data_17601 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of the MLV readthrough pseudoknot ; _BMRB_accession_number 17601 _BMRB_flat_file_name bmr17601.str _Entry_type original _Submission_date 2011-04-26 _Accession_date 2011-04-26 _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 Houck-Loomis Brian . . 2 Durney Michael A. . 3 D'Souza Victoria M. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 182 "13C chemical shifts" 92 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-03-08 update BMRB 'update entry citation' 2011-12-02 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'An equilibrium-dependent retroviral mRNA switch regulates translational recoding.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 22121021 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Houck-Loomis Brian . . 2 Durney Michael A. . 3 Salguero Carolina . . 4 Shankar Neelaabh . . 5 Nagle Julia M. . 6 Goff Stephen P. . stop_ _Journal_abbreviation Nature _Journal_name_full Nature _Journal_volume 480 _Journal_issue 7378 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 561 _Page_last 564 _Year 2011 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'MLV readthrough pseudoknot' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label RNA_(59-MER) $RNA_(59-MER) stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_RNA_(59-MER) _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_(59-MER) _Molecular_mass 111.103 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 63 _Mol_residue_sequence ; GGAGGUCAGGGUCAGGAGCC CCCCCCUGAACCCAGGAUAA CCCUCAAAGUCGGGGGGCAA CCC ; loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 A 4 G 5 G 6 U 7 C 8 A 9 G 10 G 11 G 12 U 13 C 14 A 15 G 16 G 17 A 18 G 19 C 20 C 21 C 22 C 23 C 24 C 25 C 26 C 27 U 28 G 29 A 30 A 31 C 32 C 33 C 34 A 35 G 36 G 37 A 38 U 39 A 40 A 41 C 42 C 43 C 44 U 45 C 46 A 47 A 48 A 49 G 50 U 51 C 52 G 53 G 54 G 55 G 56 G 57 G 58 C 59 A 60 A 61 C 62 C 63 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 _ICTVdb_decimal_code _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $RNA_(59-MER) MMLV 00.061.1.02.014.00.001 11801 Viruses . Moloney "murine leukemia virus (MLV)" 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 $RNA_(59-MER) 'recombinant technology' . None: "in vitro transcription" . pUC19 stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_MLV-PK _Saveframe_category sample _Sample_type solution _Details 'pH 7.4' loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $RNA_(59-MER) . mM 0.2 2.0 'natural abundance' D2O 100 % . . 'natural abundance' stop_ save_ save_MLV-PK-AC-13C_15N _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $RNA_(59-MER) . mM 0.2 2.0 '[U-100% 13C; U-100% 15N]' D2O 100 % . . 'natural abundance' stop_ save_ save_MLV-PK-AC-2H _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $RNA_(59-MER) . mM 0.2 2.0 '[U-100% 2H]' D2O 100 % . . 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CYANA _Saveframe_category software _Name CYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 700 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 900 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $MLV-PK save_ save_2D_1H-13C_HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $MLV-PK-AC-13C_15N save_ save_2D_1H-13C_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $MLV-PK-AC-13C_15N save_ save_2D_1H-1H_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $MLV-PK-AC-2H save_ save_2D_1H-1H_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $MLV-PK-AC-13C_15N save_ save_2D_1H-1H_NOESY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $MLV-PK 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' 0.02 . M pH 7.4 . pH pressure 1 . atm temperature 298 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_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 C 13 protons ppm 4.7 internal indirect . . . . water H 1 protons ppm 4.7 internal direct . . . 1 water N 15 protons ppm 4.7 internal indirect . . . . 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_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' stop_ loop_ _Sample_label $MLV-PK stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name RNA_(59-MER) _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 H8 H 8.0540 . 1 2 1 1 G C8 C 117.2960 . 1 3 2 2 G H8 H 7.9600 . 1 4 2 2 G C8 C 115.8820 . 1 5 3 3 A H1' H 6.0142 . 1 6 3 3 A H2 H 7.7280 . 1 7 3 3 A H2' H 4.7864 . 1 8 3 3 A H8 H 8.0139 . 1 9 3 3 A C1' C 127.2370 . 1 10 3 3 A C2 C 130.9750 . 1 11 3 3 A C8 C 117.6520 . 1 12 4 4 G H8 H 7.1229 . 1 13 4 4 G C8 C 113.4130 . 1 14 5 5 G H8 H 7.2680 . 1 15 5 5 G C8 C 114.0730 . 1 16 6 6 U H3 H 13.9750 . 1 17 6 6 U H5 H 5.3520 . 1 18 6 6 U H6 H 7.6560 . 1 19 6 6 U C5 C 101.7330 . 1 20 6 6 U C6 C 100.5490 . 1 21 7 7 C H1' H 5.5584 . 1 22 7 7 C H2' H 4.4320 . 1 23 7 7 C H3' H 4.3784 . 1 24 7 7 C H4' H 4.5554 . 1 25 7 7 C H5 H 5.8348 . 1 26 7 7 C H6 H 7.7770 . 1 27 7 7 C C1' C 100.3130 . 1 28 8 8 A H1' H 5.9874 . 1 29 8 8 A H2' H 4.5800 . 1 30 8 8 A H3' H 4.5041 . 1 31 8 8 A H4' H 4.1998 . 1 32 8 8 A H8 H 8.1581 . 1 33 8 8 A C1' C 108.8990 . 1 34 8 8 A C2 C 132.3860 . 1 35 8 8 A C8 C 117.8450 . 1 36 9 9 G H1 H 12.5760 . 1 37 9 9 G H8 H 7.2659 . 1 38 9 9 G C8 C 114.0940 . 1 39 10 10 G H1 H 12.8610 . 1 40 10 10 G H8 H 7.2390 . 1 41 10 10 G C8 C 113.2550 . 1 42 11 11 G H1 H 12.9720 . 1 43 11 11 G H8 H 6.9780 . 1 44 11 11 G C8 C 112.8530 . 1 45 12 12 U H3 H 13.7440 . 1 46 12 12 U H5 H 4.9750 . 1 47 12 12 U H6 H 7.4790 . 1 48 12 12 U C5 C 100.3760 . 1 49 12 12 U C6 C 100.3020 . 1 50 13 13 C H1' H 5.4177 . 1 51 13 13 C H5 H 5.6563 . 1 52 13 13 C H6 H 8.0111 . 1 53 14 14 A H1' H 5.6915 . 1 54 14 14 A H2 H 7.0770 . 1 55 14 14 A H8 H 7.9551 . 1 56 14 14 A C1' C 130.3850 . 1 57 14 14 A C2 C 109.7070 . 1 58 14 14 A C8 C 136.9100 . 1 59 15 15 G H1 H 13.0660 . 1 60 15 15 G H8 H 7.1527 . 1 61 15 15 G C8 C 113.4630 . 1 62 16 16 G H1 H 12.4880 . 1 63 16 16 G H8 H 7.3260 . 1 64 16 16 G C8 C 114.1280 . 1 65 17 17 A H1' H 6.1874 . 1 66 17 17 A H2 H 8.2570 . 1 67 17 17 A H2' H 5.0209 . 1 68 17 17 A H3' H 4.9283 . 1 69 17 17 A H4' H 4.5415 . 1 70 17 17 A H5' H 4.1239 . 2 71 17 17 A H8 H 8.4726 . 1 72 17 17 A C1' C 106.0130 . 1 73 17 17 A C2 C 112.8930 . 1 74 17 17 A C8 C 119.8730 . 1 75 18 18 G H8 H 8.0790 . 1 76 18 18 G C8 C 116.3050 . 1 77 19 19 C H1' H 5.5221 . 1 78 19 19 C H2' H 4.2472 . 1 79 19 19 C H5 H 5.1741 . 1 80 19 19 C H6 H 7.9754 . 1 81 20 20 C H1' H 5.4863 . 1 82 20 20 C H2' H 4.2001 . 1 83 20 20 C H5 H 5.3105 . 1 84 20 20 C H6 H 7.8328 . 1 85 21 21 C H1' H 5.9298 . 1 86 21 21 C H2' H 4.1992 . 1 87 21 21 C H5 H 5.3172 . 1 88 21 21 C H6 H 7.3136 . 1 89 22 22 C H1' H 5.4089 . 1 90 22 22 C H5 H 5.3449 . 1 91 22 22 C H6 H 7.7379 . 1 92 23 23 C H1' H 5.3847 . 1 93 23 23 C H5 H 5.3522 . 1 94 23 23 C H6 H 7.6505 . 1 95 24 24 C H1' H 5.3166 . 1 96 24 24 C H2' H 4.5188 . 1 97 24 24 C H5 H 5.4596 . 1 98 24 24 C H6 H 7.4835 . 1 99 24 24 C C6 C 117.9620 . 1 100 25 25 C H1' H 5.3852 . 1 101 25 25 C H5 H 5.5246 . 1 102 25 25 C H6 H 7.7828 . 1 103 25 25 C C5 C 115.3480 . 1 104 26 26 C H1' H 5.2834 . 1 105 26 26 C H2' H 4.3641 . 1 106 26 26 C H5 H 5.4945 . 1 107 26 26 C H6 H 7.7956 . 1 108 26 26 C C5 C 115.2920 . 1 109 27 27 U H3 H 13.6880 . 1 110 27 27 U H5 H 5.4660 . 1 111 27 27 U H6 H 7.8360 . 1 112 27 27 U C5 C 102.2440 . 1 113 27 27 U C6 C 100.5970 . 1 114 28 28 G H1 H 11.9480 . 1 115 28 28 G H8 H 7.7550 . 1 116 28 28 G C8 C 115.2440 . 1 117 29 29 A H1' H 6.0352 . 1 118 29 29 A H2 H 8.0870 . 1 119 29 29 A H2' H 4.9842 . 1 120 29 29 A H3' H 4.9061 . 1 121 29 29 A H8 H 8.1020 . 1 122 29 29 A C1' C 107.9350 . 1 123 29 29 A C2 C 132.7150 . 1 124 29 29 A C8 C 118.9130 . 1 125 30 30 A H1' H 6.0194 . 1 126 30 30 A H2 H 7.8316 . 1 127 30 30 A H8 H 8.3929 . 1 128 30 30 A C1' C 109.8800 . 1 129 30 30 A C2 C 111.8550 . 1 130 30 30 A C8 C 118.6910 . 1 131 31 31 C H1' H 5.4123 . 1 132 31 31 C H5 H 5.1383 . 1 133 31 31 C H6 H 7.5279 . 1 134 31 31 C C5 C 114.6490 . 1 135 31 31 C C6 C 118.7770 . 1 136 32 32 C H1' H 5.4170 . 1 137 32 32 C H5 H 5.3108 . 1 138 32 32 C H6 H 7.6732 . 1 139 33 33 C H1' H 5.3516 . 1 140 33 33 C H2' H 4.2867 . 1 141 33 33 C H5 H 5.3374 . 1 142 33 33 C H6 H 7.5817 . 1 143 34 34 A H1' H 5.4166 . 1 144 34 34 A H2 H 7.5300 . 1 145 34 34 A H8 H 8.0164 . 1 146 34 34 A C1' C 129.4480 . 1 147 34 34 A C2 C 112.0960 . 1 148 34 34 A C8 C 116.9510 . 1 149 35 35 G H8 H 7.0560 . 1 150 35 35 G C8 C 113.3720 . 1 151 36 36 G H8 H 7.1840 . 1 152 36 36 G C8 C 113.0680 . 1 153 37 37 A H1' H 5.7214 . 1 154 37 37 A H2 H 7.8370 . 1 155 37 37 A H8 H 7.8378 . 1 156 37 37 A C2 C 111.8040 . 1 157 37 37 A C8 C 117.8380 . 1 158 38 38 U H5 H 5.3270 . 1 159 38 38 U H6 H 7.3660 . 1 160 38 38 U C5 C 102.0450 . 1 161 38 38 U C6 C 100.1400 . 1 162 39 39 A H1' H 5.6038 . 1 163 39 39 A H2 H 7.9630 . 1 164 39 39 A H2' H 4.5155 . 1 165 39 39 A H8 H 8.0301 . 1 166 39 39 A C1' C 107.6070 . 1 167 39 39 A C2 C 132.3200 . 1 168 39 39 A C8 C 119.1370 . 1 169 40 40 A H1' H 5.8399 . 1 170 40 40 A H2 H 7.9620 . 1 171 40 40 A H8 H 8.1400 . 1 172 40 40 A C1' C 107.9150 . 1 173 40 40 A C2 C 132.5870 . 1 174 40 40 A C8 C 118.6310 . 1 175 41 41 C H5 H 5.6908 . 1 176 41 41 C H6 H 7.6491 . 1 177 41 41 C C5 C 116.3140 . 1 178 42 42 C H1' H 5.9270 . 1 179 42 42 C H5 H 5.6432 . 1 180 42 42 C H6 H 7.8799 . 1 181 42 42 C C1' C 109.0250 . 1 182 42 42 C C5 C 116.3990 . 1 183 43 43 C H1' H 5.7635 . 1 184 43 43 C H5 H 5.6306 . 1 185 43 43 C H6 H 7.8127 . 1 186 44 44 U H5 H 5.5000 . 1 187 44 44 U C5 C 102.2670 . 1 188 45 45 C H1' H 5.7617 . 1 189 45 45 C H2' H 4.0981 . 1 190 45 45 C H5 H 5.6905 . 1 191 45 45 C H6 H 7.7253 . 1 192 45 45 C C5 C 115.9170 . 1 193 46 46 A H1' H 5.8222 . 1 194 46 46 A H2 H 7.8020 . 1 195 46 46 A H8 H 8.1776 . 1 196 46 46 A C1' C 107.9860 . 1 197 46 46 A C2 C 112.3290 . 1 198 46 46 A C8 C 119.0160 . 1 199 47 47 A H1' H 5.7336 . 1 200 47 47 A H2 H 7.8940 . 1 201 47 47 A H8 H 8.0992 . 1 202 47 47 A C1' C 108.4590 . 1 203 47 47 A C2 C 112.2770 . 1 204 47 47 A C8 C 118.6720 . 1 205 48 48 A H1' H 5.7461 . 1 206 48 48 A H2 H 8.0300 . 1 207 48 48 A H8 H 8.0151 . 1 208 48 48 A C1' C 128.4270 . 1 209 48 48 A C2 C 112.5510 . 1 210 48 48 A C8 C 118.2590 . 1 211 49 49 G H8 H 7.7970 . 1 212 49 49 G C8 C 116.6120 . 1 213 50 50 U H5 H 5.6690 . 1 214 50 50 U H6 H 7.7100 . 1 215 50 50 U C5 C 102.3730 . 1 216 50 50 U C6 C 100.5210 . 1 217 51 51 C H1' H 5.8284 . 1 218 51 51 C H2' H 4.2836 . 1 219 51 51 C H3' H 4.4092 . 1 220 51 51 C H5 H 5.8530 . 1 221 51 51 C H6 H 7.7229 . 1 222 51 51 C C5 C 115.0780 . 1 223 52 52 G H1 H 11.7710 . 1 224 52 52 G H8 H 7.7440 . 1 225 52 52 G C8 C 115.7450 . 1 226 53 53 G H1 H 12.3920 . 1 227 53 53 G H8 H 7.5220 . 1 228 53 53 G C8 C 114.4150 . 1 229 54 54 G H1 H 13.0540 . 1 230 54 54 G H8 H 7.2390 . 1 231 54 54 G C8 C 114.0300 . 1 232 55 55 G H1 H 12.2880 . 1 233 55 55 G H8 H 7.1450 . 1 234 55 55 G C8 C 113.0600 . 1 235 56 56 G H1 H 12.4460 . 1 236 56 56 G H8 H 7.0080 . 1 237 56 56 G C8 C 112.8500 . 1 238 57 57 G H1 H 12.8580 . 1 239 57 57 G H8 H 6.9550 . 1 240 57 57 G C8 C 112.8480 . 1 241 58 58 C H1' H 5.3558 . 1 242 58 58 C H2' H 4.6020 . 1 243 58 58 C H5 H 5.1289 . 1 244 58 58 C H6 H 7.0820 . 1 245 58 58 C C6 C 117.6040 . 1 246 59 59 A H1' H 5.8210 . 1 247 59 59 A H2 H 7.1480 . 1 248 59 59 A H8 H 7.8406 . 1 249 59 59 A C1' C 110.7400 . 1 250 59 59 A C2 C 110.9520 . 1 251 59 59 A C8 C 117.0590 . 1 252 60 60 A H1' H 5.3783 . 1 253 60 60 A H2 H 7.9054 . 1 254 60 60 A H2' H 4.3098 . 1 255 60 60 A H8 H 7.6440 . 1 256 60 60 A C1' C 109.8590 . 1 257 60 60 A C2 C 112.4390 . 1 258 60 60 A C8 C 116.3600 . 1 259 61 61 C H1' H 5.1863 . 1 260 61 61 C H2' H 4.0636 . 1 261 61 61 C H5 H 5.1428 . 1 262 61 61 C H6 H 7.1889 . 1 263 61 61 C C1' C 110.8090 . 1 264 61 61 C C5 C 114.7060 . 1 265 62 62 C H1' H 5.5783 . 1 266 62 62 C H2' H 4.1418 . 1 267 62 62 C H5 H 5.6370 . 1 268 62 62 C H6 H 7.6443 . 1 269 62 62 C C1' C 118.9520 . 1 270 62 62 C C5 C 116.0650 . 1 271 63 63 C H1' H 5.7790 . 1 272 63 63 C H5 H 5.8354 . 1 273 63 63 C H6 H 7.7884 . 1 274 63 63 C C5 C 116.3750 . 1 stop_ save_