data_25415 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structural features of a 3' splice site influenza A: 19-nt duplex ; _BMRB_accession_number 25415 _BMRB_flat_file_name bmr25415.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" 140 "31P chemical shifts" 14 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' 25416 "3' splice site in influenza A: 39-nt hairpin" 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 "3' splice site influenza A: 19-nt duplex" _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_(19-MER) _Molecular_mass 6171.794 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 19 _Mol_residue_sequence ; GCAGGCCCAUGGGAGUGCA ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 7 G 2 8 C 3 9 A 4 10 G 5 11 G 6 12 C 7 13 C 8 14 C 9 15 A 10 16 U 11 17 G 12 18 G 13 19 G 14 20 A 15 21 G 16 22 U 17 23 G 18 24 C 19 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 . . . . . . 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 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '19-nt duplex' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity 4.0 mM 'natural abundance' H2O 95 % 'natural abundance' D2O 5 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '19-nt duplex' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity 1.0 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_AMBER _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_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_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 500 _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_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_TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _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-31P_HETCOR_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-31P HETCOR' _Sample_label $sample_2 save_ save_2D_1H-1H_TOCSY_7 _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 . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 101.12 . mM pH 6.0 . pH pressure 1 . atm temperature 298.15 . 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' 101.12 . mM pH 6.0 . pH pressure 1 . atm temperature 273.15 . K stop_ save_ save_sample_conditions_3 _Saveframe_category sample_conditions _Details . 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 DSS P 31 'methyl protons' ppm 0.00 na indirect . . . 0.404808636 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 $sample_2 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 7 1 G H1 H 12.666 0.01 1 2 7 1 G H1' H 5.870 0.005 1 3 7 1 G H2' H 4.785 0.005 1 4 7 1 G H3' H 4.555 0.005 1 5 7 1 G H4' H 4.437 0.005 1 6 7 1 G H5' H 4.128 0.005 4 7 7 1 G H5'' H 3.949 0.005 4 8 7 1 G H8 H 8.127 0.005 1 9 8 2 C H1' H 5.504 0.005 1 10 8 2 C H2' H 4.316 0.005 1 11 8 2 C H3' H 4.605 0.005 1 12 8 2 C H4' H 4.461 0.01 1 13 8 2 C H5 H 5.273 0.01 1 14 8 2 C H5'' H 4.169 0.005 4 15 8 2 C H6 H 7.835 0.005 1 16 8 2 C H41 H 8.543 0.005 1 17 8 2 C H42 H 6.823 0.005 1 18 8 2 C P P -4.339 0.01 1 19 9 3 A H1' H 5.878 0.005 1 20 9 3 A H2 H 7.198 0.005 1 21 9 3 A H2' H 4.491 0.005 1 22 9 3 A H3' H 4.852 0.005 1 23 9 3 A H4' H 4.391 0.005 1 24 9 3 A H5'' H 4.185 0.005 4 25 9 3 A H8 H 8.045 0.005 1 26 9 3 A P P -4.021 0.01 1 27 10 4 G H1' H 6.038 0.005 1 28 10 4 G H2' H 4.500 0.005 1 29 10 4 G H3' H 4.716 0.005 1 30 10 4 G H4' H 4.491 0.005 1 31 10 4 G H8 H 7.679 0.005 1 32 11 5 G H1 H 13.077 0.01 1 33 11 5 G H1' H 5.567 0.005 1 34 11 5 G H2' H 4.583 0.01 1 35 11 5 G H3' H 4.353 0.005 1 36 11 5 G H8 H 7.369 0.005 1 37 11 5 G H22 H 5.906 0.005 1 38 11 5 G P P -3.930 0.01 1 39 12 6 C H1' H 5.523 0.005 1 40 12 6 C H2' H 4.239 0.005 1 41 12 6 C H3' H 4.451 0.005 1 42 12 6 C H5 H 5.208 0.01 1 43 12 6 C H5'' H 4.103 0.01 4 44 12 6 C H6 H 7.512 0.005 1 45 12 6 C H41 H 8.474 0.005 1 46 12 6 C H42 H 7.058 0.005 1 47 12 6 C P P -4.489 0.01 1 48 13 7 C H1' H 5.367 0.005 1 49 13 7 C H2' H 4.290 0.005 1 50 13 7 C H3' H 4.485 0.005 1 51 13 7 C H4' H 4.363 0.01 1 52 13 7 C H5 H 5.423 0.01 1 53 13 7 C H5'' H 4.047 0.005 4 54 13 7 C H6 H 7.837 0.005 1 55 13 7 C H41 H 8.419 0.005 1 56 13 7 C H42 H 6.961 0.005 1 57 13 7 C P P -4.536 0.01 1 58 14 8 C H1' H 5.408 0.005 1 59 14 8 C H2' H 4.315 0.005 1 60 14 8 C H3' H 4.474 0.005 1 61 14 8 C H4' H 4.344 0.01 1 62 14 8 C H5 H 5.425 0.01 1 63 14 8 C H5'' H 4.050 0.005 4 64 14 8 C H6 H 7.640 0.005 1 65 14 8 C H41 H 8.249 0.005 1 66 14 8 C H42 H 6.970 0.005 1 67 14 8 C P P -4.074 0.01 1 68 15 9 A H1' H 5.982 0.005 1 69 15 9 A H2 H 7.459 0.005 1 70 15 9 A H2' H 4.080 0.005 1 71 15 9 A H3' H 4.313 0.005 1 72 15 9 A H4' H 4.239 0.005 1 73 15 9 A H5'' H 4.083 0.005 4 74 15 9 A H8 H 8.026 0.005 1 75 15 9 A P P -3.939 0.01 1 76 27 10 U H1' H 5.770 0.005 1 77 27 10 U H2' H 4.619 0.005 1 78 27 10 U H3' H 4.631 0.005 1 79 27 10 U H4' H 4.371 0.005 1 80 27 10 U H5 H 5.851 0.005 1 81 27 10 U H5' H 4.000 0.005 4 82 27 10 U H5'' H 3.903 0.005 4 83 27 10 U H6 H 8.010 0.005 1 84 28 11 G H1 H 12.157 0.01 1 85 28 11 G H1' H 5.914 0.005 1 86 28 11 G H2' H 4.791 0.005 1 87 28 11 G H3' H 4.685 0.005 1 88 28 11 G H4' H 4.555 0.005 1 89 28 11 G H8 H 8.017 0.005 1 90 28 11 G P P -3.744 0.01 1 91 29 12 G H1 H 12.811 0.01 1 92 29 12 G H1' H 5.745 0.005 1 93 29 12 G H2' H 4.560 0.005 1 94 29 12 G H3' H 4.504 0.005 1 95 29 12 G H4' H 4.507 0.005 1 96 29 12 G H5' H 4.510 0.005 4 97 29 12 G H5'' H 4.135 0.005 4 98 29 12 G H8 H 7.329 0.005 1 99 29 12 G P P -3.694 0.01 1 100 30 13 G H1 H 12.575 0.01 1 101 30 13 G H1' H 5.660 0.005 1 102 30 13 G H2' H 4.169 0.005 1 103 30 13 G H3' H 4.647 0.005 1 104 30 13 G H4' H 4.420 0.005 1 105 30 13 G H5' H 4.543 0.005 4 106 30 13 G H5'' H 4.094 0.005 4 107 30 13 G H8 H 7.264 0.005 1 108 31 14 A H1' H 6.104 0.005 1 109 31 14 A H2 H 7.948 0.005 1 110 31 14 A H2' H 4.842 0.005 1 111 31 14 A H3' H 4.678 0.005 1 112 31 14 A H4' H 4.480 0.005 1 113 31 14 A H8 H 8.078 0.005 1 114 32 15 G H1' H 5.370 0.005 1 115 32 15 G H2' H 4.358 0.005 1 116 32 15 G H3' H 4.229 0.005 1 117 32 15 G H8 H 7.100 0.005 1 118 32 15 G P P -4.000 0.01 1 119 33 16 U H1' H 5.518 0.005 1 120 33 16 U H2' H 4.600 0.005 1 121 33 16 U H3 H 13.314 0.01 1 122 33 16 U H3' H 4.533 0.005 1 123 33 16 U H4' H 4.422 0.005 1 124 33 16 U H5 H 5.040 0.005 1 125 33 16 U H5'' H 4.090 0.005 4 126 33 16 U H6 H 7.732 0.005 1 127 33 16 U P P -4.850 0.01 1 128 34 17 G H1 H 12.906 0.01 1 129 34 17 G H1' H 5.745 0.005 1 130 34 17 G H2' H 4.415 0.005 1 131 34 17 G H3' H 4.558 0.005 1 132 34 17 G H4' H 4.435 0.005 1 133 34 17 G H5'' H 4.110 0.005 4 134 34 17 G H8 H 7.693 0.005 1 135 34 17 G P P -4.047 0.01 1 136 35 18 C H1' H 5.357 0.005 1 137 35 18 C H2' H 4.303 0.005 1 138 35 18 C H3' H 4.370 0.005 1 139 35 18 C H4' H 4.330 0.01 1 140 35 18 C H5 H 5.170 0.01 1 141 35 18 C H5'' H 4.040 0.005 4 142 35 18 C H6 H 7.438 0.005 1 143 35 18 C H41 H 8.066 0.005 1 144 35 18 C H42 H 6.911 0.005 1 145 35 18 C P P -4.233 0.01 1 146 36 19 A H1' H 5.973 0.005 1 147 36 19 A H2 H 7.408 0.005 1 148 36 19 A H2' H 4.030 0.005 1 149 36 19 A H3' H 4.274 0.005 1 150 36 19 A H4' H 4.213 0.005 1 151 36 19 A H5' H 4.397 0.005 4 152 36 19 A H5'' H 4.033 0.005 4 153 36 19 A H8 H 8.008 0.005 1 154 36 19 A P P -3.845 0.01 1 stop_ save_