data_36168 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of G-quadruplex formed in vegfr-2 proximal promoter sequence ; _BMRB_accession_number 36168 _BMRB_flat_file_name bmr36168.str _Entry_type original _Submission_date 2018-02-28 _Accession_date 2018-04-17 _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 Liu Y. . . 2 Lan W. X. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 236 "13C chemical shifts" 11 "31P chemical shifts" 24 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-01-09 original BMRB . stop_ _Original_release_date 2018-04-17 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; A putative G-quadruplex structure in the proximal promoter of VEGFR-2 has implications for drug design to inhibit tumor angiogenesis. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 29666187 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Liu Yaping . . 2 Lan Wenxian . . 3 Wang Chunxi . . 4 Cao Chunyang . . stop_ _Journal_abbreviation 'J. Biol. Chem.' _Journal_name_full 'The Journal of biological chemistry' _Journal_volume 293 _Journal_issue 23 _Journal_ISSN 0021-9258 _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 8947 _Page_last 8955 _Year 2018 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name "DNA (5'-D(*GP*GP*GP*TP*AP*CP*CP*CP*GP*GP*GP*TP*GP*AP*GP*GP*TP*GP*CP*GP*GP*GP*GP*T)-3')" _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 7563.837 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 24 _Mol_residue_sequence ; GGGTACCCGGGTGAGGTGCG GGGT ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DG 2 2 DG 3 3 DG 4 4 DT 5 5 DA 6 6 DC 7 7 DC 8 8 DC 9 9 DG 10 10 DG 11 11 DG 12 12 DT 13 13 DG 14 14 DA 15 15 DG 16 16 DG 17 17 DT 18 18 DG 19 19 DC 20 20 DG 21 21 DG 22 22 DG 23 23 DG 24 24 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 $entity_1 . 32630 . . . . 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 ; 1 mM DNA (5'-D(*GP*GP*GP*TP*AP*CP*CP*CP*GP*GP*GP*TP*GP*AP*GP*GP*TP*GP*CP*GP*GP*GP*GP*T)-3'), 20 mM potassium phosphate, 80 mM potassium chloride, 90% H2O/10% D2O ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1 mM 'natural abundance' 'potassium chloride' 80 mM 'natural abundance' 'potassium phosphate' 20 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % [U-2H] stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details ; 1.0 mM DNA (5'-D(*GP*GP*GP*TP*AP*CP*CP*CP*GP*GP*GP*TP*GP*AP*GP*GP*TP*GP*CP*GP*GP*GP*GP*T)-3'), 80 mM potassium chloride, 20 mM potassium phosphate, 100% D2O ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1.0 mM 'natural abundance' 'potassium chloride' 80 mM 'natural abundance' 'potassium phosphate' 20 mM 'natural abundance' D2O 100 % [U-2H] stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type solution _Details ; 0.1 mM [U-13C; U-15N]-Gua DNA (5'-D(*GP*GP*GP*TP*AP*CP*CP*CP*GP*GP*GP*TP*GP*AP*GP*GP*TP*GP*CP*GP*GP*GP*GP*T)-3'), 80 mM potassium chloride, 20 mM potassium phosphate, 90% H2O/10% D2O ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.1 mM '[U-13C; U-15N]-Gua' 'potassium chloride' 80 mM 'natural abundance' 'potassium phosphate' 20 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % [U-2H] stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name CNS _Version . loop_ _Vendor _Address _Electronic_address 'Brunger A.T. et.al.' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 800 _Details . save_ save_NMR_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _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_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 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' 100 . mM pH 6.8 . pH pressure 1 . atm temperature 293 . 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 C 13 'methyl protons' ppm 0.000 internal indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0.000 internal direct . . . 1.0 DSS N 15 'methyl protons' ppm 0.000 internal indirect . . . 0.101329118 'phosphoric acid' P 31 phosphorus 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 DQF-COSY' '2D 1H-13C HSQC' stop_ loop_ _Sample_label $sample_1 $sample_2 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 11.711 . . 2 1 1 DG H1' H 5.703 . . 3 1 1 DG H2' H 2.461 . . 4 1 1 DG H2'' H 2.220 . . 5 1 1 DG H3' H 4.619 . . 6 1 1 DG H4' H 4.149 . . 7 1 1 DG H5' H 3.907 . . 8 1 1 DG H5'' H 3.901 . . 9 1 1 DG H8 H 7.079 . . 10 1 1 DG H21 H 5.531 . . 11 1 1 DG H22 H 8.276 . . 12 1 1 DG C8 C 119.475 . . 13 1 1 DG P P -0.888 . . 14 2 2 DG H1 H 11.580 . . 15 2 2 DG H1' H 5.592 . . 16 2 2 DG H2' H 2.102 . . 17 2 2 DG H2'' H 2.401 . . 18 2 2 DG H3' H 4.995 . . 19 2 2 DG H4' H 3.960 . . 20 2 2 DG H5' H 3.506 . . 21 2 2 DG H5'' H 3.309 . . 22 2 2 DG H8 H 7.331 . . 23 2 2 DG H21 H 6.036 . . 24 2 2 DG H22 H 8.515 . . 25 2 2 DG C8 C 117.070 . . 26 2 2 DG P P -1.242 . . 27 3 3 DG H1' H 5.317 . . 28 3 3 DG H2' H 2.216 . . 29 3 3 DG H2'' H 2.275 . . 30 3 3 DG H3' H 4.937 . . 31 3 3 DG H4' H 4.145 . . 32 3 3 DG H5' H 4.084 . . 33 3 3 DG H5'' H 3.962 . . 34 3 3 DG H8 H 7.682 . . 35 3 3 DG P P -0.323 . . 36 4 4 DT H1' H 5.087 . . 37 4 4 DT H2' H 1.654 . . 38 4 4 DT H2'' H 1.398 . . 39 4 4 DT H4' H 4.198 . . 40 4 4 DT H5' H 3.766 . . 41 4 4 DT H5'' H 4.094 . . 42 4 4 DT H6 H 6.748 . . 43 4 4 DT H71 H 1.223 . . 44 4 4 DT H72 H 1.223 . . 45 4 4 DT H73 H 1.223 . . 46 4 4 DT P P -0.771 . . 47 5 5 DA H1' H 6.366 . . 48 5 5 DA H3' H 4.992 . . 49 5 5 DA H4' H 4.300 . . 50 5 5 DA H8 H 7.738 . . 51 5 5 DA H61 H 6.552 . . 52 5 5 DA H62 H 6.552 . . 53 5 5 DA P P -1.339 . . 54 6 6 DC H3' H 5.763 . . 55 6 6 DC H4' H 4.149 . . 56 6 6 DC H5 H 5.346 . . 57 6 6 DC H6 H 7.113 . . 58 6 6 DC P P -1.006 . . 59 7 7 DC H1' H 5.629 . . 60 7 7 DC H2' H 1.628 . . 61 7 7 DC H2'' H 1.996 . . 62 7 7 DC H3' H 4.695 . . 63 7 7 DC H4' H 4.322 . . 64 7 7 DC H5 H 5.022 . . 65 7 7 DC H5' H 3.505 . . 66 7 7 DC H5'' H 3.308 . . 67 7 7 DC H6 H 7.025 . . 68 7 7 DC P P 0.224 . . 69 8 8 DC H1' H 5.533 . . 70 8 8 DC H2' H 1.848 . . 71 8 8 DC H2'' H 2.117 . . 72 8 8 DC H3' H 4.409 . . 73 8 8 DC H4' H 4.128 . . 74 8 8 DC H5 H 5.565 . . 75 8 8 DC H5' H 3.167 . . 76 8 8 DC H5'' H 3.394 . . 77 8 8 DC H6 H 7.185 . . 78 8 8 DC P P -0.326 . . 79 9 9 DG H1 H 11.996 . . 80 9 9 DG H1' H 5.665 . . 81 9 9 DG H2' H 3.167 . . 82 9 9 DG H2'' H 2.730 . . 83 9 9 DG H3' H 4.653 . . 84 9 9 DG H4' H 4.236 . . 85 9 9 DG H5' H 3.799 . . 86 9 9 DG H5'' H 4.026 . . 87 9 9 DG H8 H 7.290 . . 88 9 9 DG H21 H 7.185 . . 89 9 9 DG H22 H 8.199 . . 90 9 9 DG C8 C 119.969 . . 91 9 9 DG P P -1.673 . . 92 10 10 DG H1 H 11.335 . . 93 10 10 DG H1' H 5.733 . . 94 10 10 DG H2' H 2.671 . . 95 10 10 DG H2'' H 2.467 . . 96 10 10 DG H3' H 4.651 . . 97 10 10 DG H4' H 4.244 . . 98 10 10 DG H5' H 4.064 . . 99 10 10 DG H5'' H 3.899 . . 100 10 10 DG H8 H 8.043 . . 101 10 10 DG H21 H 6.428 . . 102 10 10 DG H22 H 9.448 . . 103 10 10 DG C8 C 116.831 . . 104 10 10 DG P P -1.343 . . 105 11 11 DG H1 H 11.004 . . 106 11 11 DG H1' H 6.183 . . 107 11 11 DG H2' H 2.378 . . 108 11 11 DG H2'' H 2.383 . . 109 11 11 DG H3' H 4.489 . . 110 11 11 DG H4' H 4.140 . . 111 11 11 DG H5' H 4.032 . . 112 11 11 DG H5'' H 4.025 . . 113 11 11 DG H8 H 7.428 . . 114 11 11 DG H21 H 6.221 . . 115 11 11 DG H22 H 8.276 . . 116 11 11 DG C8 C 116.980 . . 117 11 11 DG P P -0.778 . . 118 12 12 DT H1' H 5.847 . . 119 12 12 DT H2' H 1.946 . . 120 12 12 DT H2'' H 2.156 . . 121 12 12 DT H3' H 4.720 . . 122 12 12 DT H4' H 4.226 . . 123 12 12 DT H5' H 3.801 . . 124 12 12 DT H5'' H 3.801 . . 125 12 12 DT H6 H 7.470 . . 126 12 12 DT H71 H 1.682 . . 127 12 12 DT H72 H 1.682 . . 128 12 12 DT H73 H 1.682 . . 129 12 12 DT P P -0.977 . . 130 13 13 DG H1 H 11.226 . . 131 13 13 DG H1' H 5.828 . . 132 13 13 DG H2' H 1.936 . . 133 13 13 DG H2'' H 2.151 . . 134 13 13 DG H3' H 4.955 . . 135 13 13 DG H4' H 4.322 . . 136 13 13 DG H8 H 7.083 . . 137 13 13 DG H21 H 5.904 . . 138 13 13 DG H22 H 9.352 . . 139 13 13 DG P P 0.219 . . 140 14 14 DA H1' H 6.356 . . 141 14 14 DA H2' H 2.314 . . 142 14 14 DA H2'' H 2.548 . . 143 14 14 DA H3' H 4.735 . . 144 14 14 DA H4' H 4.184 . . 145 14 14 DA H5' H 3.774 . . 146 14 14 DA H5'' H 4.057 . . 147 14 14 DA H8 H 8.121 . . 148 14 14 DA H61 H 6.558 . . 149 14 14 DA H62 H 6.558 . . 150 14 14 DA P P -0.782 . . 151 15 15 DG H1 H 11.354 . . 152 15 15 DG H1' H 5.840 . . 153 15 15 DG H2' H 2.550 . . 154 15 15 DG H2'' H 2.033 . . 155 15 15 DG H3' H 4.598 . . 156 15 15 DG H4' H 4.268 . . 157 15 15 DG H5' H 3.621 . . 158 15 15 DG H5'' H 3.621 . . 159 15 15 DG H8 H 7.063 . . 160 15 15 DG H21 H 5.661 . . 161 15 15 DG H22 H 9.887 . . 162 15 15 DG C8 C 117.746 . . 163 15 15 DG P P -0.387 . . 164 16 16 DG H1 H 11.349 . . 165 16 16 DG H1' H 6.091 . . 166 16 16 DG H2' H 2.404 . . 167 16 16 DG H2'' H 2.543 . . 168 16 16 DG H3' H 4.688 . . 169 16 16 DG H4' H 4.315 . . 170 16 16 DG H5' H 3.858 . . 171 16 16 DG H5'' H 4.026 . . 172 16 16 DG H8 H 7.522 . . 173 16 16 DG H21 H 5.360 . . 174 16 16 DG H22 H 9.901 . . 175 16 16 DG C8 C 117.072 . . 176 16 16 DG P P -0.631 . . 177 17 17 DT H1' H 6.016 . . 178 17 17 DT H2' H 2.217 . . 179 17 17 DT H2'' H 2.071 . . 180 17 17 DT H3' H 4.513 . . 181 17 17 DT H4' H 4.053 . . 182 17 17 DT H5' H 3.895 . . 183 17 17 DT H5'' H 3.895 . . 184 17 17 DT H6 H 7.368 . . 185 17 17 DT H71 H 1.454 . . 186 17 17 DT H72 H 1.454 . . 187 17 17 DT H73 H 1.454 . . 188 17 17 DT P P -0.424 . . 189 18 18 DG H1' H 5.926 . . 190 18 18 DG H2' H 1.981 . . 191 18 18 DG H2'' H 2.373 . . 192 18 18 DG H3' H 4.761 . . 193 18 18 DG H4' H 4.283 . . 194 18 18 DG H5' H 3.864 . . 195 18 18 DG H5'' H 3.742 . . 196 18 18 DG H8 H 7.237 . . 197 18 18 DG P P -0.973 . . 198 19 19 DC H1' H 5.344 . . 199 19 19 DC H2' H 1.827 . . 200 19 19 DC H2'' H 2.041 . . 201 19 19 DC H3' H 5.003 . . 202 19 19 DC H4' H 4.405 . . 203 19 19 DC H5 H 5.338 . . 204 19 19 DC H5' H 3.703 . . 205 19 19 DC H5'' H 3.858 . . 206 19 19 DC H6 H 7.242 . . 207 19 19 DC P P -0.774 . . 208 20 20 DG H1 H 10.939 . . 209 20 20 DG H1' H 5.925 . . 210 20 20 DG H2' H 2.662 . . 211 20 20 DG H2'' H 2.505 . . 212 20 20 DG H3' H 5.534 . . 213 20 20 DG H4' H 3.967 . . 214 20 20 DG H5' H 3.753 . . 215 20 20 DG H5'' H 3.501 . . 216 20 20 DG H8 H 7.083 . . 217 20 20 DG H21 H 5.388 . . 218 20 20 DG H22 H 7.024 . . 219 20 20 DG C8 C 118.586 . . 220 20 20 DG P P -1.677 . . 221 21 21 DG H1 H 11.250 . . 222 21 21 DG H1' H 5.543 . . 223 21 21 DG H2' H 1.860 . . 224 21 21 DG H2'' H 2.120 . . 225 21 21 DG H3' H 4.554 . . 226 21 21 DG H4' H 3.969 . . 227 21 21 DG H5' H 3.391 . . 228 21 21 DG H5'' H 3.181 . . 229 21 21 DG H8 H 7.083 . . 230 21 21 DG H21 H 6.145 . . 231 21 21 DG H22 H 9.593 . . 232 21 21 DG C8 C 118.234 . . 233 21 21 DG P P -0.757 . . 234 22 22 DG H1 H 11.358 . . 235 22 22 DG H1' H 5.866 . . 236 22 22 DG H2' H 2.740 . . 237 22 22 DG H2'' H 2.302 . . 238 22 22 DG H3' H 4.595 . . 239 22 22 DG H4' H 4.045 . . 240 22 22 DG H5' H 3.674 . . 241 22 22 DG H5'' H 3.435 . . 242 22 22 DG H8 H 7.343 . . 243 22 22 DG H21 H 6.057 . . 244 22 22 DG H22 H 9.898 . . 245 22 22 DG C8 C 117.065 . . 246 22 22 DG P P -1.677 . . 247 23 23 DG H1 H 11.130 . . 248 23 23 DG H1' H 6.092 . . 249 23 23 DG H2' H 2.544 . . 250 23 23 DG H2'' H 2.404 . . 251 23 23 DG H3' H 4.942 . . 252 23 23 DG H4' H 4.346 . . 253 23 23 DG H5' H 4.037 . . 254 23 23 DG H5'' H 4.037 . . 255 23 23 DG H8 H 7.616 . . 256 23 23 DG H21 H 6.085 . . 257 23 23 DG H22 H 8.399 . . 258 23 23 DG C8 C 117.916 . . 259 23 23 DG P P -0.896 . . 260 24 24 DT H1' H 5.919 . . 261 24 24 DT H2' H 2.372 . . 262 24 24 DT H2'' H 1.985 . . 263 24 24 DT H3' H 5.544 . . 264 24 24 DT H4' H 4.374 . . 265 24 24 DT H5' H 3.694 . . 266 24 24 DT H5'' H 3.953 . . 267 24 24 DT H6 H 7.192 . . 268 24 24 DT H71 H 1.319 . . 269 24 24 DT H72 H 1.319 . . 270 24 24 DT H73 H 1.319 . . 271 24 24 DT P P -1.254 . . stop_ save_