data_17580 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Myc G-quadruplex formed at the 5'-end of NHEIII element ; _BMRB_accession_number 17580 _BMRB_flat_file_name bmr17580.str _Entry_type original _Submission_date 2011-04-07 _Accession_date 2011-04-07 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'Myc G-quadruplex formed at the 5'-end of NHEIII element.' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Mathad Raveendra . . 2 Hatzakis Emmanuel . . 3 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" 161 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-02-10 original author . stop_ _Original_release_date 2012-02-10 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'c-MYC promoter G-quadruplex formed at the 5'-end of NHE III1 element: insights into biological relevance and parallel-stranded G-quadruplex stability.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 21795379 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Mathad Raveendra I. . 2 Hatzakis Emmanuel . . 3 Dai Jixun . . 4 Yang Danzhou . . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_name_full 'Nucleic acids research' _Journal_volume 39 _Journal_issue 20 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 9023 _Page_last 9033 _Year 2011 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Myc G-quadruplex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'Myc G-quadruplex' $DNA_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_DNA_G-quadruplex _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_G-quadruplex _Molecular_mass 510.438 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 19 _Mol_residue_sequence TAGGGAGGGTAGGGAGGGT loop_ _Residue_seq_code _Residue_label 1 DT 2 DA 3 DG 4 DG 5 DG 6 DA 7 DG 8 DG 9 DG 10 DT 11 DA 12 DG 13 DG 14 DG 15 DA 16 DG 17 DG 18 DG 19 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_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 $DNA_G-quadruplex 'chemical synthesis' . Escherichia coli . . 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 $DNA_G-quadruplex 1 mM 'natural abundance' H20 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 refinement 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_ ####################### # 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 0.0 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_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 'Myc 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 DT H1' H 5.753 . 1 2 1 1 DT H2' H 1.659 . 1 3 1 1 DT H2'' H 2.079 . 1 4 1 1 DT H3' H 4.415 . 1 5 1 1 DT H4' H 3.848 . 1 6 1 1 DT H5' H 3.416 . 1 7 1 1 DT H6 H 7.102 . 1 8 1 1 DT H71 H 1.527 . 2 9 1 1 DT H72 H 1.527 . 2 10 1 1 DT H73 H 1.527 . 2 11 2 2 DA H1' H 5.788 . 1 12 2 2 DA H2 H 7.786 . 1 13 2 2 DA H2' H 2.376 . 1 14 2 2 DA H2'' H 2.572 . 1 15 2 2 DA H3' H 4.800 . 1 16 2 2 DA H4' H 4.047 . 1 17 2 2 DA H5' H 3.610 . 1 18 2 2 DA H5'' H 3.832 . 1 19 2 2 DA H8 H 7.918 . 1 20 3 3 DG H1 H 11.702 . 1 21 3 3 DG H1' H 6.050 . 1 22 3 3 DG H2' H 2.761 . 1 23 3 3 DG H2'' H 2.998 . 1 24 3 3 DG H3' H 4.955 . 1 25 3 3 DG H4' H 4.251 . 1 26 3 3 DG H5' H 4.026 . 1 27 3 3 DG H8 H 8.029 . 1 28 4 4 DG H1 H 11.299 . 1 29 4 4 DG H1' H 6.126 . 1 30 4 4 DG H2' H 2.584 . 1 31 4 4 DG H2'' H 2.866 . 1 32 4 4 DG H3' H 4.943 . 1 33 4 4 DG H4' H 4.495 . 1 34 4 4 DG H5' H 4.245 . 2 35 4 4 DG H8 H 7.672 . 1 36 5 5 DG H1 H 11.154 . 1 37 5 5 DG H1' H 6.059 . 1 38 5 5 DG H2' H 2.595 . 1 39 5 5 DG H2'' H 2.879 . 1 40 5 5 DG H3' H 4.948 . 1 41 5 5 DG H4' H 4.490 . 1 42 5 5 DG H5' H 4.256 . 2 43 5 5 DG H8 H 7.684 . 1 44 6 6 DA H1' H 6.327 . 1 45 6 6 DA H2 H 8.287 . 1 46 6 6 DA H2' H 2.580 . 1 47 6 6 DA H2'' H 2.438 . 1 48 6 6 DA H3' H 4.935 . 1 49 6 6 DA H4' H 4.405 . 1 50 6 6 DA H5' H 3.644 . 1 51 6 6 DA H8 H 7.775 . 1 52 7 7 DG H1 H 9.676 . 1 53 7 7 DG H1' H 6.120 . 1 54 7 7 DG H2' H 2.447 . 1 55 7 7 DG H2'' H 2.891 . 1 56 7 7 DG H3' H 5.115 . 1 57 7 7 DG H4' H 4.441 . 1 58 7 7 DG H5' H 4.230 . 1 59 7 7 DG H5'' H 4.329 . 1 60 7 7 DG H8 H 7.984 . 1 61 8 8 DG H1 H 11.542 . 1 62 8 8 DG H1' H 6.097 . 1 63 8 8 DG H2' H 2.623 . 1 64 8 8 DG H2'' H 2.781 . 1 65 8 8 DG H3' H 5.003 . 1 66 8 8 DG H4' H 4.039 . 1 67 8 8 DG H5' H 3.604 . 1 68 8 8 DG H5'' H 3.824 . 1 69 8 8 DG H8 H 7.914 . 1 70 9 9 DG H1 H 11.289 . 1 71 9 9 DG H1' H 6.114 . 1 72 9 9 DG H2' H 2.620 . 1 73 9 9 DG H2'' H 2.796 . 1 74 9 9 DG H3' H 4.986 . 1 75 9 9 DG H4' H 4.419 . 1 76 9 9 DG H5' H 4.197 . 1 77 9 9 DG H8 H 7.771 . 1 78 10 10 DT H1' H 6.153 . 1 79 10 10 DT H2' H 2.130 . 1 80 10 10 DT H2'' H 2.378 . 1 81 10 10 DT H3' H 4.629 . 1 82 10 10 DT H4' H 3.795 . 1 83 10 10 DT H5' H 3.643 . 2 84 10 10 DT H6 H 7.550 . 1 85 10 10 DT H71 H 1.849 . 2 86 10 10 DT H72 H 1.849 . 2 87 10 10 DT H73 H 1.849 . 2 88 11 11 DA H1' H 6.604 . 1 89 11 11 DA H2 H 8.237 . 1 90 11 11 DA H2' H 2.849 . 1 91 11 11 DA H2'' H 3.018 . 1 92 11 11 DA H3' H 5.156 . 1 93 11 11 DA H4' H 4.636 . 1 94 11 11 DA H5' H 4.238 . 2 95 11 11 DA H8 H 8.452 . 1 96 12 12 DG H1 H 11.990 . 1 97 12 12 DG H1' H 6.123 . 1 98 12 12 DG H2' H 2.607 . 1 99 12 12 DG H2'' H 2.929 . 1 100 12 12 DG H3' H 4.972 . 1 101 12 12 DG H4' H 4.401 . 1 102 12 12 DG H5' H 4.080 . 1 103 12 12 DG H5'' H 4.195 . 1 104 12 12 DG H8 H 8.092 . 1 105 13 13 DG H1 H 11.271 . 1 106 13 13 DG H1' H 6.169 . 1 107 13 13 DG H2' H 2.619 . 1 108 13 13 DG H2'' H 2.896 . 1 109 13 13 DG H3' H 4.963 . 1 110 13 13 DG H4' H 4.485 . 1 111 13 13 DG H5'' H 4.341 . 2 112 13 13 DG H8 H 7.773 . 1 113 14 14 DG H1 H 10.977 . 1 114 14 14 DG H1' H 6.383 . 1 115 14 14 DG H2' H 2.508 . 1 116 14 14 DG H2'' H 2.603 . 1 117 14 14 DG H3' H 5.046 . 1 118 14 14 DG H4' H 4.333 . 1 119 14 14 DG H5' H 4.242 . 2 120 14 14 DG H8 H 7.732 . 1 121 15 15 DA H1' H 6.373 . 1 122 15 15 DA H2' H 2.494 . 1 123 15 15 DA H2'' H 2.610 . 1 124 15 15 DA H3' H 5.042 . 1 125 15 15 DA H4' H 4.585 . 1 126 15 15 DA H5' H 4.248 . 2 127 15 15 DA H8 H 7.689 . 1 128 16 16 DG H1 H 11.235 . 1 129 16 16 DG H1' H 6.019 . 1 130 16 16 DG H2' H 2.347 . 1 131 16 16 DG H2'' H 2.775 . 1 132 16 16 DG H3' H 5.102 . 1 133 16 16 DG H4' H 4.424 . 1 134 16 16 DG H5' H 4.223 . 1 135 16 16 DG H5'' H 4.315 . 1 136 16 16 DG H8 H 7.936 . 1 137 17 17 DG H1 H 11.361 . 1 138 17 17 DG H1' H 5.979 . 1 139 17 17 DG H2' H 2.653 . 2 140 17 17 DG H3' H 5.012 . 1 141 17 17 DG H4' H 4.465 . 1 142 17 17 DG H5' H 4.200 . 2 143 17 17 DG H8 H 7.904 . 1 144 18 18 DG H1 H 11.174 . 1 145 18 18 DG H1' H 6.156 . 1 146 18 18 DG H2' H 2.528 . 1 147 18 18 DG H2'' H 2.710 . 1 148 18 18 DG H3' H 4.828 . 1 149 18 18 DG H4' H 4.452 . 1 150 18 18 DG H5' H 4.174 . 2 151 18 18 DG H8 H 7.617 . 1 152 19 19 DT H1' H 5.850 . 1 153 19 19 DT H2' H 2.007 . 2 154 19 19 DT H3' H 4.361 . 1 155 19 19 DT H4' H 4.163 . 1 156 19 19 DT H5' H 3.996 . 1 157 19 19 DT H5'' H 3.897 . 1 158 19 19 DT H6 H 7.077 . 1 159 19 19 DT H71 H 1.427 . 2 160 19 19 DT H72 H 1.427 . 2 161 19 19 DT H73 H 1.427 . 2 stop_ save_