data_27226 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; hsa-miR-34a-mSIRT1_bulge ; _BMRB_accession_number 27226 _BMRB_flat_file_name bmr27226.str _Entry_type original _Submission_date 2017-08-19 _Accession_date 2017-08-19 _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). ; 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" 94 "13C chemical shifts" 67 "15N chemical shifts" 54 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)' 27229 'hsa-miR-34a-mSIRT1 bulge U5C9mut' stop_ _Original_release_date 2017-08-21 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 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label hsa-miR-34a-mSIRT1_bulge $hsa-miR-34a-mSIRT1_bulge 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 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 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common hsa-miR-34a-mSIRT1_bulge _Molecular_mass 8458.4 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 28 _Mol_residue_sequence ; GGCACCAUUACUGCUUCGGC AGUGUGCC ; loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 C 4 A 5 C 6 C 7 A 8 U 9 U 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 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 '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 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 _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 5.787 0.000 1 2 1 1 G H8 H 8.109 0.000 1 3 1 1 G C1' C 90.870 0.000 1 4 1 1 G C8 C 139.042 0.000 1 5 1 1 G N9 N 167.996 0.000 1 6 2 2 G H1 H 13.311 0.000 1 7 2 2 G H1' H 5.880 0.000 1 8 2 2 G H8 H 7.601 0.000 1 9 2 2 G C1' C 92.989 0.000 1 10 2 2 G C8 C 136.765 0.000 1 11 2 2 G N1 N 148.436 0.000 1 12 2 2 G N9 N 169.305 0.004 1 13 3 3 C H1' H 5.485 0.000 1 14 3 3 C H6 H 7.676 0.000 1 15 3 3 C H41 H 8.524 0.000 1 16 3 3 C H42 H 6.848 0.000 1 17 3 3 C C1' C 93.821 0.000 1 18 3 3 C C6 C 140.697 0.000 1 19 3 3 C N1 N 150.620 0.000 1 20 3 3 C N3 N 197.037 0.000 1 21 3 3 C N4 N 98.442 0.001 1 22 4 4 A H1' H 5.922 0.000 1 23 4 4 A H2 H 7.405 0.000 1 24 4 4 A H8 H 8.006 0.000 1 25 4 4 A C2 C 153.317 0.000 1 26 4 4 A C8 C 139.328 0.000 1 27 4 4 A N1 N 220.504 0.000 1 28 4 4 A N9 N 170.857 0.004 1 29 5 5 C H1' H 5.367 0.000 1 30 5 5 C H5 H 5.160 0.000 1 31 5 5 C H6 H 7.270 0.000 1 32 5 5 C H41 H 8.168 0.000 1 33 5 5 C H42 H 6.904 0.000 1 34 5 5 C C1' C 93.329 0.000 1 35 5 5 C C5 C 97.429 0.000 1 36 5 5 C C6 C 140.431 0.000 1 37 5 5 C N1 N 150.867 0.000 1 38 5 5 C N3 N 197.183 0.000 1 39 5 5 C N4 N 98.034 0.000 1 40 6 6 C H1' H 5.537 0.000 1 41 6 6 C H5 H 5.484 0.000 1 42 6 6 C H6 H 7.540 0.001 1 43 6 6 C C1' C 93.119 0.000 1 44 6 6 C C5 C 97.866 0.000 1 45 6 6 C C6 C 141.894 0.000 1 46 6 6 C N1 N 151.924 0.003 1 47 7 7 A H1' H 5.827 0.000 1 48 7 7 A H2 H 7.886 0.000 1 49 7 7 A H8 H 8.140 0.001 1 50 7 7 A C1' C 90.352 0.000 1 51 7 7 A C2 C 154.977 0.000 1 52 7 7 A C8 C 141.338 0.000 1 53 7 7 A N9 N 169.122 0.001 1 54 8 8 U H1' H 5.948 0.000 1 55 8 8 U H5 H 5.746 0.000 1 56 8 8 U H6 H 7.756 0.000 1 57 8 8 U C1' C 90.230 0.000 1 58 8 8 U C5 C 105.410 0.000 1 59 8 8 U C6 C 143.762 0.000 1 60 8 8 U N1 N 143.642 0.001 1 61 9 9 U H1' H 5.521 0.000 1 62 9 9 U H5 H 5.517 0.000 1 63 9 9 U H6 H 7.373 0.001 1 64 9 9 U C1' C 89.977 0.000 1 65 9 9 U C5 C 104.997 0.000 1 66 9 9 U C6 C 142.718 0.000 1 67 9 9 U N1 N 143.202 0.000 1 68 10 10 A H2 H 7.986 0.000 1 69 10 10 A H8 H 8.428 0.000 1 70 10 10 A C2 C 154.395 0.000 1 71 10 10 A C8 C 140.984 0.000 1 72 10 10 A N9 N 170.372 0.000 1 73 11 11 C H1' H 5.522 0.000 1 74 11 11 C H5 H 5.438 0.062 1 75 11 11 C H6 H 7.640 0.001 1 76 11 11 C H41 H 8.391 0.000 1 77 11 11 C H42 H 6.985 0.000 1 78 11 11 C C1' C 93.944 0.000 1 79 11 11 C C5 C 97.989 0.380 1 80 11 11 C C6 C 141.267 0.000 1 81 11 11 C N1 N 151.453 0.000 1 82 11 11 C N3 N 197.951 0.000 1 83 11 11 C N4 N 98.077 0.009 1 84 12 12 U H1' H 5.574 0.000 1 85 12 12 U H3 H 13.489 0.035 1 86 12 12 U H5 H 5.403 0.000 1 87 12 12 U H6 H 7.885 0.000 1 88 12 12 U C1' C 93.495 0.000 1 89 12 12 U C5 C 93.740 0.000 1 90 12 12 U C6 C 141.716 0.000 1 91 12 12 U N1 N 145.857 0.000 1 92 12 12 U N3 N 162.159 0.000 1 93 13 13 G H1 H 12.536 0.000 1 94 13 13 G H1' H 5.822 0.000 1 95 13 13 G H8 H 7.768 0.000 1 96 13 13 G C1' C 92.491 0.000 1 97 13 13 G C8 C 136.327 0.000 1 98 13 13 G N1 N 147.520 0.000 1 99 13 13 G N9 N 169.707 0.000 1 100 14 14 C H1' H 5.428 0.000 1 101 14 14 C H5 H 5.184 0.000 1 102 14 14 C H6 H 7.436 0.000 1 103 14 14 C H41 H 8.486 0.000 1 104 14 14 C H42 H 6.874 0.000 1 105 14 14 C C1' C 93.794 0.000 1 106 14 14 C C5 C 97.304 0.000 1 107 14 14 C C6 C 140.394 0.000 1 108 14 14 C N1 N 151.171 0.002 1 109 14 14 C N3 N 195.951 0.000 1 110 14 14 C N4 N 99.576 0.000 1 111 15 15 U H1' H 5.618 0.000 1 112 15 15 U H3 H 11.660 0.000 1 113 15 15 U H5 H 5.701 0.000 1 114 15 15 U H6 H 7.724 0.000 1 115 15 15 U C1' C 94.505 0.000 1 116 15 15 U C5 C 105.112 0.000 1 117 15 15 U C6 C 140.595 0.000 1 118 15 15 U N1 N 146.895 0.001 1 119 15 15 U N3 N 159.769 0.000 1 120 16 16 U H1' H 6.072 0.000 1 121 16 16 U H5 H 5.833 0.000 1 122 16 16 U H6 H 7.993 0.000 1 123 16 16 U C1' C 89.202 0.000 1 124 16 16 U C5 C 105.503 0.000 1 125 16 16 U C6 C 144.671 0.000 1 126 16 16 U N1 N 143.894 0.001 1 127 17 17 C H1' H 5.929 0.000 1 128 17 17 C H5 H 6.099 0.000 1 129 17 17 C H6 H 7.661 0.003 1 130 17 17 C H41 H 7.114 0.000 1 131 17 17 C H42 H 6.262 0.000 1 132 17 17 C C1' C 89.070 0.000 1 133 17 17 C C5 C 98.641 0.000 1 134 17 17 C C6 C 142.786 0.000 1 135 17 17 C N1 N 150.630 0.002 1 136 17 17 C N4 N 93.727 0.008 1 137 18 18 G H1 H 9.852 0.000 1 138 18 18 G H1' H 5.935 0.000 1 139 18 18 G H8 H 7.835 0.000 1 140 18 18 G C1' C 94.548 0.000 1 141 18 18 G C8 C 142.907 0.000 1 142 18 18 G N1 N 143.312 0.000 1 143 18 18 G N9 N 171.681 0.001 1 144 19 19 G H1 H 13.343 0.001 1 145 19 19 G H1' H 4.335 0.000 1 146 19 19 G H8 H 8.268 0.000 1 147 19 19 G C1' C 90.498 0.000 1 148 19 19 G C8 C 138.828 0.000 1 149 19 19 G N1 N 148.270 0.000 1 150 19 19 G N9 N 170.322 0.000 1 151 20 20 C H1' H 5.470 0.000 1 152 20 20 C H41 H 8.583 0.000 1 153 20 20 C H42 H 6.824 0.000 1 154 20 20 C C1' C 93.904 0.000 1 155 20 20 C N1 N 151.097 0.000 1 156 20 20 C N3 N 197.147 0.000 1 157 20 20 C N4 N 97.650 0.005 1 158 21 21 A H1' H 5.940 0.000 1 159 21 21 A H2 H 7.080 0.000 1 160 21 21 A H8 H 7.982 0.000 1 161 21 21 A C1' C 93.021 0.000 1 162 21 21 A C2 C 152.461 0.000 1 163 21 21 A C8 C 139.449 0.000 1 164 21 21 A N1 N 220.462 0.000 1 165 21 21 A N9 N 170.532 0.001 1 166 22 22 G H1 H 13.492 0.000 1 167 22 22 G H1' H 5.590 0.000 1 168 22 22 G H8 H 7.206 0.001 1 169 22 22 G C1' C 92.901 0.000 1 170 22 22 G C8 C 136.008 0.000 1 171 22 22 G N1 N 148.209 0.000 1 172 22 22 G N9 N 168.981 0.000 1 173 23 23 U H1' H 5.880 0.000 1 174 23 23 U H6 H 7.570 0.000 1 175 23 23 U C1' C 92.135 0.000 1 176 23 23 U C6 C 141.963 0.000 1 177 23 23 U N1 N 145.592 0.002 1 178 24 24 G H1 H 12.948 0.003 1 179 24 24 G H1' H 5.748 0.000 1 180 24 24 G H8 H 7.935 0.000 1 181 24 24 G C1' C 92.663 0.000 1 182 24 24 G C8 C 138.397 0.000 1 183 24 24 G N1 N 148.122 0.000 1 184 24 24 G N9 N 168.938 0.003 1 185 25 25 U H1' H 5.588 0.000 1 186 25 25 U H3 H 13.562 0.038 1 187 25 25 U H6 H 7.816 0.001 1 188 25 25 U C1' C 93.545 0.000 1 189 25 25 U C6 C 141.872 0.000 1 190 25 25 U N1 N 146.310 0.002 1 191 25 25 U N3 N 162.222 0.000 1 192 26 26 G H1 H 12.594 0.007 1 193 26 26 G H1' H 5.805 0.000 1 194 26 26 G H8 H 7.729 0.000 1 195 26 26 G C1' C 92.770 0.000 1 196 26 26 G C8 C 136.198 0.000 1 197 26 26 G N1 N 147.627 0.000 1 198 26 26 G N9 N 169.607 0.005 1 199 27 27 C H1' H 5.449 0.000 1 200 27 27 C H5 H 5.231 0.000 1 201 27 27 C H41 H 8.540 0.000 1 202 27 27 C H42 H 6.868 0.000 1 203 27 27 C C1' C 94.067 0.000 1 204 27 27 C C5 C 97.222 0.000 1 205 27 27 C N1 N 151.228 0.000 1 206 27 27 C N3 N 198.027 0.000 1 207 27 27 C N4 N 99.428 0.001 1 208 28 28 C H1' H 5.724 0.000 1 209 28 28 C H6 H 7.631 0.000 1 210 28 28 C H41 H 8.369 0.000 1 211 28 28 C H42 H 6.969 0.000 1 212 28 28 C C1' C 92.938 0.000 1 213 28 28 C C6 C 141.665 0.000 1 214 28 28 C N1 N 152.527 0.001 1 215 28 28 C N4 N 97.559 0.005 1 stop_ save_