sing N N 129 U "C3'" "O3'" sing N N 130 U "C3'" "C2'" sing N N 131 U "C3'" "H3'" sing N N 132 U "O3'" "HO3'" sing N N 133 U "C2'" "O2'" sing N N 134 U "C2'" "C1'" sing N N 135 U "C2'" "H2'" sing N N 136 U "O2'" "HO2'" sing N N 137 U "C1'" N1 sing N N 138 U "C1'" "H1'" sing N N 139 U N1 C2 sing N N 140 U N1 C6 sing N N 141 U C2 O2 doub N N 142 U C2 N3 sing N N 143 U N3 C4 sing N N 144 U N3 H3 sing N N 145 U C4 O4 doub N N 146 U C4 C5 sing N N 147 U C5 C6 doub N N 148 U C5 H5 sing N N 149 U C6 H6 sing N N 150 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 8CQ1 'double helix' 8CQ1 'a-form double helix' 8CQ1 'hairpin loop' 8CQ1 'bulge loop' 8CQ1 '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 44 1_555 -0.271 -0.106 0.114 -1.782 -3.288 -4.082 1 A_G84:C127_A A 84 ? A 127 ? 19 1 1 A G 2 1_555 A C 43 1_555 -0.391 -0.158 0.164 2.500 -6.576 0.652 2 A_G85:C126_A A 85 ? A 126 ? 19 1 1 A G 3 1_555 A C 42 1_555 -0.028 -0.168 0.105 2.912 -7.074 -1.485 3 A_G86:C125_A A 86 ? A 125 ? 19 1 1 A U 4 1_555 A G 41 1_555 2.008 -0.430 -0.017 -3.323 -8.985 -3.929 4 A_U87:G124_A A 87 ? A 124 ? 28 1 1 A G 5 1_555 A C 40 1_555 0.036 -0.113 -0.283 -2.105 -9.596 3.223 5 A_G88:C123_A A 88 ? A 123 ? 19 1 1 A U 6 1_555 A A 39 1_555 0.163 -0.100 -0.208 1.795 -10.777 2.121 6 A_U89:A122_A A 89 ? A 122 ? 20 1 1 A G 7 1_555 A C 38 1_555 0.199 -0.141 -0.137 -7.784 -9.565 -0.069 7 A_G90:C121_A A 90 ? A 121 ? 19 1 1 A G 8 1_555 A U 37 1_555 -2.045 -0.371 -0.246 -0.760 1.399 3.229 8 A_G91:U120_A A 91 ? A 120 ? 28 1 1 A U 10 1_555 A A 35 1_555 0.218 -0.184 -0.145 1.186 -22.548 5.165 9 A_U93:A118_A A 93 ? A 118 ? 20 1 1 A G 11 1_555 A C 34 1_555 0.217 -0.091 -0.098 -8.448 -0.352 -3.268 10 A_G94:C117_A A 94 ? A 117 ? 19 1 1 A C 13 1_555 A G 33 1_555 -0.106 -0.035 -0.211 7.566 -1.926 -1.625 11 A_C96:G116_A A 96 ? A 116 ? 19 1 1 A A 14 1_555 A U 32 1_555 -0.207 -0.171 -0.105 -4.387 -13.002 5.136 12 A_A97:U115_A A 97 ? A 115 ? 20 1 1 A C 15 1_555 A G 31 1_555 -0.283 -0.068 -0.075 -0.489 -12.190 1.262 13 A_C98:G114_A A 98 ? A 114 ? 19 1 1 A U 16 1_555 A A 30 1_555 0.373 -0.107 0.471 -10.298 -0.616 -3.325 14 A_U99:A113_A A 99 ? A 113 ? 20 1 1 A C 17 1_555 A U 29 1_555 -0.247 -0.959 -0.329 11.825 -8.370 -13.478 15 A_C100:U112_A A 100 ? A 112 ? ? ? 1 A G 18 1_555 A U 28 1_555 -1.609 -0.372 0.326 0.720 -19.116 7.394 16 A_G101:U111_A A 101 ? A 111 ? 28 1 1 A G 19 1_555 A C 27 1_555 -0.280 -0.332 0.159 -4.559 -17.033 -3.535 17 A_G102:C110_A A 102 ? A 110 ? 19 1 1 A C 20 1_555 A G 26 1_555 0.270 -0.058 0.135 -5.995 -4.319 -3.298 18 A_C103:G109_A A 103 ? A 109 ? 19 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 44 1_555 A G 2 1_555 A C 43 1_555 0.341 -1.616 3.665 -1.429 -9.202 30.311 -0.939 -0.938 3.954 -17.099 2.656 31.677 1 AA_G84G85:C126C127_AA A 84 ? A 127 ? A 85 ? A 126 ? 1 A G 2 1_555 A C 43 1_555 A G 3 1_555 A C 42 1_555 -0.349 -1.960 3.385 -2.975 2.214 29.499 -4.293 0.045 3.252 4.326 5.814 29.726 2 AA_G85G86:C125C126_AA A 85 ? A 126 ? A 86 ? A 125 ? 1 A G 3 1_555 A C 42 1_555 A U 4 1_555 A G 41 1_555 -0.325 -1.774 3.541 2.707 4.413 42.931 -2.863 0.720 3.326 6.004 -3.683 43.228 3 AA_G86U87:G124C125_AA A 86 ? A 125 ? A 87 ? A 124 ? 1 A U 4 1_555 A G 41 1_555 A G 5 1_555 A C 40 1_555 0.874 -1.438 3.264 4.298 17.117 24.873 -5.795 -0.899 2.004 34.708 -8.716 30.418 4 AA_U87G88:C123G124_AA A 87 ? A 124 ? A 88 ? A 123 ? 1 A G 5 1_555 A C 40 1_555 A U 6 1_555 A A 39 1_555 0.485 -1.608 3.360 0.256 3.727 29.241 -3.954 -0.899 3.140 7.344 -0.504 29.474 5 AA_G88U89:A122C123_AA A 88 ? A 123 ? A 89 ? A 122 ? 1 A U 6 1_555 A A 39 1_555 A G 7 1_555 A C 38 1_555 -0.235 -1.209 3.588 0.805 18.144 34.553 -4.052 0.453 2.648 28.261 -1.254 38.906 6 AA_U89G90:C121A122_AA A 89 ? A 122 ? A 90 ? A 121 ? 1 A G 7 1_555 A C 38 1_555 A G 8 1_555 A U 37 1_555 0.402 -2.260 3.387 -0.268 2.207 19.613 -7.646 -1.302 3.111 6.452 0.783 19.737 7 AA_G90G91:U120C121_AA A 90 ? A 121 ? A 91 ? A 120 ? 1 A G 8 1_555 A U 37 1_555 A U 10 1_555 A A 35 1_555 -0.493 -3.139 6.619 -4.428 20.140 63.900 -4.368 0.114 5.545 18.529 4.074 66.808 8 AA_G91U93:A118U120_AA A 91 ? A 120 ? A 93 ? A 118 ? 1 A U 10 1_555 A A 35 1_555 A G 11 1_555 A C 34 1_555 -0.591 -1.645 3.557 1.349 21.125 30.565 -5.259 1.101 2.015 35.262 -2.252 37.035 9 AA_U93G94:C117A118_AA A 93 ? A 118 ? A 94 ? A 117 ? 1 A G 11 1_555 A C 34 1_555 A C 13 1_555 A G 33 1_555 -1.264 -1.093 3.179 0.333 3.909 37.239 -2.193 2.011 3.041 6.101 -0.520 37.438 10 AA_G94C96:G116C117_AA A 94 ? A 117 ? A 96 ? A 116 ? 1 A C 13 1_555 A G 33 1_555 A A 14 1_555 A U 32 1_555 -0.143 -1.875 3.532 -4.044 12.340 36.267 -4.373 -0.282 2.771 19.087 6.255 38.448 11 AA_C96A97:U115G116_AA A 96 ? A 116 ? A 97 ? A 115 ? 1 A A 14 1_555 A U 32 1_555 A C 15 1_555 A G 31 1_555 -0.302 -1.479 3.197 -0.233 7.676 32.144 -3.808 0.495 2.781 13.622 0.413 33.025 12 AA_A97C98:G114U115_AA A 97 ? A 115 ? A 98 ? A 114 ? 1 A C 15 1_555 A G 31 1_555 A U 16 1_555 A A 30 1_555 0.043 -1.920 3.454 -2.544 16.822 34.632 -4.860 -0.360 2.304 26.380 3.990 38.470 13 AA_C98U99:A113G114_AA A 98 ? A 114 ? A 99 ? A 113 ? 1 A U 16 1_555 A A 30 1_555 A C 17 1_555 A U 29 1_555 1.350 -2.270 3.292 7.341 -11.921 12.673 1.638 1.153 4.169 -40.914 -25.196 18.863 14 AA_U99C100:U112A113_AA A 99 ? A 113 ? A 100 ? A 112 ? 1 A C 17 1_555 A U 29 1_555 A G 18 1_555 A U 28 1_555 1.971 -1.323 3.390 -2.026 18.303 32.923 -4.257 -3.302 2.252 29.590 3.275 37.599 15 AA_C100G101:U111U112_AA A 100 ? A 112 ? A 101 ? A 111 ? 1 A G 18 1_555 A U 28 1_555 A G 19 1_555 A C 27 1_555 -1.355 -1.659 3.193 -7.152 10.015 40.205 -3.309 1.182 2.907 14.172 10.120 41.972 16 AA_G101G102:C110U111_AA A 101 ? A 111 ? A 102 ? A 110 ? 1 A G 19 1_555 A C 27 1_555 A C 20 1_555 A G 26 1_555 0.381 -1.800 3.343 3.041 7.594 37.909 -3.620 -0.212 2.962 11.526 -4.616 38.750 17 AA_G102C103:G109C110_AA A 102 ? A 110 ? A 103 ? A 109 ? # _pdbx_audit_support.funding_organization 'German Research Foundation (DFG)' _pdbx_audit_support.country Germany _pdbx_audit_support.grant_number CRC902 _pdbx_audit_support.ordinal 1 # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support SAXS _pdbx_struct_assembly_auth_evidence.details ? #