data_34038 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; SINEB2 element of the long non-coding RNA activator of translation AS Uchl1 ; _BMRB_accession_number 34038 _BMRB_flat_file_name bmr34038.str _Entry_type original _Submission_date 2016-09-05 _Accession_date 2016-09-05 _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 Podbevsek P. . . 2 Plavec J. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 93 "13C chemical shifts" 63 "15N chemical shifts" 18 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2018-02-28 update BMRB 'update entry citation' 2017-09-15 original author 'original release' stop_ _Original_release_date 2016-09-06 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structural determinants of the SINE B2 element embedded in the long non-coding RNA activator of translation AS Uchl1 ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 29453387 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Podbevsek P. . . 2 Fasolo F. . . 3 Bon C. . . 4 Cimatti L. . . 5 Reisser S. . . 6 Carninci P. . . 7 Bussi G. . . 8 Zucchelli S. . . 9 Plavec J. . . 10 Gustincich S. . . stop_ _Journal_abbreviation 'Sci. Rep.' _Journal_name_full 'Scientific reports' _Journal_volume 8 _Journal_issue 1 _Journal_ISSN 2045-2322 _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 3189 _Page_last 3189 _Year 2018 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'RNA (29-MER)' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity_1 stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common entity_1 _Molecular_mass 9309.521 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 29 _Mol_residue_sequence ; CCUCGUGGUGGUUGUGAACC ACCAUGUGG ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 64 C 2 65 C 3 66 U 4 67 C 5 68 G 6 69 U 7 70 G 8 71 G 9 72 U 10 73 G 11 74 G 12 75 U 13 76 U 14 77 G 15 78 U 16 79 G 17 80 A 18 81 A 19 82 C 20 83 C 21 84 A 22 85 C 23 86 C 24 87 A 25 88 U 26 89 G 27 90 U 28 91 G 29 92 G 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 $entity_1 'House Mouse' 10090 Eukaryota Metazoa Mus musculus 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 $entity_1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '0.5 mM RNA (29-MER), 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.5 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '0.5 mM RNA (29-MER), 100% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.5 mM 'natural abundance' stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type solution _Details '0.5 mM [U-99% 13C; U-99% 15N] RNA (29-MER), 100% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.5 mM '[U-99% 13C; U-99% 15N]' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name AMBER _Version . loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ save_software_2 _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_software_3 _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_4 _Saveframe_category software _Name VNMR _Version . loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task collection stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Agilent _Model VNMRS _Field_strength 600 _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_1 save_ save_2D_1H-15N_HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_3 save_ save_2D_1H-13C_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_3 save_ save_2D_DQF-COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-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_HCN_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D HCN' _Sample_label $sample_3 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7 . pH pressure 1 . atm temperature 298 . K stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7 . pH pressure 1 . atm temperature 273 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_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 water H 1 protons ppm 4.78 internal 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_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $software_3 stop_ loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-15N HSQC' '2D 1H-13C HSQC' stop_ loop_ _Sample_label $sample_1 $sample_3 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name entity_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 64 1 C H1' H 5.338 0.02 1 2 64 1 C H5 H 5.563 0.02 1 3 64 1 C H6 H 7.596 0.02 1 4 64 1 C C1' C 94.212 0.20 1 5 64 1 C C5 C 98.142 0.20 1 6 64 1 C C6 C 141.538 0.20 1 7 64 1 C N1 N 151.242 0.10 1 8 65 2 C H1' H 5.433 0.02 1 9 65 2 C H5 H 5.428 0.02 1 10 65 2 C H6 H 7.665 0.02 1 11 65 2 C C5 C 97.998 0.20 1 12 65 2 C C6 C 141.268 0.20 1 13 65 2 C N1 N 151.254 0.10 1 14 66 3 U H1' H 5.490 0.02 1 15 66 3 U H5 H 5.502 0.02 1 16 66 3 U H6 H 7.776 0.02 1 17 66 3 U C1' C 93.779 0.20 1 18 66 3 U C5 C 104.105 0.20 1 19 66 3 U C6 C 141.476 0.20 1 20 66 3 U N1 N 145.882 0.10 1 21 67 4 C H1' H 5.732 0.02 1 22 67 4 C H5 H 5.662 0.02 1 23 67 4 C H6 H 7.934 0.02 1 24 67 4 C C1' C 92.572 0.20 1 25 67 4 C C5 C 97.593 0.20 1 26 67 4 C C6 C 142.489 0.20 1 27 67 4 C N1 N 151.445 0.10 1 28 68 5 G H1' H 5.677 0.02 1 29 68 5 G H8 H 7.553 0.02 1 30 68 5 G C1' C 92.919 0.20 1 31 68 5 G C8 C 137.519 0.20 1 32 69 6 U H1' H 5.495 0.02 1 33 69 6 U H5 H 5.090 0.02 1 34 69 6 U H6 H 7.637 0.02 1 35 69 6 U C5 C 103.039 0.20 1 36 69 6 U C6 C 141.734 0.20 1 37 69 6 U N1 N 146.315 0.10 1 38 70 7 G H1 H 11.990 0.02 1 39 70 7 G H1' H 5.796 0.02 1 40 70 7 G H8 H 7.706 0.02 1 41 70 7 G C1' C 92.524 0.20 1 42 70 7 G C8 C 136.447 0.20 1 43 71 8 G H1 H 13.167 0.02 1 44 71 8 G H1' H 5.684 0.02 1 45 71 8 G H8 H 7.175 0.02 1 46 71 8 G C1' C 89.328 0.20 1 47 71 8 G C8 C 136.284 0.20 1 48 72 9 U H1' H 5.502 0.02 1 49 72 9 U H3 H 13.600 0.02 1 50 72 9 U H5 H 4.993 0.02 1 51 72 9 U H6 H 7.617 0.02 1 52 72 9 U C5 C 105.637 0.20 1 53 72 9 U C6 C 141.594 0.20 1 54 73 10 G H1 H 12.093 0.02 1 55 73 10 G H1' H 5.791 0.02 1 56 73 10 G H8 H 7.679 0.02 1 57 73 10 G C1' C 92.666 0.20 1 58 73 10 G C8 C 136.333 0.20 1 59 73 10 G N9 N 169.935 0.10 1 60 74 11 G H1 H 13.219 0.02 1 61 74 11 G H1' H 5.637 0.02 1 62 74 11 G H8 H 7.168 0.02 1 63 74 11 G C8 C 136.277 0.20 1 64 75 12 U H1' H 5.542 0.02 1 65 75 12 U H5 H 4.983 0.02 1 66 75 12 U H6 H 7.628 0.02 1 67 75 12 U C5 C 102.816 0.20 1 68 76 13 U H1' H 5.850 0.02 1 69 76 13 U H5 H 5.526 0.02 1 70 76 13 U H6 H 7.727 0.02 1 71 76 13 U C6 C 142.239 0.20 1 72 76 13 U N1 N 146.048 0.10 1 73 77 14 G H1' H 5.688 0.02 1 74 77 14 G H8 H 7.975 0.02 1 75 77 14 G C8 C 139.815 0.20 1 76 77 14 G N9 N 166.521 0.10 1 77 78 15 U H1' H 5.450 0.02 1 78 78 15 U H2' H 4.378 0.02 1 79 78 15 U H3' H 4.019 0.02 1 80 78 15 U H4' H 3.892 0.02 1 81 78 15 U H5 H 5.681 0.02 1 82 78 15 U H6 H 7.499 0.02 1 83 78 15 U C1' C 88.945 0.20 1 84 78 15 U C2' C 78.028 0.20 1 85 78 15 U C3' C 75.873 0.20 1 86 78 15 U C4' C 84.560 0.20 1 87 78 15 U C5 C 105.637 0.20 1 88 78 15 U C6 C 143.243 0.20 1 89 78 15 U N1 N 142.901 0.10 1 90 79 16 G H1' H 5.406 0.02 1 91 79 16 G H8 H 7.392 0.02 1 92 79 16 G C1' C 89.954 0.20 1 93 79 16 G C8 C 138.986 0.20 1 94 80 17 A H1' H 5.682 0.02 1 95 80 17 A H2 H 7.190 0.02 1 96 80 17 A H8 H 8.296 0.02 1 97 80 17 A C1' C 87.526 0.20 1 98 80 17 A C2 C 153.217 0.20 1 99 80 17 A C8 C 141.578 0.20 1 100 80 17 A N9 N 165.413 0.10 1 101 81 18 A H1' H 5.961 0.02 1 102 81 18 A H2 H 7.845 0.02 1 103 81 18 A H8 H 7.965 0.02 1 104 81 18 A C1' C 92.994 0.20 1 105 81 18 A C2 C 154.152 0.20 1 106 81 18 A C8 C 139.740 0.20 1 107 81 18 A N9 N 170.157 0.10 1 108 82 19 C H1' H 5.418 0.02 1 109 82 19 C H5 H 5.100 0.02 1 110 82 19 C H6 H 7.504 0.02 1 111 82 19 C H41 H 8.231 0.02 1 112 82 19 C H42 H 6.743 0.02 1 113 82 19 C C5 C 97.102 0.20 1 114 82 19 C C6 C 140.919 0.20 1 115 82 19 C N1 N 151.501 0.10 1 116 83 20 C H1' H 5.413 0.02 1 117 83 20 C H5 H 5.392 0.02 1 118 83 20 C H6 H 7.692 0.02 1 119 83 20 C H41 H 8.328 0.02 1 120 83 20 C H42 H 6.749 0.02 1 121 83 20 C C1' C 93.801 0.20 1 122 83 20 C C5 C 97.792 0.20 1 123 83 20 C C6 C 141.156 0.20 1 124 83 20 C N1 N 150.636 0.10 1 125 84 21 A H1' H 5.882 0.02 1 126 84 21 A H2 H 7.316 0.02 1 127 84 21 A H8 H 8.020 0.02 1 128 84 21 A C1' C 92.992 0.20 1 129 84 21 A C2 C 153.223 0.20 1 130 84 21 A C8 C 139.636 0.20 1 131 84 21 A N9 N 170.619 0.10 1 132 85 22 C H1' H 5.367 0.02 1 133 85 22 C H5 H 5.122 0.02 1 134 85 22 C H6 H 7.496 0.02 1 135 85 22 C H41 H 8.261 0.02 1 136 85 22 C H42 H 6.855 0.02 1 137 85 22 C C1' C 93.739 0.20 1 138 85 22 C C5 C 97.145 0.20 1 139 85 22 C C6 C 140.751 0.20 1 140 85 22 C N1 N 151.222 0.10 1 141 86 23 C H1' H 5.420 0.02 1 142 86 23 C H5 H 5.394 0.02 1 143 86 23 C H6 H 7.676 0.02 1 144 86 23 C H41 H 8.238 0.02 1 145 86 23 C H42 H 6.772 0.02 1 146 86 23 C C5 C 97.755 0.20 1 147 86 23 C N1 N 150.601 0.10 1 148 87 24 A H1' H 5.901 0.02 1 149 87 24 A H2 H 7.308 0.02 1 150 87 24 A H8 H 7.886 0.02 1 151 87 24 A C1' C 93.417 0.20 1 152 87 24 A C2 C 153.294 0.20 1 153 87 24 A C8 C 139.367 0.20 1 154 87 24 A N9 N 171.102 0.10 1 155 88 25 U H1' H 5.296 0.02 1 156 88 25 U H5 H 5.287 0.02 1 157 88 25 U H6 H 7.420 0.02 1 158 88 25 U C1' C 92.781 0.20 1 159 88 25 U C6 C 140.372 0.20 1 160 88 25 U N1 N 144.772 0.10 1 161 89 26 G H1' H 5.758 0.02 1 162 89 26 G H8 H 7.817 0.02 1 163 89 26 G C1' C 92.657 0.20 1 164 89 26 G C8 C 137.715 0.20 1 165 90 27 U H1' H 5.455 0.02 1 166 90 27 U H5 H 5.079 0.02 1 167 90 27 U H6 H 7.311 0.02 1 168 90 27 U C5 C 103.285 0.20 1 169 90 27 U C6 C 141.170 0.20 1 170 91 28 G H1' H 5.775 0.02 1 171 91 28 G H8 H 7.652 0.02 1 172 92 29 G H1' H 5.702 0.02 1 173 92 29 G H8 H 7.179 0.02 1 174 92 29 G C8 C 136.430 0.20 1 stop_ save_