data_27229 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; hsa-miR-34a-mSIRT1 bulge U5C9mut ; _BMRB_accession_number 27229 _BMRB_flat_file_name bmr27229.str _Entry_type original _Submission_date 2017-08-22 _Accession_date 2017-08-22 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details ; Sequence specific resonance assignment of an RNA hairpin construct mimicking the central bulge region of the miR-34a mSIRT1 duplex (28-mer) with the following mutation sites: C5U and U9C. ; loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Baronti Lorenzo . . 2 Steiner Emilie . . 3 Schlagnitweit Judith . . 4 Petzold Katja . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 90 "13C chemical shifts" 71 "15N chemical shifts" 41 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2020-07-03 update BMRB 'update entry citation' 2020-05-21 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 27225 'mature hsa-miR-34a-5p (22-mer)' 27226 'hsa-miR-34a-mSIRT1 bulge' stop_ _Original_release_date 2017-08-22 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Base-pair Conformational Switch Modulates miR-34a Targeting of Sirt1 mRNA ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 32461691 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Baronti Lorenzo . . 2 Guzzetti Ileana . . 3 Ebrahimi Parisa . . 4 'Friebe Sandoz' Sarah . . 5 Steiner Emilie . . 6 Schlagnitweit Judith . . 7 Fromm Bastian . . 8 Silva Luis . . 9 Fontana Carolina . . 10 Chen Alan . . 11 Petzold Katja . . stop_ _Journal_abbreviation Nature _Journal_volume 583 _Journal_issue 7814 _Journal_ISSN 1476-4687 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 139 _Page_last 144 _Year 2020 _Details . loop_ _Keyword RNA SIRT1 'Sirtuin 1' miR-34a microRNA stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'hsa-miR-34a-mSIRT1 bulge U5C9mut' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'hsa-miR-34a-mSIRT1 bulge U5C9mut' $hsa-miR-34a-mSIRT1_bulge_U5C9mut stop_ _System_molecular_weight 8458.4 _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details ; Synthetic hairpin construct mimicking the mutated central bulge region of the hsa-miR-34a-5p mSIRT1 duplex. Details about the design of this molecular assembly can be found in the associated publication. ; save_ ######################## # Monomeric polymers # ######################## save_hsa-miR-34a-mSIRT1_bulge_U5C9mut _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common hsa-miR-34a-mSIRT1_bulge_U5C9mut _Molecular_mass 8458.4 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 28 _Mol_residue_sequence ; GGCAUCAUCACUGCUUCGGC AGUGUGCC ; loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 C 4 A 5 U 6 C 7 A 8 U 9 C 10 A 11 C 12 U 13 G 14 C 15 U 16 U 17 C 18 G 19 G 20 C 21 A 22 G 23 U 24 G 25 U 26 G 27 C 28 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 $hsa-miR-34a-mSIRT1_bulge_U5C9mut 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_type _Vector_name _Details $hsa-miR-34a-mSIRT1_bulge_U5C9mut 'enzymatic semisynthesis' . . . . 'DNA template' 'DNA template' 'T7 in-vitro transcription.' 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 _Concentration_min_value _Concentration_max_value _Isotopic_labeling $hsa-miR-34a-mSIRT1_bulge_U5C9mut 750 uM 500 1000 '[U-100% 13C; U-100% 15N]' H2O 90 % . . 'natural abundance' D2O 10 % . . [U-2H] 'sodium phosphate' 15 mM . . 'natural abundance' 'sodium chloride' 25 mM . . 'natural abundance' EDTA 0.1 mM . . 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version 'v 3.2' loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'Avance III HD' _Field_strength 600 _Details 'equipped with a QCI cryoprobe' 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_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_HNN_COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D HNN COSY' _Sample_label $sample_1 save_ save_3D_HCN_5 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HCN' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.5 . pH pressure 1 . atm temperature 295.4 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference _Details '13C and 15N were referenced using indirect referencing for multidimensional heteronuclear according to Wishart et al., 1995' 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 C 13 'methyl protons' ppm 0.00 na indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 DSS N 15 'methyl protons' ppm 0.00 na indirect . . . 0.101329118 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 $SPARKY stop_ loop_ _Experiment_label '2D 1H-13C HSQC' '2D 1H-15N HSQC' '2D 1H-1H NOESY' '2D HNN COSY' '3D HCN' 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 'hsa-miR-34a-mSIRT1 bulge U5C9mut' _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 5.778 0.000 1 2 1 1 G H8 H 8.087 0.000 1 3 1 1 G C1' C 91.004 0.000 1 4 1 1 G C8 C 139.033 0.000 1 5 1 1 G N9 N 168.047 0.000 1 6 2 2 G H1' H 5.881 0.000 1 7 2 2 G H8 H 7.579 0.000 1 8 2 2 G C1' C 92.854 0.000 1 9 2 2 G C8 C 136.678 0.000 1 10 2 2 G N9 N 169.415 0.000 1 11 3 3 C H1' H 5.484 0.000 1 12 3 3 C H5 H 5.224 0.000 1 13 3 3 C H6 H 7.469 0.000 1 14 3 3 C H41 H 8.206 0.000 1 15 3 3 C H42 H 6.812 0.000 1 16 3 3 C C1' C 93.851 0.000 1 17 3 3 C C5 C 97.653 0.000 1 18 3 3 C C6 C 140.326 0.000 1 19 3 3 C N1 N 150.414 0.000 1 20 3 3 C N4 N 97.932 0.006 1 21 4 4 A H1' H 5.887 0.000 1 22 4 4 A H2 H 7.206 0.000 1 23 4 4 A H8 H 7.849 0.000 1 24 4 4 A C1' C 93.060 0.000 1 25 4 4 A C2 C 153.688 0.000 1 26 4 4 A C8 C 139.411 0.000 1 27 4 4 A N9 N 170.550 0.000 1 28 5 5 U H1' H 5.249 0.000 1 29 5 5 U H5 H 5.153 0.000 1 30 5 5 U H6 H 7.220 0.000 1 31 5 5 U C1' C 91.866 0.000 1 32 5 5 U C5 C 103.816 0.000 1 33 5 5 U C6 C 141.190 0.000 1 34 5 5 U N1 N 144.528 0.000 1 35 6 6 C H1' H 5.676 0.000 1 36 6 6 C H5 H 5.691 0.000 1 37 6 6 C H6 H 7.551 0.000 1 38 6 6 C C1' C 91.947 0.000 1 39 6 6 C C5 C 98.709 0.000 1 40 6 6 C C6 C 143.125 0.000 1 41 6 6 C N1 N 151.196 0.000 1 42 7 7 A H1' H 5.785 0.000 1 43 7 7 A H2 H 7.882 0.000 1 44 7 7 A H8 H 8.145 0.000 1 45 7 7 A C1' C 90.446 0.000 1 46 7 7 A C2 C 154.847 0.000 1 47 7 7 A C8 C 141.192 0.000 1 48 7 7 A N9 N 168.912 0.000 1 49 8 8 U H1' H 5.784 0.000 1 50 8 8 U H6 H 7.760 0.000 1 51 8 8 U C1' C 91.485 0.000 1 52 8 8 U C6 C 143.170 0.000 1 53 8 8 U N1 N 144.798 0.000 1 54 9 9 C H1' H 5.492 0.000 1 55 9 9 C H5 H 5.894 0.000 1 56 9 9 C H6 H 7.986 0.000 1 57 9 9 C H41 H 8.362 0.000 1 58 9 9 C H42 H 7.056 0.000 1 59 9 9 C C1' C 93.591 0.000 1 60 9 9 C C5 C 98.627 0.000 1 61 9 9 C C6 C 142.075 0.000 1 62 9 9 C N1 N 151.572 0.000 1 63 9 9 C N4 N 97.398 0.009 1 64 10 10 A H1' H 5.953 0.000 1 65 10 10 A H2 H 7.494 0.000 1 66 10 10 A H8 H 8.178 0.000 1 67 10 10 A C1' C 92.956 0.000 1 68 10 10 A C2 C 153.368 0.000 1 69 10 10 A C8 C 139.831 0.000 1 70 10 10 A N9 N 170.912 0.000 1 71 11 11 C H1' H 5.418 0.000 1 72 11 11 C H6 H 7.536 0.000 1 73 11 11 C C1' C 93.778 0.000 1 74 11 11 C C6 C 140.777 0.000 1 75 11 11 C N1 N 151.173 0.000 1 76 12 12 U H1' H 5.515 0.000 1 77 12 12 U H3 H 13.409 0.000 1 78 12 12 U H5 H 5.334 0.000 1 79 12 12 U H6 H 7.790 0.000 1 80 12 12 U C1' C 93.451 0.000 1 81 12 12 U C5 C 103.776 0.000 1 82 12 12 U C6 C 141.561 0.000 1 83 12 12 U N1 N 145.642 0.000 1 84 12 12 U N3 N 161.982 0.000 1 85 13 13 G H1 H 12.508 0.000 1 86 13 13 G H1' H 5.792 0.000 1 87 13 13 G H8 H 7.731 0.000 1 88 13 13 G C1' C 92.509 0.000 1 89 13 13 G C8 C 136.294 0.000 1 90 13 13 G N1 N 147.515 0.000 1 91 13 13 G N9 N 169.635 0.000 1 92 14 14 C H1' H 5.418 0.000 1 93 14 14 C H5 H 5.157 0.000 1 94 14 14 C H6 H 7.411 0.000 1 95 14 14 C C1' C 93.753 0.000 1 96 14 14 C C5 C 97.251 0.000 1 97 14 14 C C6 C 140.360 0.000 1 98 14 14 C N1 N 151.171 0.000 1 99 15 15 U H1' H 5.609 0.000 1 100 15 15 U H6 H 7.701 0.000 1 101 15 15 U C1' C 94.503 0.000 1 102 15 15 U C6 C 140.564 0.000 1 103 15 15 U N1 N 146.892 0.000 1 104 16 16 U H1' H 6.069 0.000 1 105 16 16 U H5 H 5.827 0.000 1 106 16 16 U H6 H 7.974 0.000 1 107 16 16 U C1' C 89.205 0.000 1 108 16 16 U C5 C 105.461 0.000 1 109 16 16 U C6 C 144.646 0.000 1 110 16 16 U N1 N 143.900 0.000 1 111 17 17 C H1' H 5.923 0.000 1 112 17 17 C H5 H 6.093 0.000 1 113 17 17 C H6 H 7.640 0.000 1 114 17 17 C C1' C 89.067 0.000 1 115 17 17 C C5 C 98.610 0.000 1 116 17 17 C C6 C 142.745 0.000 1 117 17 17 C N1 N 150.632 0.000 1 118 18 18 G H1 H 9.846 0.000 1 119 18 18 G H1' H 5.932 0.000 1 120 18 18 G H8 H 7.820 0.000 1 121 18 18 G C1' C 94.539 0.000 1 122 18 18 G C8 C 142.879 0.000 1 123 18 18 G N1 N 143.309 0.000 1 124 18 18 G N9 N 171.685 0.000 1 125 19 19 G H1 H 13.329 0.000 1 126 19 19 G H1' H 4.402 0.000 1 127 19 19 G H8 H 8.254 0.000 1 128 19 19 G C1' C 93.232 0.000 1 129 19 19 G C8 C 138.819 0.000 1 130 19 19 G N1 N 148.254 0.000 1 131 19 19 G N9 N 170.329 0.000 1 132 20 20 C H1' H 5.469 0.000 1 133 20 20 C H6 H 7.624 0.000 1 134 20 20 C H41 H 8.557 0.000 1 135 20 20 C H42 H 6.811 0.000 1 136 20 20 C C1' C 93.883 0.000 1 137 20 20 C C6 C 140.940 0.000 1 138 20 20 C N1 N 151.089 0.000 1 139 20 20 C N4 N 97.652 0.002 1 140 21 21 A H1' H 5.933 0.000 1 141 21 21 A H2 H 7.005 0.000 1 142 21 21 A H8 H 7.960 0.000 1 143 21 21 A C1' C 92.961 0.000 1 144 21 21 A C2 C 152.373 0.000 1 145 21 21 A C8 C 139.434 0.000 1 146 21 21 A N9 N 170.585 0.000 1 147 22 22 G H1 H 13.398 0.000 1 148 22 22 G H1' H 5.533 0.000 1 149 22 22 G H8 H 7.132 0.000 1 150 22 22 G C1' C 92.912 0.000 1 151 22 22 G C8 C 135.813 0.000 1 152 22 22 G N1 N 148.154 0.000 1 153 22 22 G N9 N 169.030 0.000 1 154 23 23 U H1' H 5.506 0.000 1 155 23 23 U H3 H 13.811 0.000 1 156 23 23 U H5 H 5.033 0.000 1 157 23 23 U H6 H 7.599 0.000 1 158 23 23 U C1' C 93.545 0.000 1 159 23 23 U C6 C 140.770 0.000 1 160 23 23 U N1 N 145.561 0.000 1 161 23 23 U N3 N 162.136 0.000 1 162 24 24 G H1 H 12.298 0.000 1 163 24 24 G H1' H 5.862 0.000 1 164 24 24 G H8 H 7.668 0.000 1 165 24 24 G C1' C 91.313 0.000 1 166 24 24 G C8 C 136.669 0.000 1 167 24 24 G N1 N 147.295 0.000 1 168 24 24 G N9 N 168.516 0.000 1 169 25 25 U H1' H 5.800 0.000 1 170 25 25 U H5 H 5.562 0.000 1 171 25 25 U H6 H 7.725 0.000 1 172 25 25 U C1' C 91.993 0.000 1 173 25 25 U C5 C 103.883 0.726 1 174 25 25 U C6 C 142.425 0.000 1 175 25 25 U N1 N 144.953 0.000 1 176 26 26 G H1 H 12.530 0.000 1 177 26 26 G H1' H 5.804 0.000 1 178 26 26 G H8 H 7.999 0.000 1 179 26 26 G C1' C 93.074 0.000 1 180 26 26 G C8 C 138.067 0.000 1 181 26 26 G N1 N 147.878 0.000 1 182 26 26 G N9 N 169.235 0.000 1 183 27 27 C H1' H 5.522 0.000 1 184 27 27 C H5 H 5.246 0.000 1 185 27 27 C H6 H 7.699 0.000 1 186 27 27 C H41 H 8.312 0.000 1 187 27 27 C H42 H 6.957 0.000 1 188 27 27 C C1' C 94.243 0.000 1 189 27 27 C C5 C 96.970 0.000 1 190 27 27 C C6 C 141.458 0.000 1 191 27 27 C N1 N 151.606 0.000 1 192 27 27 C N4 N 98.559 0.000 1 193 28 28 C H1' H 5.743 0.000 1 194 28 28 C H5 H 5.529 0.000 1 195 28 28 C H6 H 7.642 0.000 1 196 28 28 C H41 H 8.339 0.000 1 197 28 28 C H42 H 7.001 0.000 1 198 28 28 C C1' C 92.972 0.000 1 199 28 28 C C5 C 98.387 0.000 1 200 28 28 C C6 C 141.669 0.000 1 201 28 28 C N1 N 152.614 0.000 1 202 28 28 C N4 N 97.475 0.010 1 stop_ save_