data_19389 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of a stacked dimeric G-quadruplex formed by a segment of the human CEB1 minisatellite ; _BMRB_accession_number 19389 _BMRB_flat_file_name bmr19389.str _Entry_type original _Submission_date 2013-07-25 _Accession_date 2013-07-25 _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 Adrian Michael . . 2 Ang 'Ding Jie' . . 3 Lech Christopher . . 4 Heddi Brahim . . 5 Nicolas Alain . . 6 Phan 'Anh Tuan' . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 134 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-05-27 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 19381 'Locked nucleic acid into G-quadruplexes' 19386 'Parallel-stranded G-quadruplex in DNA poly-G stretches' stop_ _Original_release_date 2014-05-27 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structure and Conformational Dynamics of a Stacked Dimeric G-Quadruplex Formed by the Human CEB1 Minisatellite' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 24742225 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Adrian Michael . . 2 Ang 'Ding Jie' . . 3 Lech Christopher J. . 4 Heddi Brahim . . 5 Nicolas Alain . . 6 Phan 'Anh Tuan' . . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_volume 136 _Journal_issue 17 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 6297 _Page_last 6305 _Year 2014 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'stacked dimeric G-quadruplex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'DNA (5'-D(*AP*GP*GP*GP*GP*GP*GP*AP*GP*GP*GP*AP*GP*GP*GP*TP*GP*G)-3')_1' $DNA 'DNA (5'-D(*AP*GP*GP*GP*GP*GP*GP*AP*GP*GP*GP*AP*GP*GP*GP*TP*GP*G)-3')_2' $DNA 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 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(*AP*GP*GP*GP*GP*GP*GP*AP*GP*GP*GP*AP*GP*GP*GP*TP*GP*G)-3') _Molecular_mass 5807.783 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 18 _Mol_residue_sequence AGGGGGGAGGGAGGGTGG loop_ _Residue_seq_code _Residue_label 1 DA 2 DG 3 DG 4 DG 5 DG 6 DG 7 DG 8 DA 9 DG 10 DG 11 DG 12 DA 13 DG 14 DG 15 DG 16 DT 17 DG 18 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 $DNA 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 'chemical synthesis' . . . . . 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 1.5 mM 'natural abundance' 'potassium phosphate' 20 mM 'natural abundance' 'potassium chloride' 70 mM 'natural abundance' DSS 10 uM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DNA 1.5 mM 'natural abundance' 'potassium phosphate' 20 mM 'natural abundance' 'potassium chloride' 70 mM 'natural abundance' DSS 10 uM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_X-PLOR_NIH _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_AMBER _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_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 700 _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_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_2 save_ save_2D_1H-13C_HSQC_aromatic_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aromatic' _Sample_label $sample_1 save_ save_2D_1H-1H_ROESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H ROESY' _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 . 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 0.00 internal direct . . . 1.000000000 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' '2D 1H-1H TOCSY' '2D 1H-13C HSQC aromatic' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'DNA (5'-D(*AP*GP*GP*GP*GP*GP*GP*AP*GP*GP*GP*AP*GP*GP*GP*TP*GP*G)-3')_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 5.679 . 1 2 1 1 DA H2 H 7.501 . 1 3 1 1 DA H2' H 1.858 . 1 4 1 1 DA H2'' H 1.928 . 1 5 1 1 DA H3' H 4.256 . 1 6 1 1 DA H4' H 3.366 . 1 7 1 1 DA H5' H 3.218 . 1 8 1 1 DA H5'' H 3.253 . 1 9 1 1 DA H8 H 7.574 . 1 10 2 2 DG H1' H 5.449 . 1 11 2 2 DG H2' H 1.905 . 1 12 2 2 DG H2'' H 2.084 . 1 13 2 2 DG H3' H 4.476 . 1 14 2 2 DG H4' H 3.500 . 1 15 2 2 DG H5' H 2.832 . 1 16 2 2 DG H5'' H 3.397 . 1 17 2 2 DG H8 H 7.317 . 1 18 3 3 DG H1 H 11.009 . 1 19 3 3 DG H1' H 6.359 . 1 20 3 3 DG H2' H 3.197 . 1 21 3 3 DG H2'' H 2.789 . 1 22 3 3 DG H3' H 4.866 . 1 23 3 3 DG H4' H 4.397 . 1 24 3 3 DG H5' H 4.021 . 1 25 3 3 DG H8 H 7.437 . 1 26 4 4 DG H1' H 6.408 . 1 27 4 4 DG H2' H 2.835 . 1 28 4 4 DG H2'' H 2.762 . 1 29 4 4 DG H3' H 5.056 . 1 30 4 4 DG H4' H 4.520 . 1 31 4 4 DG H5' H 4.293 . 1 32 4 4 DG H5'' H 4.171 . 1 33 4 4 DG H8 H 8.080 . 1 34 5 5 DG H1 H 11.297 . 1 35 5 5 DG H1' H 6.095 . 1 36 5 5 DG H2' H 2.327 . 1 37 5 5 DG H2'' H 2.710 . 1 38 5 5 DG H3' H 5.044 . 1 39 5 5 DG H4' H 4.457 . 1 40 5 5 DG H5' H 4.272 . 2 41 5 5 DG H8 H 7.821 . 1 42 6 6 DG H1 H 11.071 . 1 43 6 6 DG H1' H 6.012 . 1 44 6 6 DG H2' H 2.488 . 1 45 6 6 DG H2'' H 2.790 . 1 46 6 6 DG H3' H 4.957 . 1 47 6 6 DG H4' H 4.480 . 1 48 6 6 DG H8 H 7.658 . 1 49 7 7 DG H1 H 10.818 . 1 50 7 7 DG H1' H 6.302 . 1 51 7 7 DG H2' H 2.696 . 1 52 7 7 DG H2'' H 2.510 . 1 53 7 7 DG H3' H 5.037 . 1 54 7 7 DG H4' H 4.549 . 1 55 7 7 DG H8 H 7.671 . 1 56 8 8 DA H1' H 6.584 . 1 57 8 8 DA H2 H 8.224 . 1 58 8 8 DA H2' H 2.860 . 1 59 8 8 DA H2'' H 2.861 . 1 60 8 8 DA H3' H 5.115 . 1 61 8 8 DA H4' H 4.591 . 1 62 8 8 DA H8 H 8.419 . 1 63 9 9 DG H1 H 11.256 . 1 64 9 9 DG H1' H 6.078 . 1 65 9 9 DG H2' H 2.099 . 1 66 9 9 DG H2'' H 2.677 . 1 67 9 9 DG H3' H 5.124 . 1 68 9 9 DG H4' H 4.468 . 1 69 9 9 DG H8 H 7.727 . 1 70 10 10 DG H1 H 11.023 . 1 71 10 10 DG H1' H 5.975 . 1 72 10 10 DG H2' H 2.486 . 1 73 10 10 DG H2'' H 2.792 . 1 74 10 10 DG H3' H 4.960 . 1 75 10 10 DG H4' H 4.474 . 1 76 10 10 DG H8 H 7.659 . 1 77 11 11 DG H1 H 10.749 . 1 78 11 11 DG H1' H 6.258 . 1 79 11 11 DG H2' H 2.676 . 1 80 11 11 DG H2'' H 2.508 . 1 81 11 11 DG H3' H 5.030 . 1 82 11 11 DG H4' H 4.541 . 1 83 11 11 DG H8 H 7.569 . 1 84 12 12 DA H1' H 6.584 . 1 85 12 12 DA H2 H 8.224 . 1 86 12 12 DA H2' H 2.859 . 1 87 12 12 DA H2'' H 2.860 . 1 88 12 12 DA H3' H 5.114 . 1 89 12 12 DA H4' H 4.582 . 1 90 12 12 DA H8 H 8.419 . 1 91 13 13 DG H1 H 11.263 . 1 92 13 13 DG H1' H 6.077 . 1 93 13 13 DG H2' H 2.072 . 1 94 13 13 DG H2'' H 2.654 . 1 95 13 13 DG H3' H 5.123 . 1 96 13 13 DG H4' H 4.456 . 1 97 13 13 DG H8 H 7.720 . 1 98 14 14 DG H1 H 10.934 . 1 99 14 14 DG H1' H 5.926 . 1 100 14 14 DG H2' H 2.451 . 1 101 14 14 DG H2'' H 2.700 . 1 102 14 14 DG H3' H 4.941 . 1 103 14 14 DG H4' H 4.456 . 1 104 14 14 DG H8 H 7.623 . 1 105 15 15 DG H1 H 11.009 . 1 106 15 15 DG H1' H 6.207 . 1 107 15 15 DG H2' H 2.552 . 1 108 15 15 DG H2'' H 2.443 . 1 109 15 15 DG H3' H 5.016 . 1 110 15 15 DG H4' H 4.485 . 1 111 15 15 DG H8 H 7.317 . 1 112 16 16 DT H1' H 6.435 . 1 113 16 16 DT H2' H 2.395 . 1 114 16 16 DT H2'' H 2.635 . 1 115 16 16 DT H3' H 4.993 . 1 116 16 16 DT H4' H 4.475 . 1 117 16 16 DT H5' H 4.136 . 2 118 16 16 DT H6 H 7.732 . 1 119 16 16 DT H71 H 1.896 . 2 120 16 16 DT H72 H 1.896 . 2 121 16 16 DT H73 H 1.896 . 2 122 17 17 DG H1 H 11.270 . 1 123 17 17 DG H1' H 6.084 . 1 124 17 17 DG H2' H 2.022 . 1 125 17 17 DG H2'' H 2.635 . 1 126 17 17 DG H3' H 5.068 . 1 127 17 17 DG H4' H 4.439 . 1 128 17 17 DG H8 H 7.698 . 1 129 18 18 DG H1 H 11.044 . 1 130 18 18 DG H1' H 5.992 . 1 131 18 18 DG H2' H 2.545 . 1 132 18 18 DG H2'' H 2.400 . 1 133 18 18 DG H3' H 4.664 . 1 134 18 18 DG H8 H 7.705 . 1 stop_ save_