data_34054 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of DNA tetrameric AGCGA-quadruplex adopted by 15-mer d(GCGAGGGAGCGAGGG), VK34, oligonucleotide found in regulatory region of the PLEKHG3 human gene ; _BMRB_accession_number 34054 _BMRB_flat_file_name bmr34054.str _Entry_type original _Submission_date 2016-10-13 _Accession_date 2016-10-13 _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" 103 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-05-25 original BMRB . stop_ _Original_release_date 2017-05-22 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 'entity_1, 3' $entity_1 'entity_1, 4' $entity_1 stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic no _System_thiol_state 'not present' _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 "1.0 mM DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3'), 150 mM sodium chloride, 90% H2O/10% D2O" loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1.0 mM 'natural abundance' 'sodium chloride' 150 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details ; 1 mM residue specific 15N and 13C DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3'), 150 mM sodium chloride, 90% H2O/10% D2O ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1 mM 'residue specific 15N and 13C' 'sodium chloride' 150 mM 'natural abundance' stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type solution _Details ; 1 mM D8 residue specific labeled DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3'), 150 mM sodium chloride, 90% H2O/10% D2O ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1 mM 'D8 residue specific labeled' 'sodium chloride' 150 mM 'natural abundance' stop_ save_ save_sample_4 _Saveframe_category sample _Sample_type solution _Details ; 1 mM uniformly labeled with D8 DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3'), 150 mM sodium chloride, 90% H2O/10% D2O ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1 mM 'uniformly labeled with D8' 'sodium chloride' 150 mM '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 '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_ save_software_3 _Saveframe_category software _Name spar _Version . loop_ _Task 'peak picking' 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_2 save_ save_2D_1H-1H_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_3 save_ save_2D_1H-1H_NOESY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_4 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' 150 . mM pH 6 . 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 $sample_4 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 6.019 0.008 1 2 1 1 DG H2' H 2.776 0.005 1 3 1 1 DG H2'' H 2.64 0.005 1 4 1 1 DG H3' H 4.831 0.006 1 5 1 1 DG H8 H 7.862 0.004 1 6 2 2 DC H1' H 6.082 0.008 1 7 2 2 DC H2' H 1.574 0.003 1 8 2 2 DC H2'' H 2.167 0.004 1 9 2 2 DC H3' H 4.835 0.01 1 10 2 2 DC H6 H 7.13 0.003 1 11 2 2 DC H41 H 8.476 0.01 1 12 2 2 DC H42 H 6.988 0 1 13 3 3 DG H1 H 10.468 0.01 1 14 3 3 DG H1' H 6.067 0.005 1 15 3 3 DG H2' H 2.736 0.017 1 16 3 3 DG H2'' H 2.93 0.01 1 17 3 3 DG H3' H 4.578 0.01 1 18 3 3 DG H8 H 8.217 0.006 1 19 3 3 DG H21 H 9.38 0.006 1 20 3 3 DG H22 H 6.978 0.006 1 21 4 4 DA H1' H 5.573 0.009 1 22 4 4 DA H2 H 7.858 0.001 1 23 4 4 DA H2' H 0.941 0.001 1 24 4 4 DA H2'' H 2.219 0.005 1 25 4 4 DA H3' H 4.757 0.004 1 26 4 4 DA H8 H 7.383 0.002 1 27 4 4 DA H61 H 8.186 0 1 28 4 4 DA H62 H 5.539 0.001 1 29 5 5 DG H1 H 12.854 0.005 1 30 5 5 DG H1' H 5.571 0.009 1 31 5 5 DG H2' H 2.418 0.004 1 32 5 5 DG H3' H 4.862 0.007 1 33 5 5 DG H8 H 7.705 0.006 1 34 6 6 DG H1 H 10.772 0.003 1 35 6 6 DG H1' H 5.75 0.006 1 36 6 6 DG H2' H 2.082 0.003 1 37 6 6 DG H2'' H 2.287 0.003 1 38 6 6 DG H3' H 4.891 0.007 1 39 6 6 DG H8 H 7.305 0.009 1 40 7 7 DG H1 H 10.149 0.006 1 41 7 7 DG H1' H 5.943 0.004 1 42 7 7 DG H2' H 2.702 0.003 1 43 7 7 DG H2'' H 2.857 0.005 1 44 7 7 DG H3' H 4.543 0.015 1 45 7 7 DG H8 H 8.14 0.004 1 46 7 7 DG H21 H 8.889 0.001 1 47 8 8 DA H1' H 5.383 0.009 1 48 8 8 DA H2 H 7.785 0.006 1 49 8 8 DA H2' H 2.352 0.006 1 50 8 8 DA H2'' H 0.591 0.003 1 51 8 8 DA H3' H 4.806 0.007 1 52 8 8 DA H4' H 4.535 0 1 53 8 8 DA H5' H 4.044 0.005 1 54 8 8 DA H5'' H 4.37 0.006 1 55 8 8 DA H8 H 7.436 0.009 1 56 8 8 DA H61 H 5.533 0.002 1 57 8 8 DA H62 H 5.307 0.002 1 58 9 9 DG H1 H 10.44 0.009 1 59 9 9 DG H1' H 5.797 0.004 1 60 9 9 DG H2' H 2.551 0.002 1 61 9 9 DG H2'' H 3.227 0 1 62 9 9 DG H3' H 4.791 0.012 1 63 9 9 DG H8 H 6.976 0.004 1 64 10 10 DC H1' H 5.957 0.013 1 65 10 10 DC H2' H 1.283 0.002 1 66 10 10 DC H2'' H 2.083 0.006 1 67 10 10 DC H3' H 4.81 0.002 1 68 10 10 DC H5 H 4.957 0.006 1 69 10 10 DC H6 H 6.885 0.012 1 70 10 10 DC H41 H 8.355 0.006 1 71 10 10 DC H42 H 6.924 0.002 1 72 11 11 DG H1 H 10.42 0.005 1 73 11 11 DG H1' H 6.064 0.008 1 74 11 11 DG H2' H 2.936 0.008 1 75 11 11 DG H2'' H 2.764 0.013 1 76 11 11 DG H3' H 4.59 0.005 1 77 11 11 DG H8 H 8.215 0.007 1 78 11 11 DG H21 H 9.371 0.006 1 79 11 11 DG H22 H 6.92 0.005 1 80 12 12 DA H1' H 5.657 0.014 1 81 12 12 DA H2 H 7.907 0.006 1 82 12 12 DA H2' H 2.19 0.011 1 83 12 12 DA H2'' H 0.939 0.007 1 84 12 12 DA H3' H 4.789 0.013 1 85 12 12 DA H8 H 7.367 0.007 1 86 12 12 DA H61 H 8.236 0 1 87 12 12 DA H62 H 5.585 0.005 1 88 13 13 DG H1 H 12.964 0.012 1 89 13 13 DG H1' H 5.322 0.006 1 90 13 13 DG H2' H 2.286 0.003 1 91 13 13 DG H2'' H 2.156 0 1 92 13 13 DG H3' H 4.833 0 1 93 13 13 DG H8 H 7.745 0.001 1 94 14 14 DG H1' H 5.733 0.015 1 95 14 14 DG H2' H 2.694 0.01 1 96 14 14 DG H2'' H 2.507 0.006 1 97 14 14 DG H3' H 4.938 0.004 1 98 14 14 DG H8 H 7.747 0.001 1 99 15 15 DG H1' H 6.003 0.004 1 100 15 15 DG H2' H 2.346 0.014 1 101 15 15 DG H2'' H 2.501 0.002 1 102 15 15 DG H3' H 4.625 0.008 1 103 15 15 DG H8 H 7.853 0.001 1 stop_ save_