data_5371 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; U6 RNA chemical shifts ; _BMRB_accession_number 5371 _BMRB_flat_file_name bmr5371.str _Entry_type new _Submission_date 2002-05-09 _Accession_date 2002-05-09 _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 Butcher Samuel E. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 211 "13C chemical shifts" 41 "15N chemical shifts" 14 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-06-01 update BMRB 'update entry citation' 2009-06-02 update BMRB 'complete entry citation' 2002-08-22 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Metal binding and base ionization in the U6 RNA intramolecular stem-loop structure ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 11992125 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Huppler Anna E. . 2 Nikstad Laura J. . 3 Allmann Anne M. . 4 Brow David A. . 5 Butcher Samuel E. . stop_ _Journal_abbreviation 'Nat. Struct. Biol.' _Journal_volume 9 _Journal_issue 6 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 431 _Page_last 435 _Year 2002 _Details . loop_ _Keyword U6 RNA stop_ save_ ################################## # Molecular system description # ################################## save_system_U6_snRNA_ISL _Saveframe_category molecular_system _Mol_system_name 'U6 RNA' _Abbreviation_common 'U6 snRNA ISL' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'U6 RNA 1' $ISL_monomer stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'not present' loop_ _Biological_function 'pre-mRNA splicing' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_ISL_monomer _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common 'U6 RNA' _Abbreviation_common 'U6 snRNA ISL' _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 24 _Mol_residue_sequence ; GGUUCCCCUGCAUAAGGAUG AACC ; loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 U 4 U 5 C 6 C 7 C 8 C 9 U 10 G 11 C 12 A 13 U 14 A 15 A 16 G 17 G 18 A 19 U 20 G 21 A 22 A 23 C 24 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 $ISL_monomer 'Baker's yeast' 4932 Eukaryota Fungi Saccharomyces cerevisiae 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 $ISL_monomer 'recombinant technology' . . . . . 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 $ISL_monomer 1.0 mM 0.5 1.5 '[U-100% 13C; U-15N]' stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer . _Model . _Field_strength . _Details . save_ ####################### # Sample conditions # ####################### save_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7.0 0.1 n/a temperature 303 0.5 K 'ionic strength' 0.05 0.01 M stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _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 TSP H 1 'methyl protons' ppm 0 internal indirect cylindrical internal parallel 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_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'U6 RNA 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 G H1' H 5.834 0.001 . 2 . 1 G H2' H 4.969 0.013 . 3 . 1 G H3' H 4.756 0.001 . 4 . 1 G H4' H 4.553 0.001 . 5 . 1 G H5' H 4.441 0.009 . 6 . 1 G H5'' H 4.268 0.007 . 7 . 1 G H8 H 8.169 0.001 . 8 . 1 G H1 H 12.852 0.014 . 9 . 1 G C8 C 138.7 0.020 . 10 . 1 G N1 N 146.9 0.020 . 11 . 2 G H1' H 5.933 0.003 . 12 . 2 G H2' H 4.592 0.001 . 13 . 2 G H3' H 4.559 0.006 . 14 . 2 G H4' H 4.534 0.006 . 15 . 2 G H5' H 4.502 0.010 . 16 . 2 G H5'' H 4.245 0.005 . 17 . 2 G H8 H 7.588 0.003 . 18 . 2 G H1 H 13.454 0.005 . 19 . 2 G H21 H 8.594 0.000 . 20 . 2 G H22 H 6.188 0.000 . 21 . 2 G N1 N 148 0.020 . 22 . 3 U H1' H 5.606 0.005 . 23 . 3 U H2' H 4.531 0.017 . 24 . 3 U H3' H 4.537 0.007 . 25 . 3 U H4' H 4.450 0.000 . 26 . 3 U H5 H 5.147 0.003 . 27 . 3 U H5' H 4.590 0.001 . 28 . 3 U H5'' H 4.148 0.007 . 29 . 3 U H6 H 7.828 0.009 . 30 . 3 U H3 H 14.458 0.005 . 31 . 3 U C6 C 141.1 0.020 . 32 . 3 U C5 C 102.3 0.020 . 33 . 3 U N3 N 162.3 0.020 . 34 . 4 U H1' H 5.694 0.007 . 35 . 4 U H2' H 4.513 0.008 . 36 . 4 U H3' H 4.526 0.001 . 37 . 4 U H4' H 4.507 0.000 . 38 . 4 U H5 H 5.631 0.006 . 39 . 4 U H5' H 4.554 0.005 . 40 . 4 U H5'' H 4.141 0.001 . 41 . 4 U H6 H 8.028 0.003 . 42 . 4 U H3 H 13.795 0.005 . 43 . 4 U N3 N 162.4 0.020 . 44 . 4 U C6 C 142 0.020 . 45 . 4 U C5 C 102.7 0.020 . 46 . 5 C H1' H 5.599 0.006 . 47 . 5 C H2' H 4.275 0.002 . 48 . 5 C H3' H 4.466 0.007 . 49 . 5 C H4' H 4.460 0.000 . 50 . 5 C H5 H 5.734 0.021 . 51 . 5 C H5' H 4.562 0.007 . 52 . 5 C H5'' H 4.130 0.004 . 53 . 5 C H6 H 7.859 0.007 . 54 . 5 C H41 H 8.438 0.001 . 55 . 5 C H42 H 7.130 0.000 . 56 . 5 C C6 C 141.4 0.020 . 57 . 5 C C5 C 97.1 0.020 . 58 . 5 C N4 N 98.4 0.020 . 59 . 6 C H3' H 4.601 0.003 . 60 . 6 C H4' H 4.354 0.001 . 61 . 6 C H5 H 5.656 0.004 . 62 . 6 C H5' H 4.550 0.002 . 63 . 6 C H5'' H 4.109 0.010 . 64 . 6 C H6 H 7.773 0.004 . 65 . 6 C C6 C 141.5 0.020 . 66 . 6 C C5 C 97 0.020 . 67 . 7 C H1' H 5.413 0.003 . 68 . 7 C H2' H 4.397 0.006 . 69 . 7 C H3' H 4.519 0.006 . 70 . 7 C H4' H 4.417 0.004 . 71 . 7 C H5 H 5.721 0.004 . 72 . 7 C H5' H 4.470 0.002 . 73 . 7 C H5'' H 4.063 0.014 . 74 . 7 C H6 H 7.907 0.003 . 75 . 7 C H41 H 8.452 0.000 . 76 . 7 C H42 H 7.155 0.002 . 77 . 7 C C6 C 140.7 0.020 . 78 . 7 C C5 C 97 0.020 . 79 . 7 C N4 N 97.4 0.020 . 80 . 8 C H1' H 5.391 0.005 . 81 . 8 C H2' H 4.288 0.005 . 82 . 8 C H3' H 4.325 0.005 . 83 . 8 C H4' H 4.369 0.004 . 84 . 8 C H5 H 5.538 0.005 . 85 . 8 C H5' H 4.482 0.007 . 86 . 8 C H5'' H 4.005 0.006 . 87 . 8 C H6 H 7.770 0.006 . 88 . 8 C H41 H 8.404 0.000 . 89 . 8 C H42 H 6.977 0.007 . 90 . 8 C C6 C 141.5 0.020 . 91 . 8 C C5 C 97.3 0.020 . 92 . 8 C N4 N 97.3 0.020 . 93 . 9 U H1' H 5.582 0.003 . 94 . 9 U H2' H 4.477 0.004 . 95 . 9 U H3' H 4.353 0.007 . 96 . 9 U H5 H 5.303 0.004 . 97 . 9 U H5' H 4.497 0.020 . 98 . 9 U H5'' H 4.085 0.004 . 99 . 9 U H6 H 7.621 0.005 . 100 . 9 U H4' H 4.450 0.000 . 101 . 9 U H3 H 13.691 0.009 . 102 . 9 U C6 C 140.1 0.020 . 103 . 9 U C5 C 103.6 0.020 . 104 . 9 U N3 N 160.7 0.020 . 105 . 10 G H1' H 5.552 0.004 . 106 . 10 G H2' H 4.418 0.001 . 107 . 10 G H3' H 4.530 0.002 . 108 . 10 G H4' H 4.386 0.006 . 109 . 10 G H5' H 4.336 0.006 . 110 . 10 G H5'' H 4.083 0.004 . 111 . 10 G H8 H 7.677 0.003 . 112 . 10 G H1 H 10.881 0.010 . 113 . 10 G H22 H 7.131 0.000 . 114 . 10 G C8 C 136.6 0.020 . 115 . 10 G N1 N 145.8 0.020 . 116 . 11 C H1' H 5.279 0.004 . 117 . 11 C H2' H 3.900 0.003 . 118 . 11 C H3' H 4.214 0.007 . 119 . 11 C H4' H 3.875 0.012 . 120 . 11 C H5 H 5.493 0.003 . 121 . 11 C H5' H 4.067 0.013 . 122 . 11 C H5'' H 3.856 0.017 . 123 . 11 C H6 H 7.462 0.006 . 124 . 11 C C6 C 141.8 0.020 . 125 . 11 C C5 C 97.4 0.020 . 126 . 12 A H1' H 5.952 0.002 . 127 . 12 A H2 H 8.042 0.000 . 128 . 12 A H2' H 4.698 0.007 . 129 . 12 A H3' H 4.713 0.002 . 130 . 12 A H4' H 4.403 0.005 . 131 . 12 A H5' H 4.078 0.003 . 132 . 12 A H5'' H 3.961 0.009 . 133 . 12 A H8 H 8.217 0.004 . 134 . 12 A C8 C 141.4 0.020 . 135 . 12 A C2 C 156.6 0.020 . 136 . 13 U H1' H 5.904 0.003 . 137 . 13 U H2' H 4.423 0.008 . 138 . 13 U H3' H 4.706 0.003 . 139 . 13 U H4' H 4.458 0.001 . 140 . 13 U H5 H 5.843 0.003 . 141 . 13 U H5' H 4.221 0.004 . 142 . 13 U H5'' H 4.181 0.001 . 143 . 13 U H6 H 7.782 0.004 . 144 . 13 U C6 C 143.3 0.020 . 145 . 13 U C5 C 104.7 0.020 . 146 . 14 A H1' H 5.951 0.001 . 147 . 14 A H2 H 8.112 0.001 . 148 . 14 A H2' H 4.851 0.001 . 149 . 14 A H3' H 4.597 0.005 . 150 . 14 A H4' H 4.621 0.014 . 151 . 14 A H5' H 4.360 0.004 . 152 . 14 A H5'' H 4.237 0.005 . 153 . 14 A H8 H 8.042 0.006 . 154 . 14 A C8 C 139.6 0.020 . 155 . 14 A C2 C 154.8 0.020 . 156 . 15 A H2 H 7.595 0.001 . 157 . 15 A H2' H 4.671 0.000 . 158 . 15 A H3' H 4.481 0.007 . 159 . 15 A H4' H 4.471 0.006 . 160 . 15 A H5' H 4.371 0.006 . 161 . 15 A H5'' H 4.300 0.003 . 162 . 15 A H8 H 8.042 0.005 . 163 . 15 A H62 H 6.633 0.009 . 164 . 15 A C8 C 141.3 0.020 . 165 . 15 A C2 C 153 0.020 . 166 . 16 G H1' H 5.583 0.006 . 167 . 16 G H2' H 4.498 0.006 . 168 . 16 G H3' H 4.506 0.004 . 169 . 16 G H4' H 4.402 0.023 . 170 . 16 G H5' H 4.366 0.009 . 171 . 16 G H5'' H 4.057 0.004 . 172 . 16 G H8 H 7.089 0.003 . 173 . 16 G H1 H 12.746 0.008 . 174 . 16 G H22 H 6.094 0.000 . 175 . 16 G C8 C 135.4 0.020 . 176 . 16 G N1 N 146.7 0.020 . 177 . 17 G H1' H 5.716 0.005 . 178 . 17 G H2' H 4.457 0.001 . 179 . 17 G H3' H 4.505 0.005 . 180 . 17 G H4' H 4.408 0.003 . 181 . 17 G H5' H 4.470 0.001 . 182 . 17 G H5'' H 4.050 0.002 . 183 . 17 G H8 H 7.211 0.004 . 184 . 17 G H1 H 12.665 0.005 . 185 . 17 G C8 C 135.8 0.020 . 186 . 17 G N1 N 147.7 0.020 . 187 . 18 A H1' H 5.922 0.004 . 188 . 18 A H2 H 7.776 0.000 . 189 . 18 A H2' H 4.457 0.011 . 190 . 18 A H3' H 4.350 0.007 . 191 . 18 A H4' H 4.462 0.001 . 192 . 18 A H5' H 4.395 0.007 . 193 . 18 A H5'' H 4.029 0.014 . 194 . 18 A H8 H 7.706 0.007 . 195 . 18 A C8 C 139.3 0.020 . 196 . 18 A C2 C 153.7 0.020 . 197 . 19 U H1' H 5.300 0.003 . 198 . 19 U H2' H 4.094 0.007 . 199 . 19 U H3' H 4.363 0.002 . 200 . 19 U H4' H 4.300 0.009 . 201 . 19 U H5 H 5.190 0.004 . 202 . 19 U H5' H 4.322 0.006 . 203 . 19 U H5'' H 4.026 0.001 . 204 . 19 U H6 H 7.281 0.002 . 205 . 19 U C6 C 140.7 0.020 . 206 . 19 U C5 C 103.2 0.020 . 207 . 20 G H1' H 5.738 0.003 . 208 . 20 G H2' H 4.745 0.002 . 209 . 20 G H3' H 4.610 0.007 . 210 . 20 G H4' H 4.467 0.000 . 211 . 20 G H5' H 4.322 0.006 . 212 . 20 G H5'' H 4.114 0.019 . 213 . 20 G H8 H 7.678 0.014 . 214 . 20 G H1 H 12.492 0.006 . 215 . 20 G H21 H 7.920 0.000 . 216 . 20 G H22 H 5.937 0.002 . 217 . 20 G C8 C 136.7 0.020 . 218 . 20 G N1 N 147 0.020 . 219 . 21 A H1' H 5.940 0.003 . 220 . 21 A H2 H 7.190 0.001 . 221 . 21 A H2' H 4.642 0.001 . 222 . 21 A H3' H 4.596 0.013 . 223 . 21 A H4' H 5.288 0.003 . 224 . 21 A H5' H 4.479 0.007 . 225 . 21 A H5'' H 4.315 0.004 . 226 . 21 A H8 H 7.889 0.006 . 227 . 21 A H61 H 8.069 0.007 . 228 . 21 A H62 H 6.581 0.003 . 229 . 21 A C8 C 141.4 0.020 . 230 . 21 A C2 C 152.5 0.020 . 231 . 22 A H1' H 5.946 0.002 . 232 . 22 A H2 H 7.796 0.002 . 233 . 22 A H2' H 4.506 0.002 . 234 . 22 A H3' H 4.603 0.001 . 235 . 22 A H4' H 4.600 0.000 . 236 . 22 A H5' H 4.601 0.013 . 237 . 22 A H5'' H 4.136 0.006 . 238 . 22 A H8 H 7.845 0.005 . 239 . 22 A H61 H 8.306 0.010 . 240 . 22 A H62 H 6.734 0.006 . 241 . 22 A C8 C 140 0.020 . 242 . 22 A C2 C 153.6 0.020 . 243 . 23 C H1' H 5.392 0.004 . 244 . 23 C H2' H 4.111 0.000 . 245 . 23 C H3' H 4.356 0.009 . 246 . 23 C H4' H 4.482 0.003 . 247 . 23 C H5 H 5.178 0.004 . 248 . 23 C H5' H 4.044 0.013 . 249 . 23 C H5'' H 4.013 0.010 . 250 . 23 C H6 H 7.447 0.003 . 251 . 23 C H41 H 8.388 0.000 . 252 . 23 C H42 H 7.050 0.002 . 253 . 23 C C6 C 140.2 0.020 . 254 . 23 C C5 C 96.6 0.020 . 255 . 23 C N4 N 98.9 0.020 . 256 . 24 C H1' H 5.777 0.004 . 257 . 24 C H2' H 3.999 0.002 . 258 . 24 C H3' H 4.161 0.000 . 259 . 24 C H4' H 4.141 0.000 . 260 . 24 C H5 H 5.453 0.006 . 261 . 24 C H5' H 4.448 0.004 . 262 . 24 C H5'' H 4.008 0.008 . 263 . 24 C H6 H 7.637 0.004 . 264 . 24 C C6 C 141.5 0.020 . 265 . 24 C C5 C 97.6 0.020 . 266 . 24 C N4 N 98.3 0.020 . stop_ save_