data_18656 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Major Conformation of the Internal Loop 5'GAGU/3'UGAG ; _BMRB_accession_number 18656 _BMRB_flat_file_name bmr18656.str _Entry_type original _Submission_date 2012-08-12 _Accession_date 2012-08-12 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'A novel RNA internal loop in a conformational switch: major conformation of 5'GAGU/3'UGAG' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Kennedy Scott D. . 2 Turner Douglas H. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 4 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 164 "13C chemical shifts" 13 "15N chemical shifts" 5 "31P chemical shifts" 10 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-02-18 update BMRB 'update entry citation' 2011-05-05 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Novel conformation of an RNA structural switch.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 23134175 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Kennedy Scott D. . 2 Kierzek Ryszard . . 3 Turner Douglas H. . stop_ _Journal_abbreviation Biochemistry _Journal_name_full Biochemistry _Journal_volume 51 _Journal_issue 46 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 9257 _Page_last 9259 _Year 2012 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Internal Loop 5'GAGU/3'UGAG' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'RNA (5'-R(*GP*AP*CP*GP*AP*GP*UP*GP*UP*CP*A)-3'), strand 1' $RNA_loop 'RNA (5'-R(*GP*AP*CP*GP*AP*GP*UP*GP*UP*CP*A)-3'), strand 2' $RNA_loop 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_loop _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_loop _Molecular_mass 3546.203 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 11 _Mol_residue_sequence GACGAGUGUCA loop_ _Residue_seq_code _Residue_label 1 G 2 A 3 C 4 G 5 A 6 G 7 U 8 G 9 U 10 C 11 A 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_loop . . . . . . 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_loop '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 $RNA_loop 1.5 mM 'natural abundance' 'sodium chloride' 80 mM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' EDTA 0.05 mM 'natural abundance' H2O 95 % 'natural abundance' D2O 5 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $RNA_loop 1.5 mM 'natural abundance' 'sodium chloride' 80 mM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' EDTA 0.05 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_SPARKY _Saveframe_category software _Name SPARKY _Version 3.12 loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' stop_ _Details . save_ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_AMBER _Saveframe_category software _Name AMBER _Version 10 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-13C_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_1H-15N_HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_30_ms_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY 30 ms' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_75_ms_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY 75 ms' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_150_ms_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY 150 ms' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_2 save_ save_2D_1H-1H_TOCSY_14ms_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY 14ms' _Sample_label $sample_2 save_ save_2D_1H-1H_TOCSY_36_ms_8 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY 36 ms' _Sample_label $sample_2 save_ save_2D_1H-1H_NOESY_75_ms_9 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY 75 ms' _Sample_label $sample_2 save_ save_2D_1H-1H_NOESY_175_ms_10 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY 175 ms' _Sample_label $sample_2 save_ save_2D_1H-1H_NOESY_400_ms_11 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY 400 ms' _Sample_label $sample_2 save_ save_2D_1H-31P_HETCOR_12 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-31P HETCOR' _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 temperature 274 . K pH 6.1 . pH pressure 1 . atm 'ionic strength' 0.1 . M 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 DSS C 13 'methyl protons' ppm 0.00 na indirect . . . 0.251449530 DSS N 15 'methyl protons' ppm 0.00 na indirect . . . 0.101329118 DSS P 31 'methyl protons' ppm 0.00 na indirect . . . 0.404808636 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-13C HSQC' '2D 1H-1H TOCSY 14ms' '2D 1H-1H NOESY 400 ms' '2D 1H-31P HETCOR' stop_ loop_ _Sample_label $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'RNA (5'-R(*GP*AP*CP*GP*AP*GP*UP*GP*UP*CP*A)-3'), strand 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 5.815 0.001 1 2 1 1 G H2' H 4.826 0.001 1 3 1 1 G H3' H 4.598 0.003 1 4 1 1 G H4' H 4.400 0.002 1 5 1 1 G H5' H 4.076 0.006 2 6 1 1 G H5'' H 3.931 0.005 2 7 1 1 G H8 H 8.080 0.001 1 8 1 1 G C8 C 138.693 0.200 1 9 2 2 A H1' H 5.911 0.001 1 10 2 2 A H2 H 7.553 0.002 1 11 2 2 A H2' H 4.597 0.003 1 12 2 2 A H3' H 4.557 0.002 1 13 2 2 A H4' H 4.471 0.003 1 14 2 2 A H5' H 4.582 0.002 2 15 2 2 A H5'' H 4.115 0.003 2 16 2 2 A H8 H 7.938 0.001 1 17 2 2 A C2 C 153.541 0.200 1 18 2 2 A C8 C 139.429 0.200 1 19 2 2 A P P -4.029 0.020 1 20 3 3 C H1' H 5.001 0.010 1 21 3 3 C H2' H 3.981 0.001 1 22 3 3 C H3' H 4.262 0.003 1 23 3 3 C H4' H 4.165 0.004 1 24 3 3 C H5 H 4.955 0.002 1 25 3 3 C H5' H 4.424 0.010 2 26 3 3 C H5'' H 3.873 0.003 2 27 3 3 C H6 H 7.112 0.003 1 28 3 3 C C6 C 139.764 0.200 1 29 3 3 C P P -4.029 0.020 1 30 4 4 G H1' H 5.626 0.003 1 31 4 4 G H2' H 4.922 0.002 1 32 4 4 G H3' H 4.263 0.003 1 33 4 4 G H4' H 4.277 0.001 1 34 4 4 G H5' H 4.367 0.003 2 35 4 4 G H5'' H 3.865 0.001 2 36 4 4 G H8 H 7.548 0.002 1 37 4 4 G C8 C 143.205 0.200 1 38 4 4 G P P -4.558 0.020 1 39 5 5 A H1' H 5.736 0.002 1 40 5 5 A H2 H 7.653 0.002 1 41 5 5 A H2' H 4.040 0.002 1 42 5 5 A H3' H 4.549 0.003 1 43 5 5 A H4' H 3.865 0.001 1 44 5 5 A H5' H 2.854 0.002 2 45 5 5 A H5'' H 3.652 0.003 2 46 5 5 A H8 H 7.583 0.001 1 47 5 5 A C2 C 153.596 0.200 1 48 5 5 A C8 C 140.118 0.200 1 49 5 5 A P P -2.583 0.020 1 50 6 6 G H1' H 5.926 0.002 1 51 6 6 G H2' H 6.140 0.002 1 52 6 6 G H3' H 4.832 0.002 1 53 6 6 G H4' H 4.536 0.002 1 54 6 6 G H5' H 4.138 0.004 2 55 6 6 G H5'' H 4.072 0.003 2 56 6 6 G P P -4.249 0.020 1 57 7 7 U H1' H 6.229 0.002 1 58 7 7 U H2' H 4.568 0.003 1 59 7 7 U H3' H 5.128 0.002 1 60 7 7 U H4' H 4.582 0.002 1 61 7 7 U H5 H 5.989 0.002 1 62 7 7 U H5' H 4.423 0.002 2 63 7 7 U H5'' H 4.243 0.002 2 64 7 7 U H6 H 8.120 0.002 1 65 7 7 U C6 C 144.283 0.200 1 66 7 7 U P P -3.207 0.020 1 67 8 8 G H1' H 5.196 0.001 1 68 8 8 G H2' H 4.363 0.001 1 69 8 8 G H3' H 4.566 0.001 1 70 8 8 G H4' H 4.402 0.004 1 71 8 8 G H5' H 4.523 0.001 2 72 8 8 G H5'' H 4.204 0.002 2 73 8 8 G H8 H 7.785 0.002 1 74 8 8 G C8 C 138.058 0.200 1 75 8 8 G P P -3.787 0.020 1 76 9 9 U H1' H 5.438 0.001 1 77 9 9 U H2' H 4.406 0.003 1 78 9 9 U H3' H 4.477 0.003 1 79 9 9 U H4' H 4.373 0.008 1 80 9 9 U H5 H 5.138 0.003 1 81 9 9 U H5' H 4.563 0.010 2 82 9 9 U H5'' H 4.033 0.004 2 83 9 9 U H6 H 7.853 0.004 1 84 9 9 U C6 C 141.946 0.200 1 85 9 9 U P P -5.001 0.020 1 86 10 10 C H1' H 5.458 0.001 1 87 10 10 C H2' H 4.358 0.002 1 88 10 10 C H3' H 4.420 0.004 1 89 10 10 C H4' H 4.348 0.005 1 90 10 10 C H5 H 5.539 0.002 1 91 10 10 C H5' H 4.460 0.002 2 92 10 10 C H5'' H 4.031 0.002 2 93 10 10 C H6 H 7.678 0.002 1 94 10 10 C C6 C 140.660 0.200 1 95 10 10 C P P -3.899 0.020 1 96 11 11 A H1' H 5.882 0.002 1 97 11 11 A H2 H 7.241 0.001 1 98 11 11 A H2' H 3.969 0.002 1 99 11 11 A H3' H 4.252 0.002 1 100 11 11 A H4' H 4.165 0.002 1 101 11 11 A H5' H 4.425 0.003 2 102 11 11 A H5'' H 3.994 0.001 2 103 11 11 A H8 H 7.972 0.001 1 104 11 11 A C2 C 154.086 0.200 1 105 11 11 A C8 C 139.960 0.200 1 106 11 11 A P P -3.790 0.020 1 stop_ save_ save_assigned_chem_shift_list_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-13C HSQC' '2D 1H-1H TOCSY 14ms' '2D 1H-1H NOESY 400 ms' '2D 1H-31P HETCOR' stop_ loop_ _Sample_label $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'RNA (5'-R(*GP*AP*CP*GP*AP*GP*UP*GP*UP*CP*A)-3'), strand 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 1 1 G H1 H 11.925 0.002 1 2 1 1 G H21 H 6.141 0.050 1 3 1 1 G H22 H 7.771 0.005 1 4 1 1 G HO2' H 7.048 0.008 1 5 2 2 A H61 H 8.016 0.003 1 6 2 2 A H62 H 6.564 0.001 1 7 2 2 A HO2' H 6.903 0.001 1 8 3 3 C H41 H 8.070 0.004 1 9 3 3 C H42 H 6.803 0.003 1 10 3 3 C HO2' H 6.521 0.001 1 11 4 4 G H1 H 10.277 0.002 1 12 6 6 G H1 H 13.320 0.002 1 13 8 8 G H1 H 12.976 0.002 1 14 8 8 G H21 H 5.966 0.050 1 15 8 8 G H22 H 8.020 0.019 1 16 8 8 G HO2' H 6.905 0.003 1 17 9 9 U H3 H 14.492 0.002 1 18 9 9 U HO2' H 6.960 0.001 1 19 10 10 C H41 H 8.139 0.002 1 20 10 10 C H42 H 7.015 0.002 1 21 10 10 C HO2' H 6.750 0.003 1 stop_ save_ save_assigned_chem_shift_list_2_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-15N HSQC' '2D 1H-1H TOCSY 30 ms' '2D 1H-1H NOESY 150 ms' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'RNA (5'-R(*GP*AP*CP*GP*AP*GP*UP*GP*UP*CP*A)-3'), strand 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 5.840 0.001 1 2 1 1 G H2' H 4.871 0.010 1 3 1 1 G H8 H 8.107 0.001 1 4 2 2 A H1' H 5.944 0.002 1 5 2 2 A H2 H 7.576 0.001 1 6 2 2 A H2' H 4.602 0.001 1 7 2 2 A H8 H 7.954 0.001 1 8 3 3 C H1' H 5.057 0.001 1 9 3 3 C H2' H 3.999 0.001 1 10 3 3 C H5 H 4.977 0.002 1 11 3 3 C H6 H 7.164 0.002 1 12 4 4 G H1' H 5.661 0.002 1 13 4 4 G H2' H 4.997 0.010 1 14 4 4 G H8 H 7.622 0.001 1 15 5 5 A H1' H 5.726 0.001 1 16 5 5 A H2 H 7.678 0.002 1 17 5 5 A H2' H 4.037 0.001 1 18 5 5 A H3' H 4.557 0.001 1 19 5 5 A H4' H 3.920 0.001 1 20 5 5 A H5' H 2.803 0.001 2 21 5 5 A H5'' H 3.629 0.001 2 22 5 5 A H8 H 7.597 0.001 1 23 6 6 G H1' H 5.887 0.002 1 24 6 6 G H2' H 5.676 0.002 1 25 6 6 G H3' H 4.895 0.010 1 26 6 6 G H4' H 4.513 0.010 1 27 6 6 G H8 H 7.817 0.001 1 28 7 7 U H1' H 6.208 0.002 1 29 7 7 U H2' H 4.592 0.001 1 30 7 7 U H4' H 4.618 0.001 1 31 7 7 U H5 H 6.008 0.002 1 32 7 7 U H6 H 8.085 0.002 1 33 8 8 G H1' H 5.062 0.010 1 34 8 8 G H2' H 4.424 0.010 1 35 8 8 G H8 H 7.802 0.001 1 36 9 9 U H1' H 5.462 0.001 1 37 9 9 U H2' H 4.423 0.001 1 38 9 9 U H5 H 5.122 0.002 1 39 9 9 U H6 H 7.860 0.002 1 40 10 10 C H1' H 5.486 0.001 1 41 10 10 C H2' H 4.389 0.010 1 42 10 10 C H5 H 5.560 0.010 1 43 10 10 C H6 H 7.698 0.001 1 44 11 11 A H1' H 5.916 0.003 1 45 11 11 A H2 H 7.285 0.002 1 46 11 11 A H2' H 4.014 0.001 1 47 11 11 A H8 H 8.006 0.002 1 stop_ save_ save_assigned_chem_shift_list_2_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-15N HSQC' '2D 1H-1H TOCSY 30 ms' '2D 1H-1H NOESY 150 ms' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'RNA (5'-R(*GP*AP*CP*GP*AP*GP*UP*GP*UP*CP*A)-3'), strand 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 1 1 G H1 H 11.940 0.001 1 2 1 1 G H21 H 6.180 0.010 1 3 1 1 G H22 H 7.788 0.012 1 4 1 1 G N1 N 147.212 0.300 1 5 3 3 C H41 H 6.820 0.002 1 6 3 3 C H42 H 8.178 0.004 1 7 4 4 G H1 H 10.174 0.001 1 8 4 4 G N1 N 145.284 0.300 1 9 6 6 G H1 H 13.381 0.001 1 10 6 6 G N1 N 151.420 0.300 1 11 8 8 G H1 H 12.992 0.001 1 12 8 8 G H21 H 6.464 0.003 1 13 8 8 G H22 H 8.748 0.006 1 14 8 8 G N1 N 148.549 0.300 1 15 9 9 U H3 H 14.548 0.002 1 16 9 9 U N3 N 163.849 0.300 1 17 10 10 C H41 H 7.017 0.003 1 18 10 10 C H42 H 8.153 0.002 1 stop_ save_