data_36263 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of anti-prion RNA aptamer ; _BMRB_accession_number 36263 _BMRB_flat_file_name bmr36263.str _Entry_type original _Submission_date 2019-06-11 _Accession_date 2020-05-14 _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 Mashima T. . . 2 Lee J. H. . 3 Hayashi T. . . 4 Nagata T. . . 5 Kinoshita M. . . 6 Katahira M. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 239 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2020-06-30 original BMRB . stop_ _Original_release_date 2020-05-14 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Development and structural determination of an anti-PrPCaptamer that blocks pathological conformational conversion of prion protein. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 32188933 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Mashima T. . . 2 Lee J. H. . 3 Kamatari Y. O. . 4 Hayashi T. . . 5 Nagata T. . . 6 Nishikawa F. . . 7 Nishikawa S. . . 8 Kinoshita M. . . 9 Kuwata K. . . 10 Katahira M. . . stop_ _Journal_abbreviation 'Sci. Rep.' _Journal_volume 10 _Journal_issue . _Journal_ISSN 2045-2322 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 4934 _Page_last 4934 _Year 2020 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'RNA (25-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 8441.188 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 25 _Mol_residue_sequence ; GGAGGAGGAGGAAGGAGGAG GAGGA ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 G 2 2 G 3 3 A 4 4 G 5 5 G 6 6 A 7 7 G 8 8 G 9 9 A 10 10 G 11 11 G 12 12 A 13 13 A 14 14 G 15 15 G 16 16 A 17 17 G 18 18 G 19 19 A 20 20 G 21 21 G 22 22 A 23 23 G 24 24 G 25 25 A 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 . 32630 . . . . 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 '1.0 mM RNA (25-MER), 10 mM potassium phosphate, 10 mM potassium chloride, 10 uM DSS, 95% H2O/5% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling DSS 10 uM 'natural abundance' $entity_1 1.0 mM 'natural abundance' 'potassium chloride' 10 mM 'natural abundance' 'potassium phosphate' 10 mM 'natural abundance' H2O 95 % 'natural abundance' D2O 5 % [U-2H] stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '1.0 mM RNA (25-MER), 10 mM potassium phosphate, 10 mM potassium chloride, 10 uM DSS, 100% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling DSS 10 uM 'natural abundance' $entity_1 1.0 mM 'natural abundance' 'potassium chloride' 10 mM 'natural abundance' 'potassium phosphate' 10 mM 'natural abundance' D2O 100 % [U-2H] 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 refinement stop_ _Details . save_ save_software_2 _Saveframe_category software _Name Sparky _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'AVANCE III' _Field_strength 600 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'AVANCE III' _Field_strength 950 _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_JR-HMBC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D JR-HMBC' _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_2 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_1H-13C_HSQC_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _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' 10 . mM pH 6.2 . pH pressure 1 . atm temperature 278 . 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' 10 . mM pH 6.2 . pH pressure 1 . atm temperature 288 . 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 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 JR-HMBC' '2D DQF-COSY' '2D 1H-1H TOCSY' '2D 1H-13C HSQC' 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 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 1 1 G H1 H 11.78 . . 2 1 1 G H1' H 5.613 . . 3 1 1 G H2' H 5.021 . . 4 1 1 G H3' H 4.959 . . 5 1 1 G H4' H 4.827 . . 6 1 1 G H5' H 4.126 . . 7 1 1 G H5'' H 4.083 . . 8 1 1 G H8 H 8.128 . . 9 1 1 G H21 H 9.043 . . 10 1 1 G H22 H 10.333 . . 11 2 2 G H1 H 11.534 . . 12 2 2 G H1' H 5.356 . . 13 2 2 G H2' H 4.235 . . 14 2 2 G H3' H 4.498 . . 15 2 2 G H4' H 3.76 . . 16 2 2 G H5' H 2.901 . . 17 2 2 G H5'' H 3.292 . . 18 2 2 G H8 H 7.924 . . 19 2 2 G H21 H 6.303 . . 20 2 2 G H22 H 9.07 . . 21 3 3 A H1' H 5.664 . . 22 3 3 A H2 H 8.485 . . 23 3 3 A H2' H 4.459 . . 24 3 3 A H3' H 5.136 . . 25 3 3 A H4' H 4.228 . . 26 3 3 A H5' H 3.712 . . 27 3 3 A H5'' H 3.735 . . 28 3 3 A H8 H 7.713 . . 29 3 3 A H61 H 6.373 . . 30 3 3 A H62 H 8.355 . . 31 4 4 G H1 H 11.833 . . 32 4 4 G H1' H 5.811 . . 33 4 4 G H2' H 5.053 . . 34 4 4 G H3' H 4.798 . . 35 4 4 G H4' H 4.686 . . 36 4 4 G H5' H 4.516 . . 37 4 4 G H5'' H 4.576 . . 38 4 4 G H8 H 7.716 . . 39 4 4 G H21 H 6.566 . . 40 4 4 G H22 H 10.045 . . 41 5 5 G H1 H 11.421 . . 42 5 5 G H1' H 6.183 . . 43 5 5 G H2' H 4.759 . . 44 5 5 G H3' H 4.696 . . 45 5 5 G H4' H 4.651 . . 46 5 5 G H5' H 4.128 . . 47 5 5 G H5'' H 4.296 . . 48 5 5 G H8 H 7.944 . . 49 5 5 G H21 H 5.762 . . 50 5 5 G H22 H 9.89 . . 51 6 6 A H1' H 6.21 . . 52 6 6 A H2 H 8.187 . . 53 6 6 A H2' H 5.203 . . 54 6 6 A H3' H 5.077 . . 55 6 6 A H4' H 4.727 . . 56 6 6 A H5' H 4.354 . . 57 6 6 A H5'' H 4.517 . . 58 6 6 A H8 H 8.332 . . 59 7 7 G H1 H 11.68 . . 60 7 7 G H1' H 5.793 . . 61 7 7 G H2' H 5.278 . . 62 7 7 G H3' H 5.067 . . 63 7 7 G H4' H 4.7 . . 64 7 7 G H5' H 4.511 . . 65 7 7 G H5'' H 4.587 . . 66 7 7 G H8 H 8.403 . . 67 7 7 G H21 H 9.032 . . 68 7 7 G H22 H 10.22 . . 69 8 8 G H1 H 11.414 . . 70 8 8 G H1' H 5.45 . . 71 8 8 G H2' H 4.347 . . 72 8 8 G H3' H 4.477 . . 73 8 8 G H4' H 3.726 . . 74 8 8 G H5' H 3.072 . . 75 8 8 G H5'' H 3.115 . . 76 8 8 G H8 H 8.319 . . 77 8 8 G H21 H 6.727 . . 78 8 8 G H22 H 9.481 . . 79 9 9 A H1' H 5.796 . . 80 9 9 A H2 H 8.487 . . 81 9 9 A H2' H 4.469 . . 82 9 9 A H3' H 5.282 . . 83 9 9 A H4' H 4.286 . . 84 9 9 A H5' H 3.732 . . 85 9 9 A H5'' H 3.701 . . 86 9 9 A H8 H 7.877 . . 87 9 9 A H61 H 6.433 . . 88 9 9 A H62 H 8.377 . . 89 10 10 G H1 H 11.906 . . 90 10 10 G H1' H 5.839 . . 91 10 10 G H2' H 4.833 . . 92 10 10 G H3' H 4.732 . . 93 10 10 G H4' H 4.593 . . 94 10 10 G H5' H 4.515 . . 95 10 10 G H5'' H 4.38 . . 96 10 10 G H8 H 7.775 . . 97 10 10 G H22 H 9.411 . . 98 11 11 G H1 H 11.501 . . 99 11 11 G H1' H 5.971 . . 100 11 11 G H2' H 4.696 . . 101 11 11 G H3' H 4.802 . . 102 11 11 G H4' H 4.627 . . 103 11 11 G H5' H 4.011 . . 104 11 11 G H5'' H 4.18 . . 105 11 11 G H8 H 8.16 . . 106 11 11 G H21 H 5.843 . . 107 11 11 G H22 H 9.206 . . 108 12 12 A H1' H 5.899 . . 109 12 12 A H2 H 8.279 . . 110 12 12 A H2' H 4.697 . . 111 12 12 A H3' H 4.735 . . 112 12 12 A H4' H 4.506 . . 113 12 12 A H5' H 3.995 . . 114 12 12 A H5'' H 4.024 . . 115 12 12 A H8 H 8.33 . . 116 13 13 A H1' H 6.397 . . 117 13 13 A H2 H 8.351 . . 118 13 13 A H2' H 5.253 . . 119 13 13 A H3' H 5.05 . . 120 13 13 A H4' H 4.738 . . 121 13 13 A H5' H 4.321 . . 122 13 13 A H5'' H 4.343 . . 123 13 13 A H8 H 8.655 . . 124 14 14 G H1 H 11.731 . . 125 14 14 G H1' H 5.634 . . 126 14 14 G H2' H 5.096 . . 127 14 14 G H3' H 5.042 . . 128 14 14 G H4' H 4.969 . . 129 14 14 G H5' H 4.384 . . 130 14 14 G H5'' H 4.519 . . 131 14 14 G H8 H 8.216 . . 132 14 14 G H21 H 9.021 . . 133 14 14 G H22 H 10.3 . . 134 15 15 G H1 H 11.485 . . 135 15 15 G H1' H 5.415 . . 136 15 15 G H2' H 4.34 . . 137 15 15 G H3' H 4.532 . . 138 15 15 G H4' H 3.765 . . 139 15 15 G H5' H 2.963 . . 140 15 15 G H5'' H 3.218 . . 141 15 15 G H8 H 7.944 . . 142 15 15 G H21 H 6.345 . . 143 15 15 G H22 H 9.121 . . 144 16 16 A H1' H 5.663 . . 145 16 16 A H2 H 8.487 . . 146 16 16 A H2' H 4.472 . . 147 16 16 A H3' H 5.141 . . 148 16 16 A H4' H 4.264 . . 149 16 16 A H5' H 3.753 . . 150 16 16 A H5'' H 3.773 . . 151 16 16 A H8 H 7.715 . . 152 16 16 A H61 H 6.363 . . 153 16 16 A H62 H 8.384 . . 154 17 17 G H1 H 11.755 . . 155 17 17 G H1' H 5.806 . . 156 17 17 G H2' H 5.07 . . 157 17 17 G H3' H 4.804 . . 158 17 17 G H4' H 4.69 . . 159 17 17 G H5' H 4.514 . . 160 17 17 G H5'' H 4.582 . . 161 17 17 G H8 H 7.716 . . 162 17 17 G H21 H 6.584 . . 163 17 17 G H22 H 10.037 . . 164 18 18 G H1 H 11.59 . . 165 18 18 G H1' H 6.202 . . 166 18 18 G H2' H 4.779 . . 167 18 18 G H3' H 4.705 . . 168 18 18 G H4' H 4.65 . . 169 18 18 G H5' H 4.134 . . 170 18 18 G H5'' H 4.295 . . 171 18 18 G H8 H 7.993 . . 172 18 18 G H21 H 5.786 . . 173 18 18 G H22 H 9.968 . . 174 19 19 A H1' H 6.206 . . 175 19 19 A H2 H 8.197 . . 176 19 19 A H2' H 5.207 . . 177 19 19 A H3' H 5.077 . . 178 19 19 A H4' H 4.723 . . 179 19 19 A H5' H 4.357 . . 180 19 19 A H5'' H 4.52 . . 181 19 19 A H8 H 8.333 . . 182 20 20 G H1 H 11.571 . . 183 20 20 G H1' H 5.802 . . 184 20 20 G H2' H 5.303 . . 185 20 20 G H3' H 5.084 . . 186 20 20 G H4' H 4.725 . . 187 20 20 G H5' H 4.512 . . 188 20 20 G H5'' H 4.595 . . 189 20 20 G H8 H 8.431 . . 190 20 20 G H21 H 8.954 . . 191 20 20 G H22 H 10.225 . . 192 21 21 G H1 H 11.669 . . 193 21 21 G H1' H 5.516 . . 194 21 21 G H2' H 4.371 . . 195 21 21 G H3' H 4.502 . . 196 21 21 G H4' H 3.721 . . 197 21 21 G H5' H 3.105 . . 198 21 21 G H5'' H 3.001 . . 199 21 21 G H8 H 8.35 . . 200 21 21 G H21 H 6.279 . . 201 21 21 G H22 H 9.525 . . 202 22 22 A H1' H 5.862 . . 203 22 22 A H2 H 8.512 . . 204 22 22 A H2' H 4.495 . . 205 22 22 A H3' H 5.273 . . 206 22 22 A H4' H 4.285 . . 207 22 22 A H5' H 3.813 . . 208 22 22 A H5'' H 3.81 . . 209 22 22 A H8 H 7.832 . . 210 22 22 A H61 H 6.375 . . 211 22 22 A H62 H 8.508 . . 212 23 23 G H1 H 11.608 . . 213 23 23 G H1' H 5.851 . . 214 23 23 G H2' H 4.819 . . 215 23 23 G H3' H 4.704 . . 216 23 23 G H4' H 4.598 . . 217 23 23 G H5' H 4.132 . . 218 23 23 G H5'' H 4.084 . . 219 23 23 G H8 H 7.758 . . 220 23 23 G H21 H 5.965 . . 221 23 23 G H22 H 8.959 . . 222 24 24 G H1 H 10.96 . . 223 24 24 G H1' H 5.667 . . 224 24 24 G H2' H 4.64 . . 225 24 24 G H3' H 4.761 . . 226 24 24 G H4' H 4.332 . . 227 24 24 G H5' H 4.07 . . 228 24 24 G H5'' H 4.27 . . 229 24 24 G H8 H 8.018 . . 230 24 24 G H21 H 5.489 . . 231 24 24 G H22 H 9.37 . . 232 25 25 A H1' H 5.819 . . 233 25 25 A H2 H 7.438 . . 234 25 25 A H2' H 3.99 . . 235 25 25 A H3' H 4.267 . . 236 25 25 A H4' H 4.471 . . 237 25 25 A H5' H 4.071 . . 238 25 25 A H5'' H 4.067 . . 239 25 25 A H8 H 7.867 . . stop_ save_