data_18847 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of stacked G-quadruplex formed by human TERRA sequence in potassium solution ; _BMRB_accession_number 18847 _BMRB_flat_file_name bmr18847.str _Entry_type original _Submission_date 2012-11-20 _Accession_date 2012-11-20 _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 Martadinata Herry . . 2 Phan 'Anh Tuan' . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 4 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 232 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-04-25 update BMRB 'update entry citation' 2013-03-01 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structure of Human Telomeric RNA (TERRA): Stacking of Two G-Quadruplex Blocks in K(+) Solution.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 23445442 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Martadinata Herry . . 2 Phan 'Anh Tuan' . . stop_ _Journal_abbreviation Biochemistry _Journal_name_full Biochemistry _Journal_volume 52 _Journal_issue 13 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 2176 _Page_last 2183 _Year 2013 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'stacked G-quadruplex formed by human TERRA sequence' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'GGGUUAGGGU, chain 1' $RNA_(5'-R(*GP*GP*GP*UP*UP*AP*GP*GP*GP*U)-3') 'GGGUUAGGGU, chain 2' $RNA_(5'-R(*GP*GP*GP*UP*UP*AP*GP*GP*GP*U)-3') 'GGGUUAGGGU, chain 3' $RNA_(5'-R(*GP*GP*GP*UP*UP*AP*GP*GP*GP*U)-3') 'GGGUUAGGGU, chain 4' $RNA_(5'-R(*GP*GP*GP*UP*UP*AP*GP*GP*GP*U)-3') 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_RNA_(5'-R(*GP*GP*GP*UP*UP*AP*GP*GP*GP*U)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_(5'-R(*GP*GP*GP*UP*UP*AP*GP*GP*GP*U)-3') _Molecular_mass 3274.003 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 10 _Mol_residue_sequence GGGUUAGGGU loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 G 4 U 5 U 6 A 7 G 8 G 9 G 10 U 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 $RNA_(5'-R(*GP*GP*GP*UP*UP*AP*GP*GP*GP*U)-3') 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 $RNA_(5'-R(*GP*GP*GP*UP*UP*AP*GP*GP*GP*U)-3') 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_10-nt_TERRA _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $RNA_(5'-R(*GP*GP*GP*UP*UP*AP*GP*GP*GP*U)-3') 1.25 mM 'natural abundance' 'K+ solution' 90 mM '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' refinement stop_ _Details . save_ save_Felix _Saveframe_category software _Name Felix _Version . loop_ _Vendor _Address _Electronic_address 'Accelrys Software Inc.' . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' 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-13C_HSQC_aliphatic_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aliphatic' _Sample_label $10-nt_TERRA save_ save_2D_1H-13C_HSQC_aromatic_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aromatic' _Sample_label $10-nt_TERRA save_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $10-nt_TERRA save_ save_2D_1H-1H_COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $10-nt_TERRA save_ save_2D_1H-1H_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $10-nt_TERRA save_ save_NMR_spectrometer_expt _Saveframe_category NMR_applied_experiment _Experiment_name . _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 298 . K pH 7 . pH pressure 1 . atm 'ionic strength' 90 . mM 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 . . . 1.0 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_chem_shift_list_1_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' stop_ loop_ _Sample_label $10-nt_TERRA stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'GGGUUAGGGU, chain 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 G H1' H 5.886 0.01 1 2 1 1 G H2' H 4.986 0.01 1 3 1 1 G H3' H 4.512 0.01 1 4 1 1 G H4' H 4.317 0.01 1 5 1 1 G H5' H 4.025 0.01 1 6 1 1 G H5'' H 4.119 0.01 1 7 1 1 G H8 H 7.923 0.01 1 8 2 2 G H1' H 5.637 0.01 1 9 2 2 G H2' H 4.153 0.01 1 10 2 2 G H3' H 4.648 0.01 1 11 2 2 G H4' H 3.94 0.01 1 12 2 2 G H5' H 4.089 0.01 1 13 2 2 G H5'' H 4.571 0.01 1 14 2 2 G H8 H 7.659 0.01 1 15 3 3 G H1' H 5.972 0.01 1 16 3 3 G H2' H 4.344 0.01 1 17 3 3 G H3' H 4.697 0.01 1 18 3 3 G H4' H 4.41 0.01 1 19 3 3 G H5' H 3.824 0.01 1 20 3 3 G H8 H 7.762 0.01 1 21 4 4 U H1' H 5.972 0.01 1 22 4 4 U H3' H 4.709 0.01 1 23 4 4 U H5 H 5.864 0.01 1 24 4 4 U H6 H 7.84 0.01 1 25 5 5 U H1' H 5.989 0.01 1 26 5 5 U H2' H 4.246 0.01 1 27 5 5 U H3' H 4.657 0.01 1 28 5 5 U H4' H 4.522 0.01 1 29 5 5 U H6 H 7.869 0.01 1 30 6 6 A H1' H 6.322 0.01 1 31 6 6 A H2 H 8.382 0.01 1 32 6 6 A H2' H 5.022 0.01 1 33 6 6 A H3' H 4.977 0.01 1 34 6 6 A H4' H 4.774 0.01 1 35 6 6 A H8 H 8.602 0.01 1 36 7 7 G H1' H 5.836 0.01 1 37 7 7 G H2' H 4.851 0.01 1 38 7 7 G H3' H 4.474 0.01 1 39 7 7 G H4' H 4.694 0.01 1 40 7 7 G H8 H 7.835 0.01 1 41 8 8 G H1' H 5.829 0.01 1 42 8 8 G H2' H 4.25 0.01 1 43 8 8 G H3' H 4.852 0.01 1 44 8 8 G H4' H 4.546 0.01 1 45 8 8 G H8 H 7.771 0.01 1 46 9 9 G H1' H 6.082 0.01 1 47 9 9 G H2' H 4.184 0.01 1 48 9 9 G H3' H 4.602 0.01 1 49 9 9 G H4' H 4.408 0.01 1 50 9 9 G H8 H 7.65 0.01 1 51 10 10 U H1' H 5.513 0.01 1 52 10 10 U H2' H 3.878 0.01 1 53 10 10 U H3' H 4.185 0.01 1 54 10 10 U H4' H 4.135 0.01 1 55 10 10 U H5 H 5.033 0.01 1 56 10 10 U H5' H 4.01 0.01 1 57 10 10 U H5'' H 4.179 0.01 1 58 10 10 U H6 H 7.58 0.01 1 stop_ save_ save_assigned_chem_shift_list_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' stop_ loop_ _Sample_label $10-nt_TERRA stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'GGGUUAGGGU, chain 2' _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 11 1 G H1' H 5.886 0.01 1 2 11 1 G H2' H 4.986 0.01 1 3 11 1 G H3' H 4.512 0.01 1 4 11 1 G H4' H 4.317 0.01 1 5 11 1 G H5' H 4.025 0.01 1 6 11 1 G H5'' H 4.119 0.01 1 7 11 1 G H8 H 7.923 0.01 1 8 12 2 G H1' H 5.637 0.01 1 9 12 2 G H2' H 4.153 0.01 1 10 12 2 G H3' H 4.648 0.01 1 11 12 2 G H4' H 3.94 0.01 1 12 12 2 G H5' H 4.089 0.01 1 13 12 2 G H5'' H 4.571 0.01 1 14 12 2 G H8 H 7.659 0.01 1 15 13 3 G H1' H 5.972 0.01 1 16 13 3 G H2' H 4.344 0.01 1 17 13 3 G H3' H 4.697 0.01 1 18 13 3 G H4' H 4.41 0.01 1 19 13 3 G H5' H 3.824 0.01 1 20 13 3 G H8 H 7.762 0.01 1 21 14 4 U H1' H 5.972 0.01 1 22 14 4 U H3' H 4.709 0.01 1 23 14 4 U H5 H 5.864 0.01 1 24 14 4 U H6 H 7.84 0.01 1 25 15 5 U H1' H 5.989 0.01 1 26 15 5 U H2' H 4.246 0.01 1 27 15 5 U H3' H 4.657 0.01 1 28 15 5 U H4' H 4.522 0.01 1 29 15 5 U H6 H 7.869 0.01 1 30 16 6 A H1' H 6.322 0.01 1 31 16 6 A H2 H 8.382 0.01 1 32 16 6 A H2' H 5.022 0.01 1 33 16 6 A H3' H 4.977 0.01 1 34 16 6 A H4' H 4.774 0.01 1 35 16 6 A H8 H 8.602 0.01 1 36 17 7 G H1' H 5.836 0.01 1 37 17 7 G H2' H 4.851 0.01 1 38 17 7 G H3' H 4.474 0.01 1 39 17 7 G H4' H 4.694 0.01 1 40 17 7 G H8 H 7.835 0.01 1 41 18 8 G H1' H 5.829 0.01 1 42 18 8 G H2' H 4.25 0.01 1 43 18 8 G H3' H 4.852 0.01 1 44 18 8 G H4' H 4.546 0.01 1 45 18 8 G H8 H 7.771 0.01 1 46 19 9 G H1' H 6.082 0.01 1 47 19 9 G H2' H 4.184 0.01 1 48 19 9 G H3' H 4.602 0.01 1 49 19 9 G H4' H 4.408 0.01 1 50 19 9 G H8 H 7.65 0.01 1 51 20 10 U H1' H 5.513 0.01 1 52 20 10 U H2' H 3.878 0.01 1 53 20 10 U H3' H 4.185 0.01 1 54 20 10 U H4' H 4.135 0.01 1 55 20 10 U H5 H 5.033 0.01 1 56 20 10 U H5' H 4.01 0.01 1 57 20 10 U H5'' H 4.179 0.01 1 58 20 10 U H6 H 7.58 0.01 1 stop_ save_ save_assigned_chem_shift_list_1_3 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' stop_ loop_ _Sample_label $10-nt_TERRA stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'GGGUUAGGGU, chain 3' _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 21 1 G H1' H 5.886 0.01 1 2 21 1 G H2' H 4.986 0.01 1 3 21 1 G H3' H 4.512 0.01 1 4 21 1 G H4' H 4.317 0.01 1 5 21 1 G H5' H 4.025 0.01 1 6 21 1 G H5'' H 4.119 0.01 1 7 21 1 G H8 H 7.923 0.01 1 8 22 2 G H1' H 5.637 0.01 1 9 22 2 G H2' H 4.153 0.01 1 10 22 2 G H3' H 4.648 0.01 1 11 22 2 G H4' H 3.94 0.01 1 12 22 2 G H5' H 4.089 0.01 1 13 22 2 G H5'' H 4.571 0.01 1 14 22 2 G H8 H 7.659 0.01 1 15 23 3 G H1' H 5.972 0.01 1 16 23 3 G H2' H 4.344 0.01 1 17 23 3 G H3' H 4.697 0.01 1 18 23 3 G H4' H 4.41 0.01 1 19 23 3 G H5' H 3.824 0.01 1 20 23 3 G H8 H 7.762 0.01 1 21 24 4 U H1' H 5.972 0.01 1 22 24 4 U H3' H 4.709 0.01 1 23 24 4 U H5 H 5.864 0.01 1 24 24 4 U H6 H 7.84 0.01 1 25 25 5 U H1' H 5.989 0.01 1 26 25 5 U H2' H 4.246 0.01 1 27 25 5 U H3' H 4.657 0.01 1 28 25 5 U H4' H 4.522 0.01 1 29 25 5 U H6 H 7.869 0.01 1 30 26 6 A H1' H 6.322 0.01 1 31 26 6 A H2 H 8.382 0.01 1 32 26 6 A H2' H 5.022 0.01 1 33 26 6 A H3' H 4.977 0.01 1 34 26 6 A H4' H 4.774 0.01 1 35 26 6 A H8 H 8.602 0.01 1 36 27 7 G H1' H 5.836 0.01 1 37 27 7 G H2' H 4.851 0.01 1 38 27 7 G H3' H 4.474 0.01 1 39 27 7 G H4' H 4.694 0.01 1 40 27 7 G H8 H 7.835 0.01 1 41 28 8 G H1' H 5.829 0.01 1 42 28 8 G H2' H 4.25 0.01 1 43 28 8 G H3' H 4.852 0.01 1 44 28 8 G H4' H 4.546 0.01 1 45 28 8 G H8 H 7.771 0.01 1 46 29 9 G H1' H 6.082 0.01 1 47 29 9 G H2' H 4.184 0.01 1 48 29 9 G H3' H 4.602 0.01 1 49 29 9 G H4' H 4.408 0.01 1 50 29 9 G H8 H 7.65 0.01 1 51 30 10 U H1' H 5.513 0.01 1 52 30 10 U H2' H 3.878 0.01 1 53 30 10 U H3' H 4.185 0.01 1 54 30 10 U H4' H 4.135 0.01 1 55 30 10 U H5 H 5.033 0.01 1 56 30 10 U H5' H 4.01 0.01 1 57 30 10 U H5'' H 4.179 0.01 1 58 30 10 U H6 H 7.58 0.01 1 stop_ save_ save_assigned_chem_shift_list_1_4 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' stop_ loop_ _Sample_label $10-nt_TERRA stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'GGGUUAGGGU, chain 4' _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 31 1 G H1' H 5.886 0.01 1 2 31 1 G H2' H 4.986 0.01 1 3 31 1 G H3' H 4.512 0.01 1 4 31 1 G H4' H 4.317 0.01 1 5 31 1 G H5' H 4.025 0.01 1 6 31 1 G H5'' H 4.119 0.01 1 7 31 1 G H8 H 7.923 0.01 1 8 32 2 G H1' H 5.637 0.01 1 9 32 2 G H2' H 4.153 0.01 1 10 32 2 G H3' H 4.648 0.01 1 11 32 2 G H4' H 3.94 0.01 1 12 32 2 G H5' H 4.089 0.01 1 13 32 2 G H5'' H 4.571 0.01 1 14 32 2 G H8 H 7.659 0.01 1 15 33 3 G H1' H 5.972 0.01 1 16 33 3 G H2' H 4.344 0.01 1 17 33 3 G H3' H 4.697 0.01 1 18 33 3 G H4' H 4.41 0.01 1 19 33 3 G H5' H 3.824 0.01 1 20 33 3 G H8 H 7.762 0.01 1 21 34 4 U H1' H 5.972 0.01 1 22 34 4 U H3' H 4.709 0.01 1 23 34 4 U H5 H 5.864 0.01 1 24 34 4 U H6 H 7.84 0.01 1 25 35 5 U H1' H 5.989 0.01 1 26 35 5 U H2' H 4.246 0.01 1 27 35 5 U H3' H 4.657 0.01 1 28 35 5 U H4' H 4.522 0.01 1 29 35 5 U H6 H 7.869 0.01 1 30 36 6 A H1' H 6.322 0.01 1 31 36 6 A H2 H 8.382 0.01 1 32 36 6 A H2' H 5.022 0.01 1 33 36 6 A H3' H 4.977 0.01 1 34 36 6 A H4' H 4.774 0.01 1 35 36 6 A H8 H 8.602 0.01 1 36 37 7 G H1' H 5.836 0.01 1 37 37 7 G H2' H 4.851 0.01 1 38 37 7 G H3' H 4.474 0.01 1 39 37 7 G H4' H 4.694 0.01 1 40 37 7 G H8 H 7.835 0.01 1 41 38 8 G H1' H 5.829 0.01 1 42 38 8 G H2' H 4.25 0.01 1 43 38 8 G H3' H 4.852 0.01 1 44 38 8 G H4' H 4.546 0.01 1 45 38 8 G H8 H 7.771 0.01 1 46 39 9 G H1' H 6.082 0.01 1 47 39 9 G H2' H 4.184 0.01 1 48 39 9 G H3' H 4.602 0.01 1 49 39 9 G H4' H 4.408 0.01 1 50 39 9 G H8 H 7.65 0.01 1 51 40 10 U H1' H 5.513 0.01 1 52 40 10 U H2' H 3.878 0.01 1 53 40 10 U H3' H 4.185 0.01 1 54 40 10 U H4' H 4.135 0.01 1 55 40 10 U H5 H 5.033 0.01 1 56 40 10 U H5' H 4.01 0.01 1 57 40 10 U H5'' H 4.179 0.01 1 58 40 10 U H6 H 7.58 0.01 1 stop_ save_