data_5553 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of influenza A virus C4 promoter ; _BMRB_accession_number 5553 _BMRB_flat_file_name bmr5553.str _Entry_type original _Submission_date 2002-10-10 _Accession_date 2002-10-10 _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 Lee M.-K. . . 2 Bae S.-H. . . 3 Park C.-J. . . 4 Cheong H.-K. . . 5 Cheong C. . . 6 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" 202 "13C chemical shifts" 29 "15N chemical shifts" 11 "31P chemical shifts" 18 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2003-03-14 original author . stop_ _Original_release_date 2003-03-14 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; A Single-nucleotide Natural Variation (U4 to C4) in an Influenza A Virus Promoter Exhibits a Large Structural Change: Implications for Differential Viral RNA Synthesis by RNA-dependent RNA Polymerase ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 22470239 _PubMed_ID 12582241 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Lee M.-K. . . 2 Bae S.-H. . . 3 Park C.-J. . . 4 Cheong H.-K. . . 5 Cheong C. . . 6 Choi B.-S. . . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_volume 31 _Journal_issue 4 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1216 _Page_last 1223 _Year 2003 _Details . loop_ _Keyword C4 'Influenza A virus promoter' 'internal loop' 'natural variant' 'single adenine bulge' stop_ save_ ################################## # Molecular system description # ################################## save_system_C4_promoter _Saveframe_category molecular_system _Mol_system_name 'C4 promoter of influneza A virus' _Abbreviation_common 'C4 promoter of influneza A virus' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'C4 promoter of influneza A virus' $C4_promoter stop_ _System_molecular_weight . _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_C4_promoter _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common 'C4 promoter of influneza A virus' _Abbreviation_common 'C4 promoter of influneza A virus' _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 31 _Mol_residue_sequence ; AGUAGAAACAAGGCUUCGGC CUGCUUUCGCU ; loop_ _Residue_seq_code _Residue_label 1 A 2 G 3 U 4 A 5 G 6 A 7 A 8 A 9 C 10 A 11 A 12 G 13 G 14 C 15 U 16 U 17 C 18 G 19 G 20 C 21 C 22 U 23 G 24 C 25 U 26 U 27 U 28 C 29 G 30 C 31 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 $C4_promoter 'Influenzavirus A' 197911 Viruses . '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 $C4_promoter . . . . . . 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 $C4_promoter 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 $C4_promoter 1 mM . D2O 99.96 % . stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $C4_promoter 1 mM '[U-13C; U-15N]' H2O 90 % . D2O 10 % . stop_ save_ save_sample_4 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $C4_promoter 1 mM '[U-13C; U-15N]' D2O 99.96 % . stop_ save_ ############################ # Computer software used # ############################ save_CNS _Saveframe_category software _Name CNS _Version 1.0 loop_ _Task refinement 'structure solution' stop_ _Details 'Brunger et al' save_ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version 2.1 loop_ _Task processing stop_ _Details 'Delaglio et al' 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_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label . save_ save_3D_HCCH-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HCCH-COSY' _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 DQF-COSY _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HCCH-COSY' _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 pH . . n/a temperature . . . 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_citation_label _Correction_value_citation_label . C 13 . ppm . . . . . . $entry_citation $entry_citation . H 1 . ppm . . . . . . $entry_citation $entry_citation . N 15 . ppm . . . . . . $entry_citation $entry_citation . P 31 . ppm . . . . . . $entry_citation $entry_citation 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_3 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'C4 promoter of influneza A virus' _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 A H1' H 6.048 0.000 . 2 . 1 A H2 H 7.985 0.000 . 3 . 1 A C2 C 139.585 0.000 . 4 . 1 A C8 C 126.620 0.000 . 5 . 1 A H2' H 4.827 0.000 . 6 . 1 A H3' H 4.649 0.002 . 7 . 1 A H4' H 4.703 0.000 . 8 . 1 A H8 H 8.253 0.003 . 9 . 2 G H8 H 7.786 0.001 . 10 . 2 G C8 C 123.446 0.000 . 11 . 2 G H1' H 5.679 0.000 . 12 . 2 G H2' H 4.743 0.000 . 13 . 2 G H4' H 4.462 0.000 . 14 . 3 U H1' H 5.883 0.000 . 15 . 3 U H2' H 4.361 0.001 . 16 . 3 U H3' H 4.644 0.001 . 17 . 3 U H4' H 4.479 0.001 . 18 . 3 U H5 H 5.703 0.002 . 19 . 3 U H6 H 7.725 0.001 . 20 . 3 U C6 C 128.902 0.000 . 21 . 3 U N3 N 160.245 0.000 . 22 . 3 U P P -3.824 0.000 . 23 . 4 A H2 H 8.123 0.000 . 24 . 4 A C2 C 140.468 0.000 . 25 . 4 A P P -3.812 0.156 . 26 . 5 G H1 H 12.052 0.004 . 27 . 5 G H1' H 5.810 0.003 . 28 . 5 G H2' H 4.684 0.001 . 29 . 5 G H4' H 4.616 0.002 . 30 . 5 G H5' H 3.826 0.000 . 31 . 5 G C8 C 127.920 0.000 . 32 . 5 G H5'' H 3.762 0.000 . 33 . 5 G H8 H 8.186 0.000 . 34 . 5 G N1 N 146.537 0.000 . 35 . 6 A H61 H 6.706 0.007 . 36 . 6 A H62 H 7.736 0.003 . 37 . 6 A C2 C 137.906 0.000 . 38 . 6 A C8 C 124.528 0.000 . 39 . 6 A H1' H 5.903 0.001 . 40 . 6 A H2 H 7.127 0.000 . 41 . 6 A H2' H 4.608 0.001 . 42 . 6 A H3' H 4.543 0.001 . 43 . 6 A H4' H 4.674 0.002 . 44 . 6 A H5' H 4.492 0.001 . 45 . 6 A H8 H 7.750 0.000 . 46 . 7 A H61 H 6.743 0.001 . 47 . 7 A H62 H 7.915 0.007 . 48 . 7 A HO2' H 6.747 0.000 . 49 . 7 A C2 C 137.976 0.000 . 50 . 7 A C8 C 124.026 0.000 . 51 . 7 A H1' H 5.810 0.000 . 52 . 7 A H2 H 7.285 0.000 . 53 . 7 A H2' H 4.630 0.001 . 54 . 7 A H3' H 4.546 0.002 . 55 . 7 A H4' H 4.488 0.000 . 56 . 7 A H8 H 7.608 0.001 . 57 . 8 A C2 C 138.602 0.000 . 58 . 8 A C8 C 123.676 0.000 . 59 . 8 A P P -4.035 0.000 . 60 . 8 A H1' H 5.676 0.001 . 61 . 8 A H2 H 7.804 0.000 . 62 . 8 A H2' H 4.531 0.001 . 63 . 8 A H4' H 4.268 0.000 . 64 . 8 A H8 H 7.408 0.000 . 65 . 9 C P P -3.889 0.000 . 66 . 9 C H1' H 5.172 0.001 . 67 . 9 C H2' H 4.117 0.001 . 68 . 9 C H3' H 4.390 0.000 . 69 . 9 C H4' H 4.325 0.000 . 70 . 9 C H5 H 5.202 0.001 . 71 . 9 C H5' H 4.487 0.000 . 72 . 9 C H5'' H 4.269 0.000 . 73 . 9 C H6 H 7.350 0.000 . 74 . 10 A C2 C 139.460 0.000 . 75 . 10 A C8 C 125.791 0.000 . 76 . 10 A H1' H 5.851 0.000 . 77 . 10 A H2 H 7.567 0.000 . 78 . 10 A H2' H 4.562 0.001 . 79 . 10 A H3' H 4.607 0.000 . 80 . 10 A H4' H 4.480 0.000 . 81 . 10 A H5' H 4.408 0.000 . 82 . 10 A H8 H 7.979 0.001 . 83 . 11 A C2 C 138.553 0.000 . 84 . 11 A C8 C 125.233 0.000 . 85 . 11 A P P -4.049 0.000 . 86 . 11 A H1' H 5.764 0.003 . 87 . 11 A H2 H 7.597 0.001 . 88 . 11 A H2' H 4.672 0.001 . 89 . 11 A H3' H 4.618 0.001 . 90 . 11 A H4' H 4.488 0.001 . 91 . 11 A H5' H 4.408 0.000 . 92 . 11 A H5'' H 4.212 0.000 . 93 . 11 A H8 H 8.072 0.004 . 94 . 12 G H1 H 12.742 0.005 . 95 . 12 G C8 C 121.193 0.000 . 96 . 12 G N1 N 147.419 0.000 . 97 . 12 G H1' H 5.519 0.001 . 98 . 12 G H2' H 4.530 0.001 . 99 . 12 G H3' H 4.371 0.002 . 100 . 12 G H4' H 4.330 0.000 . 101 . 12 G H5' H 4.121 0.000 . 102 . 12 G H8 H 7.162 0.002 . 103 . 13 G H1 H 13.406 0.003 . 104 . 13 G C8 C 121.153 0.000 . 105 . 13 G N1 N 148.606 0.000 . 106 . 13 G H1' H 5.803 0.001 . 107 . 13 G H2' H 4.527 0.000 . 108 . 13 G H3' H 4.497 0.000 . 109 . 13 G H4' H 4.457 0.000 . 110 . 13 G H5' H 4.285 0.000 . 111 . 13 G H5'' H 4.066 0.001 . 112 . 13 G H8 H 7.339 0.001 . 113 . 14 C H41 H 7.026 0.003 . 114 . 14 C H42 H 8.634 0.003 . 115 . 14 C P P -4.195 0.000 . 116 . 14 C H1' H 5.512 0.000 . 117 . 14 C H2' H 4.523 0.001 . 118 . 14 C H3' H 4.221 0.001 . 119 . 14 C H4' H 4.428 0.000 . 120 . 14 C H5 H 5.205 0.001 . 121 . 14 C H5' H 4.408 0.000 . 122 . 14 C H5'' H 4.228 0.002 . 123 . 14 C H6 H 7.395 0.001 . 124 . 15 U HO2' H 6.679 0.005 . 125 . 15 U C6 C 125.749 0.000 . 126 . 15 U N3 N 160.170 0.000 . 127 . 15 U P P -4.312 0.000 . 128 . 15 U H1' H 5.682 0.001 . 129 . 15 U H2' H 3.807 0.001 . 130 . 15 U H3' H 4.529 0.003 . 131 . 15 U H4' H 4.374 0.000 . 132 . 15 U H5 H 5.715 0.001 . 133 . 15 U H5'' H 4.089 0.003 . 134 . 15 U H6 H 7.772 0.002 . 135 . 16 U C6 C 129.724 0.000 . 136 . 16 U N3 N 158.343 0.000 . 137 . 16 U P P -3.559 0.001 . 138 . 16 U H1' H 6.107 0.001 . 139 . 16 U H2' H 4.691 0.001 . 140 . 16 U H3' H 4.019 0.002 . 141 . 16 U H4' H 4.482 0.001 . 142 . 16 U H5 H 5.859 0.002 . 143 . 16 U H5'' H 4.237 0.001 . 144 . 16 U H6 H 8.030 0.002 . 145 . 17 C H1' H 5.965 0.002 . 146 . 17 C H2' H 4.099 0.001 . 147 . 17 C H3' H 4.476 0.000 . 148 . 17 C H4' H 3.791 0.002 . 149 . 17 C H5 H 6.135 0.002 . 150 . 17 C H5' H 3.603 0.002 . 151 . 17 C H5'' H 2.705 0.001 . 152 . 17 C H6 H 7.694 0.001 . 153 . 17 C H41 H 7.160 0.006 . 154 . 17 C H42 H 6.434 0.005 . 155 . 17 C P P -5.127 0.004 . 156 . 18 G H1' H 5.958 0.001 . 157 . 18 G H2' H 4.849 0.001 . 158 . 18 G H3' H 5.629 0.001 . 159 . 18 G H4' H 4.396 0.002 . 160 . 18 G H5' H 4.178 0.002 . 161 . 18 G H5'' H 4.387 0.001 . 162 . 18 G H8 H 7.853 0.000 . 163 . 18 G H1 H 9.918 0.004 . 164 . 18 G C8 C 127.980 0.000 . 165 . 18 G N1 N 143.233 0.000 . 166 . 18 G P P -5.064 0.000 . 167 . 19 G H1' H 4.451 0.001 . 168 . 19 G H2' H 4.435 0.001 . 169 . 19 G H3' H 4.244 0.000 . 170 . 19 G H4' H 4.262 0.000 . 171 . 19 G H5'' H 4.497 0.000 . 172 . 19 G H8 H 8.285 0.001 . 173 . 19 G H1 H 13.559 0.003 . 174 . 19 G H21 H 6.512 0.004 . 175 . 19 G H22 H 8.978 0.002 . 176 . 19 G C8 C 123.805 0.000 . 177 . 19 G N1 N 148.501 0.000 . 178 . 19 G P P -2.584 0.003 . 179 . 20 C H2' H 4.457 0.003 . 180 . 20 C H3' H 4.407 0.000 . 181 . 20 C H5 H 5.262 0.001 . 182 . 20 C H6 H 7.678 0.001 . 183 . 20 C H41 H 6.972 0.004 . 184 . 20 C H42 H 8.830 0.004 . 185 . 20 C C6 C 127.835 0.000 . 186 . 20 C P P -4.722 0.000 . 187 . 21 C H1' H 5.530 0.003 . 188 . 21 C H2' H 4.466 0.001 . 189 . 21 C H3' H 4.401 0.001 . 190 . 21 C H5 H 5.526 0.001 . 191 . 21 C H6 H 7.724 0.000 . 192 . 21 C H41 H 6.960 0.008 . 193 . 21 C H42 H 8.553 0.008 . 194 . 21 C C6 C 126.255 0.000 . 195 . 22 U H1' H 5.597 0.000 . 196 . 22 U H2' H 4.333 0.000 . 197 . 22 U H3' H 4.291 0.001 . 198 . 22 U H4' H 4.389 0.000 . 199 . 22 U H5 H 5.435 0.001 . 200 . 22 U H6 H 7.698 0.001 . 201 . 22 U C6 C 127.478 0.000 . 202 . 22 U P P -3.934 0.000 . 203 . 23 G H1' H 5.587 0.001 . 204 . 23 G H2' H 4.551 0.000 . 205 . 23 G H3' H 4.479 0.012 . 206 . 23 G H4' H 4.622 0.000 . 207 . 23 G H5' H 4.138 0.000 . 208 . 23 G H8 H 7.893 0.001 . 209 . 23 G C8 C 123.438 0.000 . 210 . 23 G P P -4.486 0.000 . 211 . 24 C H1' H 5.728 0.001 . 212 . 24 C H2' H 4.131 0.004 . 213 . 24 C H3' H 4.188 0.001 . 214 . 24 C H4' H 4.084 0.000 . 215 . 24 C H5 H 5.540 0.000 . 216 . 24 C H6 H 7.677 0.002 . 217 . 24 C P P -4.444 0.000 . 218 . 25 U H1' H 5.567 0.001 . 219 . 25 U H2' H 4.494 0.000 . 220 . 25 U H3' H 4.401 0.001 . 221 . 25 U H4' H 4.535 0.000 . 222 . 25 U H5 H 5.562 0.000 . 223 . 25 U H5' H 4.113 0.002 . 224 . 25 U H6 H 7.838 0.001 . 225 . 25 U C6 C 127.370 0.000 . 226 . 26 U H1' H 5.635 0.000 . 227 . 26 U H2' H 4.496 0.000 . 228 . 26 U H3' H 4.449 0.000 . 229 . 26 U H5 H 5.630 0.000 . 230 . 26 U H6 H 7.947 0.001 . 231 . 26 U H3 H 13.435 0.003 . 232 . 26 U N3 N 162.763 0.000 . 233 . 27 U H1' H 5.636 0.001 . 234 . 27 U H2' H 4.498 0.000 . 235 . 27 U H3' H 4.389 0.001 . 236 . 27 U H4' H 4.467 0.000 . 237 . 27 U H5 H 5.562 0.000 . 238 . 27 U H6 H 7.998 0.001 . 239 . 27 U H3 H 13.787 0.010 . 240 . 27 U C6 C 127.709 0.000 . 241 . 27 U N3 N 163.057 0.000 . 242 . 27 U P P -4.012 0.000 . 243 . 28 C H1' H 5.554 0.000 . 244 . 28 C H2' H 4.451 0.001 . 245 . 28 C H3' H 4.413 0.000 . 246 . 28 C H4' H 4.392 0.000 . 247 . 28 C H5 H 5.567 0.000 . 248 . 28 C H6 H 7.754 0.001 . 249 . 28 C H41 H 6.861 0.007 . 250 . 28 C H42 H 8.150 0.005 . 251 . 28 C P P -4.231 0.000 . 252 . 29 G H1' H 5.625 0.000 . 253 . 29 G H2' H 4.407 0.001 . 254 . 29 G H3' H 4.484 0.000 . 255 . 29 G H8 H 7.540 0.000 . 256 . 29 G C8 C 122.255 0.000 . 257 . 29 G N1 N 146.268 0.000 . 258 . 29 G P P -3.777 0.000 . 259 . 30 C H5 H 5.250 0.000 . 260 . 30 C H6 H 7.418 0.002 . stop_ save_