data_25686 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of a G-quadruplex in the Long Terminal Repeat of the proviral HIV-1 genome ; _BMRB_accession_number 25686 _BMRB_flat_file_name bmr25686.str _Entry_type original _Submission_date 2015-07-02 _Accession_date 2015-07-02 _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 'De Nicola' Beatrice . . 2 Lech 'Christopher Jacques' . . 3 Regmi Sagar . . 4 Heddi Brahim . . 5 Richter Sara . . 6 Phan 'Anh Tuan' . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 209 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2016-08-12 update BMRB 'update entry citation' 2016-06-27 original author 'original release' stop_ _Original_release_date 2016-06-27 save_ ############################# # Citation for this entry # ############################# save_citation1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structure of a G-quadruplex in the Long Terminal Repeat of the proviral HIV-1 genome ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 27298260 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 'de Nicola' Beatrice . . 2 Lech 'Christopher Jacques' . . 3 Regmi Sagar . . 4 Heddi Brahim . . 5 Richter Sara . . 6 Phan 'Anh Tuan' . . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_volume 44 _Journal_issue 13 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 6442 _Page_last 6451 _Year 2016 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'G-quadruplex in the Long Terminal Repeat of the proviral HIV-1 genome' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label "DNA (5'-D(*CP*TP*GP*GP*GP*CP*GP*GP*GP*AP*CP*TP*GP*GP*GP*GP*AP*GP*TP*GP*GP*T)-3')" $DNA_(5'-D(*CP*TP*GP*GP*GP*CP*GP*GP*GP*AP*CP*TP*GP*GP*GP*GP*AP*GP*TP*GP*GP*T)-3') stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_DNA_(5'-D(*CP*TP*GP*GP*GP*CP*GP*GP*GP*AP*CP*TP*GP*GP*GP*GP*AP*GP*TP*GP*GP*T)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(*CP*TP*GP*GP*GP*CP*GP*GP*GP*AP*CP*TP*GP*GP*GP*GP*AP*GP*TP*GP*GP*T)-3') _Molecular_mass 6945.505 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 22 _Mol_residue_sequence ; CTGGGCGGGACTGGGGAGTG GT ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DC 2 2 DT 3 3 DG 4 4 DG 5 5 DG 6 6 DC 7 7 DG 8 8 DG 9 9 DG 10 10 DA 11 11 DC 12 12 DT 13 13 DG 14 14 DG 15 15 DG 16 16 DG 17 17 DA 18 18 DG 19 19 DT 20 20 DG 21 21 DG 22 22 DT 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 $DNA_(5'-D(*CP*TP*GP*GP*GP*CP*GP*GP*GP*AP*CP*TP*GP*GP*GP*GP*AP*GP*TP*GP*GP*T)-3') viruses 12721 Viruses . Lentivirus . 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 $DNA_(5'-D(*CP*TP*GP*GP*GP*CP*GP*GP*GP*AP*CP*TP*GP*GP*GP*GP*AP*GP*TP*GP*GP*T)-3') 'chemical synthesis' . . . . . 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 $DNA_(5'-D(*CP*TP*GP*GP*GP*CP*GP*GP*GP*AP*CP*TP*GP*GP*GP*GP*AP*GP*TP*GP*GP*T)-3') . mM 0.1 1 'natural abundance' K+ 10 mM . . 'natural abundance' H2O 90 % . . 'natural abundance' D2O 10 % . . 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' 'peak picking' stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection stop_ _Details . save_ save_X-PLOR_NIH _Saveframe_category software _Name X-PLOR_NIH _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'geometry optimization' 'structure solution' stop_ _Details . save_ save_AMBER _Saveframe_category software _Name AMBER _Version . loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task refinement 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _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_aliphatic_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aliphatic' _Sample_label $sample_1 save_ save_1D_JR-HMQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '1D JR-HMQC' _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 . atm temperature 298 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_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 0.00 internal direct . . . 1.000000000 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_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $SPARKY stop_ loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-1H TOCSY' '1D JR-HMQC' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name "DNA (5'-D(*CP*TP*GP*GP*GP*CP*GP*GP*GP*AP*CP*TP*GP*GP*GP*GP*AP*GP*TP*GP*GP*T)-3')" _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 DC H1' H 5.882 0.05 1 2 1 1 DC H2' H 1.926 0.05 1 3 1 1 DC H2'' H 2.422 0.05 1 4 1 1 DC H3' H 4.594 0.05 1 5 1 1 DC H4' H 3.972 0.05 1 6 1 1 DC H5 H 5.737 0.05 1 7 1 1 DC H5' H 3.566 0.05 2 8 1 1 DC H5'' H 3.566 0.05 2 9 1 1 DC H6 H 7.561 0.05 1 10 2 2 DT H1' H 5.802 0.05 1 11 2 2 DT H2' H 2.091 0.05 1 12 2 2 DT H2'' H 2.398 0.05 1 13 2 2 DT H3' H 4.734 0.05 1 14 2 2 DT H4' H 4.030 0.05 1 15 2 2 DT H5' H 3.793 0.05 1 16 2 2 DT H5'' H 3.585 0.05 1 17 2 2 DT H6 H 7.344 0.05 1 18 2 2 DT H71 H 1.483 0.05 2 19 2 2 DT H72 H 1.483 0.05 2 20 2 2 DT H73 H 1.483 0.05 2 21 3 3 DG H1 H 12.034 0.05 1 22 3 3 DG H1' H 6.171 0.05 1 23 3 3 DG H2' H 2.867 0.05 1 24 3 3 DG H2'' H 3.102 0.05 1 25 3 3 DG H3' H 4.999 0.05 1 26 3 3 DG H4' H 4.467 0.05 1 27 3 3 DG H5' H 4.113 0.05 2 28 3 3 DG H5'' H 4.113 0.05 2 29 3 3 DG H8 H 8.147 0.05 1 30 4 4 DG H1 H 11.393 0.05 1 31 4 4 DG H1' H 6.216 0.05 1 32 4 4 DG H2' H 2.706 0.05 1 33 4 4 DG H2'' H 2.961 0.05 1 34 4 4 DG H3' H 5.017 0.05 1 35 4 4 DG H4' H 4.586 0.05 1 36 4 4 DG H5' H 4.333 0.05 1 37 4 4 DG H5'' H 4.366 0.05 2 38 4 4 DG H8 H 7.802 0.05 1 39 4 4 DG H21 H 6.815 0.05 1 40 4 4 DG H22 H 9.260 0.05 1 41 5 5 DG H1 H 11.206 0.05 1 42 5 5 DG H1' H 6.460 0.05 1 43 5 5 DG H2' H 2.688 0.05 1 44 5 5 DG H2'' H 2.585 0.05 1 45 5 5 DG H3' H 5.104 0.05 1 46 5 5 DG H4' H 4.663 0.05 1 47 5 5 DG H5' H 4.309 0.05 2 48 5 5 DG H5'' H 4.309 0.05 2 49 5 5 DG H8 H 7.808 0.05 1 50 6 6 DC H1' H 6.507 0.05 1 51 6 6 DC H2' H 2.413 0.05 1 52 6 6 DC H2'' H 2.748 0.05 1 53 6 6 DC H3' H 5.118 0.05 1 54 6 6 DC H4' H 4.657 0.05 1 55 6 6 DC H5 H 6.191 0.05 1 56 6 6 DC H5' H 4.382 0.05 1 57 6 6 DC H5'' H 4.300 0.05 1 58 6 6 DC H6 H 8.027 0.05 1 59 7 7 DG H1 H 11.617 0.05 1 60 7 7 DG H1' H 6.179 0.05 1 61 7 7 DG H2' H 2.499 0.05 1 62 7 7 DG H2'' H 2.924 0.05 1 63 7 7 DG H3' H 5.175 0.05 1 64 7 7 DG H4' H 4.484 0.05 1 65 7 7 DG H5' H 4.363 0.05 1 66 7 7 DG H5'' H 4.288 0.05 1 67 7 7 DG H8 H 8.042 0.05 1 68 8 8 DG H1 H 11.689 0.05 1 69 8 8 DG H1' H 6.021 0.05 1 70 8 8 DG H2' H 2.658 0.05 1 71 8 8 DG H2'' H 2.681 0.05 1 72 8 8 DG H3' H 4.956 0.05 1 73 8 8 DG H4' H 4.483 0.05 1 74 8 8 DG H5' H 4.274 0.05 2 75 8 8 DG H5'' H 4.274 0.05 2 76 8 8 DG H8 H 7.995 0.05 1 77 9 9 DG H1 H 11.344 0.05 1 78 9 9 DG H1' H 6.302 0.05 1 79 9 9 DG H2' H 2.488 0.05 2 80 9 9 DG H2'' H 2.488 0.05 2 81 9 9 DG H3' H 4.798 0.05 1 82 9 9 DG H4' H 4.000 0.05 1 83 9 9 DG H5' H 3.299 0.05 1 84 9 9 DG H5'' H 3.555 0.05 1 85 9 9 DG H8 H 7.736 0.05 1 86 10 10 DA H1' H 6.436 0.05 1 87 10 10 DA H2 H 8.183 0.05 1 88 10 10 DA H2' H 2.974 0.05 1 89 10 10 DA H2'' H 2.845 0.05 1 90 10 10 DA H3' H 5.021 0.05 1 91 10 10 DA H4' H 4.440 0.05 1 92 10 10 DA H5' H 4.203 0.05 1 93 10 10 DA H5'' H 4.120 0.05 1 94 10 10 DA H8 H 8.419 0.05 1 95 11 11 DC H1' H 6.347 0.05 1 96 11 11 DC H2' H 2.384 0.05 1 97 11 11 DC H2'' H 2.637 0.05 1 98 11 11 DC H3' H 4.913 0.05 1 99 11 11 DC H4' H 4.467 0.05 1 100 11 11 DC H5 H 6.090 0.05 1 101 11 11 DC H5' H 4.171 0.05 2 102 11 11 DC H5'' H 4.171 0.05 2 103 11 11 DC H6 H 7.965 0.05 1 104 12 12 DT H1' H 6.124 0.05 1 105 12 12 DT H2' H 1.817 0.05 1 106 12 12 DT H2'' H 2.297 0.05 1 107 12 12 DT H3' H 4.745 0.05 1 108 12 12 DT H4' H 4.219 0.05 1 109 12 12 DT H5' H 4.022 0.05 2 110 12 12 DT H5'' H 4.022 0.05 2 111 12 12 DT H6 H 7.578 0.05 1 112 12 12 DT H71 H 1.917 0.05 1 113 12 12 DT H72 H 1.917 0.05 1 114 12 12 DT H73 H 1.917 0.05 1 115 13 13 DG H1' H 6.067 0.05 1 116 13 13 DG H2' H 2.889 0.05 1 117 13 13 DG H2'' H 2.765 0.05 1 118 13 13 DG H3' H 5.047 0.05 1 119 13 13 DG H4' H 4.356 0.05 1 120 13 13 DG H5' H 3.980 0.05 2 121 13 13 DG H5'' H 3.980 0.05 2 122 13 13 DG H8 H 7.898 0.05 1 123 14 14 DG H1 H 11.959 0.05 1 124 14 14 DG H1' H 6.213 0.05 1 125 14 14 DG H2' H 2.821 0.05 1 126 14 14 DG H2'' H 3.113 0.05 1 127 14 14 DG H3' H 5.081 0.05 1 128 14 14 DG H4' H 4.496 0.05 1 129 14 14 DG H5' H 4.156 0.05 1 130 14 14 DG H5'' H 4.155 0.05 2 131 14 14 DG H8 H 8.178 0.05 1 132 15 15 DG H1 H 11.355 0.05 1 133 15 15 DG H1' H 6.260 0.05 1 134 15 15 DG H2' H 2.733 0.05 1 135 15 15 DG H2'' H 2.997 0.05 1 136 15 15 DG H3' H 5.078 0.05 1 137 15 15 DG H4' H 4.616 0.05 1 138 15 15 DG H5' H 4.338 0.05 1 139 15 15 DG H5'' H 4.338 0.05 1 140 15 15 DG H8 H 7.878 0.05 1 141 15 15 DG H21 H 7.010 0.05 1 142 15 15 DG H22 H 9.530 0.05 1 143 16 16 DG H1 H 11.086 0.05 1 144 16 16 DG H1' H 6.521 0.05 1 145 16 16 DG H2' H 2.673 0.05 1 146 16 16 DG H2'' H 2.611 0.05 1 147 16 16 DG H3' H 5.120 0.05 1 148 16 16 DG H4' H 4.735 0.05 1 149 16 16 DG H5' H 4.478 0.05 1 150 16 16 DG H5'' H 4.478 0.05 1 151 16 16 DG H8 H 7.802 0.05 1 152 17 17 DA H1' H 6.653 0.05 1 153 17 17 DA H2 H 8.136 0.05 1 154 17 17 DA H2' H 2.680 0.05 1 155 17 17 DA H2'' H 2.943 0.05 1 156 17 17 DA H3' H 5.287 0.05 1 157 17 17 DA H4' H 4.528 0.05 1 158 17 17 DA H5' H 4.337 0.05 1 159 17 17 DA H5'' H 4.410 0.05 1 160 17 17 DA H8 H 8.454 0.05 1 161 18 18 DG H1 H 11.579 0.05 1 162 18 18 DG H1' H 6.305 0.05 1 163 18 18 DG H2' H 2.917 0.05 1 164 18 18 DG H2'' H 2.730 0.05 1 165 18 18 DG H3' H 5.046 0.05 1 166 18 18 DG H4' H 4.794 0.05 1 167 18 18 DG H5' H 4.440 0.05 2 168 18 18 DG H5'' H 4.440 0.05 2 169 18 18 DG H8 H 8.175 0.05 1 170 19 19 DT H1' H 5.715 0.05 1 171 19 19 DT H2' H 2.055 0.05 1 172 19 19 DT H2'' H 2.501 0.05 1 173 19 19 DT H3' H 4.711 0.05 1 174 19 19 DT H4' H 4.323 0.05 1 175 19 19 DT H5' H 4.038 0.05 2 176 19 19 DT H5'' H 4.038 0.05 2 177 19 19 DT H6 H 7.137 0.05 1 178 19 19 DT H71 H 1.819 0.05 1 179 19 19 DT H72 H 1.819 0.05 1 180 19 19 DT H73 H 1.819 0.05 1 181 20 20 DG H1 H 11.519 0.05 1 182 20 20 DG H1' H 6.110 0.05 1 183 20 20 DG H2' H 2.602 0.05 1 184 20 20 DG H2'' H 2.791 0.05 1 185 20 20 DG H3' H 5.068 0.05 1 186 20 20 DG H4' H 4.537 0.05 1 187 20 20 DG H5' H 4.265 0.05 2 188 20 20 DG H5'' H 4.265 0.05 2 189 20 20 DG H8 H 7.613 0.05 1 190 21 21 DG H1 H 11.324 0.05 1 191 21 21 DG H1' H 6.262 0.05 1 192 21 21 DG H2' H 2.588 0.05 1 193 21 21 DG H2'' H 2.848 0.05 1 194 21 21 DG H3' H 4.968 0.05 1 195 21 21 DG H4' H 4.550 0.05 1 196 21 21 DG H5' H 4.240 0.05 2 197 21 21 DG H5'' H 4.240 0.05 2 198 21 21 DG H8 H 7.919 0.05 1 199 22 22 DT H1' H 5.969 0.05 1 200 22 22 DT H2' H 2.112 0.05 2 201 22 22 DT H2'' H 2.112 0.05 2 202 22 22 DT H3' H 4.471 0.05 1 203 22 22 DT H4' H 3.999 0.05 1 204 22 22 DT H5' H 4.248 0.05 1 205 22 22 DT H5'' H 4.096 0.05 1 206 22 22 DT H6 H 7.188 0.05 1 207 22 22 DT H71 H 1.545 0.05 1 208 22 22 DT H72 H 1.545 0.05 1 209 22 22 DT H73 H 1.545 0.05 1 stop_ save_