data_25291 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; RNA duplex ; _BMRB_accession_number 25291 _BMRB_flat_file_name bmr25291.str _Entry_type original _Submission_date 2014-10-20 _Accession_date 2014-10-20 _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 Lynch Stephen R. . 2 Kool Eric T. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 77 "13C chemical shifts" 48 "31P chemical shifts" 8 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2015-09-28 original BMRB . stop_ _Original_release_date 2015-09-28 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structure and thermodynamics of N6-methyladenosine in RNA: a spring-loaded base modification ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 25611135 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Roost Caroline . . 2 Lynch Stephen R. . 3 Batista Pedro J. . 4 Qu Kun . . 5 Chang Howard Y. . 6 Kool Eric T. . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_volume 137 _Journal_issue 5 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 2107 _Page_last 2115 _Year 2015 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'RNA duplex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'RNA, chain 1' $RNA 'RNA, chain 2' $RNA 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 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 10 _Mol_residue_sequence ; GGACUAGUCC ; loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 A 4 C 5 U 6 A 7 G 8 U 9 C 10 C 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 . . . . . . 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 '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 0.2 mM 'natural abundance' 'sodium chloride' 100 mM 'natural abundance' EDTA 0.1 mM 'natural abundance' 'sodium phosphate' 10 mM '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 0.2 mM 'natural abundance' 'sodium chloride' 100 mM 'natural abundance' EDTA 0.1 mM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_VNMR _Saveframe_category software _Name VNMR _Version 6.1C loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task collection processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version 3.115 loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' stop_ _Details . save_ save_X-PLOR_NIH _Saveframe_category software _Name X-PLOR_NIH _Version 2.36 loop_ _Vendor _Address _Electronic_address Brunger . . 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_ save_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_2 save_ save_2D_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_2 save_ save_2D_1H-13C_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _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-1H_TOCSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_2 save_ save_2D_1H-1H_NOESY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-31P_COSY_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-31P COSY' _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' 100 . mM pH 6.4 . 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 TMS C 13 'methyl carbon' ppm 0 external indirect . . . 1.0 water H 1 protons ppm 4.77 internal direct . . . 1.0 'phosphoric acid (85%)' P 31 phosphorus ppm 0 external indirect . . . 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 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $VNMR $SPARKY $X-PLOR_NIH stop_ loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-13C HSQC' '2D 1H-31P COSY' 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, 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 C1' C 91.48 0.5 1 2 1 1 G C2' C 73.96 0.5 1 3 1 1 G C3' C 72.91 0.5 1 4 1 1 G C4' C 83.42 0.5 1 5 1 1 G C8 C 137.4 0.5 1 6 1 1 G H1' H 5.683 0.005 1 7 1 1 G H2' H 4.832 0.005 1 8 1 1 G H3' H 4.542 0.005 1 9 1 1 G H4' H 4.296 0.005 1 10 1 1 G H5' H 3.986 0.005 2 11 1 1 G H5'' H 3.882 0.005 2 12 1 1 G H8 H 7.964 0.005 1 13 2 2 G C1' C 91.72 0.5 1 14 2 2 G C2' C 74.34 0.5 1 15 2 2 G C3' C 71.64 0.5 1 16 2 2 G C8 C 135.4 0.5 1 17 2 2 G H1' H 5.854 0.005 1 18 2 2 G H2' H 4.640 0.005 1 19 2 2 G H3' H 4.662 0.005 1 20 2 2 G H4' H 4.530 0.005 1 21 2 2 G H5' H 4.176 0.005 1 22 2 2 G H1 H 12.62 0.005 1 23 2 2 G H8 H 7.510 0.005 1 24 2 2 G P P 0.07900 0.05 1 25 3 3 A C1' C 91.84 0.5 1 26 3 3 A C2 C 152.7 0.5 1 27 3 3 A C2' C 74.44 0.5 1 28 3 3 A C3' C 71.02 0.5 1 29 3 3 A C8 C 137.9 0.5 1 30 3 3 A H1' H 5.985 0.005 1 31 3 3 A H2 H 7.788 0.005 1 32 3 3 A H2' H 4.593 0.005 1 33 3 3 A H3' H 4.616 0.005 1 34 3 3 A H4' H 4.520 0.005 1 35 3 3 A H5' H 4.160 0.005 1 36 3 3 A H8 H 7.860 0.005 1 37 3 3 A H61 H 8.414 0.005 1 38 3 3 A H62 H 6.968 0.005 1 39 3 3 A P P -0.1160 0.05 1 40 4 4 C C1' C 92.70 0.5 1 41 4 4 C C2' C 74.50 0.5 1 42 4 4 C C3' C 72.30 0.5 1 43 4 4 C C5 C 96.11 0.5 1 44 4 4 C C6 C 139.4 0.5 1 45 4 4 C H1' H 5.370 0.005 1 46 4 4 C H2' H 4.251 0.005 1 47 4 4 C H3' H 4.332 0.005 1 48 4 4 C H4' H 4.417 0.005 1 49 4 4 C H5 H 5.218 0.005 1 50 4 4 C H5' H 4.053 0.005 1 51 4 4 C H6 H 7.455 0.005 1 52 4 4 C H41 H 8.377 0.005 1 53 4 4 C H42 H 6.962 0.005 1 54 4 4 C P P -0.2760 0.05 1 55 5 5 U C1' C 92.46 0.5 1 56 5 5 U C2' C 74.14 0.5 1 57 5 5 U C3' C 71.60 0.5 1 58 5 5 U C5 C 102.4 0.5 1 59 5 5 U C6 C 140.4 0.5 1 60 5 5 U H1' H 5.511 0.005 1 61 5 5 U H2' H 4.538 0.005 1 62 5 5 U H3' H 4.622 0.005 1 63 5 5 U H5 H 5.412 0.005 1 64 5 5 U H5' H 4.095 0.005 1 65 5 5 U H6 H 7.869 0.005 1 66 5 5 U H3 H 13.30 0.005 1 67 5 5 U P P -0.4370 0.05 1 68 6 6 A C1' C 91.38 0.5 1 69 6 6 A C2 C 151.3 0.5 1 70 6 6 A C2' C 74.58 0.5 1 71 6 6 A C3' C 71.81 0.5 1 72 6 6 A C8 C 138.4 0.5 1 73 6 6 A H1' H 5.973 0.005 1 74 6 6 A H2 H 6.730 0.005 1 75 6 6 A H2' H 4.633 0.005 1 76 6 6 A H3' H 4.743 0.005 1 77 6 6 A H4' H 4.531 0.005 1 78 6 6 A H5' H 4.186 0.005 1 79 6 6 A H8 H 8.132 0.005 1 80 6 6 A H61 H 7.706 0.005 1 81 6 6 A P P 0.02300 0.05 1 82 7 7 G C1' C 91.55 0.5 1 83 7 7 G C2' C 74.17 0.5 1 84 7 7 G C3' C 71.12 0.5 1 85 7 7 G C8 C 134.5 0.5 1 86 7 7 G H1' H 5.540 0.005 1 87 7 7 G H2' H 4.322 0.005 1 88 7 7 G H3' H 4.425 0.005 1 89 7 7 G H4' H 4.440 0.005 1 90 7 7 G H5' H 4.072 0.005 1 91 7 7 G H1 H 13.47 0.005 1 92 7 7 G H8 H 7.244 0.005 1 93 8 8 U C1' C 92.45 0.5 1 94 8 8 U C2' C 74.19 0.5 1 95 8 8 U C3' C 71.10 0.5 1 96 8 8 U C5 C 101.4 0.5 1 97 8 8 U C6 C 140.4 0.5 1 98 8 8 U H1' H 5.520 0.005 1 99 8 8 U H2' H 4.459 0.005 1 100 8 8 U H3' H 4.447 0.005 1 101 8 8 U H5 H 5.005 0.005 1 102 8 8 U H5' H 4.059 0.005 1 103 8 8 U H6 H 7.741 0.005 1 104 8 8 U H3 H 14.40 0.005 1 105 8 8 U P P -0.7580 0.05 1 106 9 9 C C1' C 93.04 0.5 1 107 9 9 C C2' C 74.59 0.5 1 108 9 9 C C3' C 71.75 0.5 1 109 9 9 C C5 C 96.43 0.5 1 110 9 9 C C6 C 140.3 0.5 1 111 9 9 C H1' H 5.588 0.005 1 112 9 9 C H2' H 4.269 0.005 1 113 9 9 C H3' H 4.443 0.005 1 114 9 9 C H4' H 4.430 0.005 1 115 9 9 C H5 H 5.621 0.005 1 116 9 9 C H5' H 4.059 0.005 1 117 9 9 C H6 H 7.868 0.005 1 118 9 9 C H41 H 8.454 0.005 1 119 9 9 C H42 H 6.976 0.005 1 120 9 9 C P P -0.2580 0.05 1 121 10 10 C C1' C 91.86 0.5 1 122 10 10 C C2' C 76.35 0.5 1 123 10 10 C C3' C 68.44 0.5 1 124 10 10 C C5 C 97.09 0.5 1 125 10 10 C C6 C 140.3 0.5 1 126 10 10 C H1' H 5.691 0.005 1 127 10 10 C H2' H 4.007 0.005 1 128 10 10 C H3' H 4.155 0.005 1 129 10 10 C H4' H 4.516 0.005 1 130 10 10 C H5 H 5.516 0.005 1 131 10 10 C H6 H 7.663 0.005 1 132 10 10 C H41 H 8.267 0.005 1 133 10 10 C P P -0.2230 0.05 1 stop_ save_