data_4780 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR Structure of Stem-loop SL2 of the HIV-1 Psi RNA Packaging Signal Reveals a Novel A-U-A Base-triple Platform ; _BMRB_accession_number 4780 _BMRB_flat_file_name bmr4780.str _Entry_type original _Submission_date 2000-07-10 _Accession_date 2000-07-10 _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 Amarasinghe Gaya K. . 2 'De Guzman' Roberto N. . 3 Turner Ryan B. . 4 Summers Michael F. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 134 "13C chemical shifts" 106 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2002-04-04 original author . stop_ _Original_release_date 2002-04-04 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; NMR Structure of Stem-loop SL2 of the HIV-1 Psi RNA Packaging Signal Reveals a Novel A-U-A Base-triple Platform ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 20328605 _PubMed_ID 10860728 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Amarasinghe Gaya K. . 2 'De Guzman' Roberto N. . 3 Turner Ryan B. . 4 Summers Michael F. . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_name_full 'Journal of Molecular Biology' _Journal_volume 299 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 145 _Page_last 156 _Year 2000 _Details ; SL2 RNA stem loop is the major 5' splice donor site. Located in the Psi-RNA packaging signal, SL2 is also involved in nucleocapsid protein mediated RNA packaging. ; loop_ _Keyword HIV-1 'NMR assingment' 'Platform motif' RNA 'Splice donor site' stop_ save_ ################################## # Molecular system description # ################################## save_system_SL2 _Saveframe_category molecular_system _Mol_system_name 'SL2 stem loop RNA from HIV-1' _Abbreviation_common SL2 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label SL2 $SL2 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'not present' loop_ _Biological_function ; Major splice donor site Viral genome packaging ; stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_SL2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common 'HIV-1 SL2 stem loop' _Name_variant SL2 _Abbreviation_common SL2 _Molecular_mass 6371 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 19 _Mol_residue_sequence GGCGACUGGUGAGUACGCC loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 C 4 G 5 A 6 C 7 U 8 G 9 G 10 U 11 G 12 A 13 G 14 U 15 A 16 C 17 G 18 C 19 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 $SL2 HIV-1 12721 viruses . Lentivirus 'Human Immunodeficiency 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 $SL2 'enzymatic semisynthesis' . . . . . 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 _Concentration_min_value _Concentration_max_value _Isotopic_labeling $SL2 . mM 0.6 1.2 . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $SL2 0.8 mM '[U-13C; U-15N]' stop_ save_ ############################ # Computer software used # ############################ save_XWINNMR _Saveframe_category software _Name xwinnmr _Version 2.6 loop_ _Task 'Data aquisition from the NMR' stop_ _Details . save_ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version 1.0 loop_ _Task 'Data processing' stop_ _Details . save_ save_NMRView _Saveframe_category software _Name NMRView _Version 3.0 loop_ _Task 'Data analysis' stop_ _Details . save_ save_DYANA _Saveframe_category software _Name DYANA _Version 1.5 loop_ _Task 'Structure calculation' stop_ _Details . save_ save_CNS _Saveframe_category software _Name CNS _Version 1.0 loop_ _Task 'Structure refinement and energy minimization' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'AVANCE DMX' _Field_strength 600 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'AVANCE DRX' _Field_strength 800 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label . save_ save_2D_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label . save_ save_2D_DQF_COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF COSY' _Sample_label . save_ save_1H-13C_HMQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-13C HMQC' _Sample_label . save_ save_1H,1H,13C_HMQC-NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '1H,1H,13C HMQC-NOESY' _Sample_label . save_ save_1H,1H,13C_HCCH-COSY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '1H,1H,13C HCCH-COSY' _Sample_label . save_ save_1H,1H,13C_HCCH-TOCSY_7 _Saveframe_category NMR_applied_experiment _Experiment_name '1H,1H,13C HCCH-TOCSY' _Sample_label . save_ save_1H,1H,15N_HSQC-NOESY_8 _Saveframe_category NMR_applied_experiment _Experiment_name '1H,1H,15N HSQC-NOESY' _Sample_label . save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF COSY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_4 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-13C HMQC' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_5 _Saveframe_category NMR_applied_experiment _Experiment_name '1H,1H,13C HMQC-NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_6 _Saveframe_category NMR_applied_experiment _Experiment_name '1H,1H,13C HCCH-COSY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_7 _Saveframe_category NMR_applied_experiment _Experiment_name '1H,1H,13C HCCH-TOCSY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_8 _Saveframe_category NMR_applied_experiment _Experiment_name '1H,1H,15N HSQC-NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_Ex-cond-1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH* 6.5 0.3 n/a temperature 298 2 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 . . . . 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_sl2rna _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $Ex-cond-1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name SL2 _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 12.913 0.02 1 2 . 1 G H8 H 8.170 0.02 1 3 . 1 G C8 C 107.807 0.20 1 4 . 1 G H1' H 5.807 0.02 1 5 . 1 G H2' H 4.923 0.02 1 6 . 1 G H3' H 4.722 0.02 1 7 . 1 G H4' H 4.509 0.02 1 8 . 1 G H5' H 4.167 0.02 1 9 . 1 G H5'' H 4.052 0.02 1 10 . 1 G C1' C 91.661 0.20 1 11 . 1 G C2' C 75.066 0.20 1 12 . 1 G C3' C 75.321 0.20 1 13 . 1 G C4' C 83.955 0.20 1 14 . 1 G C5' C 65.820 0.20 1 15 . 2 G H1 H 13.357 0.02 1 16 . 2 G H8 H 7.596 0.02 1 17 . 2 G C8 C 136.705 0.20 1 18 . 2 G H1' H 5.916 0.02 1 19 . 2 G H2' H 4.577 0.02 1 20 . 2 G H3' H 4.549 0.02 1 21 . 2 G H4' H 4.557 0.02 1 22 . 2 G C1' C 92.922 0.20 1 23 . 2 G C2' C 75.250 0.20 1 24 . 2 G C3' C 73.207 0.20 1 25 . 2 G C4' C 82.679 0.20 1 26 . 3 C H41 H 8.663 0.02 1 27 . 3 C H6 H 7.580 0.02 1 28 . 3 C C2 C 6.786 0.02 1 29 . 3 C C6 C 140.463 0.20 1 30 . 3 C H1' H 5.579 0.02 1 31 . 3 C H2' H 4.663 0.02 1 32 . 3 C H3' H 4.503 0.02 1 33 . 3 C H4' H 4.420 0.02 1 34 . 3 C C1' C 93.660 0.20 1 35 . 3 C C2' C 75.622 0.20 1 36 . 3 C C3' C 72.484 0.20 1 37 . 3 C C4' C 81.848 0.20 1 38 . 4 G H1 H 12.193 0.02 1 39 . 4 G H8 H 7.477 0.02 1 40 . 4 G C8 C 136.206 0.20 1 41 . 4 G H1' H 7.618 0.02 1 42 . 4 G H2' H 4.679 0.02 1 43 . 4 G H3' H 4.512 0.02 1 44 . 4 G H4' H 4.516 0.02 1 45 . 4 G H5' H 4.427 0.02 1 46 . 4 G H5'' H 4.149 0.02 1 47 . 4 G C2' C 75.423 0.20 1 48 . 4 G C3' C 73.726 0.20 1 49 . 4 G C4' C 82.404 0.20 1 50 . 4 G C5' C 66.907 0.20 1 51 . 5 A H2 H 7.696 0.02 1 52 . 5 A H8 H 7.849 0.02 1 53 . 5 A C2 C 154.264 0.20 1 54 . 5 A C8 C 139.298 0.20 1 55 . 5 A H1' H 5.917 0.02 1 56 . 5 A H2' H 4.553 0.02 1 57 . 5 A H3' H 4.611 0.02 1 58 . 5 A H4' H 4.496 0.02 1 59 . 5 A C1' C 92.969 0.20 1 60 . 5 A C2' C 75.359 0.20 1 61 . 5 A C3' C 72.555 0.20 1 62 . 5 A C4' C 83.171 0.20 1 63 . 6 C H41 H 8.274 0.02 1 64 . 6 C H42 H 7.021 0.02 1 65 . 6 C H6 H 7.555 0.02 1 66 . 6 C C6 C 140.579 0.20 1 67 . 6 C H1' H 5.417 0.02 1 68 . 6 C H2' H 4.185 0.02 1 69 . 6 C H3' H 4.358 0.02 1 70 . 6 C H4' H 4.354 0.02 1 71 . 6 C H5' H 4.492 0.02 1 72 . 6 C H5'' H 4.060 0.02 1 73 . 6 C C1' C 93.519 0.20 1 74 . 6 C C2' C 75.612 0.20 1 75 . 6 C C3' C 72.134 0.20 1 76 . 6 C C4' C 81.815 0.20 1 77 . 6 C C5' C 64.279 0.20 1 78 . 7 U H5 H 5.337 0.02 1 79 . 7 U H6 H 7.783 0.02 1 80 . 7 U C5 C 103.995 0.20 1 81 . 7 U C6 C 141.210 0.20 1 82 . 7 U H1' H 5.638 0.02 1 83 . 7 U H2' H 4.543 0.02 1 84 . 7 U H3' H 4.436 0.02 1 85 . 7 U H4' H 4.352 0.02 1 86 . 7 U H5' H 4.571 0.02 1 87 . 7 U H5'' H 4.131 0.02 1 88 . 7 U C1' C 93.315 0.20 1 89 . 7 U C2' C 75.354 0.20 1 90 . 7 U C3' C 72.854 0.20 1 91 . 7 U C4' C 82.370 0.20 1 92 . 7 U C5' C 64.626 0.20 1 93 . 8 G H8 H 7.630 0.02 1 94 . 8 G C8 C 137.423 0.20 1 95 . 8 G H1' H 5.693 0.02 1 96 . 8 G H2' H 3.928 0.02 1 97 . 8 G H3' H 4.503 0.02 1 98 . 8 G H4' H 4.355 0.02 1 99 . 8 G H5' H 4.568 0.02 1 100 . 8 G H5'' H 4.077 0.02 1 101 . 8 G C1' C 92.927 0.20 1 102 . 8 G C2' C 76.595 0.20 1 103 . 8 G C3' C 73.605 0.20 1 104 . 8 G C4' C 82.653 0.20 1 105 . 8 G C5' C 64.482 0.20 1 106 . 9 G H8 H 7.614 0.02 1 107 . 9 G C8 C 139.047 0.20 1 108 . 9 G H1' H 5.628 0.02 1 109 . 9 G H2' H 4.498 0.02 1 110 . 9 G H3' H 4.496 0.02 1 111 . 9 G H4' H 2.660 0.02 1 112 . 9 G H5' H 2.981 0.02 1 113 . 9 G H5'' H 2.927 0.02 1 114 . 9 G C1' C 89.623 0.20 1 115 . 9 G C2' C 76.813 0.20 1 116 . 9 G C3' C 80.646 0.20 1 117 . 9 G C4' C 86.542 0.20 1 118 . 9 G C5' C 67.467 0.20 1 119 . 10 U H5 H 6.298 0.02 1 120 . 10 U H6 H 7.916 0.02 1 121 . 10 U C5 C 106.702 0.20 1 122 . 10 U C6 C 142.724 0.20 1 123 . 10 U H1' H 5.804 0.02 1 124 . 10 U H2' H 4.348 0.02 1 125 . 10 U H3' H 4.782 0.02 1 126 . 10 U H4' H 4.118 0.02 1 127 . 10 U H5' H 3.581 0.02 1 128 . 10 U H5'' H 3.930 0.02 1 129 . 10 U C1' C 90.048 0.20 1 130 . 10 U C2' C 77.469 0.20 1 131 . 10 U C3' C 80.133 0.20 1 132 . 10 U C4' C 85.745 0.20 1 133 . 10 U C5' C 67.755 0.20 1 134 . 11 G H8 H 8.328 0.02 1 135 . 11 G C8 C 140.198 0.20 1 136 . 11 G H1' H 5.844 0.02 1 137 . 11 G H2' H 5.126 0.02 1 138 . 11 G H3' H 5.069 0.02 1 139 . 11 G H4' H 4.841 0.02 1 140 . 11 G H5' H 4.249 0.02 1 141 . 11 G H5'' H 3.997 0.02 1 142 . 11 G C1' C 90.547 0.20 1 143 . 11 G C2' C 75.376 0.20 1 144 . 11 G C3' C 79.486 0.20 1 145 . 11 G C4' C 86.861 0.20 1 146 . 11 G C5' C 69.172 0.20 1 147 . 12 A H2 H 7.584 0.02 1 148 . 12 A H8 H 8.653 0.02 1 149 . 12 A C2 C 153.023 0.20 1 150 . 12 A C8 C 141.359 0.20 1 151 . 12 A H1' H 5.874 0.02 1 152 . 12 A H2' H 4.979 0.02 1 153 . 12 A H3' H 4.711 0.02 1 154 . 12 A H4' H 4.631 0.02 1 155 . 12 A H5' H 4.357 0.02 1 156 . 12 A H5'' H 4.328 0.02 1 157 . 12 A C1' C 91.436 0.20 1 158 . 12 A C2' C 75.663 0.20 1 159 . 12 A C3' C 74.516 0.20 1 160 . 12 A C4' C 82.661 0.20 1 161 . 12 A C5' C 68.775 0.20 1 162 . 13 G H1 H 13.244 0.02 1 163 . 13 G H8 H 7.266 0.02 1 164 . 13 G C8 C 136.529 0.20 1 165 . 13 G H1' H 5.557 0.02 1 166 . 13 G H2' H 4.512 0.02 1 167 . 13 G H3' H 4.407 0.02 1 168 . 13 G H4' H 4.502 0.02 1 169 . 13 G C1' C 93.304 0.20 1 170 . 13 G C2' C 75.155 0.20 1 171 . 13 G C3' C 73.762 0.20 1 172 . 13 G C4' C 82.988 0.20 1 173 . 14 U H5 H 5.198 0.02 1 174 . 14 U H6 H 7.688 0.02 1 175 . 14 U C5 C 103.995 0.20 1 176 . 14 U C6 C 142.166 0.20 1 177 . 14 U H1' H 5.880 0.02 1 178 . 14 U H2' H 4.297 0.02 1 179 . 14 U H3' H 4.660 0.02 1 180 . 14 U H4' H 4.478 0.02 1 181 . 14 U C1' C 91.656 0.20 1 182 . 14 U C2' C 76.369 0.20 1 183 . 14 U C3' C 75.485 0.20 1 184 . 14 U C4' C 84.640 0.20 1 185 . 15 A H2 H 8.016 0.02 1 186 . 15 A H8 H 8.393 0.02 1 187 . 15 A C2 C 155.399 0.20 1 188 . 15 A C8 C 141.795 0.20 1 189 . 15 A H1' H 6.119 0.02 1 190 . 15 A H2' H 4.752 0.02 1 191 . 15 A H3' H 4.833 0.02 1 192 . 15 A H4' H 4.571 0.02 1 193 . 15 A H5' H 4.331 0.02 1 194 . 15 A H5'' H 4.201 0.02 1 195 . 15 A C1' C 90.481 0.20 1 196 . 15 A C2' C 76.156 0.20 1 197 . 15 A C3' C 75.979 0.20 1 198 . 15 A C4' C 84.785 0.20 1 199 . 15 A C5' C 67.039 0.20 1 200 . 16 C H41 H 8.141 0.02 1 201 . 16 C H42 H 6.855 0.02 1 202 . 16 C H5 H 5.640 0.02 1 203 . 16 C H6 H 7.682 0.02 1 204 . 16 C C5 C 98.405 0.20 1 205 . 16 C C6 C 142.072 0.20 1 206 . 16 C H1' H 5.562 0.02 1 207 . 16 C C1' C 93.940 0.20 1 208 . 17 G H1 H 12.790 0.02 1 209 . 17 G H8 H 7.725 0.02 1 210 . 17 G C8 C 136.853 0.20 1 211 . 17 G H1' H 5.745 0.02 1 212 . 17 G H2' H 4.592 0.02 1 213 . 17 G H5' H 4.515 0.02 1 214 . 17 G H5'' H 4.165 0.02 1 215 . 17 G C1' C 93.046 0.20 1 216 . 17 G C2' C 75.061 0.20 1 217 . 17 G C5' C 65.894 0.20 1 218 . 18 C H41 H 8.552 0.02 1 219 . 18 C H42 H 6.933 0.02 1 220 . 18 C H5 H 5.211 0.02 1 221 . 18 C H6 H 7.711 0.02 1 222 . 18 C H1' H 5.560 0.02 1 223 . 18 C C1' C 94.228 0.20 1 224 . 19 C H41 H 8.377 0.02 1 225 . 19 C H42 H 7.055 0.02 1 226 . 19 C H5 H 5.512 0.02 1 227 . 19 C H6 H 7.675 0.02 1 228 . 19 C C5 C 98.211 0.20 1 229 . 19 C C6 C 141.690 0.20 1 230 . 19 C H1' H 5.763 0.02 1 231 . 19 C H2' H 4.010 0.02 1 232 . 19 C H3' H 4.175 0.02 1 233 . 19 C H4' H 4.165 0.02 1 234 . 19 C H5' H 4.486 0.02 1 235 . 19 C H5'' H 4.032 0.02 1 236 . 19 C C1' C 92.942 0.20 1 237 . 19 C C2' C 77.547 0.20 1 238 . 19 C C3' C 69.650 0.20 1 239 . 19 C C4' C 83.371 0.20 1 240 . 19 C C5' C 65.043 0.20 1 stop_ save_