data_30622 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution Structure of lncRNA (LINK-A) 20-nt Hexaloop Hairpin ; _BMRB_accession_number 30622 _BMRB_flat_file_name bmr30622.str _Entry_type original _Submission_date 2019-06-28 _Accession_date 2019-06-28 _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 Amado A. Y. . 2 Walker M. . . 3 Varani G. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 163 "13C chemical shifts" 109 "15N chemical shifts" 8 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2020-06-26 original BMRB . stop_ _Original_release_date 2019-08-02 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structure of the lncRNA LINK-A Hexaloop Hairpin in PI(3,4,5)P3 Interaction ; _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 Amado A. Y. . 2 Walker M. . . 3 Varani G. . . stop_ _Journal_abbreviation . _Journal_volume . _Journal_issue . _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name LINK-A _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 6414.854 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 20 _Mol_residue_sequence ; GGAGGGUAGACUCGCUCUCC ; loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 A 4 G 5 G 6 G 7 U 8 A 9 G 10 A 11 C 12 U 13 C 14 G 15 C 16 U 17 C 18 U 19 C 20 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 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_name $entity_1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '0.9 mM RNA, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.9 mM 'natural abundance' 'Sodium Phosphate' 20 mM 'natural abundance' EDTA 0.01 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '0.6 mM RNA, 100% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.6 mM 'natural abundance' 'Sodium Phosphate' 20 mM 'natural abundance' EDTA 0.01 mM 'natural abundance' stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type solution _Details '0.5 mM [U-13C; U-15N] RNA, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.5 mM '[U-13C; U-15N]' 'Sodium Phosphate' 20 mM 'natural abundance' EDTA 0.01 mM 'natural abundance' stop_ save_ save_sample_4 _Saveframe_category sample _Sample_type solution _Details '0.5 mM [U-13C; U-15N] RNA, 100% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.5 mM '[U-13C; U-15N]' 'Sodium Phosphate' 20 mM 'natural abundance' EDTA 0.01 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name TopSpin _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing stop_ _Details . save_ save_software_2 _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name Sparky _Version . 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_ ############################# # 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-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_2 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_1H-1H_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ save_2D_1H-15N_HSQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_3 save_ save_2D_1H-13C_HSQC_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_4 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.0 . 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 pH 6.0 . pH pressure 1 . atm temperature 298 . K stop_ save_ save_sample_conditions_3 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.0 . pH pressure 1 . atm temperature 298 . 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 C 13 'methyl protons' ppm 0.000 internal indirect . . . 0.10132912 DSS H 1 'methyl protons' ppm 0.0000 internal direct . . . 1.0 DSS N 15 'methyl protons' ppm 0.000 internal indirect . . . 0.25144953 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-1H TOCSY' '2D 1H-15N HSQC' '2D 1H-13C HSQC' stop_ loop_ _Sample_label $sample_1 $sample_2 $sample_3 $sample_4 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 12.112 . . 2 1 1 G H1' H 5.642 . . 3 1 1 G H3' H 4.954 . . 4 1 1 G H4' H 4.531 . . 5 1 1 G H5' H 4.399 . . 6 1 1 G H5'' H 4.232 . . 7 1 1 G H8 H 8.079 . . 8 1 1 G C1' C 88.746 . . 9 1 1 G C2' C 72.385 . . 10 1 1 G C3' C 71.928 . . 11 1 1 G C4' C 80.652 . . 12 1 1 G C5' C 63.341 . . 13 1 1 G C8 C 136.206 . . 14 1 1 G HO2' H 4.907 . . 15 2 2 G H1 H 12.119 . . 16 2 2 G H1' H 5.872 . . 17 2 2 G H3' H 4.555 . . 18 2 2 G H4' H 4.464 . . 19 2 2 G H5' H 4.455 . . 20 2 2 G H5'' H 4.245 . . 21 2 2 G H8 H 7.495 . . 22 2 2 G H22 H 5.685 . . 23 2 2 G C1' C 90.192 . . 24 2 2 G C2' C 72.975 . . 25 2 2 G C3' C 70.394 . . 26 2 2 G C5' C 64.073 . . 27 2 2 G C8 C 134.253 . . 28 2 2 G N1 N 146.86 . . 29 2 2 G HO2' H 4.643 . . 30 3 3 A H1' H 5.962 . . 31 3 3 A H2 H 7.442 . . 32 3 3 A H3' H 4.566 . . 33 3 3 A H4' H 4.485 . . 34 3 3 A H5' H 4.136 . . 35 3 3 A H5'' H 4.138 . . 36 3 3 A H8 H 7.722 . . 37 3 3 A H61 H 7.945 . . 38 3 3 A H62 H 6.747 . . 39 3 3 A C1' C 90.162 . . 40 3 3 A C2 C 150.957 . . 41 3 3 A C2' C 72.65 . . 42 3 3 A C3' C 73.517 . . 43 3 3 A C4' C 79.224 . . 44 3 3 A C5' C 62.2 . . 45 3 3 A C8 C 136.453 . . 46 3 3 A HO2' H 4.641 . . 47 4 4 G H1 H 12.407 . . 48 4 4 G H1' H 5.667 . . 49 4 4 G H3' H 4.397 . . 50 4 4 G H4' H 4.269 . . 51 4 4 G H5'' H 4.019 . . 52 4 4 G H8 H 7.124 . . 53 4 4 G H21 H 7.848 . . 54 4 4 G H22 H 5.765 . . 55 4 4 G C1' C 89.464 . . 56 4 4 G C2' C 73.329 . . 57 4 4 G C3' C 70.413 . . 58 4 4 G C5' C 62.868 . . 59 4 4 G C8 C 133.144 . . 60 4 4 G N1 N 147.6 . . 61 4 4 G HO2' H 4.456 . . 62 5 5 G H1 H 10.716 . . 63 5 5 G H1' H 5.706 . . 64 5 5 G H3' H 4.244 . . 65 5 5 G H4' H 4.272 . . 66 5 5 G H5' H 3.958 . . 67 5 5 G H5'' H 4.013 . . 68 5 5 G H8 H 7.008 . . 69 5 5 G H21 H 6.111 . . 70 5 5 G H22 H 5.515 . . 71 5 5 G C1' C 90.744 . . 72 5 5 G C2' C 72.395 . . 73 5 5 G C3' C 70.88 . . 74 5 5 G C5' C 64.453 . . 75 5 5 G C8 C 134.042 . . 76 5 5 G N1 N 143.24 . . 77 5 5 G HO2' H 4.732 . . 78 6 6 G H1 H 13.15 . . 79 6 6 G H1' H 5.767 . . 80 6 6 G H3' H 4.41 . . 81 6 6 G H5'' H 4.045 . . 82 6 6 G H8 H 7.158 . . 83 6 6 G H21 H 8.463 . . 84 6 6 G H22 H 6.323 . . 85 6 6 G C1' C 90.272 . . 86 6 6 G C2' C 74.103 . . 87 6 6 G C3' C 69.394 . . 88 6 6 G C5' C 61.595 . . 89 6 6 G C8 C 133.127 . . 90 6 6 G N1 N 148.03 . . 91 6 6 G HO2' H 4.545 . . 92 7 7 U H1' H 5.493 . . 93 7 7 U H3 H 11.364 . . 94 7 7 U H3' H 4.394 . . 95 7 7 U H4' H 4.456 . . 96 7 7 U H5 H 5.434 . . 97 7 7 U H5' H 4.085 . . 98 7 7 U H5'' H 4.037 . . 99 7 7 U H6 H 7.522 . . 100 7 7 U C1' C 90.611 . . 101 7 7 U C2' C 73.145 . . 102 7 7 U C4' C 79.567 . . 103 7 7 U C5 C 101.777 . . 104 7 7 U C5' C 64.195 . . 105 7 7 U C6 C 137.461 . . 106 7 7 U N3 N 158.36 . . 107 7 7 U HO2' H 4.256 . . 108 8 8 A H1' H 5.819 . . 109 8 8 A H2 H 7.462 . . 110 8 8 A H3' H 4.493 . . 111 8 8 A H4' H 4.559 . . 112 8 8 A H5' H 4.091 . . 113 8 8 A H8 H 8.096 . . 114 8 8 A C1' C 89.594 . . 115 8 8 A C2 C 150.604 . . 116 8 8 A C2' C 73.004 . . 117 8 8 A C5' C 63.98 . . 118 8 8 A C8 C 137.998 . . 119 8 8 A HO2' H 4.471 . . 120 9 9 G H1' H 5.474 . . 121 9 9 G H3' H 4.583 . . 122 9 9 G H4' H 4.377 . . 123 9 9 G H5' H 4.266 . . 124 9 9 G H5'' H 4.061 . . 125 9 9 G H8 H 7.598 . . 126 9 9 G C1' C 88.187 . . 127 9 9 G C2' C 72.083 . . 128 9 9 G C4' C 81.738 . . 129 9 9 G C5' C 64.168 . . 130 9 9 G C8 C 136.506 . . 131 9 9 G HO2' H 4.546 . . 132 10 10 A H1' H 5.956 . . 133 10 10 A H2 H 8.064 . . 134 10 10 A H3' H 4.716 . . 135 10 10 A H4' H 4.442 . . 136 10 10 A H5' H 4.236 . . 137 10 10 A H5'' H 4.078 . . 138 10 10 A H8 H 8.234 . . 139 10 10 A C1' C 87.529 . . 140 10 10 A C2 C 152.197 . . 141 10 10 A C2' C 73.768 . . 142 10 10 A C3' C 73.357 . . 143 10 10 A C4' C 82.5 . . 144 10 10 A C5' C 63.577 . . 145 10 10 A C8 C 139.12 . . 146 10 10 A HO2' H 4.656 . . 147 11 11 C H1' H 5.758 . . 148 11 11 C H3' H 4.542 . . 149 11 11 C H4' H 4.349 . . 150 11 11 C H5 H 5.698 . . 151 11 11 C H6 H 7.613 . . 152 11 11 C C1' C 88.456 . . 153 11 11 C C2' C 73.697 . . 154 11 11 C C3' C 69.676 . . 155 11 11 C C4' C 82.104 . . 156 11 11 C C5 C 94.741 . . 157 11 11 C C6 C 140.506 . . 158 11 11 C HO2' H 4.197 . . 159 12 12 U H1' H 5.86 . . 160 12 12 U H4' H 4.418 . . 161 12 12 U H5 H 5.798 . . 162 12 12 U H5' H 4.569 . . 163 12 12 U H5'' H 4.077 . . 164 12 12 U H6 H 7.751 . . 165 12 12 U C1' C 88.596 . . 166 12 12 U C2' C 73.2 . . 167 12 12 U C4' C 81.904 . . 168 12 12 U C5 C 102.509 . . 169 12 12 U C5' C 62.121 . . 170 12 12 U C6 C 141.065 . . 171 12 12 U HO2' H 4.379 . . 172 13 13 C H1' H 5.987 . . 173 13 13 C H3' H 4.522 . . 174 13 13 C H4' H 4.273 . . 175 13 13 C H5 H 6.037 . . 176 13 13 C H5' H 4.199 . . 177 13 13 C H5'' H 4.073 . . 178 13 13 C H6 H 7.898 . . 179 13 13 C C1' C 89.025 . . 180 13 13 C C2' C 72.763 . . 181 13 13 C C5 C 96.217 . . 182 13 13 C C5' C 64.821 . . 183 13 13 C C6 C 139.679 . . 184 13 13 C HO2' H 4.439 . . 185 14 14 G H1 H 10.813 . . 186 14 14 G H1' H 5.728 . . 187 14 14 G H3' H 4.374 . . 188 14 14 G H4' H 4.339 . . 189 14 14 G H5' H 4.25 . . 190 14 14 G H5'' H 4.066 . . 191 14 14 G H8 H 7.95 . . 192 14 14 G H21 H 6.03 . . 193 14 14 G H22 H 5.522 . . 194 14 14 G C1' C 90.616 . . 195 14 14 G C2' C 72.338 . . 196 14 14 G C3' C 69.04 . . 197 14 14 G C5' C 64.921 . . 198 14 14 G C8 C 135.472 . . 199 14 14 G N1 N 143.64 . . 200 14 14 G HO2' H 4.664 . . 201 15 15 C H1' H 5.434 . . 202 15 15 C H3' H 4.375 . . 203 15 15 C H5 H 5.351 . . 204 15 15 C H5'' H 4.056 . . 205 15 15 C H6 H 7.557 . . 206 15 15 C H41 H 8.123 . . 207 15 15 C H42 H 6.793 . . 208 15 15 C C1' C 91.11 . . 209 15 15 C C2' C 72.267 . . 210 15 15 C C5 C 94.671 . . 211 15 15 C C6 C 137.76 . . 212 15 15 C HO2' H 4.472 . . 213 16 16 U H1' H 5.67 . . 214 16 16 U H3 H 11.643 . . 215 16 16 U H3' H 4.531 . . 216 16 16 U H5 H 5.778 . . 217 16 16 U H5' H 4.347 . . 218 16 16 U H5'' H 4.058 . . 219 16 16 U H6 H 7.836 . . 220 16 16 U C1' C 91.275 . . 221 16 16 U C2' C 73.032 . . 222 16 16 U C3' C 72.631 . . 223 16 16 U C5 C 102.338 . . 224 16 16 U C5' C 64.593 . . 225 16 16 U C6 C 138.355 . . 226 16 16 U N3 N 157.74 . . 227 16 16 U HO2' H 4.144 . . 228 17 17 C H1' H 5.678 . . 229 17 17 C H3' H 4.126 . . 230 17 17 C H4' H 4.38 . . 231 17 17 C H5 H 5.694 . . 232 17 17 C H5' H 4.308 . . 233 17 17 C H5'' H 3.984 . . 234 17 17 C H6 H 7.919 . . 235 17 17 C H41 H 8.198 . . 236 17 17 C H42 H 6.691 . . 237 17 17 C C1' C 90.025 . . 238 17 17 C C2' C 74.745 . . 239 17 17 C C3' C 66.973 . . 240 17 17 C C5 C 95.728 . . 241 17 17 C C5' C 62.801 . . 242 17 17 C C6 C 141.263 . . 243 17 17 C HO2' H 3.946 . . 244 18 18 U H1' H 5.538 . . 245 18 18 U H3 H 13.808 . . 246 18 18 U H3' H 4.462 . . 247 18 18 U H4' H 4.094 . . 248 18 18 U H5 H 5.441 . . 249 18 18 U H6 H 7.614 . . 250 18 18 U C1' C 91.479 . . 251 18 18 U C2' C 72.876 . . 252 18 18 U C3' C 69.394 . . 253 18 18 U C4' C 80.742 . . 254 18 18 U C5 C 95.249 . . 255 18 18 U C6 C 139.071 . . 256 18 18 U N3 N 162.55 . . 257 18 18 U HO2' H 4.161 . . 258 19 19 C H1' H 5.535 . . 259 19 19 C H3' H 4.372 . . 260 19 19 C H5 H 5.618 . . 261 19 19 C H5' H 4.208 . . 262 19 19 C H5'' H 4.516 . . 263 19 19 C H6 H 7.877 . . 264 19 19 C H41 H 7.747 . . 265 19 19 C H42 H 6.763 . . 266 19 19 C C1' C 91.08 . . 267 19 19 C C2' C 72.664 . . 268 19 19 C C5 C 94.451 . . 269 19 19 C C5' C 61.707 . . 270 19 19 C C6 C 140.623 . . 271 19 19 C HO2' H 4.31 . . 272 20 20 C H1' H 5.465 . . 273 20 20 C H3' H 4.405 . . 274 20 20 C H5 H 5.397 . . 275 20 20 C H6 H 7.893 . . 276 20 20 C C1' C 91.071 . . 277 20 20 C C2' C 72.735 . . 278 20 20 C C5 C 100.411 . . 279 20 20 C C6 C 139.172 . . 280 20 20 C HO2' H 4.471 . . stop_ save_