data_34051 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of DNA AGCGA-quadruplex adopted by 15-mer d(GCGAGGGAGCGAGGG), VK34, oligonucleotide found in regulatory region of the PLEKHG3 human gene ; _BMRB_accession_number 34051 _BMRB_flat_file_name bmr34051.str _Entry_type original _Submission_date 2016-10-09 _Accession_date 2016-10-09 _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 Kocman V. . . 2 Plavec J. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 137 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-05-25 original BMRB . stop_ _Original_release_date 2016-10-10 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Tetrahelical structural family adopted by AGCGA-rich regulatory DNA regions. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 28513602 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Kocman V. . . 2 Plavec J. . . stop_ _Journal_abbreviation 'Nat. Commun.' _Journal_volume 8 _Journal_issue . _Journal_ISSN 2041-1723 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 15355 _Page_last 15355 _Year 2017 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name "DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3')" _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'entity_1, 1' $entity_1 'entity_1, 2' $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 4765.084 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 15 _Mol_residue_sequence ; GCGAGGGAGCGAGGG ; loop_ _Residue_seq_code _Residue_label 1 DG 2 DC 3 DG 4 DA 5 DG 6 DG 7 DG 8 DA 9 DG 10 DC 11 DG 12 DA 13 DG 14 DG 15 DG 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 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 $entity_1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details "0.8 mM DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3'), 90% H2O/10% D2O" loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.8 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details "0.8 mM [10 % 15N] residue specific Gua DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3'), 90% H2O/10% D2O" loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.8 mM '[10 % 15N] residue specific Gua' stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type solution _Details "0.8 mM [10% 13C] residues specific adenine DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3'), 90% H2O/10% D2O" loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.8 mM '[10% 13C] residues specific adenine' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name 'AMBER 14' _Version . loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollman' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Agilent-Varian _Model 'Uniform NMR System' _Field_strength 600 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Agilent-Varian _Model 'Uniform NMR System' _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_1D_1H-15N_HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '1D 1H-15N HSQC' _Sample_label $sample_2 save_ save_2D_1H-15N_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_2 save_ save_2D_1H-13C_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_3 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 6.25 0.25 pH pressure 1 . atm temperature 273 . 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 TMS H 1 'methyl protons' ppm 0 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_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '1D 1H-15N HSQC' '2D 1H-15N HSQC' '2D 1H-13C HSQC' stop_ loop_ _Sample_label $sample_1 $sample_2 $sample_3 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name 'entity_1, 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 6.063 0.012 1 2 1 1 DG H2' H 2.635 0.003 1 3 1 1 DG H2'' H 2.764 0.007 1 4 1 1 DG H3' H 4.859 0.006 1 5 1 1 DG H4' H 4.323 0.004 1 6 1 1 DG H5' H 4.133 0 1 7 1 1 DG H5'' H 3.801 0.002 1 8 1 1 DG H8 H 7.885 0.006 1 9 2 2 DC H1' H 6.132 0.014 1 10 2 2 DC H2' H 1.625 0.009 1 11 2 2 DC H2'' H 2.226 0.003 1 12 2 2 DC H3' H 4.873 0.01 1 13 2 2 DC H5 H 5.209 0.003 1 14 2 2 DC H5' H 4.145 0.002 1 15 2 2 DC H5'' H 4.309 0.006 1 16 2 2 DC H6 H 7.194 0.013 1 17 2 2 DC H41 H 8.562 0.014 1 18 2 2 DC H42 H 7.053 0.009 1 19 3 3 DG H1 H 10.603 0.014 1 20 3 3 DG H1' H 6.199 0.016 1 21 3 3 DG H2' H 3.013 0.009 1 22 3 3 DG H2'' H 2.866 0.012 1 23 3 3 DG H3' H 5.174 0.008 1 24 3 3 DG H4' H 4.663 0.008 1 25 3 3 DG H5' H 4.181 0.003 1 26 3 3 DG H5'' H 4.264 0.004 1 27 3 3 DG H8 H 8.315 0.011 1 28 3 3 DG H21 H 9.525 0.009 1 29 3 3 DG H22 H 8.395 0.01 1 30 4 4 DA H1' H 5.673 0.01 1 31 4 4 DA H2 H 7.979 0.012 1 32 4 4 DA H2' H 0.839 0.012 1 33 4 4 DA H2'' H 2.1 0.006 1 34 4 4 DA H3' H 4.781 0.008 1 35 4 4 DA H4' H 4.654 0.009 1 36 4 4 DA H5' H 4.139 0.003 1 37 4 4 DA H5'' H 4.396 0.002 1 38 4 4 DA H8 H 7.445 0.016 1 39 4 4 DA H61 H 6.201 0.014 1 40 4 4 DA H62 H 5.752 0 1 41 5 5 DG H1 H 12.854 0.008 1 42 5 5 DG H1' H 5.623 0.011 1 43 5 5 DG H2' H 1.633 0.003 1 44 5 5 DG H2'' H 1.843 0.002 1 45 5 5 DG H3' H 4.758 0.017 1 46 5 5 DG H4' H 4.302 0.016 1 47 5 5 DG H5' H 4.124 0.008 1 48 5 5 DG H5'' H 3.982 0.016 1 49 5 5 DG H8 H 7.48 0.002 1 50 5 5 DG H21 H 6.283 0.005 1 51 5 5 DG H22 H 5.577 0.012 1 52 6 6 DG H1' H 5.68 0.019 1 53 6 6 DG H2' H 2.797 0.016 1 54 6 6 DG H2'' H 2.418 0.007 1 55 6 6 DG H3' H 4.854 0.001 1 56 6 6 DG H8 H 7.994 0.012 1 57 7 7 DG H1' H 5.399 0.003 1 58 7 7 DG H2' H 2.486 0.002 1 59 7 7 DG H2'' H 2.564 0 1 60 7 7 DG H3' H 4.786 0.002 1 61 7 7 DG H4' H 4.391 0 1 62 7 7 DG H5' H 4.122 0 1 63 7 7 DG H5'' H 4.024 0 1 64 7 7 DG H8 H 7.839 0.012 1 65 8 8 DA H1' H 6.295 0.002 1 66 8 8 DA H2' H 2.559 0.002 1 67 8 8 DA H2'' H 2.691 0.003 1 68 8 8 DA H3' H 4.783 0.004 1 69 8 8 DA H4' H 3.863 0.009 1 70 8 8 DA H8 H 8.182 0.012 1 71 9 9 DG H1 H 11.457 0.014 1 72 9 9 DG H1' H 6.208 0.014 1 73 9 9 DG H2' H 2.737 0.008 1 74 9 9 DG H2'' H 2.94 0.009 1 75 9 9 DG H3' H 4.911 0.001 1 76 9 9 DG H4' H 4.464 0.001 1 77 9 9 DG H5' H 4.001 0.001 1 78 9 9 DG H5'' H 4.197 0.003 1 79 9 9 DG H8 H 8.11 0.011 1 80 10 10 DC H1' H 6.018 0.013 1 81 10 10 DC H2' H 1.518 0.003 1 82 10 10 DC H2'' H 2.185 0.008 1 83 10 10 DC H3' H 4.857 0.002 1 84 10 10 DC H5 H 5.189 0.008 1 85 10 10 DC H5' H 4.275 0.013 1 86 10 10 DC H5'' H 4.201 0.007 1 87 10 10 DC H6 H 7.13 0.015 1 88 10 10 DC H41 H 8.385 0.008 1 89 10 10 DC H42 H 7.026 0.004 1 90 11 11 DG H1 H 10.604 0.015 1 91 11 11 DG H1' H 6.198 0.017 1 92 11 11 DG H2' H 2.858 0.011 1 93 11 11 DG H2'' H 3.004 0.01 1 94 11 11 DG H3' H 5.151 0.003 1 95 11 11 DG H4' H 4.658 0.001 1 96 11 11 DG H5' H 4.184 0.004 1 97 11 11 DG H5'' H 4.257 0.004 1 98 11 11 DG H8 H 8.27 0.004 1 99 11 11 DG H21 H 9.455 0.005 1 100 11 11 DG H22 H 8.409 0.005 1 101 12 12 DA H1' H 5.65 0.007 1 102 12 12 DA H2 H 7.956 0.007 1 103 12 12 DA H2' H 0.962 0.012 1 104 12 12 DA H2'' H 2.215 0.008 1 105 12 12 DA H3' H 4.851 0.001 1 106 12 12 DA H4' H 4.662 0 1 107 12 12 DA H5' H 4.395 0.004 1 108 12 12 DA H5'' H 4.127 0.012 1 109 12 12 DA H8 H 7.472 0.005 1 110 12 12 DA H61 H 6.195 0.015 1 111 12 12 DA H62 H 5.736 0 1 112 13 13 DG H1 H 13.001 0.003 1 113 13 13 DG H1' H 5.325 0.006 1 114 13 13 DG H2' H 2.1 0.004 1 115 13 13 DG H2'' H 2.291 0.004 1 116 13 13 DG H3' H 4.854 0.003 1 117 13 13 DG H4' H 4.283 0.009 1 118 13 13 DG H5' H 4.021 0.011 1 119 13 13 DG H5'' H 4.112 0.002 1 120 13 13 DG H8 H 7.751 0.004 1 121 13 13 DG H21 H 9.526 0 1 122 13 13 DG H22 H 5.645 0.009 1 123 14 14 DG H1' H 5.768 0.003 1 124 14 14 DG H2' H 2.544 0.009 1 125 14 14 DG H2'' H 2.671 0.013 1 126 14 14 DG H3' H 4.974 0.013 1 127 14 14 DG H4' H 4.393 0.004 1 128 14 14 DG H5' H 4.072 0.007 1 129 14 14 DG H5'' H 4.142 0 1 130 14 14 DG H8 H 7.784 0.012 1 131 15 15 DG H1' H 6.032 0.002 1 132 15 15 DG H2' H 2.36 0.018 1 133 15 15 DG H2'' H 2.54 0.015 1 134 15 15 DG H3' H 4.655 0.005 1 135 15 15 DG H5' H 4.194 0 1 136 15 15 DG H5'' H 4.072 0.007 1 137 15 15 DG H8 H 7.902 0.013 1 stop_ save_