data_34302 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; The major G-quadruplex form of HIV-1 LTR ; _BMRB_accession_number 34302 _BMRB_flat_file_name bmr34302.str _Entry_type original _Submission_date 2018-07-11 _Accession_date 2018-07-11 _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 Phan A. T. . 2 Heddi B. . . 3 Butovskaya E. . . 4 Bakalar B. . . 5 Richter S. N. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 229 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-07-31 update BMRB 'update entry citation' 2018-10-12 original author 'original release' stop_ _Original_release_date 2018-07-13 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Major G-Quadruplex Form of HIV-1 LTR Reveals a (3 + 1) Folding Topology Containing a Stem-Loop ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 30299955 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Butovskaya E. . . 2 Heddi B. . . 3 Bakalar B. . . 4 Richter S. N. . 5 Phan A. T. . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_volume 140 _Journal_issue 42 _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 13654 _Page_last 13662 _Year 2018 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'DNA (28-MER)' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity_1 stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common entity_1 _Molecular_mass 8865.647 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 28 _Mol_residue_sequence ; GGGAGGCGTGGCCTGGGCGG GACTGGGG ; loop_ _Residue_seq_code _Residue_label 1 DG 2 DG 3 DG 4 DA 5 DG 6 DG 7 DC 8 DG 9 DT 10 DG 11 DG 12 DC 13 DC 14 DT 15 DG 16 DG 17 DG 18 DC 19 DG 20 DG 21 DG 22 DA 23 DC 24 DT 25 DG 26 DG 27 DG 28 DG 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 $entity_1 HIV-1 11676 Viruses . Lentivirus HIV-1 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 $entity_1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '70 mM NA potassium chloride, 20 mM NA potassium phosphate, 1 mM DNA (28-MER), 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling 'potassium chloride' 70 mM 'natural abundance' 'potassium phosphate' 20 mM 'natural abundance' $entity_1 1 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceII _Field_strength 600 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceII _Field_strength 700 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_1H-13C_HMBC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HMBC' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_aromatic_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aromatic' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 90 . mM pH 7.0 . pH pressure 1 . Pa temperature 298 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_shift_reference_1 _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 H 1 'methyl protons' ppm 0.000 internal direct . . . 1.0 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_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-1H TOCSY' '2D 1H-13C HSQC' '2D 1H-13C HMBC' '2D 1H-13C HSQC aromatic' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name entity_1 _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 1 DG H1 H 11.801 0.002 . 2 1 1 DG H1' H 5.854 0.001 . 3 1 1 DG H2' H 2.692 0.002 . 4 1 1 DG H2'' H 2.771 0.002 . 5 1 1 DG H3' H 4.976 0.002 . 6 1 1 DG H4' H 4.362 0.075 . 7 1 1 DG H8 H 7.173 0.001 . 8 2 2 DG H1 H 11.543 0.002 . 9 2 2 DG H1' H 5.794 0.002 . 10 2 2 DG H2' H 2.455 0.003 . 11 2 2 DG H2'' H 2.683 0.001 . 12 2 2 DG H3' H 4.994 0.003 . 13 2 2 DG H4' H 4.390 0.004 . 14 2 2 DG H8 H 7.790 0.001 . 15 3 3 DG H1' H 5.318 0.001 . 16 3 3 DG H2' H 2.242 0.003 . 17 3 3 DG H2'' H 2.334 0.001 . 18 3 3 DG H3' H 4.863 0.003 . 19 3 3 DG H4' H 4.190 0.005 . 20 3 3 DG H8 H 7.570 0.002 . 21 4 4 DA H1' H 5.467 0.002 . 22 4 4 DA H2 H 7.485 0.004 . 23 4 4 DA H2' H 2.283 0.002 . 24 4 4 DA H2'' H 2.456 0.001 . 25 4 4 DA H3' H 4.803 0.002 . 26 4 4 DA H4' H 4.116 0.005 . 27 4 4 DA H5' H 4.015 0.005 . 28 4 4 DA H5'' H 3.979 0.002 . 29 4 4 DA H8 H 7.836 0.001 . 30 5 5 DG H1 H 12.713 0.002 . 31 5 5 DG H1' H 5.498 0.002 . 32 5 5 DG H2' H 2.553 0.002 . 33 5 5 DG H2'' H 2.649 0.002 . 34 5 5 DG H3' H 4.901 0.003 . 35 5 5 DG H4' H 4.227 0.003 . 36 5 5 DG H5' H 4.026 0.002 . 37 5 5 DG H5'' H 3.909 0.004 . 38 5 5 DG H8 H 7.668 0.002 . 39 6 6 DG H1 H 12.855 0.003 . 40 6 6 DG H1' H 5.780 0.002 . 41 6 6 DG H2' H 2.283 0.001 . 42 6 6 DG H2'' H 2.536 0.001 . 43 6 6 DG H3' H 4.855 0.002 . 44 6 6 DG H4' H 4.200 0.043 . 45 6 6 DG H8 H 7.502 0.001 . 46 7 7 DC H1' H 5.913 0.001 . 47 7 7 DC H2' H 1.661 0.003 . 48 7 7 DC H2'' H 2.020 0.003 . 49 7 7 DC H3' H 4.717 0.004 . 50 7 7 DC H4' H 4.022 0.001 . 51 7 7 DC H5 H 5.217 0.002 . 52 7 7 DC H5'' H 4.137 0.001 . 53 7 7 DC H6 H 7.060 0.002 . 54 8 8 DG H1' H 5.894 0.003 . 55 8 8 DG H2' H 2.666 0.001 . 56 8 8 DG H2'' H 2.601 0.001 . 57 8 8 DG H3' H 4.842 0.002 . 58 8 8 DG H4' H 4.308 0.002 . 59 8 8 DG H5' H 3.828 0.163 . 60 8 8 DG H8 H 7.976 0.001 . 61 9 9 DT H1' H 5.780 0.004 . 62 9 9 DT H2' H 1.825 0.002 . 63 9 9 DT H2'' H 2.044 0.002 . 64 9 9 DT H3' H 4.597 0.001 . 65 9 9 DT H4' H 3.467 0.014 . 66 9 9 DT H5' H 3.703 0.012 . 67 9 9 DT H5'' H 3.727 0.002 . 68 9 9 DT H6 H 7.160 0.001 . 69 9 9 DT H71 H 1.440 0.002 . 70 9 9 DT H72 H 1.440 0.002 . 71 9 9 DT H73 H 1.440 0.002 . 72 10 10 DG H1' H 5.586 0.002 . 73 10 10 DG H2' H 2.530 0.003 . 74 10 10 DG H2'' H 2.492 0.003 . 75 10 10 DG H3' H 4.722 0.004 . 76 10 10 DG H4' H 4.109 0.003 . 77 10 10 DG H5' H 3.865 0.001 . 78 10 10 DG H5'' H 3.721 0.003 . 79 10 10 DG H8 H 7.743 0.001 . 80 11 11 DG H1' H 5.810 0.003 . 81 11 11 DG H2' H 2.610 0.000 . 82 11 11 DG H2'' H 2.713 0.002 . 83 11 11 DG H3' H 4.907 0.005 . 84 11 11 DG H4' H 4.360 0.003 . 85 11 11 DG H5' H 4.217 0.166 . 86 11 11 DG H8 H 7.943 0.001 . 87 12 12 DC H1' H 5.974 0.002 . 88 12 12 DC H2' H 2.108 0.002 . 89 12 12 DC H2'' H 2.422 0.002 . 90 12 12 DC H3' H 4.754 0.003 . 91 12 12 DC H4' H 4.216 0.003 . 92 12 12 DC H5 H 5.391 0.001 . 93 12 12 DC H6 H 7.449 0.002 . 94 13 13 DC H1' H 6.061 0.003 . 95 13 13 DC H2' H 1.876 0.002 . 96 13 13 DC H2'' H 2.002 0.002 . 97 13 13 DC H3' H 4.632 0.003 . 98 13 13 DC H4' H 4.194 0.001 . 99 13 13 DC H5 H 5.578 0.003 . 100 13 13 DC H5' H 3.957 0.003 . 101 13 13 DC H6 H 7.464 0.002 . 102 14 14 DT H1' H 5.836 0.004 . 103 14 14 DT H2' H 2.209 0.001 . 104 14 14 DT H2'' H 2.304 0.004 . 105 14 14 DT H3' H 4.827 0.002 . 106 14 14 DT H4' H 3.812 0.005 . 107 14 14 DT H5' H 4.079 0.002 . 108 14 14 DT H6 H 7.243 0.001 . 109 14 14 DT H71 H 1.583 0.004 . 110 14 14 DT H72 H 1.583 0.004 . 111 14 14 DT H73 H 1.583 0.004 . 112 15 15 DG H1 H 12.006 0.002 . 113 15 15 DG H1' H 6.087 0.003 . 114 15 15 DG H2' H 3.577 0.002 . 115 15 15 DG H2'' H 3.057 0.001 . 116 15 15 DG H3' H 4.977 0.001 . 117 15 15 DG H4' H 4.444 0.001 . 118 15 15 DG H5' H 4.444 0.002 . 119 15 15 DG H5'' H 4.393 0.008 . 120 15 15 DG H8 H 7.490 0.001 . 121 16 16 DG H1 H 11.662 0.003 . 122 16 16 DG H1' H 6.102 0.003 . 123 16 16 DG H2' H 2.751 0.002 . 124 16 16 DG H2'' H 3.045 0.005 . 125 16 16 DG H3' H 5.128 0.004 . 126 16 16 DG H4' H 4.561 0.004 . 127 16 16 DG H5' H 4.482 0.104 . 128 16 16 DG H5'' H 4.296 0.002 . 129 16 16 DG H8 H 8.200 0.001 . 130 17 17 DG H1 H 11.116 0.003 . 131 17 17 DG H1' H 6.522 0.002 . 132 17 17 DG H2' H 2.786 0.003 . 133 17 17 DG H2'' H 2.699 0.001 . 134 17 17 DG H3' H 5.156 0.004 . 135 17 17 DG H4' H 4.692 0.004 . 136 17 17 DG H5' H 4.466 0.000 . 137 17 17 DG H5'' H 4.396 0.000 . 138 17 17 DG H8 H 7.771 0.002 . 139 18 18 DC H1' H 6.488 0.002 . 140 18 18 DC H2' H 2.371 0.001 . 141 18 18 DC H2'' H 2.811 0.001 . 142 18 18 DC H3' H 5.079 0.003 . 143 18 18 DC H4' H 4.837 0.007 . 144 18 18 DC H5 H 6.192 0.000 . 145 18 18 DC H5' H 4.389 0.002 . 146 18 18 DC H5'' H 4.331 0.000 . 147 18 18 DC H6 H 8.034 0.002 . 148 19 19 DG H1 H 11.661 0.002 . 149 19 19 DG H1' H 5.986 0.002 . 150 19 19 DG H2' H 2.977 0.001 . 151 19 19 DG H2'' H 2.746 0.003 . 152 19 19 DG H3' H 5.069 0.002 . 153 19 19 DG H4' H 4.219 0.000 . 154 19 19 DG H8 H 7.294 0.002 . 155 20 20 DG H1 H 11.735 0.004 . 156 20 20 DG H1' H 5.844 0.003 . 157 20 20 DG H2' H 2.628 0.000 . 158 20 20 DG H2'' H 2.629 0.000 . 159 20 20 DG H3' H 5.057 0.004 . 160 20 20 DG H4' H 4.442 0.003 . 161 20 20 DG H5' H 4.220 0.000 . 162 20 20 DG H8 H 8.135 0.002 . 163 21 21 DG H1 H 11.580 0.003 . 164 21 21 DG H1' H 6.115 0.003 . 165 21 21 DG H2' H 2.452 0.003 . 166 21 21 DG H2'' H 2.693 0.002 . 167 21 21 DG H3' H 4.905 0.005 . 168 21 21 DG H4' H 4.442 0.010 . 169 21 21 DG H8 H 7.277 0.002 . 170 22 22 DA H1' H 6.019 0.002 . 171 22 22 DA H2 H 8.127 0.004 . 172 22 22 DA H2' H 2.612 0.000 . 173 22 22 DA H2'' H 2.612 0.001 . 174 22 22 DA H3' H 4.683 0.004 . 175 22 22 DA H4' H 4.293 0.007 . 176 22 22 DA H5' H 4.164 0.006 . 177 22 22 DA H5'' H 4.145 0.000 . 178 22 22 DA H8 H 8.256 0.001 . 179 23 23 DC H1' H 5.608 0.002 . 180 23 23 DC H2' H 1.744 0.001 . 181 23 23 DC H2'' H 2.148 0.004 . 182 23 23 DC H3' H 4.574 0.004 . 183 23 23 DC H4' H 3.841 0.025 . 184 23 23 DC H5 H 5.386 0.002 . 185 23 23 DC H5' H 3.850 0.003 . 186 23 23 DC H6 H 7.207 0.002 . 187 24 24 DT H1' H 5.614 0.002 . 188 24 24 DT H2' H 1.862 0.001 . 189 24 24 DT H2'' H 2.216 0.004 . 190 24 24 DT H3' H 4.626 0.003 . 191 24 24 DT H4' H 3.874 0.008 . 192 24 24 DT H5' H 3.362 0.007 . 193 24 24 DT H5'' H 3.630 0.005 . 194 24 24 DT H6 H 6.958 0.003 . 195 24 24 DT H71 H 1.471 0.002 . 196 24 24 DT H72 H 1.471 0.002 . 197 24 24 DT H73 H 1.471 0.002 . 198 25 25 DG H1 H 11.047 0.003 . 199 25 25 DG H1' H 6.132 0.002 . 200 25 25 DG H2' H 2.808 0.000 . 201 25 25 DG H2'' H 2.868 0.003 . 202 25 25 DG H3' H 4.400 0.003 . 203 25 25 DG H4' H 3.979 0.000 . 204 25 25 DG H5' H 3.980 0.000 . 205 25 25 DG H8 H 7.245 0.006 . 206 26 26 DG H1 H 11.298 0.003 . 207 26 26 DG H1' H 5.989 0.004 . 208 26 26 DG H2' H 2.973 0.001 . 209 26 26 DG H2'' H 2.738 0.003 . 210 26 26 DG H3' H 4.964 0.003 . 211 26 26 DG H4' H 4.126 0.002 . 212 26 26 DG H8 H 7.398 0.001 . 213 27 27 DG H1 H 11.762 0.004 . 214 27 27 DG H1' H 6.157 0.003 . 215 27 27 DG H2' H 2.957 0.002 . 216 27 27 DG H2'' H 2.603 0.002 . 217 27 27 DG H3' H 4.858 0.002 . 218 27 27 DG H4' H 4.553 0.003 . 219 27 27 DG H5' H 4.310 0.000 . 220 27 27 DG H5'' H 4.393 0.000 . 221 27 27 DG H8 H 7.689 0.000 . 222 28 28 DG H1 H 11.501 0.006 . 223 28 28 DG H1' H 6.457 0.003 . 224 28 28 DG H2' H 2.654 0.002 . 225 28 28 DG H2'' H 2.548 0.001 . 226 28 28 DG H3' H 4.742 0.002 . 227 28 28 DG H4' H 4.431 0.001 . 228 28 28 DG H5' H 4.287 0.002 . 229 28 28 DG H8 H 7.942 0.001 . stop_ save_