data_25416 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structural features of a 3' splice site in influenza A: 39-nt hairpin ; _BMRB_accession_number 25416 _BMRB_flat_file_name bmr25416.str _Entry_type original _Submission_date 2015-01-06 _Accession_date 2015-01-06 _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 Turner Douglas H. . 2 Kennedy Scott D. . 3 Chen Jonathan L. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 166 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2016-02-18 update BMRB 'update entry citation' 2015-05-04 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 25414 '3 splice site influenza A: 11-nt hairpin' 25415 '3 splice site influenza A: 19-nt duplex' stop_ _Original_release_date 2015-05-04 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structural features of a 3' splice site in influenza A ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 25909229 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Chen Jonathan L. . 2 Kennedy Scott D. . 3 Turner Douglas H. . stop_ _Journal_abbreviation Biochemistry _Journal_volume 54 _Journal_issue 21 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 3269 _Page_last 3285 _Year 2015 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name "RNA (39-MER), 3' splice site in influenza A: 39-nt hairpin" _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity $entity 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_entity _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_(39-MER) _Molecular_mass 12688.705 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 39 _Mol_residue_sequence ; GGAUUUGCAGGCCUACCAGA AACGGAUGGGAGUGCAGAU ; loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 A 4 U 5 U 6 U 7 G 8 C 9 A 10 G 11 G 12 C 13 C 14 U 15 A 16 C 17 C 18 A 19 G 20 A 21 A 22 A 23 C 24 G 25 G 26 A 27 U 28 G 29 G 30 G 31 A 32 G 33 U 34 G 35 C 36 A 37 G 38 A 39 U 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 . . . . . . 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 'cell free synthesis' . . . . pUC18 stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '39-nt hairpin' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity 1.1 mM 'natural abundance' H2O 95 % 'natural abundance' D2O 5 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_AMBER _Saveframe_category software _Name AMBER _Version 11 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' 'peak picking' stop_ _Details . save_ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_VNMR _Saveframe_category software _Name VNMR _Version . loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task collection stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _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_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details '80 mM KCl, 20 mM KH2PO4/K2HPO4 and 0.02 mM Na2EDTA at pH 6.0' loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 101.12 . mM pH 6.0 . pH pressure 1 . atm temperature 293.15 . K stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details '80 mM KCl, 20 mM KH2PO4/K2HPO4 and 0.02 mM Na2EDTA at pH 6.0' loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 101.12 . mM pH 6.0 . pH pressure 1 . atm temperature 271.15 . 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 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 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 $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name entity _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 2 2 G H1' H 5.783 0.005 1 2 2 2 G H2' H 4.760 0.005 1 3 2 2 G H8 H 7.890 0.005 1 4 3 3 A H1' H 5.882 0.005 1 5 3 3 A H2 H 7.880 0.005 1 6 3 3 A H2' H 4.713 0.005 1 7 3 3 A H8 H 8.380 0.005 1 8 4 4 U H1' H 5.544 0.005 1 9 4 4 U H2' H 4.564 0.005 1 10 4 4 U H3 H 14.139 0.01 1 11 4 4 U H5 H 5.140 0.005 1 12 4 4 U H6 H 7.600 0.005 1 13 5 5 U H1' H 5.476 0.005 1 14 5 5 U H3 H 11.925 0.01 1 15 5 5 U H5 H 5.510 0.005 1 16 5 5 U H6 H 7.935 0.005 1 17 6 6 U H1' H 5.465 0.005 1 18 6 6 U H2' H 4.558 0.005 1 19 6 6 U H3 H 13.506 0.01 1 20 6 6 U H5 H 5.529 0.005 1 21 6 6 U H6 H 7.941 0.005 1 22 7 7 G H1 H 12.414 0.01 1 23 7 7 G H1' H 5.681 0.005 1 24 7 7 G H2' H 4.415 0.005 1 25 7 7 G H8 H 7.677 0.005 1 26 8 8 C H1' H 5.320 0.005 1 27 8 8 C H5 H 5.169 0.01 1 28 8 8 C H6 H 7.612 0.01 1 29 8 8 C H41 H 8.283 0.005 1 30 8 8 C H42 H 6.868 0.005 1 31 9 9 A H1' H 5.781 0.005 1 32 9 9 A H2 H 7.056 0.005 1 33 9 9 A H2' H 4.467 0.005 1 34 9 9 A H8 H 7.898 0.005 1 35 10 10 G H1' H 5.883 0.005 1 36 10 10 G H8 H 7.595 0.005 1 37 11 11 G H1 H 13.079 0.01 1 38 11 11 G H1' H 5.514 0.005 1 39 11 11 G H2' H 4.580 0.01 1 40 11 11 G H22 H 5.878 0.005 1 41 12 12 C H1' H 5.522 0.005 1 42 12 12 C H2' H 4.259 0.005 1 43 12 12 C H5 H 5.130 0.01 1 44 12 12 C H6 H 7.500 0.01 1 45 12 12 C H41 H 8.416 0.005 1 46 12 12 C H42 H 6.976 0.005 1 47 13 13 C H1' H 5.352 0.005 1 48 13 13 C H2' H 4.507 0.005 1 49 13 13 C H5 H 5.373 0.01 1 50 13 13 C H6 H 7.673 0.01 1 51 13 13 C H41 H 8.222 0.005 1 52 13 13 C H42 H 6.912 0.005 1 53 14 14 U H1' H 5.516 0.005 1 54 14 14 U H2' H 4.252 0.005 1 55 14 14 U H3 H 11.665 0.01 1 56 14 14 U H5 H 5.736 0.005 1 57 14 14 U H6 H 7.802 0.005 1 58 15 15 A H1' H 5.939 0.005 1 59 15 15 A H2 H 7.417 0.005 1 60 15 15 A H2' H 4.519 0.005 1 61 15 15 A H3' H 4.613 0.005 1 62 15 15 A H8 H 8.250 0.005 1 63 16 16 C H1' H 5.139 0.005 1 64 16 16 C H5 H 5.360 0.01 1 65 16 16 C H6 H 7.421 0.01 1 66 16 16 C H41 H 8.096 0.005 1 67 16 16 C H42 H 6.921 0.005 1 68 17 17 C H1' H 5.302 0.005 1 69 17 17 C H2' H 4.178 0.005 1 70 17 17 C H5 H 5.365 0.01 1 71 17 17 C H6 H 7.596 0.01 1 72 17 17 C H41 H 8.224 0.005 1 73 17 17 C H42 H 6.933 0.005 1 74 18 18 A H1' H 5.822 0.005 1 75 18 18 A H2 H 7.425 0.005 1 76 18 18 A H2' H 4.357 0.005 1 77 18 18 A H3' H 4.690 0.005 1 78 18 18 A H8 H 8.000 0.005 1 79 19 19 G H1 H 10.464 0.01 1 80 19 19 G H1' H 5.449 0.005 1 81 19 19 G H2' H 4.363 0.005 1 82 19 19 G H3' H 4.544 0.005 1 83 19 19 G H8 H 7.340 0.005 1 84 20 20 A H1' H 5.668 0.005 1 85 20 20 A H2 H 7.775 0.005 1 86 20 20 A H2' H 4.617 0.005 1 87 20 20 A H3' H 4.482 0.005 1 88 20 20 A H8 H 8.162 0.005 1 89 21 21 A H1' H 5.573 0.005 1 90 21 21 A H2 H 7.725 0.005 1 91 21 21 A H2' H 4.552 0.005 1 92 21 21 A H8 H 7.959 0.005 1 93 22 22 A H1' H 5.814 0.005 1 94 22 22 A H2' H 4.637 0.005 1 95 22 22 A H8 H 7.981 0.005 1 96 23 23 C H5 H 5.600 0.005 1 97 23 23 C H6 H 7.643 0.005 1 98 24 24 G H1 H 11.919 0.01 1 99 24 24 G H1' H 5.528 0.005 1 100 24 24 G H2' H 4.698 0.005 1 101 24 24 G H8 H 7.596 0.005 1 102 25 25 G H1 H 12.411 0.01 1 103 25 25 G H1' H 5.640 0.005 1 104 25 25 G H2' H 4.391 0.005 1 105 25 25 G H3' H 4.564 0.005 1 106 25 25 G H8 H 7.307 0.005 1 107 26 26 A H1' H 5.924 0.005 1 108 26 26 A H2 H 7.960 0.005 1 109 26 26 A H2' H 4.387 0.005 1 110 26 26 A H8 H 8.036 0.005 1 111 27 27 U H1' H 5.598 0.005 1 112 27 27 U H2' H 4.401 0.005 1 113 27 27 U H3 H 12.235 0.01 1 114 27 27 U H5 H 5.262 0.005 1 115 27 27 U H6 H 7.479 0.005 1 116 28 28 G H1 H 10.296 0.01 1 117 28 28 G H1' H 5.769 0.005 1 118 28 28 G H2' H 4.719 0.005 1 119 28 28 G H8 H 7.700 0.005 1 120 29 29 G H1 H 12.698 0.01 1 121 29 29 G H1' H 5.622 0.005 1 122 29 29 G H2' H 4.511 0.005 1 123 29 29 G H3' H 4.424 0.005 1 124 29 29 G H8 H 7.099 0.005 1 125 30 30 G H1 H 12.490 0.01 1 126 30 30 G H1' H 5.651 0.005 1 127 30 30 G H2' H 4.226 0.005 1 128 30 30 G H3' H 4.562 0.005 1 129 30 30 G H8 H 7.155 0.005 1 130 31 31 A H1' H 6.060 0.005 1 131 31 31 A H2' H 4.858 0.005 1 132 31 31 A H3' H 4.640 0.005 1 133 31 31 A H4' H 4.458 0.005 1 134 31 31 A H8 H 8.027 0.005 1 135 32 32 G H2' H 4.367 0.005 1 136 33 33 U H1' H 5.492 0.005 1 137 33 33 U H2' H 4.600 0.005 1 138 33 33 U H3 H 13.389 0.01 1 139 33 33 U H5 H 4.992 0.005 1 140 33 33 U H6 H 7.682 0.005 1 141 34 34 G H1' H 5.707 0.005 1 142 34 34 G H2' H 4.368 0.005 1 143 34 34 G H8 H 7.684 0.005 1 144 35 35 C H1' H 5.324 0.005 1 145 35 35 C H2' H 4.356 0.005 1 146 35 35 C H5 H 5.191 0.01 1 147 35 35 C H6 H 7.610 0.01 1 148 35 35 C H41 H 8.308 0.005 1 149 35 35 C H42 H 6.857 0.005 1 150 36 36 A H1' H 5.909 0.005 1 151 36 36 A H2 H 6.811 0.005 1 152 36 36 A H2' H 4.588 0.005 1 153 36 36 A H8 H 7.916 0.005 1 154 37 37 G H1 H 10.672 0.01 1 155 37 37 G H1' H 5.478 0.005 1 156 37 37 G H2' H 4.612 0.005 1 157 37 37 G H8 H 6.867 0.005 1 158 38 38 A H1' H 5.894 0.005 1 159 38 38 A H2 H 7.878 0.005 1 160 38 38 A H2' H 4.336 0.005 1 161 38 38 A H8 H 7.706 0.005 1 162 39 39 U H1' H 5.707 0.005 1 163 39 39 U H2' H 4.103 0.005 1 164 39 39 U H3 H 13.665 0.01 1 165 39 39 U H5 H 5.084 0.005 1 166 39 39 U H6 H 7.450 0.005 1 stop_ save_