data_30012 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR structure of a new G-quadruplex forming sequence within the KRAS proto-oncogene promoter region ; _BMRB_accession_number 30012 _BMRB_flat_file_name bmr30012.str _Entry_type original _Submission_date 2016-02-09 _Accession_date 2016-02-09 _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 Salgado G. F. . 2 Kerkour A. . . 3 Mergny J.-L. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 218 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-08-15 update BMRB 'update entry citation' 2016-03-14 original author 'original release' stop_ _Original_release_date 2016-03-14 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; High-resolution three-dimensional NMR structure of the KRAS proto-oncogene promoter reveals key features of a G-quadruplex involved in transcriptional regulation ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 28330874 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Kerkour Abdelaziz . . 2 Marquevielle Julien . . 3 Ivashchenko Stefaniia . . 4 Yatsunyk Liliya A. . 5 Mergny Jean-Louis L. . 6 Salgado Gilmar F. . stop_ _Journal_abbreviation 'J. Biol. Chem.' _Journal_name_full 'The Journal of biological chemistry' _Journal_volume 292 _Journal_issue 19 _Journal_ISSN 1083-351X _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 8082 _Page_last 8091 _Year 2017 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name "DNA (5'-D(*AP*GP*GP*GP*CP*GP*GP*TP*GP*TP*GP*GP*GP*AP*AP*TP*AP*GP*GP*GP*AP*A)-3')" _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity_1 'potassium ion' $entity_K 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 "DNA (5'-D(*AP*GP*GP*GP*CP*GP*GP*TP*GP*TP*GP*GP*GP*AP*AP*TP*AP*GP*GP*GP*AP*A)-3')" _Molecular_mass 6986.514 _Mol_thiol_state 'not present' _Details 'DNA G-quadruplex from the nuclease hypersensitive element of KRAS promotor region' ############################## # Polymer residue sequence # ############################## _Residue_count 22 _Mol_residue_sequence ; AGGGCGGTGTGGGAATAGGG AA ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DA 2 2 DG 3 3 DG 4 4 DG 5 5 DC 6 6 DG 7 7 DG 8 8 DT 9 9 DG 10 10 DT 11 11 DG 12 12 DG 13 13 DG 14 14 DA 15 15 DA 16 16 DT 17 17 DA 18 18 DG 19 19 DG 20 20 DG 21 21 DA 22 22 DA stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ############# # Ligands # ############# save_K _Saveframe_category ligand _Mol_type NON-POLYMER _Name_common 'POTASSIUM ION' _BMRB_code K _PDB_code K _Molecular_mass 39.098 _Mol_charge 1 _Mol_paramagnetic . _Mol_aromatic no _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons K K K . 1 . ? stop_ 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 human 9606 Eukaryota Metazoa homo . 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 '2 mM KRAS 22RT, 2 mM dG (5% 15N) KRAS 22RT 15N, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 2 mM 'natural abundance' $entity_1 2 mM 'dG (5% 15N)' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _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 stop_ _Details . save_ save_software_2 _Saveframe_category software _Name ARIA _Version . loop_ _Vendor _Address _Electronic_address "Linge, O'Donoghue and Nilges" . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name CNS _Version . loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ save_software_4 _Saveframe_category software _Name CcpNMR _Version . loop_ _Vendor _Address _Electronic_address CCPN . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_software_5 _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_6 _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceIII _Field_strength 700 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceIII _Field_strength 800 _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_COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _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-1H_TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-15N_HSQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_2D_1H-13C_HMBC_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HMBC' _Sample_label $sample_1 save_ save_1D_1H-15N_HSQC_7 _Saveframe_category NMR_applied_experiment _Experiment_name '1D 1H-15N HSQC' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_8 _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' 90 2 mM pH 6.6 0.1 pH pressure 1 . atm temperature 293 0.2 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 'KRAS 22RT' C 13 'methylene protons' ppm 0.000 internal indirect . . . 0.25144953 'KRAS 22RT' H 1 protons ppm 4.7 internal direct . . . 0.25144953 'KRAS 22RT' N 15 nitrogen ppm 143 internal direct . . . 0.25144953 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_ _Software_label $software_1 $software_2 $software_3 stop_ loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-13C HSQC' '2D 1H-15N HSQC' '2D 1H-13C HMBC' '1D 1H-15N HSQC' 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 DA H1' H 5.8213 . . 2 1 1 DA H2' H 2.3630 . . 3 1 1 DA H2'' H 2.4990 . . 4 1 1 DA H3' H 4.7203 . . 5 1 1 DA H4' H 4.0390 . . 6 1 1 DA H5'' H 3.5488 . . 7 1 1 DA H8 H 7.7944 . . 8 2 2 DG H1 H 11.5983 . . 9 2 2 DG H1' H 5.9272 . . 10 2 2 DG H2' H 2.6377 . . 11 2 2 DG H2'' H 2.8711 . . 12 2 2 DG H21 H 9.3830 . . 13 2 2 DG H22 H 6.5430 . . 14 2 2 DG H3' H 4.9166 . . 15 2 2 DG H4' H 4.3464 . . 16 2 2 DG H5'' H 4.0172 . . 17 2 2 DG H8 H 7.9169 . . 18 3 3 DG H1 H 11.0811 . . 19 3 3 DG H1' H 5.9911 . . 20 3 3 DG H2' H 2.3838 . . 21 3 3 DG H2'' H 2.7579 . . 22 3 3 DG H21 H 9.3970 . . 23 3 3 DG H22 H 6.5490 . . 24 3 3 DG H3' H 4.8197 . . 25 3 3 DG H4' H 4.4203 . . 26 3 3 DG H5' H 4.1945 . . 27 3 3 DG H5'' H 4.0905 . . 28 3 3 DG H8 H 7.4793 . . 29 4 4 DG H1 H 11.1386 . . 30 4 4 DG H1' H 6.1834 . . 31 4 4 DG H2' H 2.5835 . . 32 4 4 DG H2'' H 2.6848 . . 33 4 4 DG H21 H 8.8520 . . 34 4 4 DG H22 H 6.5990 . . 35 4 4 DG H3' H 5.0203 . . 36 4 4 DG H4' H 4.5110 . . 37 4 4 DG H5' H 4.2750 . . 38 4 4 DG H5'' H 4.1960 . . 39 4 4 DG H8 H 7.5807 . . 40 5 5 DC H1' H 6.3802 . . 41 5 5 DC H2' H 2.3013 . . 42 5 5 DC H2'' H 2.6310 . . 43 5 5 DC H3' H 4.9822 . . 44 5 5 DC H4' H 4.5227 . . 45 5 5 DC H5 H 6.0865 . . 46 5 5 DC H5' H 4.1710 . . 47 5 5 DC H5'' H 4.2780 . . 48 5 5 DC H6 H 7.9117 . . 49 6 6 DG H1 H 11.7907 . . 50 6 6 DG H1' H 6.0918 . . 51 6 6 DG H2' H 2.2995 . . 52 6 6 DG H2'' H 2.8475 . . 53 6 6 DG H21 H 6.3250 . . 54 6 6 DG H22 H 9.4050 . . 55 6 6 DG H3' H 5.0885 . . 56 6 6 DG H4' H 4.3762 . . 57 6 6 DG H5' H 4.2258 . . 58 6 6 DG H5'' H 4.1257 . . 59 6 6 DG H8 H 7.9586 . . 60 7 7 DG H1 H 11.2150 . . 61 7 7 DG H1' H 6.1774 . . 62 7 7 DG H2' H 2.5963 . . 63 7 7 DG H2'' H 2.7522 . . 64 7 7 DG H21 H 9.2120 . . 65 7 7 DG H22 H 6.7660 . . 66 7 7 DG H3' H 5.0754 . . 67 7 7 DG H4' H 4.5230 . . 68 7 7 DG H5' H 4.3400 . . 69 7 7 DG H5'' H 4.2195 . . 70 7 7 DG H8 H 7.8969 . . 71 8 8 DT H1' H 6.4540 . . 72 8 8 DT H2' H 2.4295 . . 73 8 8 DT H2'' H 2.5340 . . 74 8 8 DT H3' H 5.0803 . . 75 8 8 DT H4' H 4.4810 . . 76 8 8 DT H71 H 1.8710 . . 77 8 8 DT H72 H 1.8710 . . 78 8 8 DT H73 H 1.8710 . . 79 8 8 DT H5' H 4.2040 . . 80 8 8 DT H5'' H 4.3490 . . 81 8 8 DT H6 H 7.8784 . . 82 9 9 DG H1 H 11.1255 . . 83 9 9 DG H1' H 6.3636 . . 84 9 9 DG H2' H 2.3590 . . 85 9 9 DG H2'' H 2.9585 . . 86 9 9 DG H21 H 8.6160 . . 87 9 9 DG H22 H 6.1889 . . 88 9 9 DG H3' H 4.9055 . . 89 9 9 DG H4' H 4.5555 . . 90 9 9 DG H5' H 4.3165 . . 91 9 9 DG H5'' H 4.1176 . . 92 9 9 DG H8 H 7.5659 . . 93 10 10 DT H1' H 5.6489 . . 94 10 10 DT H2' H 2.0888 . . 95 10 10 DT H2'' H 2.0890 . . 96 10 10 DT H3' H 4.5245 . . 97 10 10 DT H4' H 4.3143 . . 98 10 10 DT H71 H 1.6676 . . 99 10 10 DT H72 H 1.6676 . . 100 10 10 DT H73 H 1.6676 . . 101 10 10 DT H5' H 4.2330 . . 102 10 10 DT H5'' H 3.9900 . . 103 10 10 DT H6 H 7.3156 . . 104 11 11 DG H1 H 11.8266 . . 105 11 11 DG H1' H 6.0702 . . 106 11 11 DG H2' H 2.5138 . . 107 11 11 DG H2'' H 2.8899 . . 108 11 11 DG H21 H 9.0200 . . 109 11 11 DG H22 H 6.9146 . . 110 11 11 DG H3' H 5.0203 . . 111 11 11 DG H4' H 4.3707 . . 112 11 11 DG H5' H 4.2246 . . 113 11 11 DG H5'' H 4.1999 . . 114 11 11 DG H8 H 8.0277 . . 115 12 12 DG H1 H 11.3626 . . 116 12 12 DG H1' H 5.9173 . . 117 12 12 DG H2' H 2.5157 . . 118 12 12 DG H2'' H 2.8720 . . 119 12 12 DG H21 H 9.2030 . . 120 12 12 DG H22 H 6.3330 . . 121 12 12 DG H3' H 5.0236 . . 122 12 12 DG H4' H 4.7650 . . 123 12 12 DG H5' H 4.3590 . . 124 12 12 DG H5'' H 4.3160 . . 125 12 12 DG H8 H 7.8463 . . 126 13 13 DG H1 H 11.1032 . . 127 13 13 DG H1' H 6.2153 . . 128 13 13 DG H2' H 2.3587 . . 129 13 13 DG H2'' H 2.5124 . . 130 13 13 DG H21 H 8.7160 . . 131 13 13 DG H22 H 6.8713 . . 132 13 13 DG H3' H 4.6117 . . 133 13 13 DG H4' H 3.7816 . . 134 13 13 DG H5' H 3.1374 . . 135 13 13 DG H5'' H 3.1374 . . 136 13 13 DG H8 H 7.6030 . . 137 14 14 DA H1' H 6.1588 . . 138 14 14 DA H2' H 2.6089 . . 139 14 14 DA H2'' H 2.7132 . . 140 14 14 DA H3' H 4.7980 . . 141 14 14 DA H4' H 4.2600 . . 142 14 14 DA H5' H 4.0313 . . 143 14 14 DA H5'' H 3.9162 . . 144 14 14 DA H8 H 8.1564 . . 145 15 15 DA H1' H 6.3342 . . 146 15 15 DA H2' H 2.7136 . . 147 15 15 DA H2'' H 2.8663 . . 148 15 15 DA H3' H 4.9890 . . 149 15 15 DA H4' H 4.4240 . . 150 15 15 DA H5' H 4.1920 . . 151 15 15 DA H5'' H 4.0200 . . 152 15 15 DA H8 H 8.3538 . . 153 16 16 DT H1' H 5.9462 . . 154 16 16 DT H2' H 1.5443 . . 155 16 16 DT H2'' H 2.0180 . . 156 16 16 DT H3' H 4.9815 . . 157 16 16 DT H4' H 4.5640 . . 158 16 16 DT H71 H 1.7950 . . 159 16 16 DT H72 H 1.7950 . . 160 16 16 DT H73 H 1.7950 . . 161 16 16 DT H5' H 4.0117 . . 162 16 16 DT H5'' H 4.1705 . . 163 16 16 DT H6 H 7.4329 . . 164 17 17 DA H1' H 6.1316 . . 165 17 17 DA H2 H 7.3597 . . 166 17 17 DA H2'' H 2.6732 . . 167 17 17 DA H3' H 4.9773 . . 168 17 17 DA H4' H 4.1280 . . 169 17 17 DA H5' H 3.9853 . . 170 17 17 DA H5'' H 3.8267 . . 171 17 17 DA H8 H 7.9382 . . 172 18 18 DG H1 H 11.3470 . . 173 18 18 DG H1' H 5.9855 . . 174 18 18 DG H2' H 2.6158 . . 175 18 18 DG H2'' H 2.8551 . . 176 18 18 DG H21 H 8.8780 . . 177 18 18 DG H22 H 5.9310 . . 178 18 18 DG H3' H 4.9470 . . 179 18 18 DG H4' H 4.3932 . . 180 18 18 DG H5'' H 4.1204 . . 181 18 18 DG H8 H 8.0649 . . 182 19 19 DG H1 H 11.2095 . . 183 19 19 DG H1' H 5.9622 . . 184 19 19 DG H2' H 2.3824 . . 185 19 19 DG H2'' H 2.6590 . . 186 19 19 DG H21 H 8.8910 . . 187 19 19 DG H22 H 6.5400 . . 188 19 19 DG H3' H 4.9783 . . 189 19 19 DG H5' H 4.3445 . . 190 19 19 DG H5'' H 4.1813 . . 191 19 19 DG H8 H 7.8354 . . 192 20 20 DG H1 H 10.6856 . . 193 20 20 DG H1' H 5.9046 . . 194 20 20 DG H2' H 2.3837 . . 195 20 20 DG H2'' H 2.6542 . . 196 20 20 DG H21 H 8.3010 . . 197 20 20 DG H22 H 6.5871 . . 198 20 20 DG H3' H 4.8417 . . 199 20 20 DG H4' H 4.3917 . . 200 20 20 DG H5' H 4.1909 . . 201 20 20 DG H5'' H 4.0292 . . 202 20 20 DG H8 H 7.5041 . . 203 21 21 DA H1' H 5.8090 . . 204 21 21 DA H2' H 2.2390 . . 205 21 21 DA H2'' H 2.3904 . . 206 21 21 DA H3' H 4.7124 . . 207 21 21 DA H4' H 4.1918 . . 208 21 21 DA H5'' H 4.0290 . . 209 21 21 DA H8 H 7.6761 . . 210 22 22 DA H1' H 5.9073 . . 211 22 22 DA H2 H 7.3610 . . 212 22 22 DA H2' H 2.1883 . . 213 22 22 DA H2'' H 2.2970 . . 214 22 22 DA H3' H 4.7360 . . 215 22 22 DA H4' H 4.4417 . . 216 22 22 DA H5' H 3.9370 . . 217 22 22 DA H5'' H 4.0288 . . 218 22 22 DA H8 H 7.8150 . . stop_ save_