data_4175 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; SL3 Hairpin from the Packaging Signal of HIV-1 ; _BMRB_accession_number 4175 _BMRB_flat_file_name bmr4175.str _Entry_type original _Submission_date 1998-08-11 _Accession_date 1998-08-11 _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 Pappalardo L. . . 2 Kerwood D. J. . 3 Pelczer I. . . 4 Borer P. N. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 175 "31P chemical shifts" 19 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2000-04-04 original author . stop_ _Original_release_date 2000-04-04 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Three-dimensional Folding of an RNA Hairpin Required for Packaging HIV-1' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 98417646 _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Pappalardo L. . . 2 Kerwood D. J. . 3 Pelczer I. . . 4 Borer P. N. . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_name_full 'Journal of Molecular Biology' _Journal_volume 282 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 801 _Page_last 818 _Year 1998 _Details . loop_ _Keyword HIV-1 NMR packaging RNA tetraloop stop_ save_ ################################## # Molecular system description # ################################## save_system_SL3_RNA_hairpin _Saveframe_category molecular_system _Mol_system_name 'SL3 RNA hairpin' _Abbreviation_common SL3_RNA_hairpin _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'SL3 RNA hairpin' $SL3_RNA_hairpin stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state oligomer _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_SL3_RNA_hairpin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common 'SL3 RNA hairpin' _Abbreviation_common SL3_RNA_hairpin _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 20 _Mol_residue_sequence ; GGACUAGCGGAGGCUAGUCC ; loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 A 4 C 5 U 6 A 7 G 8 C 9 G 10 G 11 A 12 G 13 G 14 C 15 U 16 A 17 G 18 U 19 C 20 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 $SL3_RNA_hairpin 'Human Immunodeficiency virus, type 1' 11676 virus . . . 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 $SL3_RNA_hairpin 'recombinant technology' . . . . . 'T7 transcript' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_one _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $SL3_RNA_hairpin 30 mM . stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_one _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _Sample_label $sample_one save_ save_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label $sample_one save_ save_H-PCOSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name H-PCOSY _Sample_label $sample_one save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name H-PCOSY _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_conditions_one _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7 0.5 n/a temperature 303 0.5 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_one _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 DSS H 1 'methyl protons' ppm 0.03 external direct cylindrical external parallel . P 31 . . . . . . . . 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_assigned_chemical_shifts_one _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_one stop_ _Sample_conditions_label $sample_conditions_one _Chem_shift_reference_set_label $chemical_shift_reference_one _Mol_system_component_name 'SL3 RNA hairpin' _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 H1 H 12.9 0.01 1 2 . 1 G H8 H 8.15 0.01 1 3 . 1 G H1' H 5.82 0.01 1 4 . 1 G H2' H 4.95 0.01 1 5 . 1 G H3' H 4.76 0.01 1 6 . 1 G H4' H 4.57 0.01 1 7 . 1 G H5' H 4.28 0.01 2 8 . 1 G H5'' H 4.42 0.01 2 9 . 2 G H1 H 12.6 0.01 1 10 . 2 G H8 H 7.62 0.01 1 11 . 2 G H1' H 5.90 0.01 1 12 . 2 G H2' H 4.70 0.01 1 13 . 2 G H3' H 4.61 0.01 1 14 . 2 G H4' H 4.63 0.01 1 15 . 2 G H5' H 4.34 0.01 2 16 . 2 G H5'' H 4.51 0.01 2 17 . 2 G P P -3.00 0.01 1 18 . 3 A H2 H 7.80 0.01 1 19 . 3 A H62 H 7.00 0.01 2 20 . 3 A H8 H 7.88 0.01 1 21 . 3 A H1' H 6.02 0.01 1 22 . 3 A H2' H 4.63 0.01 1 23 . 3 A H3' H 4.63 0.01 1 24 . 3 A H4' H 4.54 0.01 1 25 . 3 A H5' H 4.20 0.01 2 26 . 3 A H5'' H 4.53 0.01 2 27 . 3 A P P -3.56 0.01 1 28 . 4 C H41 H 8.36 0.01 2 29 . 4 C H42 H 7.05 0.01 2 30 . 4 C H5 H 5.26 0.01 1 31 . 4 C H6 H 7.40 0.01 1 32 . 4 C H1' H 5.36 0.01 1 33 . 4 C H2' H 4.28 0.01 1 34 . 4 C H3' H 4.33 0.01 1 35 . 4 C H4' H 4.44 0.01 1 36 . 4 C H5' H 4.06 0.01 2 37 . 4 C H5'' H 4.49 0.01 2 38 . 4 C P P -3.70 0.01 1 39 . 5 U H3 H 13.2 0.01 1 40 . 5 U H5 H 5.43 0.01 1 41 . 5 U H6 H 7.84 0.01 1 42 . 5 U H1' H 5.53 0.01 1 43 . 5 U H2' H 4.56 0.01 1 44 . 5 U H3' H 4.64 0.01 1 45 . 5 U H4' H 4.43 0.01 1 46 . 5 U H5' H 4.12 0.01 2 47 . 5 U H5'' H 4.57 0.01 2 48 . 5 U P P -3.90 0.01 1 49 . 6 A H2 H 6.71 0.01 1 50 . 6 A H8 H 8.13 0.01 1 51 . 6 A H1' H 5.95 0.01 1 52 . 6 A H2' H 4.56 0.01 1 53 . 6 A H3' H 4.76 0.01 1 54 . 6 A H4' H 4.53 0.01 1 55 . 6 A H5' H 4.20 0.01 2 56 . 6 A H5'' H 4.53 0.01 2 57 . 6 A P P -3.56 0.01 1 58 . 7 G H1 H 13.3 0.01 1 59 . 7 G H8 H 7.32 0.01 1 60 . 7 G H1' H 5.60 0.01 1 61 . 7 G H2' H 4.32 0.01 1 62 . 7 G H3' H 4.45 0.01 1 63 . 7 G H4' H 4.43 0.01 1 64 . 7 G H5' H 4.09 0.01 2 65 . 7 G H5'' H 4.50 0.01 2 66 . 7 G P P -3.64 0.01 1 67 . 8 C H41 H 8.16 0.01 2 68 . 8 C H42 H 6.66 0.01 2 69 . 8 C H5 H 5.01 0.01 1 70 . 8 C H6 H 7.31 0.01 1 71 . 8 C H1' H 5.46 0.01 1 72 . 8 C H2' H 4.46 0.01 1 73 . 8 C H3' H 4.32 0.01 1 74 . 8 C H4' H 4.32 0.01 1 75 . 8 C H5' H 4.04 0.01 2 76 . 8 C H5'' H 4.17 0.01 2 77 . 8 C P P -3.78 0.01 1 78 . 9 G H8 H 7.55 0.01 1 79 . 9 G H1' H 5.60 0.01 1 80 . 9 G H2' H 4.53 0.01 1 81 . 9 G H3' H 4.57 0.01 1 82 . 9 G H4' H 4.40 0.01 1 83 . 9 G H5' H 4.07 0.01 2 84 . 9 G H5'' H 4.32 0.01 2 85 . 9 G P P -3.34 0.01 1 86 . 10 G H8 H 7.76 0.01 1 87 . 10 G H1' H 5.41 0.01 1 88 . 10 G H2' H 4.60 0.01 1 89 . 10 G H3' H 4.54 0.01 1 90 . 10 G H4' H 4.07 0.01 1 91 . 10 G H5' H 3.95 0.01 2 92 . 10 G H5'' H 4.07 0.01 2 93 . 10 G P P -3.04 0.01 1 94 . 11 A H2 H 8.00 0.01 1 95 . 11 A H8 H 8.19 0.01 1 96 . 11 A H1' H 5.94 0.01 1 97 . 11 A H2' H 4.80 0.01 1 98 . 11 A H3' H 4.86 0.01 1 99 . 11 A H4' H 4.41 0.01 1 100 . 11 A H5' H 3.94 0.01 2 101 . 11 A H5'' H 4.06 0.01 2 102 . 11 A P P -3.07 0.01 1 103 . 12 G H8 H 7.90 0.01 1 104 . 12 G H1' H 5.98 0.01 1 105 . 12 G H2' H 4.84 0.01 1 106 . 12 G H3' H 4.94 0.01 1 107 . 12 G H4' H 4.62 0.01 1 108 . 12 G H5' H 4.30 0.01 2 109 . 12 G H5'' H 4.36 0.01 2 110 . 12 G P P -3.56 0.01 1 111 . 13 G H1 H 12.9 0.01 1 112 . 13 G H8 H 7.97 0.01 1 113 . 13 G H1' H 5.07 0.01 1 114 . 13 G H2' H 4.58 0.01 1 115 . 13 G H3' H 4.40 0.01 1 116 . 13 G H4' H 4.47 0.01 1 117 . 13 G H5' H 4.30 0.01 2 118 . 13 G H5'' H 4.33 0.01 2 119 . 13 G P P -2.62 0.01 1 120 . 14 C H41 H 8.60 0.01 2 121 . 14 C H42 H 6.83 0.01 2 122 . 14 C H5 H 5.28 0.01 1 123 . 14 C H6 H 7.68 0.01 1 124 . 14 C H1' H 5.54 0.01 1 125 . 14 C H2' H 4.45 0.01 1 126 . 14 C H3' H 4.43 0.01 1 127 . 14 C H4' H 4.41 0.01 1 128 . 14 C H5' H 4.14 0.01 2 129 . 14 C H5'' H 4.52 0.01 2 130 . 14 C P P -3.83 0.01 1 131 . 15 U H3 H 13.3 0.01 1 132 . 15 U H5 H 5.49 0.01 1 133 . 15 U H6 H 7.89 0.01 1 134 . 15 U H1' H 5.53 0.01 1 135 . 15 U H2' H 4.56 0.01 1 136 . 15 U H3' H 4.64 0.01 1 137 . 15 U H4' H 4.35 0.01 1 138 . 15 U H5' H 4.14 0.01 2 139 . 15 U H5'' H 4.45 0.01 2 140 . 15 U P P -3.75 0.01 1 141 . 16 A H2 H 6.75 0.01 1 142 . 16 A H61 H 7.71 0.01 2 143 . 16 A H62 H 6.41 0.01 2 144 . 16 A H8 H 8.13 0.01 1 145 . 16 A H1' H 5.97 0.01 1 146 . 16 A H2' H 4.67 0.01 1 147 . 16 A H3' H 4.74 0.01 1 148 . 16 A H4' H 4.56 0.01 1 149 . 16 A H5' H 4.20 0.01 2 150 . 16 A H5'' H 4.53 0.01 2 151 . 16 A P P -3.42 0.01 1 152 . 17 G H1 H 13.5 0.01 1 153 . 17 G H21 H 8.57 0.01 2 154 . 17 G H22 H 6.22 0.01 2 155 . 17 G H8 H 7.18 0.01 1 156 . 17 G H1' H 5.52 0.01 1 157 . 17 G H2' H 4.37 0.01 1 158 . 17 G H3' H 4.37 0.01 1 159 . 17 G H4' H 4.45 0.01 1 160 . 17 G H5' H 4.07 0.01 2 161 . 17 G H5'' H 4.45 0.01 2 162 . 17 G P P -3.49 0.01 1 163 . 18 U H3 H 14.4 0.01 1 164 . 18 U H5 H 5.01 0.01 1 165 . 18 U H6 H 7.73 0.01 1 166 . 18 U H1' H 5.53 0.01 1 167 . 18 U H2' H 4.48 0.01 1 168 . 18 U H3' H 4.48 0.01 1 169 . 18 U H4' H 4.44 0.01 1 170 . 18 U H5' H 4.07 0.01 2 171 . 18 U H5'' H 4.54 0.01 2 172 . 18 U P P -4.29 0.01 1 173 . 19 C H41 H 8.46 0.01 2 174 . 19 C H42 H 6.99 0.01 2 175 . 19 C H5 H 5.64 0.01 1 176 . 19 C H6 H 7.88 0.01 1 177 . 19 C H1' H 5.62 0.01 1 178 . 19 C H2' H 4.26 0.01 1 179 . 19 C H3' H 4.49 0.01 1 180 . 19 C H4' H 4.42 0.01 1 181 . 19 C H5' H 4.08 0.01 2 182 . 19 C H5'' H 4.52 0.01 2 183 . 19 C P P -3.85 0.01 1 184 . 20 C H41 H 8.28 0.01 2 185 . 20 C H42 H 7.04 0.01 2 186 . 20 C H5 H 5.54 0.01 1 187 . 20 C H6 H 7.68 0.01 1 188 . 20 C H1' H 5.76 0.01 1 189 . 20 C H2' H 4.00 0.01 1 190 . 20 C H3' H 4.18 0.01 1 191 . 20 C H4' H 4.19 0.01 1 192 . 20 C H5' H 4.04 0.01 2 193 . 20 C H5'' H 4.50 0.01 2 194 . 20 C P P -3.80 0.01 1 stop_ save_