data_34483 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Constitutive decay element CDE1 from human 3'UTR ; _BMRB_accession_number 34483 _BMRB_flat_file_name bmr34483.str _Entry_type original _Submission_date 2020-01-27 _Accession_date 2020-01-27 _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 Schwalbe H. . . 2 Binas O. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 135 "13C chemical shifts" 112 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2020-05-25 original BMRB . stop_ _Original_release_date 2020-05-22 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structural basis for the recognition of transiently structured AU-rich elements by Roquin ; _Citation_status 'in preparation' _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Binas O. . . 2 Tants J. N. . 3 Peter S. . . 4 Janowski R. . . 5 Davydova E. . . 6 Braun J. . . 7 Niessing D. . . 8 Schwalbe H. . . 9 Weigand J. E. . 10 Schlundt A. . . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_volume . _Journal_issue . _Journal_ASTM NARHAD _Journal_ISSN 1362-4962 _Journal_CSD 0389 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year 2020 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name "RNA (5'-R(*GP*GP*UP*GP*CP*CP*UP*AP*AP*UP*AP*UP*UP*UP*AP*GP*GP*CP*AP*CP*C)-3')" _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label unit_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 6009.584 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 19 _Mol_residue_sequence ; GGAAAUUAUAUUAAUUUCC ; loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 A 4 A 5 A 6 U 7 U 8 A 9 U 10 A 11 U 12 U 13 A 14 A 15 U 16 U 17 U 18 C 19 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 $entity_1 'Thermosinus carboxydivorans Nor1' 401526 Bacteria . Thermosinus carboxydivorans 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 '350 uM CDE1, 100% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 350 uM 'natural abundance' KCl 50 mM 'natural abundance' 'potassium phosphate buffer' 25 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '300 uM [U-99% 13C; U-99% 15N] CDE1, 100% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 300 uM '[U-99% 13C; U-99% 15N]' KCl 50 mM 'natural abundance' 'potassium phosphate buffer' 25 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name CNS _Version 1.2 loop_ _Vendor _Address _Electronic_address 'Brunger A. T. et.al.' . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name Sparky _Version 3.2 loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'AVANCE III' _Field_strength 800 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'AVANCE III' _Field_strength 600 _Details . save_ save_NMR_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'AVANCE III' _Field_strength 700 _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-13C_HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_3D_HCCH-TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HCCH-TOCSY' _Sample_label $sample_2 save_ save_fwHCC-TOCSY-CCH-E.COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name fwHCC-TOCSY-CCH-E.COSY _Sample_label $sample_2 save_ save_3D_HCP_5 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HCP' _Sample_label $sample_2 save_ save_3D_HCN_6 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HCN' _Sample_label $sample_2 save_ save_2D_gamma_HCN_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D gamma HCN' _Sample_label $sample_2 save_ save_2D_PFIDS_8 _Saveframe_category NMR_applied_experiment _Experiment_name '2D PFIDS' _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' 75 . mM pH 6.2 . pH pressure 1 . bar 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 'ionic strength' 75 . mM pH 6.2 . pH pressure 1 . bar temperature 298 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_shift_reference_1 _Saveframe_category chemical_shift_reference _Details ; 13C 15N referencing was achieved with the au program calc_wishart.rw in Topspin 3.5 written by Ruediger Weisemann (Bruker Biospin) after Wishart et al. ; 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 H 1 'methyl protons' ppm 0.000 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_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-13C HSQC' '3D HCCH-TOCSY' fwHCC-TOCSY-CCH-E.COSY '3D HCP' '3D HCN' '2D gamma HCN' '2D PFIDS' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name unit_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 5.844 0.001 . 2 1 1 G H3' H 4.700 0.001 . 3 1 1 G H4' H 4.569 0.002 . 4 1 1 G H5' H 4.454 0.002 . 5 1 1 G H5'' H 4.297 0.005 . 6 1 1 G H8 H 8.139 0.002 . 7 1 1 G C1' C 91.840 0.039 . 8 1 1 G C2' C 75.177 0.000 . 9 1 1 G C3' C 74.587 0.000 . 10 1 1 G C4' C 83.264 0.000 . 11 1 1 G C5' C 67.283 0.016 . 12 1 1 G C8 C 139.022 0.000 . 13 1 1 G HO2' H 4.947 0.003 . 14 2 2 G H1' H 5.915 0.003 . 15 2 2 G H3' H 4.582 0.004 . 16 2 2 G H4' H 4.569 0.012 . 17 2 2 G H5' H 4.503 0.000 . 18 2 2 G H5'' H 4.261 0.000 . 19 2 2 G H8 H 7.493 0.001 . 20 2 2 G C1' C 92.986 0.015 . 21 2 2 G C2' C 75.481 0.007 . 22 2 2 G C3' C 73.255 0.003 . 23 2 2 G C4' C 82.436 0.025 . 24 2 2 G C5' C 66.322 0.025 . 25 2 2 G C8 C 136.865 0.000 . 26 2 2 G HO2' H 4.695 0.002 . 27 3 3 A H1' H 5.954 0.001 . 28 3 3 A H2 H 7.146 0.002 . 29 3 3 A H3' H 4.676 0.002 . 30 3 3 A H4' H 4.534 0.004 . 31 3 3 A H5' H 4.608 0.001 . 32 3 3 A H5'' H 4.173 0.001 . 33 3 3 A H8 H 7.730 0.002 . 34 3 3 A C1' C 93.172 0.031 . 35 3 3 A C2 C 152.873 0.000 . 36 3 3 A C2' C 75.767 0.007 . 37 3 3 A C3' C 72.941 0.017 . 38 3 3 A C4' C 82.174 0.012 . 39 3 3 A C5' C 65.160 0.004 . 40 3 3 A C8 C 139.416 0.000 . 41 3 3 A HO2' H 4.675 0.000 . 42 4 4 A H1' H 5.813 0.001 . 43 4 4 A H2 H 7.204 0.001 . 44 4 4 A H3' H 4.609 0.002 . 45 4 4 A H4' H 4.521 0.009 . 46 4 4 A H8 H 7.608 0.001 . 47 4 4 A C1' C 92.856 0.027 . 48 4 4 A C2 C 152.767 0.000 . 49 4 4 A C2' C 75.739 0.011 . 50 4 4 A C3' C 73.245 0.000 . 51 4 4 A C4' C 82.133 0.007 . 52 4 4 A C8 C 139.234 0.000 . 53 4 4 A HO2' H 4.616 0.005 . 54 5 5 A H1' H 5.849 0.002 . 55 5 5 A H2 H 7.763 0.000 . 56 5 5 A H3' H 4.505 0.002 . 57 5 5 A H4' H 4.508 0.001 . 58 5 5 A H5' H 4.530 0.000 . 59 5 5 A H5'' H 4.109 0.000 . 60 5 5 A H8 H 7.666 0.001 . 61 5 5 A C1' C 93.006 0.005 . 62 5 5 A C2 C 153.695 0.000 . 63 5 5 A C2' C 75.561 0.008 . 64 5 5 A C3' C 73.004 0.024 . 65 5 5 A C4' C 82.223 0.015 . 66 5 5 A C5' C 65.539 0.005 . 67 5 5 A C8 C 139.312 0.000 . 68 5 5 A HO2' H 4.459 0.003 . 69 6 6 U H1' H 5.463 0.002 . 70 6 6 U H3' H 4.398 0.003 . 71 6 6 U H4' H 4.406 0.000 . 72 6 6 U H5 H 4.959 0.003 . 73 6 6 U H6 H 7.536 0.003 . 74 6 6 U C1' C 93.541 0.023 . 75 6 6 U C2' C 75.456 0.031 . 76 6 6 U C3' C 72.360 0.000 . 77 6 6 U C4' C 82.130 0.000 . 78 6 6 U C6 C 141.401 0.000 . 79 6 6 U HO2' H 4.288 0.002 . 80 7 7 U H1' H 5.617 0.008 . 81 7 7 U H3' H 4.530 0.003 . 82 7 7 U H4' H 4.459 0.028 . 83 7 7 U H5 H 5.470 0.001 . 84 7 7 U H5' H 4.529 0.013 . 85 7 7 U H5'' H 4.102 0.000 . 86 7 7 U H6 H 7.804 0.003 . 87 7 7 U C1' C 93.506 0.025 . 88 7 7 U C2' C 75.528 0.004 . 89 7 7 U C3' C 72.865 0.000 . 90 7 7 U C4' C 82.328 0.058 . 91 7 7 U C5' C 64.973 0.036 . 92 7 7 U C6 C 141.916 0.000 . 93 7 7 U HO2' H 4.334 0.001 . 94 8 8 A H1' H 5.889 0.006 . 95 8 8 A H2 H 7.192 0.001 . 96 8 8 A H3' H 4.693 0.003 . 97 8 8 A H4' H 4.492 0.001 . 98 8 8 A H5' H 4.450 0.004 . 99 8 8 A H5'' H 4.132 0.003 . 100 8 8 A H8 H 8.082 0.001 . 101 8 8 A C1' C 91.377 0.009 . 102 8 8 A C2 C 153.961 0.000 . 103 8 8 A C2' C 76.353 0.016 . 104 8 8 A C3' C 75.171 0.014 . 105 8 8 A C4' C 83.684 0.010 . 106 8 8 A C5' C 66.190 0.014 . 107 8 8 A C8 C 140.304 0.000 . 108 8 8 A HO2' H 4.515 0.004 . 109 9 9 U H1' H 5.631 0.001 . 110 9 9 U H3' H 4.453 0.001 . 111 9 9 U H4' H 4.243 0.003 . 112 9 9 U H5 H 5.636 0.000 . 113 9 9 U H5' H 4.105 0.004 . 114 9 9 U H5'' H 3.992 0.001 . 115 9 9 U H6 H 7.642 0.002 . 116 9 9 U C1' C 90.618 0.008 . 117 9 9 U C2' C 75.682 0.052 . 118 9 9 U C3' C 76.902 0.016 . 119 9 9 U C4' C 85.125 0.001 . 120 9 9 U C5' C 67.349 0.014 . 121 9 9 U C6 C 143.238 0.000 . 122 9 9 U HO2' H 4.276 0.003 . 123 10 10 A H1' H 5.748 0.002 . 124 10 10 A H2 H 7.976 0.002 . 125 10 10 A H3' H 4.628 0.005 . 126 10 10 A H4' H 4.399 0.002 . 127 10 10 A H5' H 4.117 0.006 . 128 10 10 A H5'' H 3.998 0.002 . 129 10 10 A H8 H 7.995 0.001 . 130 10 10 A C1' C 90.082 0.003 . 131 10 10 A C2 C 154.861 0.000 . 132 10 10 A C2' C 77.412 0.041 . 133 10 10 A C3' C 78.103 0.047 . 134 10 10 A C4' C 86.172 0.015 . 135 10 10 A C5' C 67.905 0.019 . 136 10 10 A C8 C 141.696 0.000 . 137 10 10 A HO2' H 4.523 0.003 . 138 11 11 U H1' H 5.908 0.004 . 139 11 11 U H3' H 4.691 0.005 . 140 11 11 U H4' H 4.437 0.005 . 141 11 11 U H5 H 5.781 0.000 . 142 11 11 U H5' H 4.129 0.001 . 143 11 11 U H5'' H 4.081 0.004 . 144 11 11 U H6 H 7.738 0.003 . 145 11 11 U C1' C 90.430 0.021 . 146 11 11 U C2' C 75.707 0.058 . 147 11 11 U C3' C 76.995 0.025 . 148 11 11 U C4' C 85.217 0.040 . 149 11 11 U C5' C 68.014 0.035 . 150 11 11 U C6 C 143.823 0.000 . 151 11 11 U HO2' H 4.374 0.001 . 152 12 12 U H1' H 5.873 0.001 . 153 12 12 U H3' H 4.633 0.002 . 154 12 12 U H4' H 4.527 0.001 . 155 12 12 U H5 H 5.918 0.003 . 156 12 12 U H5' H 4.258 0.001 . 157 12 12 U H5'' H 4.227 0.002 . 158 12 12 U H6 H 7.913 0.003 . 159 12 12 U C1' C 91.254 0.041 . 160 12 12 U C2' C 75.055 0.057 . 161 12 12 U C3' C 76.309 0.003 . 162 12 12 U C4' C 84.542 0.002 . 163 12 12 U C5' C 68.475 0.012 . 164 12 12 U C6 C 143.797 0.000 . 165 12 12 U HO2' H 4.591 0.002 . 166 13 13 A H1' H 6.005 0.001 . 167 13 13 A H2 H 6.811 0.001 . 168 13 13 A H3' H 4.681 0.002 . 169 13 13 A H4' H 4.619 0.005 . 170 13 13 A H5' H 4.448 0.003 . 171 13 13 A H5'' H 4.379 0.002 . 172 13 13 A H8 H 8.319 0.001 . 173 13 13 A C1' C 92.374 0.050 . 174 13 13 A C2 C 152.440 0.000 . 175 13 13 A C2' C 75.434 0.019 . 176 13 13 A C3' C 74.569 0.029 . 177 13 13 A C4' C 83.268 0.003 . 178 13 13 A C5' C 67.678 0.004 . 179 13 13 A C8 C 141.101 0.000 . 180 13 13 A HO2' H 4.750 0.005 . 181 14 14 A H1' H 5.914 0.002 . 182 14 14 A H2 H 7.717 0.001 . 183 14 14 A H3' H 4.548 0.003 . 184 14 14 A H8 H 7.865 0.000 . 185 14 14 A C1' C 92.859 0.000 . 186 14 14 A C2 C 153.704 0.000 . 187 14 14 A C2' C 75.587 0.000 . 188 14 14 A C3' C 73.082 0.000 . 189 14 14 A C8 C 139.657 0.000 . 190 14 14 A HO2' H 4.457 0.002 . 191 15 15 U H1' H 5.468 0.005 . 192 15 15 U H3' H 4.414 0.003 . 193 15 15 U H5 H 5.001 0.001 . 194 15 15 U H6 H 7.561 0.003 . 195 15 15 U C1' C 93.382 0.058 . 196 15 15 U C2' C 75.426 0.000 . 197 15 15 U C3' C 72.412 0.000 . 198 15 15 U C6 C 141.395 0.000 . 199 15 15 U HO2' H 4.350 0.002 . 200 16 16 U H1' H 5.645 0.005 . 201 16 16 U H3' H 4.474 0.002 . 202 16 16 U H5 H 5.518 0.001 . 203 16 16 U H6 H 7.911 0.004 . 204 16 16 U C1' C 93.837 0.022 . 205 16 16 U C2' C 75.533 0.015 . 206 16 16 U C3' C 72.758 0.012 . 207 16 16 U C6 C 142.348 0.000 . 208 16 16 U HO2' H 4.447 0.003 . 209 17 17 U H1' H 5.599 0.003 . 210 17 17 U H3' H 4.471 0.005 . 211 17 17 U H4' H 4.473 0.000 . 212 17 17 U H5 H 5.560 0.000 . 213 17 17 U H6 H 7.978 0.004 . 214 17 17 U C1' C 93.873 0.019 . 215 17 17 U C2' C 75.310 0.005 . 216 17 17 U C3' C 72.519 0.009 . 217 17 17 U C4' C 82.195 0.000 . 218 17 17 U C6 C 142.596 0.000 . 219 17 17 U HO2' H 4.434 0.002 . 220 18 18 C H1' H 5.517 0.003 . 221 18 18 C H3' H 4.456 0.007 . 222 18 18 C H4' H 4.382 0.003 . 223 18 18 C H5 H 5.620 0.000 . 224 18 18 C H5' H 4.533 0.000 . 225 18 18 C H5'' H 4.062 0.000 . 226 18 18 C H6 H 7.847 0.004 . 227 18 18 C C1' C 94.591 0.026 . 228 18 18 C C2' C 75.675 0.019 . 229 18 18 C C3' C 72.337 0.006 . 230 18 18 C C4' C 82.148 0.009 . 231 18 18 C C5' C 64.596 0.031 . 232 18 18 C C6 C 141.967 0.000 . 233 18 18 C HO2' H 4.130 0.002 . 234 19 19 C H1' H 6.052 0.002 . 235 19 19 C H3' H 4.932 0.007 . 236 19 19 C H4' H 4.397 0.002 . 237 19 19 C H5 H 5.479 0.000 . 238 19 19 C H5' H 4.522 0.003 . 239 19 19 C H5'' H 4.083 0.004 . 240 19 19 C H6 H 7.457 0.004 . 241 19 19 C C1' C 91.959 0.021 . 242 19 19 C C2' C 85.135 0.020 . 243 19 19 C C3' C 77.986 0.023 . 244 19 19 C C4' C 85.551 0.013 . 245 19 19 C C5' C 65.810 0.017 . 246 19 19 C C6 C 141.852 0.000 . 247 19 19 C HO2' H 4.605 0.001 . stop_ save_