data_5834 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of the HIV-1 frameshift inducing stem-loop RNA ; _BMRB_accession_number 5834 _BMRB_flat_file_name bmr5834.str _Entry_type original _Submission_date 2003-06-17 _Accession_date 2003-06-17 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Staple David W. . 2 Butcher Samuel E. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 155 "13C chemical shifts" 59 "15N chemical shifts" 31 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2003-09-12 original author . stop_ _Original_release_date 2003-09-12 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Solution Structure of the HIV-1 Frameshift Inducing Stem-loop RNA' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 22770795 _PubMed_ID 12888491 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Staple David W . 2 Butcher Samuel E . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_volume 31 _Journal_issue 15 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 4326 _Page_last 4331 _Year 2003 _Details . loop_ _Keyword frameshift HIV RNA tetraloop stop_ save_ ################################## # Molecular system description # ################################## save_system_HIVFSL _Saveframe_category molecular_system _Mol_system_name 'HIV-1 frameshift inducing stem-loop RNA' _Abbreviation_common HIVfsl _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'HIV-1 frameshift inducing stem-loop RNA' $HIVfsl stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monmer _System_paramagnetic no _System_thiol_state 'not present' loop_ _Biological_function 'induces a programmed -1 frameshift during translation of the HIV-1 genes' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_HIVfsl _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common 'HIV-1 frameshift inducing stem-loop RNA' _Abbreviation_common HIVfsl _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 22 _Mol_residue_sequence ; GGCCUUCCCACAAGGGAAGG CC ; loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 C 4 C 5 U 6 U 7 C 8 C 9 C 10 A 11 C 12 A 13 A 14 G 15 G 16 G 17 A 18 A 19 G 20 G 21 C 22 C stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $HIVfsl HIV 12721 Viruses . Lentivirus HIV stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name _Details $HIVfsl 'enzymatic semisynthesis' . . . . . 'The RNA was transcribed in vitro using T7 RNA polymerase.' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_Sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $HIVfsl 1.0 mM . stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DMX _Field_strength 750 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DMX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H NOESY' _Sample_label . save_ save_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H TOCSY' _Sample_label . save_ save_1H-13C_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-13C HSQC' _Sample_label . save_ save_HCCH-TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name HCCH-TOCSY _Sample_label . save_ save_HCCH-COSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name HCCH-COSY _Sample_label . save_ save_HNN-COSY_6 _Saveframe_category NMR_applied_experiment _Experiment_name HNN-COSY _Sample_label . save_ save_1H-13C-1H_NOESY_HMQC_7 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-13C-1H NOESY HMQC' _Sample_label . save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H NOESY' _BMRB_pulse_sequence_accession_number . _Details '600 MHz spectrometer was equipped with a cryoprobe.' save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H TOCSY' _BMRB_pulse_sequence_accession_number . _Details '600 MHz spectrometer was equipped with a cryoprobe.' save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-13C HSQC' _BMRB_pulse_sequence_accession_number . _Details '600 MHz spectrometer was equipped with a cryoprobe.' save_ save_NMR_spec_expt__0_4 _Saveframe_category NMR_applied_experiment _Experiment_name HCCH-TOCSY _BMRB_pulse_sequence_accession_number . _Details '600 MHz spectrometer was equipped with a cryoprobe.' save_ save_NMR_spec_expt__0_5 _Saveframe_category NMR_applied_experiment _Experiment_name HCCH-COSY _BMRB_pulse_sequence_accession_number . _Details '600 MHz spectrometer was equipped with a cryoprobe.' save_ save_NMR_spec_expt__0_6 _Saveframe_category NMR_applied_experiment _Experiment_name HNN-COSY _BMRB_pulse_sequence_accession_number . _Details '600 MHz spectrometer was equipped with a cryoprobe.' save_ save_NMR_spec_expt__0_7 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-13C-1H NOESY HMQC' _BMRB_pulse_sequence_accession_number . _Details '600 MHz spectrometer was equipped with a cryoprobe.' save_ ####################### # Sample conditions # ####################### save_condition_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.8 0.1 n/a temperature 303 1 K stop_ save_ save_condition_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.8 0.1 n/a temperature 283 1 K stop_ save_ save_condition_3 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.8 0.1 n/a temperature 298 1 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _Saveframe_category chemical_shift_reference _Details . loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis _Indirect_shift_ratio DSS C 13 'methyl protons' ppm 0.0 . indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0.0 internal direct . . . 1.0 DSS N 15 'methyl protons' ppm 0.0 . indirect . . . 0.101329118 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_chemical_shift_list _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $Sample_1 stop_ _Sample_conditions_label $condition_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'HIV-1 frameshift inducing stem-loop RNA' _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 . 1 G C1' C 90.224 . 1 2 . 1 G C8 C 139.005 . 1 3 . 1 G H1 H 12.955 . 1 4 . 1 G H1' H 5.755 . 1 5 . 1 G H2' H 4.882 . 1 6 . 1 G H3' H 4.76 . 1 7 . 1 G H4' H 4.501 . 1 8 . 1 G H8 H 8.13 . 1 9 . 1 G N1 N 147.359 . 1 10 . 1 G N3 N 162.186 . 1 11 . 1 G N7 N 217.632 . 1 12 . 2 G C1' C 92.722 . 1 13 . 2 G C8 C 136.992 . 1 14 . 2 G H1 H 13.407 . 1 15 . 2 G H1' H 5.874 . 1 16 . 2 G H2' H 4.529 . 1 17 . 2 G H21 H 8.373 . 1 18 . 2 G H22 H 7.585 . 1 19 . 2 G H3' H 4.507 . 1 20 . 2 G H4' H 4.565 . 1 21 . 2 G H8 H 7.67 . 1 22 . 2 G N1 N 148.384 . 1 23 . 2 G N3 N 161.55 . 1 24 . 2 G N7 N 218.419 . 1 25 . 3 C C1' C 93.773 . 1 26 . 3 C C5 C 97.005 . 1 27 . 3 C C6 C 140.864 . 1 28 . 3 C H1' H 5.528 . 1 29 . 3 C H2' H 4.412 . 1 30 . 3 C H3' H 4.34 . 1 31 . 3 C H41 H 8.603 . 1 32 . 3 C H42 H 6.847 . 1 33 . 3 C H5 H 5.25 . 1 34 . 3 C H6 H 7.672 . 1 35 . 3 C N3 N 197.487 . 1 36 . 4 C C1' C 94.105 . 1 37 . 4 C C5 C 97.88 . 1 38 . 4 C C6 C 141.513 . 1 39 . 4 C H1' H 5.483 . 1 40 . 4 C H2' H 4.392 . 1 41 . 4 C H3' H 4.384 . 1 42 . 4 C H4' H 4.399 . 1 43 . 4 C H41 H 8.482 . 1 44 . 4 C H42 H 6.877 . 1 45 . 4 C H5 H 5.536 . 1 46 . 4 C H6 H 7.717 . 1 47 . 4 C N3 N 196.969 . 1 48 . 5 U C1' C 93.986 . 1 49 . 5 U C5 C 103.154 . 1 50 . 5 U C6 C 139.823 . 1 51 . 5 U H1' H 5.491 . 1 52 . 5 U H2' H 4.424 . 1 53 . 5 U H3 H 13.843 . 1 54 . 5 U H3' H 4.486 . 1 55 . 5 U H4' H 4.412 . 1 56 . 5 U H5 H 5.399 . 1 57 . 5 U H6 H 7.88 . 1 58 . 5 U N3 N 161.656 . 1 59 . 6 U C1' C 93.565 . 1 60 . 6 U C5 C 102.868 . 1 61 . 6 U C6 C 140.304 . 1 62 . 6 U H1' H 5.595 . 1 63 . 6 U H2' H 4.376 . 1 64 . 6 U H3 H 13.691 . 1 65 . 6 U H3' H 4.505 . 1 66 . 6 U H4' H 4.419 . 1 67 . 6 U H5 H 5.557 . 1 68 . 6 U H6 H 8.022 . 1 69 . 6 U N3 N 162.344 . 1 70 . 7 C C1' C 93.796 . 1 71 . 7 C C5 C 97.037 . 1 72 . 7 C C6 C 141.704 . 1 73 . 7 C H1' H 5.455 . 1 74 . 7 C H2' H 4.193 . 1 75 . 7 C H3' H 4.409 . 1 76 . 7 C H4' H 4.38 . 1 77 . 7 C H41 H 8.23 . 1 78 . 7 C H42 H 6.732 . 1 79 . 7 C H5 H 5.572 . 1 80 . 7 C H6 H 7.843 . 1 81 . 7 C N3 N 197.983 . 1 82 . 8 C C2' C 93.761 . 1 83 . 8 C C5 C 97.14 . 1 84 . 8 C C6 C 141.083 . 1 85 . 8 C H1' H 5.347 . 1 86 . 8 C H2' H 4.258 . 1 87 . 8 C H3' H 4.404 . 1 88 . 8 C H4' H 4.311 . 1 89 . 8 C H41 H 8.239 . 1 90 . 8 C H42 H 6.708 . 1 91 . 8 C H5 H 5.331 . 1 92 . 8 C H6 H 7.702 . 1 93 . 8 C N3 N 196.661 . 1 94 . 9 C C1' C 93.695 . 1 95 . 9 C C5 C 97.061 . 1 96 . 9 C C6 C 140.729 . 1 97 . 9 C H1' H 5.407 . 1 98 . 9 C H2' H 4.558 . 1 99 . 9 C H3' H 4.334 . 1 100 . 9 C H4' H 4.319 . 1 101 . 9 C H41 H 7.698 . 1 102 . 9 C H42 H 5.688 . 1 103 . 9 C H5 H 5.148 . 1 104 . 9 C H6 H 7.493 . 1 105 . 9 C N3 N 195.496 . 1 106 . 10 A C1' C 93.184 . 1 107 . 10 A C2 C 152.073 . 1 108 . 10 A C8 C 137.454 . 1 109 . 10 A H1' H 5.698 . 1 110 . 10 A H2 H 7.564 . 1 111 . 10 A H2' H 4.4 . 1 112 . 10 A H3' H 4.458 . 1 113 . 10 A H4' H 4.392 . 1 114 . 10 A H8 H 8.029 . 1 115 . 11 C C1' C 89.872 . 1 116 . 11 C C5 C 98.08 . 1 117 . 11 C C6 C 142.691 . 1 118 . 11 C H1' H 5.576 . 1 119 . 11 C H2' H 3.997 . 1 120 . 11 C H3' H 4.275 . 1 121 . 11 C H4' H 3.66 . 1 122 . 11 C H5 H 5.425 . 1 123 . 11 C H5'' H 3.777 . 1 124 . 11 C H6 H 7.444 . 1 125 . 12 A C1' C 89.971 . 1 126 . 12 A C2 C 152.663 . 1 127 . 12 A C8 C 139.299 . 1 128 . 12 A H1' H 5.77 . 1 129 . 12 A H2 H 7.968 . 1 130 . 12 A H2' H 4.523 . 1 131 . 12 A H3' H 4.648 . 1 132 . 12 A H4' H 4.32 . 1 133 . 12 A H8 H 8.079 . 1 134 . 13 A C1' C 90.538 . 1 135 . 13 A C2 C 152.788 . 1 136 . 13 A C8 C 139.66 . 1 137 . 13 A H1' H 6.058 . 1 138 . 13 A H2 H 8.062 . 1 139 . 13 A H2' H 4.775 . 1 140 . 13 A H3' H 4.902 . 1 141 . 13 A H4' H 4.552 . 1 142 . 13 A H8 H 8.331 . 1 143 . 14 G C1' C 92.42 . 1 144 . 14 G C8 C 137.303 . 1 145 . 14 G H1 H 12.022 . 1 146 . 14 G H1' H 5.014 . 1 147 . 14 G H2' H 4.539 . 1 148 . 14 G H21 H 8.216 . 1 149 . 14 G H22 H 6.038 . 1 150 . 14 G H3' H 4.26 . 1 151 . 14 G H4' H 4.441 . 1 152 . 14 G H8 H 7.685 . 1 153 . 14 G N1 N 146.803 . 1 154 . 14 G N3 N 162.976 . 1 155 . 14 G N7 N 217.005 . 1 156 . 15 G C1' C 92.713 . 1 157 . 15 G C8 C 135.971 . 1 158 . 15 G H1 H 12.333 . 1 159 . 15 G H1' H 5.754 . 1 160 . 15 G H2' H 4.421 . 1 161 . 15 G H21 H 8.217 . 1 162 . 15 G H22 H 5.784 . 1 163 . 15 G H3' H 4.577 . 1 164 . 15 G H8 H 7.199 . 1 165 . 15 G N1 N 147.26 . 1 166 . 15 G N3 N 162.551 . 1 167 . 15 G N7 N 217.259 . 1 168 . 16 G C1' C 92.833 . 1 169 . 16 G C8 C 136.05 . 1 170 . 16 G H1 H 12.1 . 1 171 . 16 G H1' H 5.695 . 1 172 . 16 G H2' H 4.54 . 1 173 . 16 G H21 H 7.824 . 1 174 . 16 G H22 H 5.684 . 1 175 . 16 G H8 H 7.091 . 1 176 . 16 G N1 N 147.004 . 1 177 . 16 G N3 N 162.784 . 1 178 . 16 G N7 N 217.082 . 1 179 . 17 A C1' C 92.99 . 1 180 . 17 A C2 C 150.46 . 1 181 . 17 A C8 C 136.632 . 1 182 . 17 A H1' H 5.847 . 1 183 . 17 A H2 H 7.047 . 1 184 . 17 A H2' H 4.542 . 1 185 . 17 A H3' H 4.57 . 1 186 . 17 A H4' H 4.445 . 1 187 . 17 A H61 H 7.749 . 1 188 . 17 A H62 H 6.527 . 1 189 . 17 A H8 H 7.595 . 1 190 . 17 A N1 N 220.173 . 1 191 . 18 A C1' C 92.411 . 1 192 . 18 A C2 C 150.732 . 1 193 . 18 A C8 C 136.623 . 1 194 . 18 A H1' H 5.837 . 1 195 . 18 A H2 H 7.414 . 1 196 . 18 A H2' H 4.554 . 1 197 . 18 A H3' H 4.356 . 1 198 . 18 A H4' H 4.428 . 1 199 . 18 A H61 H 7.881 . 1 200 . 18 A H62 H 6.492 . 1 201 . 18 A H8 H 7.615 . 1 202 . 18 A N1 N 219.986 . 1 203 . 19 G C1' C 92.42 . 1 204 . 19 G C8 C 135.597 . 1 205 . 19 G H1 H 12.857 . 1 206 . 19 G H1' H 5.524 . 1 207 . 19 G H2' H 4.463 . 1 208 . 19 G H21 H 8.225 . 1 209 . 19 G H22 H 6.002 . 1 210 . 19 G H3' H 4.515 . 1 211 . 19 G H8 H 7.002 . 1 212 . 19 G N1 N 147.464 . 1 213 . 19 G N3 N 162.374 . 1 214 . 19 G N7 N 217.519 . 1 215 . 20 G C1' C 92.833 . 1 216 . 20 G C8 C 136.21 . 1 217 . 20 G H1 H 13.278 . 1 218 . 20 G H1' H 5.701 . 1 219 . 20 G H2' H 4.46 . 1 220 . 20 G H21 H 8.453 . 1 221 . 20 G H22 H 7.668 . 1 222 . 20 G H8 H 7.208 . 1 223 . 20 G N1 N 148.747 . 1 224 . 20 G N7 N 218.748 . 1 225 . 21 C C1' C 93.996 . 1 226 . 21 C C5 C 96.898 . 1 227 . 21 C C6 C 140.921 . 1 228 . 21 C H1' H 5.502 . 1 229 . 21 C H2' H 4.25 . 1 230 . 21 C H3' H 4.49 . 1 231 . 21 C H4' H 4.357 . 1 232 . 21 C H41 H 8.543 . 1 233 . 21 C H42 H 6.877 . 1 234 . 21 C H5 H 5.162 . 1 235 . 21 C H6 H 7.583 . 1 236 . 21 C N3 N 197.988 . 1 237 . 22 C C1' C 92.713 . 1 238 . 22 C C5 C 98.072 . 1 239 . 22 C C6 C 141.674 . 1 240 . 22 C H1' H 5.739 . 1 241 . 22 C H2' H 3.964 . 1 242 . 22 C H4' H 4.127 . 1 243 . 22 C H5 H 5.5 . 1 244 . 22 C H6 H 7.644 . 1 245 . 22 C N3 N 196.9 . 1 stop_ save_