data_25220 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; N6-Methyladenosine RNA ; _BMRB_accession_number 25220 _BMRB_flat_file_name bmr25220.str _Entry_type original _Submission_date 2014-09-12 _Accession_date 2014-09-12 _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 . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 83 "13C chemical shifts" 28 "31P chemical shifts" 9 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2015-09-04 original BMRB . stop_ _Original_release_date 2015-09-04 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 duplex, chain 1' $N-6_Methyl_Adenosine_RNA 'RNA duplex, chain 2' $N-6_Methyl_Adenosine_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_N-6_Methyl_Adenosine_RNA _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common N-6_Methyl_Adenosine_RNA _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 10 _Mol_residue_sequence ; GGXCUAGUCC ; loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 6MD 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_ ###################### # Polymer residues # ###################### save_chem_comp_6MD _Saveframe_category polymer_residue _Mol_type NON-POLYMER _Name_common N-methyladenosine _BMRB_code 6MD _PDB_code 6MD _Standard_residue_derivative . _Molecular_mass 281.268 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons O5' O5' O . 0 . ? C5' C5' C . 0 . ? C4' C4' C . 0 . ? O4' O4' O . 0 . ? C3' C3' C . 0 . ? O3' O3' O . 0 . ? C2' C2' C . 0 . ? O2' O2' O . 0 . ? C1' C1' C . 0 . ? N9 N9 N . 0 . ? C8 C8 C . 0 . ? N7 N7 N . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? N6 N6 N . 0 . ? N1 N1 N . 0 . ? C2 C2 C . 0 . ? N3 N3 N . 0 . ? C4 C4 C . 0 . ? CZ CZ C . 0 . ? H1 H1 H . 0 . ? H2 H2 H . 0 . ? H3 H3 H . 0 . ? H4 H4 H . 0 . ? H5 H5 H . 0 . ? H6 H6 H . 0 . ? H7 H7 H . 0 . ? H8 H8 H . 0 . ? H9 H9 H . 0 . ? H10 H10 H . 0 . ? H11 H11 H . 0 . ? H12 H12 H . 0 . ? H13 H13 H . 0 . ? H14 H14 H . 0 . ? H15 H15 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 C2 N1 ? ? SING C2 N3 ? ? SING N1 C6 ? ? DOUB N3 C4 ? ? SING CZ N6 ? ? SING C6 N6 ? ? DOUB C6 C5 ? ? SING C4 C5 ? ? SING C4 N9 ? ? SING C4' O4' ? ? SING C4' C5' ? ? SING C4' C3' ? ? SING O4' C1' ? ? SING C5 N7 ? ? SING C5' O5' ? ? SING O3' C3' ? ? SING C1' N9 ? ? SING C1' C2' ? ? SING N9 C8 ? ? SING C3' C2' ? ? SING C2' O2' ? ? DOUB N7 C8 ? ? SING O5' H1 ? ? SING C5' H2 ? ? SING C5' H3 ? ? SING C4' H4 ? ? SING C3' H5 ? ? SING O3' H6 ? ? SING C2' H7 ? ? SING O2' H8 ? ? SING C1' H9 ? ? SING C8 H10 ? ? SING N6 H11 ? ? SING C2 H12 ? ? SING CZ H13 ? ? SING CZ H14 ? ? SING CZ H15 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $N-6_Methyl_Adenosine_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 $N-6_Methyl_Adenosine_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 $N-6_Methyl_Adenosine_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 $N-6_Methyl_Adenosine_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 direct . . . 1.0 water H 1 protons ppm 4.77 internal direct . . . 1.0 'phosphoric acid (85%)' P 31 phosphorus ppm 0 external 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 _Saveframe_category assigned_chemical_shifts _Details . 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 duplex, 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 12.54 0.005 1 2 1 1 G H1' H 5.718 0.005 1 3 1 1 G H2' H 4.858 0.005 1 4 1 1 G H3' H 4.581 0.005 1 5 1 1 G H4' H 4.33 0.005 1 6 1 1 G H5' H 4.001 0.005 2 7 1 1 G H5'' H 3.903 0.005 2 8 1 1 G H8 H 7.993 0.005 1 9 1 1 G C1' C 90.84 0.5 1 10 1 1 G C8 C 137.2 0.5 1 11 2 2 G H1 H 12.7 0.005 1 12 2 2 G H1' H 5.836 0.005 1 13 2 2 G H2' H 4.633 0.005 1 14 2 2 G H3' H 4.684 0.005 1 15 2 2 G H4' H 4.55 0.005 1 16 2 2 G H5' H 4.201 0.005 1 17 2 2 G H8 H 7.52 0.005 1 18 2 2 G C1' C 91.51 0.5 1 19 2 2 G C8 C 135.3 0.5 1 20 2 2 G P P 0.221 0.05 1 21 3 3 6MD H1' H 6.007 0.005 1 22 3 3 6MD H2 H 7.712 0.005 1 23 3 3 6MD H2' H 4.618 0.005 1 24 3 3 6MD H3' H 4.688 0.005 1 25 3 3 6MD H3C H 3.017 0.005 1 26 3 3 6MD H4' H 4.521 0.005 1 27 3 3 6MD H5' H 4.187 0.005 1 28 3 3 6MD H8 H 8.098 0.005 1 29 3 3 6MD H61 H 8.343 0.005 1 30 3 3 6MD C1' C 91.17 0.5 1 31 3 3 6MD C2 C 152.3 0.5 1 32 3 3 6MD C8 C 137.3 0.5 1 33 3 3 6MD CH3 C 31.73 0.5 1 34 3 3 6MD P P -0.045 0.05 1 35 4 4 C H1' H 5.35 0.005 1 36 4 4 C H2' H 4.201 0.005 1 37 4 4 C H3' H 4.314 0.005 1 38 4 4 C H4' H 4.424 0.005 1 39 4 4 C H5 H 5.318 0.005 1 40 4 4 C H5' H 4.057 0.005 1 41 4 4 C H6 H 7.417 0.005 1 42 4 4 C H41 H 8.306 0.005 1 43 4 4 C H42 H 7.274 0.005 1 44 4 4 C C1' C 92.48 0.5 1 45 4 4 C C5 C 95.88 0.5 1 46 4 4 C C6 C 139.1 0.5 1 47 4 4 C P P -0.431 0.05 1 48 5 5 U H1' H 5.521 0.005 1 49 5 5 U H2' H 4.543 0.005 1 50 5 5 U H3 H 13.27 0.005 1 51 5 5 U H3' H 4.63 0.005 1 52 5 5 U H4' H 4.423 0.005 1 53 5 5 U H5 H 5.415 0.005 1 54 5 5 U H5' H 4.11 0.005 1 55 5 5 U H6 H 7.867 0.005 1 56 5 5 U C1' C 92.17 0.5 1 57 5 5 U C5 C 102.2 0.5 1 58 5 5 U C6 C 140.3 0.5 1 59 5 5 U P P -0.404 0.05 1 60 6 6 A H1' H 5.984 0.005 1 61 6 6 A H2 H 6.759 0.005 1 62 6 6 A H2' H 4.67 0.005 1 63 6 6 A H3' H 4.753 0.005 1 64 6 6 A H4' H 4.537 0.005 1 65 6 6 A H5' H 4.186 0.005 1 66 6 6 A H8 H 8.142 0.005 1 67 6 6 A H61 H 7.706 0.005 1 68 6 6 A H62 H 6.261 0.005 1 69 6 6 A C1' C 91.01 0.5 1 70 6 6 A C2 C 151.1 0.5 1 71 6 6 A C8 C 138.3 0.5 1 72 6 6 A P P 0.092 0.05 1 73 7 7 G H1 H 13.48 0.005 1 74 7 7 G H1' H 5.499 0.005 1 75 7 7 G H2' H 4.328 0.005 1 76 7 7 G H3' H 4.372 0.005 1 77 7 7 G H4' H 4.452 0.005 1 78 7 7 G H5' H 4.067 0.005 1 79 7 7 G H8 H 7.193 0.005 1 80 7 7 G H21 H 8.505 0.005 1 81 7 7 G H22 H 6.239 0.005 1 82 7 7 G C1' C 91.4 0.5 1 83 7 7 G C8 C 134.4 0.5 1 84 7 7 G P P 0.021 0.05 1 85 8 8 U H1' H 5.52 0.005 1 86 8 8 U H2' H 4.467 0.005 1 87 8 8 U H3 H 14.4 0.005 1 88 8 8 U H3' H 4.454 0.005 1 89 8 8 U H4' H 4.502 0.005 1 90 8 8 U H5 H 4.968 0.005 1 91 8 8 U H5' H 4.066 0.005 1 92 8 8 U H6 H 7.799 0.005 1 93 8 8 U C1' C 92.25 0.5 1 94 8 8 U C5 C 102.1 0.5 1 95 8 8 U C6 C 140.5 0.5 1 96 8 8 U P P -0.82 0.05 1 97 9 9 C H1' H 5.627 0.005 1 98 9 9 C H2' H 4.292 0.005 1 99 9 9 C H3' H 4.494 0.005 1 100 9 9 C H4' H 4.427 0.005 1 101 9 9 C H5 H 5.622 0.005 1 102 9 9 C H5' H 4.072 0.005 1 103 9 9 C H6 H 7.962 0.005 1 104 9 9 C H41 H 8.588 0.005 1 105 9 9 C H42 H 7.052 0.005 1 106 9 9 C C1' C 92.55 0.5 1 107 9 9 C C5 C 95.89 0.5 1 108 9 9 C C6 C 140.4 0.5 1 109 9 9 C P P -0.295 0.05 1 110 10 10 C H1' H 5.705 0.005 1 111 10 10 C H2' H 3.999 0.005 1 112 10 10 C H3' H 4.159 0.005 1 113 10 10 C H5 H 5.534 0.005 1 114 10 10 C H6 H 7.665 0.005 1 115 10 10 C H41 H 8.344 0.005 1 116 10 10 C H42 H 7.096 0.005 1 117 10 10 C C1' C 91.58 0.5 1 118 10 10 C C5 C 96.76 0.5 1 119 10 10 C C6 C 140.1 0.5 1 120 10 10 C P P -0.082 0.05 1 stop_ save_