data_9A9V # _entry.id 9A9V # loop_ _atom_type.symbol C H N O P # loop_ _audit_author.name _audit_author.pdbx_ordinal "Szewczyk, M." 1 "Loharch, S." 2 "Lopez-Nunez, S." 3 "Gallego J." 4 # loop_ _audit_conform.dict_location _audit_conform.dict_name _audit_conform.dict_version https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_ihm_ext.dic mmcif_ihm_ext.dic 1.28 http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic mmcif_pdbx.dic 5.403 # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 9A9V _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2025-05-06 # 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 2025-11-05 # _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 ? # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 9A9V pdb_00009a9v 10.2210/pdb9a9v/pdb # loop_ _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.type "C10 H14 N5 O7 P" 347.224 A . "ADENOSINE-5'-MONOPHOSPHATE" . "RNA linking" "C9 H14 N3 O8 P" 323.198 C . "CYTIDINE-5'-MONOPHOSPHATE" . "RNA linking" "C10 H14 N5 O8 P" 363.223 G . "GUANOSINE-5'-MONOPHOSPHATE" . "RNA linking" "C9 H13 N2 O9 P" 324.182 U . "URIDINE-5'-MONOPHOSPHATE" . "RNA linking" # _citation.country . _citation.id 1 _citation.journal_abbrev J.Mol.Biol. _citation.journal_id_ASTM . _citation.journal_id_CSD . _citation.journal_id_ISSN . _citation.journal_issue 24 _citation.journal_volume 437 _citation.page_first . _citation.page_last . _citation.pdbx_database_id_DOI 10.1016/j.jmb.2025.169451 _citation.pdbx_database_id_PubMed 40976347 _citation.title "Insights About the Structure and Recognition Mechanism of the Rev Response Element of HIV-1 Revealed by FRET-monitored Mutagenesis and Modeling" _citation.year 2025 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal 1 "Szewczyk, M.P." 1 1 "Loharch, S." 2 1 "Lopez-Nunez, S." 3 1 "Gallego J." 4 # _entity.details . _entity.formula_weight 79866.79 _entity.id 1 _entity.pdbx_description "RNA (234-MER)" _entity.pdbx_number_of_molecules 1 _entity.src_method MAN _entity.type POLYMER # _entity_name_com.entity_id 1 _entity_name_com.name "Rev Recognition Element (RRE) of HIV-1 genomic RNA (subtype B, isolate ARV-2/SF2)" # _entity_poly.entity_id 1 _entity_poly.nstd_chirality . _entity_poly.nstd_linkage NO _entity_poly.nstd_monomer NO _entity_poly.pdbx_seq_one_letter_code GGGAGCUUUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGUGUCAUUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAACAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCC _entity_poly.pdbx_seq_one_letter_code_can GGGAGCUUUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGUGUCAUUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAACAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCC _entity_poly.pdbx_sequence_evidence_code . _entity_poly.pdbx_strand_id A _entity_poly.type polyribonucleotide # loop_ _entity_poly_seq.entity_id _entity_poly_seq.hetero _entity_poly_seq.mon_id _entity_poly_seq.num 1 . G 1 1 . G 2 1 . G 3 1 . A 4 1 . G 5 1 . C 6 1 . U 7 1 . U 8 1 . U 9 1 . G 10 1 . U 11 1 . U 12 1 . C 13 1 . C 14 1 . U 15 1 . U 16 1 . G 17 1 . G 18 1 . G 19 1 . U 20 1 . U 21 1 . C 22 1 . U 23 1 . U 24 1 . G 25 1 . G 26 1 . G 27 1 . A 28 1 . G 29 1 . C 30 1 . A 31 1 . G 32 1 . C 33 1 . A 34 1 . G 35 1 . G 36 1 . A 37 1 . A 38 1 . G 39 1 . C 40 1 . A 41 1 . C 42 1 . U 43 1 . A 44 1 . U 45 1 . G 46 1 . G 47 1 . G 48 1 . C 49 1 . G 50 1 . C 51 1 . A 52 1 . G 53 1 . U 54 1 . G 55 1 . U 56 1 . C 57 1 . A 58 1 . U 59 1 . U 60 1 . G 61 1 . A 62 1 . C 63 1 . G 64 1 . C 65 1 . U 66 1 . G 67 1 . A 68 1 . C 69 1 . G 70 1 . G 71 1 . U 72 1 . A 73 1 . C 74 1 . A 75 1 . G 76 1 . G 77 1 . C 78 1 . C 79 1 . A 80 1 . G 81 1 . A 82 1 . C 83 1 . A 84 1 . A 85 1 . U 86 1 . U 87 1 . A 88 1 . U 89 1 . U 90 1 . G 91 1 . U 92 1 . C 93 1 . U 94 1 . G 95 1 . G 96 1 . U 97 1 . A 98 1 . U 99 1 . A 100 1 . G 101 1 . U 102 1 . G 103 1 . C 104 1 . A 105 1 . A 106 1 . C 107 1 . A 108 1 . G 109 1 . C 110 1 . A 111 1 . G 112 1 . A 113 1 . A 114 1 . C 115 1 . A 116 1 . A 117 1 . U 118 1 . U 119 1 . U 120 1 . G 121 1 . C 122 1 . U 123 1 . G 124 1 . A 125 1 . G 126 1 . G 127 1 . G 128 1 . C 129 1 . U 130 1 . A 131 1 . U 132 1 . U 133 1 . G 134 1 . A 135 1 . G 136 1 . G 137 1 . C 138 1 . G 139 1 . C 140 1 . A 141 1 . A 142 1 . C 143 1 . A 144 1 . A 145 1 . C 146 1 . A 147 1 . U 148 1 . C 149 1 . U 150 1 . G 151 1 . U 152 1 . U 153 1 . G 154 1 . C 155 1 . A 156 1 . A 157 1 . C 158 1 . U 159 1 . C 160 1 . A 161 1 . C 162 1 . A 163 1 . G 164 1 . U 165 1 . C 166 1 . U 167 1 . G 168 1 . G 169 1 . G 170 1 . G 171 1 . C 172 1 . A 173 1 . U 174 1 . C 175 1 . A 176 1 . A 177 1 . G 178 1 . C 179 1 . A 180 1 . G 181 1 . C 182 1 . U 183 1 . C 184 1 . C 185 1 . A 186 1 . G 187 1 . G 188 1 . C 189 1 . A 190 1 . A 191 1 . G 192 1 . A 193 1 . G 194 1 . U 195 1 . C 196 1 . C 197 1 . U 198 1 . G 199 1 . G 200 1 . C 201 1 . U 202 1 . G 203 1 . U 204 1 . G 205 1 . G 206 1 . A 207 1 . A 208 1 . A 209 1 . G 210 1 . A 211 1 . U 212 1 . A 213 1 . C 214 1 . C 215 1 . U 216 1 . A 217 1 . A 218 1 . A 219 1 . G 220 1 . G 221 1 . A 222 1 . U 223 1 . C 224 1 . A 225 1 . A 226 1 . C 227 1 . A 228 1 . G 229 1 . C 230 1 . U 231 1 . C 232 1 . C 233 1 . C 234 # _ihm_dataset_external_reference.dataset_list_id 1 _ihm_dataset_external_reference.file_id 1 _ihm_dataset_external_reference.id 1 # _ihm_dataset_group.application . _ihm_dataset_group.details . _ihm_dataset_group.id 1 _ihm_dataset_group.name . # loop_ _ihm_dataset_group_link.dataset_list_id _ihm_dataset_group_link.group_id 1 1 2 1 # loop_ _ihm_dataset_list.data_type _ihm_dataset_list.database_hosted _ihm_dataset_list.details _ihm_dataset_list.id "Ensemble FRET data" NO "Steady-state FRET ratio A values obtained for the Rev Response Element (RRE) of HIV-1 as a function of magnesium concentration and changes in helix IIA length and junction IIA-IIB-IIC and I-II-III-IV nucleotides" 1 "Predicted contacts" NO "Predicted contacts are based on RRE base-pairings derived from a previous SHAPE study (Bai et al. Elife 3, e03656, 2014)." 2 # _ihm_derived_distance_restraint.dataset_list_id 1 _ihm_derived_distance_restraint.distance_lower_limit 50 _ihm_derived_distance_restraint.distance_lower_limit_esd . _ihm_derived_distance_restraint.distance_threshold_esd . _ihm_derived_distance_restraint.distance_threshold_mean . _ihm_derived_distance_restraint.distance_upper_limit 70 _ihm_derived_distance_restraint.distance_upper_limit_esd . _ihm_derived_distance_restraint.feature_id_1 1 _ihm_derived_distance_restraint.feature_id_2 2 _ihm_derived_distance_restraint.group_conditionality . _ihm_derived_distance_restraint.group_id 1 _ihm_derived_distance_restraint.id 1 _ihm_derived_distance_restraint.mic_value . _ihm_derived_distance_restraint.probability . _ihm_derived_distance_restraint.random_exclusion_fraction . _ihm_derived_distance_restraint.restraint_type "lower and upper bound" # _ihm_entity_poly_segment.comp_id_begin G _ihm_entity_poly_segment.comp_id_end C _ihm_entity_poly_segment.entity_id 1 _ihm_entity_poly_segment.id 1 _ihm_entity_poly_segment.seq_id_begin 1 _ihm_entity_poly_segment.seq_id_end 234 # _ihm_external_files.content_type "Input data or restraints" _ihm_external_files.details . _ihm_external_files.file_format . _ihm_external_files.file_path . _ihm_external_files.file_size_bytes . _ihm_external_files.id 1 _ihm_external_files.reference_id 1 # _ihm_external_reference_info.associated_url https://zenodo.org/records/17380954/files/FRET-data-final.zip _ihm_external_reference_info.details "Fluorescence Resonance Energy Transfer (FRET) data of wild-type and mutant sequences of the Rev Response RNA Element of HIV-1" _ihm_external_reference_info.reference 10.5281/zenodo.17380954 _ihm_external_reference_info.reference_id 1 _ihm_external_reference_info.reference_provider . _ihm_external_reference_info.reference_type DOI _ihm_external_reference_info.refers_to Archive # loop_ _ihm_feature_list.details _ihm_feature_list.entity_type _ihm_feature_list.feature_id _ihm_feature_list.feature_type . polymer 1 atom . polymer 2 atom # _ihm_model_group.details . _ihm_model_group.id 1 _ihm_model_group.name . # _ihm_model_group_link.group_id 1 _ihm_model_group_link.model_id 1 # _ihm_model_list.assembly_id 1 _ihm_model_list.model_id 1 _ihm_model_list.model_name . _ihm_model_list.protocol_id 1 _ihm_model_list.representation_id 1 # _ihm_model_representation.details "No starting models were used" _ihm_model_representation.id 1 _ihm_model_representation.name . # _ihm_model_representation_details.description . _ihm_model_representation_details.entity_asym_id A _ihm_model_representation_details.entity_description "RNA (234-MER)" _ihm_model_representation_details.entity_id 1 _ihm_model_representation_details.entity_poly_segment_id 1 _ihm_model_representation_details.id 1 _ihm_model_representation_details.model_granularity by-atom _ihm_model_representation_details.model_mode flexible _ihm_model_representation_details.model_object_count . _ihm_model_representation_details.model_object_primitive atomistic _ihm_model_representation_details.representation_id 1 _ihm_model_representation_details.starting_model_id . # _ihm_modeling_protocol.details . _ihm_modeling_protocol.id 1 _ihm_modeling_protocol.num_steps 1 _ihm_modeling_protocol.protocol_name "Mutagenesis and FRET-guided selection from FARFAR2-generated model ensemble" # _ihm_modeling_protocol_details.dataset_group_id 1 _ihm_modeling_protocol_details.description "An ensemble of 89,187 all-atom models of the 234-nt ARV-2/SF2 RRE structure was generated using the Rosetta 3.13 FARFAR2 algorithm. The calculations employed 20,000 Monte Carlo cycles per model with default parameters and used RRE base-pairings derived from a previous SHAPE study (Bai et al. Elife 3, e03656, 2014) as the only restraint. The models were scored with the rna_res_level_energy4 function and a set of 400 lowest-energy models was selected from the ensemble. The separation between subdomains IA and IIB, experimentally determined by FRET, was assessed by measuring the distance between A58 O2' and A219 C4', located close to the cy5 and cy3 fluorophores, respectively, in the cy3/cy5-labeled RRE construct. The model deposited in this entry was selected from a subset of 34 low-energy models exhibiting a subdomain IA-IIB separation distance consistent with the experimental FRET ratios (50-70 A)." _ihm_modeling_protocol_details.ensemble_flag NO _ihm_modeling_protocol_details.id 1 _ihm_modeling_protocol_details.multi_scale_flag NO _ihm_modeling_protocol_details.multi_state_flag NO _ihm_modeling_protocol_details.num_models_begin . _ihm_modeling_protocol_details.num_models_end . _ihm_modeling_protocol_details.ordered_flag NO _ihm_modeling_protocol_details.protocol_id 1 _ihm_modeling_protocol_details.script_file_id 1 _ihm_modeling_protocol_details.software_id 1 _ihm_modeling_protocol_details.step_id 1 _ihm_modeling_protocol_details.step_method . _ihm_modeling_protocol_details.step_name . _ihm_modeling_protocol_details.struct_assembly_description . _ihm_modeling_protocol_details.struct_assembly_id 1 # loop_ _ihm_poly_atom_feature.asym_id _ihm_poly_atom_feature.atom_id _ihm_poly_atom_feature.comp_id _ihm_poly_atom_feature.entity_id _ihm_poly_atom_feature.feature_id _ihm_poly_atom_feature.ordinal_id _ihm_poly_atom_feature.seq_id A "O2'" A 1 1 1 58 A "C4'" A 1 2 2 219 # loop_ _ihm_predicted_contact_restraint.asym_id_1 _ihm_predicted_contact_restraint.asym_id_2 _ihm_predicted_contact_restraint.comp_id_1 _ihm_predicted_contact_restraint.comp_id_2 _ihm_predicted_contact_restraint.dataset_list_id _ihm_predicted_contact_restraint.distance_lower_limit _ihm_predicted_contact_restraint.distance_upper_limit _ihm_predicted_contact_restraint.entity_description_1 _ihm_predicted_contact_restraint.entity_description_2 _ihm_predicted_contact_restraint.entity_id_1 _ihm_predicted_contact_restraint.entity_id_2 _ihm_predicted_contact_restraint.group_id _ihm_predicted_contact_restraint.id _ihm_predicted_contact_restraint.model_granularity _ihm_predicted_contact_restraint.probability _ihm_predicted_contact_restraint.rep_atom_1 _ihm_predicted_contact_restraint.rep_atom_2 _ihm_predicted_contact_restraint.restraint_type _ihm_predicted_contact_restraint.seq_id_1 _ihm_predicted_contact_restraint.seq_id_2 _ihm_predicted_contact_restraint.software_id A A G C 2 . 3.5 . . 1 1 1 1 by-residue . . . "upper bound" 1 234 . A A G C 2 . 3.5 . . 1 1 1 2 by-residue . . . "upper bound" 2 233 . A A G C 2 . 3.5 . . 1 1 1 3 by-residue . . . "upper bound" 3 232 . A A A U 2 . 3.5 . . 1 1 1 4 by-residue . . . "upper bound" 4 231 . A A G C 2 . 3.5 . . 1 1 1 5 by-residue . . . "upper bound" 5 230 . A A C G 2 . 3.5 . . 1 1 1 6 by-residue . . . "upper bound" 6 229 . A A U A 2 . 3.5 . . 1 1 1 7 by-residue . . . "upper bound" 7 228 . A A U A 2 . 3.5 . . 1 1 1 8 by-residue . . . "upper bound" 8 226 . A A U A 2 . 3.5 . . 1 1 1 9 by-residue . . . "upper bound" 9 225 . A A G C 2 . 3.5 . . 1 1 1 10 by-residue . . . "upper bound" 10 224 . A A U A 2 . 3.5 . . 1 1 1 11 by-residue . . . "upper bound" 12 222 . A A C G 2 . 3.5 . . 1 1 1 12 by-residue . . . "upper bound" 13 221 . A A C G 2 . 3.5 . . 1 1 1 13 by-residue . . . "upper bound" 14 220 . A A U A 2 . 3.5 . . 1 1 1 14 by-residue . . . "upper bound" 15 219 . A A U A 2 . 3.5 . . 1 1 1 15 by-residue . . . "upper bound" 16 218 . A A G U 2 . 3.5 . . 1 1 1 16 by-residue . . . "upper bound" 17 216 . A A G C 2 . 3.5 . . 1 1 1 17 by-residue . . . "upper bound" 18 215 . A A G C 2 . 3.5 . . 1 1 1 18 by-residue . . . "upper bound" 19 214 . A A U A 2 . 3.5 . . 1 1 1 19 by-residue . . . "upper bound" 20 213 . A A U A 2 . 3.5 . . 1 1 1 20 by-residue . . . "upper bound" 21 211 . A A C G 2 . 3.5 . . 1 1 1 21 by-residue . . . "upper bound" 22 210 . A A U A 2 . 3.5 . . 1 1 1 22 by-residue . . . "upper bound" 23 209 . A A U A 2 . 3.5 . . 1 1 1 23 by-residue . . . "upper bound" 24 208 . A A G U 2 . 3.5 . . 1 1 1 24 by-residue . . . "upper bound" 29 204 . A A C G 2 . 3.5 . . 1 1 1 25 by-residue . . . "upper bound" 30 203 . A A A U 2 . 3.5 . . 1 1 1 26 by-residue . . . "upper bound" 31 202 . A A G C 2 . 3.5 . . 1 1 1 27 by-residue . . . "upper bound" 32 201 . A A C G 2 . 3.5 . . 1 1 1 28 by-residue . . . "upper bound" 33 200 . A A G C 2 . 3.5 . . 1 1 1 29 by-residue . . . "upper bound" 39 104 . A A C G 2 . 3.5 . . 1 1 1 30 by-residue . . . "upper bound" 40 103 . A A A U 2 . 3.5 . . 1 1 1 31 by-residue . . . "upper bound" 41 102 . A A C G 2 . 3.5 . . 1 1 1 32 by-residue . . . "upper bound" 42 101 . A A U A 2 . 3.5 . . 1 1 1 33 by-residue . . . "upper bound" 43 100 . A A A U 2 . 3.5 . . 1 1 1 34 by-residue . . . "upper bound" 44 99 . A A U A 2 . 3.5 . . 1 1 1 35 by-residue . . . "upper bound" 45 75 . A A G C 2 . 3.5 . . 1 1 1 36 by-residue . . . "upper bound" 46 74 . A A C G 2 . 3.5 . . 1 1 1 37 by-residue . . . "upper bound" 49 70 . A A G C 2 . 3.5 . . 1 1 1 38 by-residue . . . "upper bound" 50 69 . A A C G 2 . 3.5 . . 1 1 1 39 by-residue . . . "upper bound" 51 67 . A A A U 2 . 3.5 . . 1 1 1 40 by-residue . . . "upper bound" 52 66 . A A G C 2 . 3.5 . . 1 1 1 41 by-residue . . . "upper bound" 53 65 . A A U G 2 . 3.5 . . 1 1 1 42 by-residue . . . "upper bound" 54 64 . A A G C 2 . 3.5 . . 1 1 1 43 by-residue . . . "upper bound" 55 63 . A A U A 2 . 3.5 . . 1 1 1 44 by-residue . . . "upper bound" 56 62 . A A C G 2 . 3.5 . . 1 1 1 45 by-residue . . . "upper bound" 57 61 . A A G U 2 . 3.5 . . 1 1 1 46 by-residue . . . "upper bound" 77 97 . A A C G 2 . 3.5 . . 1 1 1 47 by-residue . . . "upper bound" 78 96 . A A C G 2 . 3.5 . . 1 1 1 48 by-residue . . . "upper bound" 79 95 . A A A U 2 . 3.5 . . 1 1 1 49 by-residue . . . "upper bound" 80 94 . A A G C 2 . 3.5 . . 1 1 1 50 by-residue . . . "upper bound" 81 93 . A A A U 2 . 3.5 . . 1 1 1 51 by-residue . . . "upper bound" 82 92 . A A C G 2 . 3.5 . . 1 1 1 52 by-residue . . . "upper bound" 83 91 . A A A U 2 . 3.5 . . 1 1 1 53 by-residue . . . "upper bound" 84 90 . A A A U 2 . 3.5 . . 1 1 1 54 by-residue . . . "upper bound" 85 89 . A A C G 2 . 3.5 . . 1 1 1 55 by-residue . . . "upper bound" 107 124 . A A A U 2 . 3.5 . . 1 1 1 56 by-residue . . . "upper bound" 108 123 . A A G C 2 . 3.5 . . 1 1 1 57 by-residue . . . "upper bound" 109 122 . A A C G 2 . 3.5 . . 1 1 1 58 by-residue . . . "upper bound" 110 121 . A A A U 2 . 3.5 . . 1 1 1 59 by-residue . . . "upper bound" 111 120 . A A G U 2 . 3.5 . . 1 1 1 60 by-residue . . . "upper bound" 112 119 . A A A U 2 . 3.5 . . 1 1 1 61 by-residue . . . "upper bound" 113 118 . A A A U 2 . 3.5 . . 1 1 1 62 by-residue . . . "upper bound" 125 198 . A A G C 2 . 3.5 . . 1 1 1 63 by-residue . . . "upper bound" 126 197 . A A G C 2 . 3.5 . . 1 1 1 64 by-residue . . . "upper bound" 127 196 . A A G U 2 . 3.5 . . 1 1 1 65 by-residue . . . "upper bound" 128 195 . A A C G 2 . 3.5 . . 1 1 1 66 by-residue . . . "upper bound" 129 194 . A A U A 2 . 3.5 . . 1 1 1 67 by-residue . . . "upper bound" 130 193 . A A U A 2 . 3.5 . . 1 1 1 68 by-residue . . . "upper bound" 133 161 . A A G C 2 . 3.5 . . 1 1 1 69 by-residue . . . "upper bound" 134 160 . A A A U 2 . 3.5 . . 1 1 1 70 by-residue . . . "upper bound" 135 159 . A A G C 2 . 3.5 . . 1 1 1 71 by-residue . . . "upper bound" 136 158 . A A G C 2 . 3.5 . . 1 1 1 72 by-residue . . . "upper bound" 139 155 . A A C G 2 . 3.5 . . 1 1 1 73 by-residue . . . "upper bound" 140 154 . A A A U 2 . 3.5 . . 1 1 1 74 by-residue . . . "upper bound" 141 153 . A A A U 2 . 3.5 . . 1 1 1 75 by-residue . . . "upper bound" 142 152 . A A C G 2 . 3.5 . . 1 1 1 76 by-residue . . . "upper bound" 143 151 . A A A U 2 . 3.5 . . 1 1 1 77 by-residue . . . "upper bound" 144 150 . A A G C 2 . 3.5 . . 1 1 1 78 by-residue . . . "upper bound" 164 189 . A A U G 2 . 3.5 . . 1 1 1 79 by-residue . . . "upper bound" 165 188 . A A C G 2 . 3.5 . . 1 1 1 80 by-residue . . . "upper bound" 166 187 . A A U A 2 . 3.5 . . 1 1 1 81 by-residue . . . "upper bound" 167 186 . A A G C 2 . 3.5 . . 1 1 1 82 by-residue . . . "upper bound" 168 185 . A A G C 2 . 3.5 . . 1 1 1 83 by-residue . . . "upper bound" 169 184 . A A G U 2 . 3.5 . . 1 1 1 84 by-residue . . . "upper bound" 170 183 . A A G C 2 . 3.5 . . 1 1 1 85 by-residue . . . "upper bound" 171 182 . A A C G 2 . 3.5 . . 1 1 1 86 by-residue . . . "upper bound" 172 181 . # _ihm_struct_assembly.description "All-atom model of the Rev Response RNA Element of HIV-1 generated by mutagenesis- and FRET-guided FARFAR2 model selection" _ihm_struct_assembly.id 1 _ihm_struct_assembly.name "Rev Response RNA Element of HIV-1" # _ihm_struct_assembly_details.assembly_id 1 _ihm_struct_assembly_details.asym_id A _ihm_struct_assembly_details.entity_description "RNA (234-MER)" _ihm_struct_assembly_details.entity_id 1 _ihm_struct_assembly_details.entity_poly_segment_id 1 _ihm_struct_assembly_details.id 1 _ihm_struct_assembly_details.parent_assembly_id 1 # _software.citation_id . _software.classification "Model building" _software.description . _software.location https://rosettacommons.org/software/ _software.name Rosetta _software.pdbx_ordinal 1 _software.type package _software.version "3.13 FARFAR2" # _struct.entry_id 9A9V _struct.pdbx_CASP_flag . _struct.pdbx_descriptor . _struct.pdbx_details . _struct.pdbx_model_details ;MODEL GENERATED BY ROSETTA VERSION 2024.09+release.06b3cf8 ; _struct.pdbx_model_type_details . _struct.pdbx_structure_determination_methodology integrative _struct.title "All-atom model of the Rev Response RNA Element of HIV-1 generated by mutagenesis- and FRET-guided FARFAR2 model selection." # _struct_asym.details . _struct_asym.entity_id 1 _struct_asym.id A _struct_asym.pdbx_PDB_id . _struct_asym.pdbx_alt_id . _struct_asym.pdbx_blank_PDB_chainid_flag . _struct_asym.pdbx_modified . _struct_asym.pdbx_order . _struct_asym.pdbx_type . # _struct_ref.db_code K02007 _struct_ref.db_name GB _struct_ref.details . _struct_ref.entity_id 1 _struct_ref.id 1 _struct_ref.pdbx_align_begin . _struct_ref.pdbx_align_end . _struct_ref.pdbx_db_accession K02007 _struct_ref.pdbx_db_isoform . _struct_ref.pdbx_seq_one_letter_code . # _struct_ref_seq.align_id 1 _struct_ref_seq.db_align_beg 7774 _struct_ref_seq.db_align_end 8007 _struct_ref_seq.ref_id 1 _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.seq_align_end 234 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.details _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_ordinal _struct_ref_seq_dif.seq_num 1 A "modified residue" G 1 1 1 T "modified residue" C 2 234 1 A variant U 3 8 1 G variant A 4 219 # 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.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 A 1 1 G 1 1 G G A . A 1 2 G 2 2 G G A . A 1 3 G 3 3 G G A . A 1 4 A 4 4 A A A . A 1 5 G 5 5 G G A . A 1 6 C 6 6 C C A . A 1 7 U 7 7 U U A . A 1 8 U 8 8 U U A . A 1 9 U 9 9 U U A . A 1 10 G 10 10 G G A . A 1 11 U 11 11 U U A . A 1 12 U 12 12 U U A . A 1 13 C 13 13 C C A . A 1 14 C 14 14 C C A . A 1 15 U 15 15 U U A . A 1 16 U 16 16 U U A . A 1 17 G 17 17 G G A . A 1 18 G 18 18 G G A . A 1 19 G 19 19 G G A . A 1 20 U 20 20 U U A . A 1 21 U 21 21 U U A . A 1 22 C 22 22 C C A . A 1 23 U 23 23 U U A . A 1 24 U 24 24 U U A . A 1 25 G 25 25 G G A . A 1 26 G 26 26 G G A . A 1 27 G 27 27 G G A . A 1 28 A 28 28 A A A . A 1 29 G 29 29 G G A . A 1 30 C 30 30 C C A . A 1 31 A 31 31 A A A . A 1 32 G 32 32 G G A . A 1 33 C 33 33 C C A . A 1 34 A 34 34 A A A . A 1 35 G 35 35 G G A . A 1 36 G 36 36 G G A . A 1 37 A 37 37 A A A . A 1 38 A 38 38 A A A . A 1 39 G 39 39 G G A . A 1 40 C 40 40 C C A . A 1 41 A 41 41 A A A . A 1 42 C 42 42 C C A . A 1 43 U 43 43 U U A . A 1 44 A 44 44 A A A . A 1 45 U 45 45 U U A . A 1 46 G 46 46 G G A . A 1 47 G 47 47 G G A . A 1 48 G 48 48 G G A . A 1 49 C 49 49 C C A . A 1 50 G 50 50 G G A . A 1 51 C 51 51 C C A . A 1 52 A 52 52 A A A . A 1 53 G 53 53 G G A . A 1 54 U 54 54 U U A . A 1 55 G 55 55 G G A . A 1 56 U 56 56 U U A . A 1 57 C 57 57 C C A . A 1 58 A 58 58 A A A . A 1 59 U 59 59 U U A . A 1 60 U 60 60 U U A . A 1 61 G 61 61 G G A . A 1 62 A 62 62 A A A . A 1 63 C 63 63 C C A . A 1 64 G 64 64 G G A . A 1 65 C 65 65 C C A . A 1 66 U 66 66 U U A . A 1 67 G 67 67 G G A . A 1 68 A 68 68 A A A . A 1 69 C 69 69 C C A . A 1 70 G 70 70 G G A . A 1 71 G 71 71 G G A . A 1 72 U 72 72 U U A . A 1 73 A 73 73 A A A . A 1 74 C 74 74 C C A . A 1 75 A 75 75 A A A . A 1 76 G 76 76 G G A . A 1 77 G 77 77 G G A . A 1 78 C 78 78 C C A . A 1 79 C 79 79 C C A . A 1 80 A 80 80 A A A . A 1 81 G 81 81 G G A . A 1 82 A 82 82 A A A . A 1 83 C 83 83 C C A . A 1 84 A 84 84 A A A . A 1 85 A 85 85 A A A . A 1 86 U 86 86 U U A . A 1 87 U 87 87 U U A . A 1 88 A 88 88 A A A . A 1 89 U 89 89 U U A . A 1 90 U 90 90 U U A . A 1 91 G 91 91 G G A . A 1 92 U 92 92 U U A . A 1 93 C 93 93 C C A . A 1 94 U 94 94 U U A . A 1 95 G 95 95 G G A . A 1 96 G 96 96 G G A . A 1 97 U 97 97 U U A . A 1 98 A 98 98 A A A . A 1 99 U 99 99 U U A . A 1 100 A 100 100 A A A . A 1 101 G 101 101 G G A . A 1 102 U 102 102 U U A . A 1 103 G 103 103 G G A . A 1 104 C 104 104 C C A . A 1 105 A 105 105 A A A . A 1 106 A 106 106 A A A . A 1 107 C 107 107 C C A . A 1 108 A 108 108 A A A . A 1 109 G 109 109 G G A . A 1 110 C 110 110 C C A . A 1 111 A 111 111 A A A . A 1 112 G 112 112 G G A . A 1 113 A 113 113 A A A . A 1 114 A 114 114 A A A . A 1 115 C 115 115 C C A . A 1 116 A 116 116 A A A . A 1 117 A 117 117 A A A . A 1 118 U 118 118 U U A . A 1 119 U 119 119 U U A . A 1 120 U 120 120 U U A . A 1 121 G 121 121 G G A . A 1 122 C 122 122 C C A . A 1 123 U 123 123 U U A . A 1 124 G 124 124 G G A . A 1 125 A 125 125 A A A . A 1 126 G 126 126 G G A . A 1 127 G 127 127 G G A . A 1 128 G 128 128 G G A . A 1 129 C 129 129 C C A . A 1 130 U 130 130 U U A . A 1 131 A 131 131 A A A . A 1 132 U 132 132 U U A . A 1 133 U 133 133 U U A . A 1 134 G 134 134 G G A . A 1 135 A 135 135 A A A . A 1 136 G 136 136 G G A . A 1 137 G 137 137 G G A . A 1 138 C 138 138 C C A . A 1 139 G 139 139 G G A . A 1 140 C 140 140 C C A . A 1 141 A 141 141 A A A . A 1 142 A 142 142 A A A . A 1 143 C 143 143 C C A . A 1 144 A 144 144 A A A . A 1 145 A 145 145 A A A . A 1 146 C 146 146 C C A . A 1 147 A 147 147 A A A . A 1 148 U 148 148 U U A . A 1 149 C 149 149 C C A . A 1 150 U 150 150 U U A . A 1 151 G 151 151 G G A . A 1 152 U 152 152 U U A . A 1 153 U 153 153 U U A . A 1 154 G 154 154 G G A . A 1 155 C 155 155 C C A . A 1 156 A 156 156 A A A . A 1 157 A 157 157 A A A . A 1 158 C 158 158 C C A . A 1 159 U 159 159 U U A . A 1 160 C 160 160 C C A . A 1 161 A 161 161 A A A . A 1 162 C 162 162 C C A . A 1 163 A 163 163 A A A . A 1 164 G 164 164 G G A . A 1 165 U 165 165 U U A . A 1 166 C 166 166 C C A . A 1 167 U 167 167 U U A . A 1 168 G 168 168 G G A . A 1 169 G 169 169 G G A . A 1 170 G 170 170 G G A . A 1 171 G 171 171 G G A . A 1 172 C 172 172 C C A . A 1 173 A 173 173 A A A . A 1 174 U 174 174 U U A . A 1 175 C 175 175 C C A . A 1 176 A 176 176 A A A . A 1 177 A 177 177 A A A . A 1 178 G 178 178 G G A . A 1 179 C 179 179 C C A . A 1 180 A 180 180 A A A . A 1 181 G 181 181 G G A . A 1 182 C 182 182 C C A . A 1 183 U 183 183 U U A . A 1 184 C 184 184 C C A . A 1 185 C 185 185 C C A . A 1 186 A 186 186 A A A . A 1 187 G 187 187 G G A . A 1 188 G 188 188 G G A . A 1 189 C 189 189 C C A . A 1 190 A 190 190 A A A . A 1 191 A 191 191 A A A . A 1 192 G 192 192 G G A . A 1 193 A 193 193 A A A . A 1 194 G 194 194 G G A . A 1 195 U 195 195 U U A . A 1 196 C 196 196 C C A . A 1 197 C 197 197 C C A . A 1 198 U 198 198 U U A . A 1 199 G 199 199 G G A . A 1 200 G 200 200 G G A . A 1 201 C 201 201 C C A . A 1 202 U 202 202 U U A . A 1 203 G 203 203 G G A . A 1 204 U 204 204 U U A . A 1 205 G 205 205 G G A . A 1 206 G 206 206 G G A . A 1 207 A 207 207 A A A . A 1 208 A 208 208 A A A . A 1 209 A 209 209 A A A . A 1 210 G 210 210 G G A . A 1 211 A 211 211 A A A . A 1 212 U 212 212 U U A . A 1 213 A 213 213 A A A . A 1 214 C 214 214 C C A . A 1 215 C 215 215 C C A . A 1 216 U 216 216 U U A . A 1 217 A 217 217 A A A . A 1 218 A 218 218 A A A . A 1 219 A 219 219 A A A . A 1 220 G 220 220 G G A . A 1 221 G 221 221 G G A . A 1 222 A 222 222 A A A . A 1 223 U 223 223 U U A . A 1 224 C 224 224 C C A . A 1 225 A 225 225 A A A . A 1 226 A 226 226 A A A . A 1 227 C 227 227 C C A . A 1 228 A 228 228 A A A . A 1 229 G 229 229 G G A . A 1 230 C 230 230 C C A . A 1 231 U 231 231 U U A . A 1 232 C 232 232 C C A . A 1 233 C 233 233 C C A . A 1 234 C 234 234 C C A . # # loop_ # #