data_36116 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; The structure of a chair-type G-quadruplex of the human telomeric variant in K+ solution ; _BMRB_accession_number 36116 _BMRB_flat_file_name bmr36116.str _Entry_type original _Submission_date 2017-09-20 _Accession_date 2017-10-20 _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 Liu C. . . 2 Zhou B. . . 3 Kuryavyi V. V. . 4 Zhu G. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 175 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-03-08 update BMRB 'update entry citation' 2018-09-24 original author 'original release' stop_ _Original_release_date 2017-10-20 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; A chair-type G-quadruplex structure formed by a human telomeric variant DNA in K ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 30713633 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Liu Changdong . . 2 Zhou Bo . . 3 Geng Yanyan . . 4 'Yan Tam' Dick . . 5 Feng Rui . . 6 Miao Haitao . . 7 Xu Naining . . 8 Shi Xiao . . 9 You Yingying . . 10 Hong Yuning . . 11 Tang 'Ben Zhong' Z. . 12 'Kwan Lo' Pik . . 13 Kuryavyi Vitaly . . 14 Zhu Guang . . stop_ _Journal_abbreviation 'Chem. Sci.' _Journal_name_full 'Chemical science' _Journal_volume 10 _Journal_issue 1 _Journal_ISSN 2041-6520 _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 218 _Page_last 226 _Year 2019 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name "DNA (5'-D(*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*TP*GP*GP*G)-3')" _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $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 "DNA (5'-D(*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*TP*GP*GP*G)-3')" _Molecular_mass 6661.276 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 21 _Mol_residue_sequence ; GGGTTAGGGTTAGGGTTTGG G ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DG 2 2 DG 3 3 DG 4 4 DT 5 5 DT 6 6 DA 7 7 DG 8 8 DG 9 9 DG 10 10 DT 11 11 DT 12 12 DA 13 13 DG 14 14 DG 15 15 DG 16 16 DT 17 17 DT 18 18 DT 19 19 DG 20 20 DG 21 21 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 "2.5 mM DNA (5'-D(*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*TP*GP*GP*G)-3'), 90% H2O/10% D2O" loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 2.5 mM 'natural abundance' 'Potassium Phosphate' 20 mM 'natural abundance' KCl 70 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % [U-2H] stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details "2.5 mM DNA (5'-D(*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*TP*GP*GP*G)-3'), 100% D2O" loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 2.5 mM 'natural abundance' 'Potassium Phosphate' 20 mM 'natural abundance' KCl 70 mM 'natural abundance' D2O 100 % [U-2H] stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task 'chemical shift 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' 'data analysis' 'peak picking' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name VNMR _Version . loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task collection stop_ _Details . save_ save_software_4 _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 800 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 500 _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-1H_COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $sample_2 save_ save_2D_1H-13C_HSQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _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' 90 . mM pH 7 . pH pressure 1 . atm temperature 284 . 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 water H 1 protons ppm 4.78 internal 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' '2D 1H-1H TOCSY' '2D 1H-1H COSY' '2D 1H-13C HSQC' stop_ loop_ _Sample_label $sample_1 $sample_2 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 DG H1 H 11.395 0.003 . 2 1 1 DG H1' H 5.799 0.003 . 3 1 1 DG H2' H 2.195 0.000 . 4 1 1 DG H2'' H 2.852 0.004 . 5 1 1 DG H3' H 4.181 0.008 . 6 1 1 DG H8 H 7.046 0.000 . 7 2 2 DG H1 H 11.826 0.000 . 8 2 2 DG H1' H 5.417 0.000 . 9 2 2 DG H2' H 2.199 0.007 . 10 2 2 DG H2'' H 2.858 0.000 . 11 2 2 DG H8 H 7.525 0.002 . 12 2 2 DG H21 H 9.786 0.003 . 13 2 2 DG H22 H 5.717 0.000 . 14 3 3 DG H1 H 11.324 0.003 . 15 3 3 DG H1' H 5.859 0.001 . 16 3 3 DG H2' H 1.701 0.000 . 17 3 3 DG H2'' H 2.315 0.007 . 18 3 3 DG H8 H 7.510 0.000 . 19 4 4 DT H1' H 6.005 0.003 . 20 4 4 DT H2' H 1.866 0.002 . 21 4 4 DT H2'' H 2.147 0.002 . 22 4 4 DT H3' H 4.478 0.000 . 23 4 4 DT H4' H 4.037 0.000 . 24 4 4 DT H5' H 3.900 0.004 . 25 4 4 DT H5'' H 3.755 0.005 . 26 4 4 DT H6 H 7.573 0.001 . 27 4 4 DT H71 H 1.693 0.000 . 28 4 4 DT H72 H 1.694 0.000 . 29 4 4 DT H73 H 1.693 0.000 . 30 5 5 DT H1' H 5.250 0.002 . 31 5 5 DT H2' H 0.560 0.003 . 32 5 5 DT H2'' H 1.480 0.002 . 33 5 5 DT H3 H 9.595 0.001 . 34 5 5 DT H3' H 4.293 0.001 . 35 5 5 DT H5' H 3.548 0.005 . 36 5 5 DT H5'' H 3.471 0.002 . 37 5 5 DT H6 H 6.505 0.001 . 38 5 5 DT H71 H 0.977 0.000 . 39 5 5 DT H72 H 0.977 0.000 . 40 5 5 DT H73 H 0.977 0.000 . 41 6 6 DA H1' H 5.406 0.003 . 42 6 6 DA H2 H 7.713 0.001 . 43 6 6 DA H2' H 2.273 0.002 . 44 6 6 DA H2'' H 2.461 0.001 . 45 6 6 DA H5' H 3.640 0.001 . 46 6 6 DA H5'' H 3.394 0.001 . 47 6 6 DA H8 H 7.497 0.005 . 48 6 6 DA H61 H 6.293 0.000 . 49 7 7 DG H1 H 10.297 0.001 . 50 7 7 DG H1' H 5.842 0.003 . 51 7 7 DG H2' H 2.798 0.003 . 52 7 7 DG H2'' H 3.159 0.002 . 53 7 7 DG H8 H 7.050 0.002 . 54 7 7 DG H21 H 7.687 0.000 . 55 7 7 DG H22 H 6.715 0.000 . 56 8 8 DG H1 H 11.053 0.001 . 57 8 8 DG H1' H 5.522 0.004 . 58 8 8 DG H2' H 2.106 0.002 . 59 8 8 DG H2'' H 2.390 0.000 . 60 8 8 DG H5' H 4.139 0.003 . 61 8 8 DG H5'' H 3.943 0.002 . 62 8 8 DG H8 H 7.136 0.002 . 63 8 8 DG H21 H 8.931 0.000 . 64 8 8 DG H22 H 5.788 0.000 . 65 9 9 DG H1 H 11.624 0.000 . 66 9 9 DG H1' H 5.686 0.002 . 67 9 9 DG H2' H 2.228 0.005 . 68 9 9 DG H2'' H 2.422 0.002 . 69 9 9 DG H5' H 3.856 0.005 . 70 9 9 DG H8 H 7.806 0.000 . 71 10 10 DT H1' H 5.434 0.006 . 72 10 10 DT H2' H 1.649 0.001 . 73 10 10 DT H2'' H 1.893 0.001 . 74 10 10 DT H3' H 4.388 0.000 . 75 10 10 DT H4' H 3.777 0.008 . 76 10 10 DT H5' H 3.926 0.000 . 77 10 10 DT H5'' H 3.753 0.000 . 78 10 10 DT H6 H 6.758 0.010 . 79 10 10 DT H71 H 1.297 0.000 . 80 10 10 DT H72 H 1.297 0.000 . 81 10 10 DT H73 H 1.298 0.000 . 82 11 11 DT H1' H 4.859 0.008 . 83 11 11 DT H2' H 1.324 0.004 . 84 11 11 DT H2'' H 1.709 0.004 . 85 11 11 DT H3' H 3.929 0.006 . 86 11 11 DT H4' H 3.464 0.002 . 87 11 11 DT H5' H 3.720 0.009 . 88 11 11 DT H5'' H 3.350 0.004 . 89 11 11 DT H6 H 6.620 0.003 . 90 11 11 DT H71 H 1.114 0.000 . 91 11 11 DT H72 H 1.114 0.000 . 92 11 11 DT H73 H 1.115 0.000 . 93 12 12 DA H1' H 5.503 0.002 . 94 12 12 DA H2 H 6.860 0.001 . 95 12 12 DA H2' H 1.805 0.001 . 96 12 12 DA H2'' H 2.328 0.003 . 97 12 12 DA H5' H 3.403 0.002 . 98 12 12 DA H5'' H 2.986 0.003 . 99 12 12 DA H8 H 7.332 0.003 . 100 13 13 DG H1 H 10.864 0.001 . 101 13 13 DG H1' H 5.784 0.005 . 102 13 13 DG H2' H 2.713 0.001 . 103 13 13 DG H2'' H 3.143 0.004 . 104 13 13 DG H4' H 2.990 0.000 . 105 13 13 DG H5' H 3.805 0.002 . 106 13 13 DG H5'' H 3.461 0.000 . 107 13 13 DG H8 H 7.173 0.001 . 108 14 14 DG H1 H 11.730 0.000 . 109 14 14 DG H1' H 5.511 0.001 . 110 14 14 DG H2' H 2.066 0.002 . 111 14 14 DG H2'' H 2.391 0.000 . 112 14 14 DG H5' H 3.999 0.002 . 113 14 14 DG H5'' H 3.921 0.006 . 114 14 14 DG H8 H 7.449 0.001 . 115 14 14 DG H21 H 9.737 0.000 . 116 14 14 DG H22 H 5.786 0.000 . 117 15 15 DG H1 H 11.458 0.000 . 118 15 15 DG H1' H 5.808 0.004 . 119 15 15 DG H2' H 2.039 0.005 . 120 15 15 DG H2'' H 2.389 0.002 . 121 15 15 DG H3' H 4.833 0.000 . 122 15 15 DG H8 H 7.609 0.002 . 123 16 16 DT H1' H 6.019 0.002 . 124 16 16 DT H2' H 1.764 0.005 . 125 16 16 DT H2'' H 2.230 0.003 . 126 16 16 DT H3' H 4.444 0.002 . 127 16 16 DT H4' H 4.083 0.001 . 128 16 16 DT H5' H 3.877 0.007 . 129 16 16 DT H5'' H 3.765 0.003 . 130 16 16 DT H6 H 7.597 0.003 . 131 16 16 DT H71 H 1.754 0.000 . 132 16 16 DT H72 H 1.755 0.000 . 133 16 16 DT H73 H 1.754 0.000 . 134 17 17 DT H1' H 5.699 0.002 . 135 17 17 DT H2' H 1.354 0.002 . 136 17 17 DT H2'' H 1.750 0.002 . 137 17 17 DT H3' H 4.490 0.000 . 138 17 17 DT H4' H 3.896 0.002 . 139 17 17 DT H5' H 3.664 0.006 . 140 17 17 DT H5'' H 3.630 0.003 . 141 17 17 DT H6 H 7.054 0.006 . 142 17 17 DT H71 H 1.223 0.000 . 143 17 17 DT H72 H 1.223 0.000 . 144 17 17 DT H73 H 1.223 0.000 . 145 18 18 DT H1' H 5.613 0.003 . 146 18 18 DT H2' H 2.083 0.002 . 147 18 18 DT H2'' H 2.198 0.002 . 148 18 18 DT H3 H 13.348 0.002 . 149 18 18 DT H4' H 3.823 0.000 . 150 18 18 DT H5' H 3.683 0.001 . 151 18 18 DT H5'' H 3.610 0.007 . 152 18 18 DT H6 H 7.024 0.001 . 153 18 18 DT H71 H 0.923 0.000 . 154 18 18 DT H72 H 0.923 0.000 . 155 18 18 DT H73 H 0.923 0.000 . 156 19 19 DG H1 H 11.191 0.000 . 157 19 19 DG H1' H 5.789 0.002 . 158 19 19 DG H2' H 2.841 0.001 . 159 19 19 DG H2'' H 3.204 0.003 . 160 19 19 DG H5'' H 4.079 0.003 . 161 19 19 DG H8 H 7.005 0.002 . 162 20 20 DG H1 H 10.963 0.003 . 163 20 20 DG H1' H 5.443 0.004 . 164 20 20 DG H2' H 2.010 0.002 . 165 20 20 DG H2'' H 2.119 0.002 . 166 20 20 DG H5'' H 4.167 0.003 . 167 20 20 DG H8 H 7.032 0.001 . 168 20 20 DG H21 H 9.151 0.000 . 169 20 20 DG H22 H 5.811 0.009 . 170 21 21 DG H1 H 11.255 0.000 . 171 21 21 DG H1' H 5.795 0.001 . 172 21 21 DG H2' H 2.058 0.004 . 173 21 21 DG H2'' H 2.312 0.001 . 174 21 21 DG H5' H 3.792 0.003 . 175 21 21 DG H8 H 7.769 0.001 . stop_ save_