data_5528 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of the complementary RNA promoter of influenza a virus ; _BMRB_accession_number 5528 _BMRB_flat_file_name bmr5528.str _Entry_type original _Submission_date 2002-09-13 _Accession_date 2002-09-13 _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 Park C.-J. . . 2 Bae S.-H. . . 3 Varani G. . . 4 Lee M.-K. . . 5 Choi B.-S. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 219 "31P chemical shifts" 13 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2003-07-07 original author . stop_ _Original_release_date 2003-07-07 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Solution Structure of the Influenza A Virus cRNA Promoter: Implications for Differential Recognition of Viral Promoter Structures by RNA-dependent RNA Polymerase ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 22656697 _PubMed_ID 12771209 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Park C.-J. . . 2 Bae S.-H. . . 3 Lee M.-K. . . 4 Varani G. . . 5 Choi B.-S. . . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_volume 31 _Journal_issue 11 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 2824 _Page_last 2832 _Year 2003 _Details . loop_ _Keyword 'A-form helix' 'asymmetric internal loop' stop_ save_ ################################## # Molecular system description # ################################## save_system_cRNA_promoter _Saveframe_category molecular_system _Mol_system_name 'RNA (25-MER):the complementary RNA promoter of influenza a virus' _Abbreviation_common 'cRNA promoter of influenza virus' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'complementary RNA promoter' $cRNA_promoter stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_cRNA_promoter _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common 'complementary RNA promoter of influenza virus' _Abbreviation_common 'cRNA promoter' _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 25 _Mol_residue_sequence ; GGAAGCAGGCUUCGGCCUUG UUUCC ; loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 A 4 A 5 G 6 C 7 A 8 G 9 G 10 C 11 U 12 U 13 C 14 G 15 G 16 C 17 C 18 U 19 U 20 G 21 U 22 U 23 U 24 C 25 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 $cRNA_promoter 'influenza A virus' 11320 . . 'influenzavirus A' . 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 $cRNA_promoter 'enzymatic semisynthesis' . . . . . 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 _Isotopic_labeling $cRNA_promoter 1 mM . 'phosphate buffer' 20 mM . EDTA 0.1 mM . H2O 90 % . D2O 10 % . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $cRNA_promoter 1 mM '[U-15N; U-13C]' 'phosphate buffer' 20 mM . EDTA 0.1 mM . D2O 100 % . stop_ save_ ############################ # Computer software used # ############################ save_FELIX _Saveframe_category software _Name FELIX _Version 95 loop_ _Task processing stop_ _Details 'Biosym, inc.' save_ save_VNMR _Saveframe_category software _Name VNMR _Version 6.1c loop_ _Task collection stop_ _Details 'Varian, inc.' save_ save_CNS _Saveframe_category software _Name CNS _Version 1.0 loop_ _Task refinement 'structure solution' stop_ _Details Brunger save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label . save_ save_2D_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label . save_ save_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label . save_ save_HETCOR_4 _Saveframe_category NMR_applied_experiment _Experiment_name HETCOR _Sample_label . save_ save_3D_13C_NOESY-HSQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 13C NOESY-HSQC' _Sample_label . save_ save_3D_HCCH-COSY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HCCH-COSY' _Sample_label . save_ save_3D_HCCH-COSY-TOCSY_7 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HCCH-COSY-TOCSY' _Sample_label . save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_4 _Saveframe_category NMR_applied_experiment _Experiment_name HETCOR _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_5 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 13C NOESY-HSQC' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_6 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HCCH-COSY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_7 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HCCH-COSY-TOCSY' _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 20 . mM pH 6.0 0.1 n/a pressure 1 . atm temperature 300 1 K stop_ save_ save_sample_cond_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 20 . mM pH 6.0 0.1 n/a pressure 1 . atm temperature 280 1 K stop_ save_ save_sample_cond_3 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 20 . mM pH 6.0 0.1 n/a pressure 1 . atm temperature 290 1 K stop_ save_ save_sample_cond_4 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 20 . mM pH 6.0 0.1 n/a pressure 1 . atm temperature 310 1 K 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 DSS H 1 'methyl protons' ppm 0.0 internal direct . . . 1.0 DSS P 31 'methyl protons' ppm 0.0 . 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_chemical_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'complementary RNA promoter' _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 H8 H 8.13 . 1 2 . 1 G H1' H 5.82 . 1 3 . 1 G H2' H 4.92 . 1 4 . 1 G H3' H 4.68 . 1 5 . 1 G H4' H 4.54 . 1 6 . 1 G H5' H 4.45 . 1 7 . 1 G H5'' H 4.27 . 1 8 . 2 G H1 H 12.42 . 1 9 . 2 G H21 H 8.02 . 1 10 . 2 G H22 H 5.93 . 1 11 . 2 G H8 H 7.49 . 1 12 . 2 G H1' H 5.89 . 1 13 . 2 G H2' H 4.65 . 1 14 . 2 G H3' H 4.58 . 1 15 . 2 G H4' H 4.43 . 1 16 . 2 G H5'' H 4.22 . 1 17 . 3 A H2 H 7.15 . 1 18 . 3 A H61 H 7.92 . 1 19 . 3 A H62 H 6.72 . 1 20 . 3 A H8 H 7.73 . 1 21 . 3 A H1' H 5.93 . 1 22 . 3 A H2' H 4.56 . 1 23 . 3 A H3' H 4.68 . 1 24 . 3 A H4' H 4.51 . 1 25 . 3 A H5'' H 4.15 . 1 26 . 4 A H2 H 7.41 . 1 27 . 4 A H61 H 8.03 . 1 28 . 4 A H62 H 6.71 . 1 29 . 4 A H8 H 7.69 . 1 30 . 4 A H1' H 5.94 . 1 31 . 4 A H2' H 4.56 . 1 32 . 4 A H4' H 4.47 . 1 33 . 4 A H5'' H 4.11 . 1 34 . 5 G H1 H 11.60 . 1 35 . 5 G H21 H 6.43 . 1 36 . 5 G H22 H 6.43 . 1 37 . 5 G H8 H 6.89 . 1 38 . 5 G H1' H 5.49 . 1 39 . 5 G H2' H 4.55 . 1 40 . 5 G H3' H 4.08 . 1 41 . 5 G H4' H 4.45 . 1 42 . 5 G H5' H 4.30 . 1 43 . 5 G H5'' H 3.96 . 1 44 . 6 C H41 H 8.08 . 1 45 . 6 C H42 H 6.97 . 1 46 . 6 C H5 H 5.18 . 1 47 . 6 C H6 H 7.49 . 1 48 . 6 C H1' H 5.46 . 1 49 . 6 C H2' H 4.50 . 1 50 . 6 C H3' H 4.08 . 1 51 . 6 C H4' H 4.39 . 1 52 . 6 C H5'' H 4.07 . 1 53 . 6 C P P -4.32 . 1 54 . 7 A H2 H 7.06 . 1 55 . 7 A H8 H 7.95 . 1 56 . 7 A H1' H 5.97 . 1 57 . 7 A H2' H 4.68 . 1 58 . 7 A H3' H 4.69 . 1 59 . 7 A H4' H 4.47 . 1 60 . 7 A H5' H 4.54 . 1 61 . 7 A H5'' H 4.14 . 1 62 . 7 A P P -3.76 . 1 63 . 8 G H1 H 12.99 . 1 64 . 8 G H21 H 8.26 . 1 65 . 8 G H22 H 5.98 . 1 66 . 8 G H8 H 7.14 . 1 67 . 8 G H1' H 5.47 . 1 68 . 8 G H2' H 4.41 . 1 69 . 8 G H3' H 4.48 . 1 70 . 8 G H4' H 4.43 . 1 71 . 8 G H5'' H 4.06 . 1 72 . 9 G H1 H 13.49 . 1 73 . 9 G H21 H 8.60 . 1 74 . 9 G H22 H 6.15 . 1 75 . 9 G H8 H 7.30 . 1 76 . 9 G H1' H 5.73 . 1 77 . 9 G H2' H 4.47 . 1 78 . 9 G H3' H 4.49 . 1 79 . 9 G H4' H 4.42 . 1 80 . 9 G H5'' H 4.04 . 1 81 . 10 C H41 H 8.63 . 1 82 . 10 C H42 H 7.03 . 1 83 . 10 C H5 H 5.19 . 1 84 . 10 C H6 H 7.41 . 1 85 . 10 C H1' H 5.51 . 1 86 . 10 C H2' H 4.51 . 1 87 . 10 C H3' H 4.22 . 1 88 . 10 C H4' H 4.41 . 1 89 . 10 C H5'' H 4.01 . 1 90 . 11 U H3 H 11.85 . 1 91 . 11 U H5 H 5.71 . 1 92 . 11 U H6 H 7.77 . 1 93 . 11 U H1' H 5.69 . 1 94 . 11 U H2' H 3.80 . 1 95 . 11 U H3' H 4.51 . 1 96 . 11 U H4' H 4.37 . 1 97 . 11 U H5' H 4.47 . 1 98 . 11 U H5'' H 4.09 . 1 99 . 11 U P P -4.09 . 1 100 . 12 U H3 H 11.27 . 1 101 . 12 U H5 H 5.86 . 1 102 . 12 U H6 H 8.03 . 1 103 . 12 U H1' H 6.10 . 1 104 . 12 U H2' H 4.67 . 1 105 . 12 U H3' H 4.03 . 1 106 . 12 U H4' H 4.49 . 1 107 . 12 U H5' H 4.23 . 1 108 . 12 U H5'' H 4.02 . 1 109 . 12 U P P -3.43 . 1 110 . 13 C H41 H 7.17 . 1 111 . 13 C H42 H 6.43 . 1 112 . 13 C H5 H 6.13 . 1 113 . 13 C H6 H 7.69 . 1 114 . 13 C H1' H 5.96 . 1 115 . 13 C H2' H 4.09 . 1 116 . 13 C H3' H 4.48 . 1 117 . 13 C H4' H 3.79 . 1 118 . 13 C H5' H 3.60 . 1 119 . 13 C H5'' H 2.71 . 1 120 . 13 C P P -4.99 . 1 121 . 14 G H1 H 9.92 . 1 122 . 14 G H8 H 7.85 . 1 123 . 14 G H1' H 5.95 . 1 124 . 14 G H2' H 4.84 . 1 125 . 14 G H3' H 5.61 . 1 126 . 14 G H4' H 4.39 . 1 127 . 14 G H5' H 4.46 . 1 128 . 14 G H5'' H 4.17 . 1 129 . 14 G P P -4.89 . 1 130 . 15 G H1 H 13.58 . 1 131 . 15 G H21 H 8.98 . 1 132 . 15 G H22 H 6.52 . 1 133 . 15 G H8 H 8.29 . 1 134 . 15 G H1' H 4.44 . 1 135 . 15 G H2' H 4.46 . 1 136 . 15 G H3' H 4.25 . 1 137 . 15 G H4' H 4.40 . 1 138 . 15 G H5' H 4.49 . 1 139 . 15 G H5'' H 4.27 . 1 140 . 15 G P P -2.42 . 1 141 . 16 C H41 H 8.79 . 1 142 . 16 C H42 H 7.00 . 1 143 . 16 C H5 H 5.29 . 1 144 . 16 C H6 H 7.68 . 1 145 . 16 C H1' H 5.52 . 1 146 . 16 C H2' H 4.45 . 1 147 . 16 C H3' H 4.40 . 1 148 . 16 C H4' H 4.36 . 1 149 . 16 C H5'' H 4.01 . 1 150 . 16 C P P -4.51 . 1 151 . 17 C H41 H 8.56 . 1 152 . 17 C H42 H 7.00 . 1 153 . 17 C H5 H 5.58 . 1 154 . 17 C H6 H 7.72 . 1 155 . 17 C H1' H 5.64 . 1 156 . 17 C H2' H 4.25 . 1 157 . 17 C H3' H 4.50 . 1 158 . 17 C H4' H 4.40 . 1 159 . 17 C H5'' H 4.08 . 1 160 . 17 C P P -4.03 . 1 161 . 18 U H5 H 5.58 . 1 162 . 18 U H6 H 7.81 . 1 163 . 18 U H1' H 5.95 . 1 164 . 18 U H2' H 4.38 . 1 165 . 18 U H3' H 4.75 . 1 166 . 18 U H4' H 4.46 . 1 167 . 18 U H5' H 4.40 . 1 168 . 18 U H5'' H 4.16 . 1 169 . 19 U H5 H 5.81 . 1 170 . 19 U H6 H 7.88 . 1 171 . 19 U H1' H 5.89 . 1 172 . 19 U H2' H 4.56 . 1 173 . 19 U H3' H 4.71 . 1 174 . 19 U H4' H 4.52 . 1 175 . 19 U H5' H 4.32 . 1 176 . 19 U H5'' H 4.23 . 1 177 . 19 U P P -3.22 . 1 178 . 20 G H1 H 12.62 . 1 179 . 20 G H21 H 8.28 . 1 180 . 20 G H22 H 6.39 . 1 181 . 20 G H8 H 7.87 . 1 182 . 20 G H1' H 5.84 . 1 183 . 20 G H2' H 4.83 . 1 184 . 20 G H3' H 4.35 . 1 185 . 20 G H4' H 4.57 . 1 186 . 20 G H5' H 4.50 . 1 187 . 20 G H5'' H 4.11 . 1 188 . 20 G P P -3.50 . 1 189 . 21 U H3 H 11.84 . 1 190 . 21 U H5 H 5.40 . 1 191 . 21 U H6 H 7.70 . 1 192 . 21 U H1' H 5.55 . 1 193 . 21 U H2' H 4.18 . 1 194 . 21 U H3' H 4.56 . 1 195 . 21 U H4' H 4.45 . 1 196 . 21 U H5' H 4.50 . 1 197 . 21 U H5'' H 4.11 . 1 198 . 21 U P P -4.24 . 1 199 . 22 U H3 H 14.15 . 1 200 . 22 U H5 H 5.60 . 1 201 . 22 U H6 H 8.04 . 1 202 . 22 U H1' H 5.61 . 1 203 . 22 U H2' H 4.49 . 1 204 . 22 U H3' H 4.54 . 1 205 . 22 U H4' H 4.47 . 1 206 . 22 U H5'' H 4.12 . 1 207 . 23 U H3 H 13.83 . 1 208 . 23 U H5 H 5.60 . 1 209 . 23 U H6 H 8.03 . 1 210 . 23 U H1' H 5.63 . 1 211 . 23 U H2' H 4.45 . 1 212 . 23 U H3' H 4.26 . 1 213 . 23 U H5'' H 4.14 . 1 214 . 24 C H41 H 8.38 . 1 215 . 24 C H42 H 7.02 . 1 216 . 24 C H5 H 5.63 . 1 217 . 24 C H6 H 7.90 . 1 218 . 24 C H1' H 5.53 . 1 219 . 24 C H2' H 4.16 . 1 220 . 24 C H3' H 4.47 . 1 221 . 24 C H4' H 4.39 . 1 222 . 24 C H5'' H 4.06 . 1 223 . 25 C H41 H 8.26 . 1 224 . 25 C H42 H 7.00 . 1 225 . 25 C H5 H 5.45 . 1 226 . 25 C H6 H 7.63 . 1 227 . 25 C H1' H 5.69 . 1 228 . 25 C H2' H 3.97 . 1 229 . 25 C H3' H 4.14 . 1 230 . 25 C H4' H 4.14 . 1 231 . 25 C H5'' H 4.01 . 1 232 . 25 C P P -4.12 . 1 stop_ save_