data_25596 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of DNA G-quadruplex adopted by ALS and FTD related GGGGCC repeat with G21 to Br-G21 substitution ; _BMRB_accession_number 25596 _BMRB_flat_file_name bmr25596.str _Entry_type original _Submission_date 2015-05-06 _Accession_date 2015-05-06 _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 Brcic J. . . 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" 166 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2016-08-24 update BMRB 'update entry citation' 2015-09-21 original author 'original release' stop_ _Original_release_date 2015-09-21 save_ ############################# # Citation for this entry # ############################# save_citations _Saveframe_category entry_citation _Citation_full . _Citation_title ; Solution structure of a DNA quadruplex containing ALS and FTD related GGGGCC repeat stabilized by 8-bromodeoxyguanosine substitution ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 26253741 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Brcic J. . . 2 Plavec J. . . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_volume 43 _Journal_issue 17 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 8590 _Page_last 8600 _Year 2015 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name G-quadruplex _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label G-quadruplex $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_G-quadruplex _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common GGGGCC_repeat_G-quadruplex _Molecular_mass 6957.481 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 22 _Mol_residue_sequence ; GGGGCCGGGGCCGGGGCCGG XG ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DG 2 2 DG 3 3 DG 4 4 DG 5 5 DC 6 6 DC 7 7 DG 8 8 DG 9 9 DG 10 10 DG 11 11 DC 12 12 DC 13 13 DG 14 14 DG 15 15 DG 16 16 DG 17 17 DC 18 18 DC 19 19 DG 20 20 DG 21 21 BGM 22 22 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value NCBI NM_018325 'chromosome 9 open reading frame 72' . . . . . stop_ save_ ###################### # Polymer residues # ###################### save_chem_comp_BGM _Saveframe_category polymer_residue _Mol_type 'DNA LINKING' _Name_common 8-BROMO-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE _BMRB_code BGM _PDB_code BGM _Standard_residue_derivative . _Molecular_mass 426.117 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons P P P . 0 . ? OP1 OP1 O . 0 . ? OP2 OP2 O . 0 . ? O5' O5' O . 0 . ? C5' C5' C . 0 . ? C4' C4' C . 0 . ? O4' O4' O . 0 . ? C1' C1' C . 0 . ? N9 N9 N . 0 . ? C8 C8 C . 0 . ? N7 N7 N . 0 . ? C5 C5 C . 0 . ? C4 C4 C . 0 . ? N3 N3 N . 0 . ? C2 C2 C . 0 . ? N2 N2 N . 0 . ? N1 N1 N . 0 . ? C6 C6 C . 0 . ? O6 O6 O . 0 . ? C2' C2' C . 0 . ? C3' C3' C . 0 . ? O3' O3' O . 0 . ? OP3 OP3 O . 0 . ? BR BR BR . 0 . ? HOP2 HOP2 H . 0 . ? H5' H5' H . 0 . ? H5'' H5'' H . 0 . ? H4' H4' H . 0 . ? H1' H1' H . 0 . ? H21 H21 H . 0 . ? H22 H22 H . 0 . ? H1 H1 H . 0 . ? H2' H2' H . 0 . ? H2'' H2'' H . 0 . ? H3' H3' H . 0 . ? HO3' HO3' H . 0 . ? HOP3 HOP3 H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name DOUB P OP1 ? ? SING P OP2 ? ? SING P O5' ? ? SING P OP3 ? ? SING OP2 HOP2 ? ? SING O5' C5' ? ? SING C5' C4' ? ? SING C5' H5' ? ? SING C5' H5'' ? ? SING C4' O4' ? ? SING C4' C3' ? ? SING C4' H4' ? ? SING O4' C1' ? ? SING C1' N9 ? ? SING C1' C2' ? ? SING C1' H1' ? ? SING N9 C8 ? ? SING N9 C4 ? ? DOUB C8 N7 ? ? SING C8 BR ? ? SING N7 C5 ? ? DOUB C5 C4 ? ? SING C5 C6 ? ? SING C4 N3 ? ? DOUB N3 C2 ? ? SING C2 N2 ? ? SING C2 N1 ? ? SING N2 H21 ? ? SING N2 H22 ? ? SING N1 C6 ? ? SING N1 H1 ? ? DOUB C6 O6 ? ? SING C2' C3' ? ? SING C2' H2' ? ? SING C2' H2'' ? ? SING C3' O3' ? ? SING C3' H3' ? ? SING O3' HO3' ? ? SING OP3 HOP3 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Gene_mnemonic _Details $G-quadruplex Human 9606 Eukaryota Metazoa Homo sapiens C9orf72 'expanded repeat within C9orf72, linked to ALS and FTD' 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 $G-quadruplex 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '0.5 mM DNA, 120 mM KCl, 20 mM potassium phosphate buffer pH 7.2, 90% H2O, 10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $G-quadruplex 0.5 mM 'natural abundance' 'potassium chloride' 120 mM 'natural abundance' 'potassium phosphate' 20 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '0.5 mM DNA, 120 mM KCl, 20 mM potassium phosphate buffer pH 7.2, 100% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $G-quadruplex 0.5 mM 'natural abundance' 'potassium chloride' 120 mM 'natural abundance' 'potassium phosphate' 20 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type solution _Details '0.3-0.6 mM 8% 15, 8% 13C N DNA, 120 mM KCl, 20 mM potassium phosphate buffer pH 7.2, 90% H2O, 10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $G-quadruplex . mM 0.3 0.6 '8% 13C, 8% 15 N' 'potassium chloride' 120 mM . . 'natural abundance' 'potassium phosphate' 20 mM . . 'natural abundance' H2O 90 % . . 'natural abundance' D2O 10 % . . 'natural abundance' stop_ save_ save_sample_4 _Saveframe_category sample _Sample_type solution _Details '0.3-0.6 mM 8% 15 N DNA, 120 mM KCl, 20 mM potassium phosphate buffer pH 7.2, 90% H2O, 10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $G-quadruplex . mM 0.3 0.6 '8% 15 N' 'potassium chloride' 120 mM . . 'natural abundance' 'potassium phosphate' 20 mM . . 'natural abundance' H2O 90 % . . 'natural abundance' D2O 10 % . . 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_AMBER _Saveframe_category software _Name AMBER _Version 14 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'peak picking' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Agilent-Varian _Model 'Uniform NMR System' _Field_strength 600 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Agilent-Varian _Model 'Uniform NMR System' _Field_strength 800 _Details . save_ ############################# # NMR applied experiments # ############################# save_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name 1H-1H_TOCSY _Sample_label $sample_2 save_ save_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name 1H-1H_NOESY _Sample_label $sample_1 save_ save_1H_1H_DQF_COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name 1H_1H_DQF_COSY _Sample_label $sample_2 save_ save_1D_13C__HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name 1D_13C__HSQC _Sample_label $sample_3 save_ save_1D_15N_HSQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name 1D_15N_HSQC _Sample_label $sample_4 save_ save_1H-1H_NOESY_6 _Saveframe_category NMR_applied_experiment _Experiment_name 1H-1H_NOESY _Sample_label $sample_2 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' 140 . mM pH 7.2 . pH pressure 1 . atm temperature 273 . K stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 140 . mM pH 7.2 . 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 external direct . 'separate tube (no insert) similar to the experimental sample tube' . 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_ _Software_label $SPARKY stop_ loop_ _Experiment_label 1H-1H_TOCSY 1H-1H_NOESY 1H_1H_DQF_COSY stop_ loop_ _Sample_label $sample_2 $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 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 DG H1 H 11.760 0.004 1 2 1 1 DG H1' H 6.210 0.004 1 3 1 1 DG H2' H 2.804 0.008 1 4 1 1 DG H2'' H 3.251 0.007 1 5 1 1 DG H3' H 5.000 0.008 1 6 1 1 DG H8 H 7.520 0.002 1 7 2 2 DG H1 H 11.482 0.003 1 8 2 2 DG H1' H 6.259 0.006 1 9 2 2 DG H2' H 2.511 0.002 1 10 2 2 DG H2'' H 2.815 0.009 1 11 2 2 DG H3' H 5.105 0.003 1 12 2 2 DG H8 H 7.967 0.007 1 13 2 2 DG H21 H 6.619 0.005 1 14 2 2 DG H22 H 9.099 0.009 1 15 3 3 DG H1 H 11.240 0.005 1 16 3 3 DG H1' H 5.985 0.007 1 17 3 3 DG H2' H 3.156 0.007 1 18 3 3 DG H2'' H 2.754 0.007 1 19 3 3 DG H3' H 5.107 0.004 1 20 3 3 DG H8 H 7.348 0.001 1 21 3 3 DG H21 H 6.543 0.003 1 22 3 3 DG H22 H 8.817 0.002 1 23 4 4 DG H1 H 11.922 0.005 1 24 4 4 DG H1' H 5.968 0.005 1 25 4 4 DG H2' H 2.963 0.006 1 26 4 4 DG H2'' H 2.235 0.004 1 27 4 4 DG H3' H 5.105 0.005 1 28 4 4 DG H4' H 4.445 0.003 1 29 4 4 DG H8 H 8.378 0.005 1 30 4 4 DG H21 H 6.591 0.008 1 31 4 4 DG H22 H 10.194 0.008 1 32 5 5 DC H1' H 5.941 0.004 1 33 5 5 DC H2' H 2.116 0.006 1 34 5 5 DC H2'' H 2.541 0.004 1 35 5 5 DC H3' H 4.783 0.007 1 36 5 5 DC H4' H 4.274 0.002 1 37 5 5 DC H5 H 6.077 0.002 1 38 5 5 DC H6 H 8.111 0.005 1 39 5 5 DC H41 H 7.138 0.004 1 40 5 5 DC H42 H 6.865 0.003 1 41 6 6 DC H1' H 5.974 0.004 1 42 6 6 DC H2' H 2.001 0.005 1 43 6 6 DC H2'' H 2.619 0.005 1 44 6 6 DC H3' H 4.842 0.009 1 45 6 6 DC H5 H 4.370 0.008 1 46 6 6 DC H6 H 7.037 0.003 1 47 7 7 DG H1 H 11.411 0.005 1 48 7 7 DG H1' H 6.183 0.007 1 49 7 7 DG H2' H 3.634 0.009 1 50 7 7 DG H2'' H 3.069 0.007 1 51 7 7 DG H3' H 4.926 0.005 1 52 7 7 DG H8 H 7.537 0.006 1 53 7 7 DG H21 H 6.900 0.005 1 54 7 7 DG H22 H 9.508 0.005 1 55 8 8 DG H1 H 11.727 0.001 1 56 8 8 DG H1' H 6.177 0.008 1 57 8 8 DG H2' H 2.622 0.007 1 58 8 8 DG H2'' H 2.773 0.006 1 59 8 8 DG H3' H 5.066 0.002 1 60 8 8 DG H8 H 8.003 0.006 1 61 8 8 DG H21 H 6.357 0.006 1 62 8 8 DG H22 H 9.807 0.007 1 63 9 9 DG H1 H 11.208 0.006 1 64 9 9 DG H1' H 5.986 0.005 1 65 9 9 DG H2' H 3.078 0.005 1 66 9 9 DG H2'' H 2.745 0.008 1 67 9 9 DG H3' H 5.069 0.000 1 68 9 9 DG H8 H 7.245 0.002 1 69 9 9 DG H21 H 6.328 0.003 1 70 9 9 DG H22 H 8.691 0.004 1 71 10 10 DG H1 H 11.789 0.003 1 72 10 10 DG H1' H 6.117 0.010 1 73 10 10 DG H2' H 2.609 0.005 1 74 10 10 DG H2'' H 2.817 0.009 1 75 10 10 DG H3' H 4.978 0.004 1 76 10 10 DG H8 H 8.072 0.003 1 77 10 10 DG H21 H 6.496 0.003 1 78 10 10 DG H22 H 10.248 0.004 1 79 11 11 DC H1' H 4.780 0.008 1 80 11 11 DC H2' H 1.446 0.006 1 81 11 11 DC H2'' H 1.920 0.006 1 82 11 11 DC H3' H 4.277 0.005 1 83 11 11 DC H5 H 5.753 0.006 1 84 11 11 DC H6 H 7.268 0.002 1 85 12 12 DC H1' H 5.623 0.010 1 86 12 12 DC H2' H 1.616 0.010 1 87 12 12 DC H2'' H 2.241 0.005 1 88 12 12 DC H3' H 4.440 0.005 1 89 12 12 DC H5 H 5.714 0.003 1 90 12 12 DC H6 H 7.172 0.004 1 91 13 13 DG H1 H 11.389 0.002 1 92 13 13 DG H1' H 6.276 0.006 1 93 13 13 DG H2' H 3.971 0.002 1 94 13 13 DG H2'' H 2.994 0.005 1 95 13 13 DG H3' H 4.906 0.007 1 96 13 13 DG H8 H 7.570 0.004 1 97 14 14 DG H1 H 11.658 0.003 1 98 14 14 DG H1' H 6.275 0.004 1 99 14 14 DG H2' H 2.436 0.005 1 100 14 14 DG H2'' H 2.827 0.007 1 101 14 14 DG H3' H 4.981 0.003 1 102 14 14 DG H8 H 7.809 0.004 1 103 14 14 DG H21 H 6.267 0.006 1 104 14 14 DG H22 H 9.569 0.007 1 105 15 15 DG H1 H 11.214 0.007 1 106 15 15 DG H1' H 5.978 0.008 1 107 15 15 DG H2' H 3.184 0.009 1 108 15 15 DG H2'' H 2.742 0.009 1 109 15 15 DG H3' H 5.107 0.003 1 110 15 15 DG H8 H 7.280 0.002 1 111 15 15 DG H21 H 6.482 0.003 1 112 15 15 DG H22 H 8.707 0.004 1 113 16 16 DG H1 H 11.920 0.008 1 114 16 16 DG H1' H 5.966 0.004 1 115 16 16 DG H2' H 2.965 0.006 1 116 16 16 DG H2'' H 2.236 0.004 1 117 16 16 DG H3' H 5.103 0.006 1 118 16 16 DG H4' H 4.448 0.005 1 119 16 16 DG H8 H 8.382 0.005 1 120 16 16 DG H21 H 6.593 0.009 1 121 16 16 DG H22 H 10.215 0.008 1 122 17 17 DC H1' H 5.940 0.004 1 123 17 17 DC H2' H 2.116 0.006 1 124 17 17 DC H2'' H 2.542 0.004 1 125 17 17 DC H3' H 4.782 0.006 1 126 17 17 DC H4' H 4.274 0.002 1 127 17 17 DC H5 H 6.079 0.002 1 128 17 17 DC H6 H 8.109 0.006 1 129 17 17 DC H41 H 7.138 0.004 1 130 17 17 DC H42 H 6.865 0.003 1 131 18 18 DC H1' H 5.973 0.003 1 132 18 18 DC H2' H 2.000 0.005 1 133 18 18 DC H2'' H 2.624 0.006 1 134 18 18 DC H3' H 4.843 0.005 1 135 18 18 DC H5 H 4.369 0.007 1 136 18 18 DC H6 H 7.036 0.003 1 137 19 19 DG H1 H 11.410 0.006 1 138 19 19 DG H1' H 6.188 0.008 1 139 19 19 DG H2' H 3.592 0.013 1 140 19 19 DG H2'' H 3.046 0.006 1 141 19 19 DG H3' H 4.920 0.008 1 142 19 19 DG H8 H 7.539 0.004 1 143 19 19 DG H21 H 6.843 0.008 1 144 19 19 DG H22 H 9.580 0.006 1 145 20 20 DG H1 H 11.774 0.004 1 146 20 20 DG H1' H 6.179 0.014 1 147 20 20 DG H2' H 2.624 0.006 1 148 20 20 DG H2'' H 2.790 0.007 1 149 20 20 DG H3' H 5.063 0.000 1 150 20 20 DG H8 H 8.044 0.008 1 151 20 20 DG H21 H 6.364 0.002 1 152 20 20 DG H22 H 9.807 0.004 1 153 21 21 BGM H1 H 11.446 0.002 1 154 21 21 BGM H1' H 6.109 0.005 1 155 21 21 BGM H2' H 3.323 0.008 1 156 21 21 BGM H2'' H 2.709 0.009 1 157 21 21 BGM H21 H 6.618 0.005 1 158 21 21 BGM H22 H 9.172 0.003 1 159 21 21 BGM H3' H 5.103 0.005 1 160 22 22 DG H1 H 11.502 0.007 1 161 22 22 DG H1' H 6.111 0.006 1 162 22 22 DG H2' H 2.668 0.007 1 163 22 22 DG H2'' H 2.385 0.005 1 164 22 22 DG H3' H 4.758 0.008 1 165 22 22 DG H4' H 4.212 0.003 1 166 22 22 DG H8 H 8.111 0.001 1 stop_ save_