data_18902 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of the major G-quadruplex formed in the human VEGF promoter: Insights into loop interactions of the parallel G-quadruplexes ; _BMRB_accession_number 18902 _BMRB_flat_file_name bmr18902.str _Entry_type original _Submission_date 2012-12-14 _Accession_date 2012-12-14 _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 Agrawal Prashansa . . 2 Hatzakis Emmanuel . . 3 Guo Kexiao . . 4 Carver Megan . . 5 Yang Danzhou . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 202 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-12-11 update BMRB 'update entry citation' 2013-09-16 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Solution structure of the major G-quadruplex formed in the human VEGF promoter in K+: insights into loop interactions of the parallel G-quadruplexes.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 24005038 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Agrawal Prashansa . . 2 Hatzakis Emmanuel . . 3 Guo Kexiao . . 4 Carver Megan . . 5 Yang Danzhou . . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_name_full 'Nucleic acids research' _Journal_volume 41 _Journal_issue 22 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 10584 _Page_last 10592 _Year 2013 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'major G-quadruplex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label major_G-quadruplex $major_G-quadruplex 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_major_G-quadruplex _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common major_G-quadruplex _Molecular_mass 6922.468 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 22 _Mol_residue_sequence ; CGGGGCGGGCCTTGGGCGGG GT ; loop_ _Residue_seq_code _Residue_label 1 DC 2 DG 3 DG 4 DG 5 DG 6 DC 7 DG 8 DG 9 DG 10 DC 11 DC 12 DT 13 DT 14 DG 15 DG 16 DG 17 DC 18 DG 19 DG 20 DG 21 DG 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 $major_G-quadruplex Human 9606 Eukaryota Metazoa Homo sapiens 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 $major_G-quadruplex 'recombinant technology' . . . . . 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 _Isotopic_labeling $major_G-quadruplex 0.2 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_X-PLOR_NIH _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address Brunger . . stop_ loop_ _Task 'geometry optimization' 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_ ############################# # 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-1H_COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _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' 100 . 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 0.2 external 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_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' 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 major_G-quadruplex _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 5.665 . . 2 1 1 DC H2' H 1.171 . . 3 1 1 DC H2'' H 1.947 . . 4 1 1 DC H3' H 4.297 . . 5 1 1 DC H4' H 4.225 . . 6 1 1 DC H5 H 5.554 . . 7 1 1 DC H5' H 3.373 . . 8 1 1 DC H5'' H 3.768 . . 9 1 1 DC H6 H 7.239 . . 10 2 2 DG H1' H 5.330 . . 11 2 2 DG H2' H 2.477 . . 12 2 2 DG H2'' H 2.508 . . 13 2 2 DG H3' H 4.753 . . 14 2 2 DG H4' H 4.441 . . 15 2 2 DG H5' H 3.777 . . 16 2 2 DG H5'' H 4.068 . . 17 2 2 DG H8 H 7.567 . . 18 3 3 DG H1 H 11.694 . . 19 3 3 DG H1' H 6.055 . . 20 3 3 DG H2' H 2.762 . . 21 3 3 DG H2'' H 2.979 . . 22 3 3 DG H3' H 4.968 . . 23 3 3 DG H4' H 4.401 . . 24 3 3 DG H5' H 4.030 . . 25 3 3 DG H5'' H 4.239 . . 26 3 3 DG H8 H 7.998 . . 27 4 4 DG H1 H 11.188 . . 28 4 4 DG H1' H 6.111 . . 29 4 4 DG H2' H 2.583 . . 30 4 4 DG H2'' H 2.879 . . 31 4 4 DG H3' H 4.957 . . 32 4 4 DG H4' H 4.493 . . 33 4 4 DG H5' H 4.232 . . 34 4 4 DG H5'' H 4.264 . . 35 4 4 DG H8 H 7.673 . . 36 5 5 DG H1 H 11.006 . . 37 5 5 DG H1' H 6.362 . . 38 5 5 DG H2' H 2.626 . . 39 5 5 DG H2'' H 2.493 . . 40 5 5 DG H3' H 5.027 . . 41 5 5 DG H4' H 4.559 . . 42 5 5 DG H5' H 4.358 . . 43 5 5 DG H5'' H 4.220 . . 44 5 5 DG H8 H 7.716 . . 45 6 6 DC H1' H 6.393 . . 46 6 6 DC H2' H 2.330 . . 47 6 6 DC H2'' H 2.646 . . 48 6 6 DC H3' H 4.962 . . 49 6 6 DC H4' H 4.507 . . 50 6 6 DC H5 H 6.090 . . 51 6 6 DC H5' H 4.218 . . 52 6 6 DC H5'' H 4.275 . . 53 6 6 DC H6 H 7.911 . . 54 7 7 DG H1 H 11.641 . . 55 7 7 DG H1' H 6.082 . . 56 7 7 DG H2' H 2.413 . . 57 7 7 DG H2'' H 2.864 . . 58 7 7 DG H3' H 5.096 . . 59 7 7 DG H4' H 4.394 . . 60 7 7 DG H5' H 4.181 . . 61 7 7 DG H5'' H 4.283 . . 62 7 7 DG H8 H 7.974 . . 63 8 8 DG H1 H 11.487 . . 64 8 8 DG H1' H 6.050 . . 65 8 8 DG H2' H 2.638 . . 66 8 8 DG H2'' H 2.804 . . 67 8 8 DG H3' H 4.998 . . 68 8 8 DG H4' H 4.471 . . 69 8 8 DG H5' H 4.237 . . 70 8 8 DG H5'' H 4.313 . . 71 8 8 DG H8 H 7.937 . . 72 9 9 DG H1 H 11.293 . . 73 9 9 DG H1' H 6.342 . . 74 9 9 DG H2' H 2.542 . . 75 9 9 DG H2'' H 2.519 . . 76 9 9 DG H3' H 4.914 . . 77 9 9 DG H4' H 4.405 . . 78 9 9 DG H5' H 4.145 . . 79 9 9 DG H5'' H 4.269 . . 80 9 9 DG H8 H 7.774 . . 81 10 10 DC H1' H 6.258 . . 82 10 10 DC H2' H 2.250 . . 83 10 10 DC H2'' H 2.525 . . 84 10 10 DC H3' H 4.773 . . 85 10 10 DC H4' H 4.407 . . 86 10 10 DC H5 H 6.102 . . 87 10 10 DC H5' H 3.991 . . 88 10 10 DC H5'' H 4.130 . . 89 10 10 DC H6 H 7.846 . . 90 11 11 DC H1' H 6.268 . . 91 11 11 DC H2' H 2.303 . . 92 11 11 DC H2'' H 2.564 . . 93 11 11 DC H3' H 4.810 . . 94 11 11 DC H4' H 4.329 . . 95 11 11 DC H5 H 6.078 . . 96 11 11 DC H5' H 4.046 . . 97 11 11 DC H5'' H 4.114 . . 98 11 11 DC H6 H 7.855 . . 99 12 12 DT H1' H 6.275 . . 100 12 12 DT H2' H 2.357 . . 101 12 12 DT H2'' H 2.513 . . 102 12 12 DT H3' H 4.853 . . 103 12 12 DT H4' H 4.323 . . 104 12 12 DT H5' H 4.235 . . 105 12 12 DT H5'' H 4.101 . . 106 12 12 DT H6 H 7.711 . . 107 12 12 DT H71 H 1.872 . . 108 12 12 DT H72 H 1.872 . . 109 12 12 DT H73 H 1.872 . . 110 13 13 DT H1' H 5.992 . . 111 13 13 DT H2' H 2.210 . . 112 13 13 DT H2'' H 2.386 . . 113 13 13 DT H3' H 4.858 . . 114 13 13 DT H4' H 4.195 . . 115 13 13 DT H5' H 3.931 . . 116 13 13 DT H5'' H 4.007 . . 117 13 13 DT H6 H 7.513 . . 118 13 13 DT H71 H 1.567 . . 119 13 13 DT H72 H 1.567 . . 120 13 13 DT H73 H 1.567 . . 121 14 14 DG H1 H 11.940 . . 122 14 14 DG H1' H 6.082 . . 123 14 14 DG H2' H 2.766 . . 124 14 14 DG H2'' H 3.009 . . 125 14 14 DG H3' H 4.958 . . 126 14 14 DG H4' H 4.391 . . 127 14 14 DG H5' H 4.024 . . 128 14 14 DG H5'' H 4.268 . . 129 14 14 DG H8 H 8.125 . . 130 15 15 DG H1 H 11.257 . . 131 15 15 DG H1' H 6.157 . . 132 15 15 DG H2' H 2.669 . . 133 15 15 DG H2'' H 2.888 . . 134 15 15 DG H3' H 4.954 . . 135 15 15 DG H4' H 4.515 . . 136 15 15 DG H5' H 4.157 . . 137 15 15 DG H5'' H 4.282 . . 138 15 15 DG H8 H 7.771 . . 139 16 16 DG H1 H 11.030 . . 140 16 16 DG H1' H 6.393 . . 141 16 16 DG H2' H 2.601 . . 142 16 16 DG H2'' H 2.525 . . 143 16 16 DG H3' H 5.031 . . 144 16 16 DG H4' H 4.578 . . 145 16 16 DG H5' H 4.222 . . 146 16 16 DG H5'' H 4.335 . . 147 16 16 DG H8 H 7.748 . . 148 17 17 DC H1' H 6.417 . . 149 17 17 DC H2' H 2.332 . . 150 17 17 DC H2'' H 2.671 . . 151 17 17 DC H3' H 5.029 . . 152 17 17 DC H4' H 4.561 . . 153 17 17 DC H5 H 6.106 . . 154 17 17 DC H5' H 4.223 . . 155 17 17 DC H5'' H 4.301 . . 156 17 17 DC H6 H 7.936 . . 157 18 18 DG H1 H 11.155 . . 158 18 18 DG H1' H 6.070 . . 159 18 18 DG H2' H 2.347 . . 160 18 18 DG H2'' H 2.812 . . 161 18 18 DG H3' H 5.091 . . 162 18 18 DG H4' H 4.397 . . 163 18 18 DG H5' H 4.185 . . 164 18 18 DG H5'' H 4.278 . . 165 18 18 DG H8 H 7.957 . . 166 19 19 DG H1 H 11.317 . . 167 19 19 DG H1' H 5.928 . . 168 19 19 DG H2' H 2.620 . . 169 19 19 DG H2'' H 2.620 . . 170 19 19 DG H3' H 4.999 . . 171 19 19 DG H4' H 4.446 . . 172 19 19 DG H5' H 4.128 . . 173 19 19 DG H5'' H 4.186 . . 174 19 19 DG H8 H 7.900 . . 175 20 20 DG H1 H 10.968 . . 176 20 20 DG H1' H 5.972 . . 177 20 20 DG H2' H 2.342 . . 178 20 20 DG H2'' H 2.715 . . 179 20 20 DG H3' H 4.870 . . 180 20 20 DG H4' H 4.418 . . 181 20 20 DG H5' H 4.125 . . 182 20 20 DG H5'' H 4.199 . . 183 20 20 DG H8 H 7.420 . . 184 21 21 DG H1' H 5.604 . . 185 21 21 DG H2' H 2.257 . . 186 21 21 DG H2'' H 2.360 . . 187 21 21 DG H3' H 4.726 . . 188 21 21 DG H4' H 4.424 . . 189 21 21 DG H5' H 4.117 . . 190 21 21 DG H5'' H 4.188 . . 191 21 21 DG H8 H 7.628 . . 192 22 22 DT H1' H 5.826 . . 193 22 22 DT H2' H 1.972 . . 194 22 22 DT H2'' H 2.017 . . 195 22 22 DT H3' H 4.306 . . 196 22 22 DT H4' H 3.922 . . 197 22 22 DT H5' H 3.655 . . 198 22 22 DT H5'' H 3.829 . . 199 22 22 DT H6 H 7.180 . . 200 22 22 DT H71 H 1.401 . . 201 22 22 DT H72 H 1.401 . . 202 22 22 DT H73 H 1.401 . . stop_ save_