data_15697 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Mutational and Structural Analysis of Stem-loop IIId of the Hepatitis C Virus and GB Virus B Internal Ribosome Entry Sites ; _BMRB_accession_number 15697 _BMRB_flat_file_name bmr15697.str _Entry_type new _Submission_date 2008-03-28 _Accession_date 2008-03-28 _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 Thiviyanathan Varatharasa . . 2 Kulasegaran Raghav . . 3 Kaluarachchi Kumaralal . . 4 Gorenstein David . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 179 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2009-10-13 original author . stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Mutational and Structural Analysis of Stem-loop IIId of the Hepatitis C Virus and GB Virus B Internal Ribosome Entry Sites ; _Citation_status 'in preparation' _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Thiviyanathan Varatharasa . . 2 Kulasegaran Raghav . . 3 Kaluarachchi Kumaralal . . 4 Rijnbrand Rene . . 5 Gorenstein David . . stop_ _Journal_abbreviation 'J. Virology' _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . loop_ _Keyword HCV GBV-B IRES stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'IRES domain IIId' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'domain IIId' $GBV_B_IRES stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . loop_ _Biological_function 'Translation initiation' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_GBV_B_IRES _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common GBV_B_IRES _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 22 _Mol_residue_sequence ; GGAUGGUUGGGGUUAGCCAU CC ; loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 A 4 U 5 G 6 G 7 U 8 U 9 G 10 G 11 G 12 G 13 U 14 U 15 A 16 G 17 C 18 C 19 A 20 U 21 C 22 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 $GBV_B_IRES 'GB virus B' 39113 Viruses . . . stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_type _Vector_name $GBV_B_IRES 'enzymatic synthesis' . . . . n/a n/a 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 $GBV_B_IRES 1.2 mM 'natural abundance' 'potassium chloride' 10 mM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' EDTA 0.05 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_VNMR _Saveframe_category software _Name VNMR _Version . loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 750 _Details . save_ save_spectrometer_2 _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-15N_HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_DQF-COSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _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 temperature 298 . K pH 6.8 . pH pressure 1 . atm 'ionic strength' 10 . mM 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 H 1 protons ppm 4.76 internal direct . . . 1 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 DQF-COSY' 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 'domain IIId' _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 H1' H 5.87 0.01 1 2 1 1 G H2' H 4.99 0.01 1 3 1 1 G H3' H 4.89 0.01 1 4 1 1 G H4' H 4.61 0.01 1 5 1 1 G H5' H 4.2 0.01 2 6 1 1 G H5'' H 4.19 0.01 2 7 1 1 G H8 H 8.17 0.01 1 8 2 2 G H1 H 12.31 0.01 1 9 2 2 G H1' H 5.96 0.01 1 10 2 2 G H2' H 4.48 0.01 1 11 2 2 G H3' H 4.71 0.01 1 12 2 2 G H4' H 4.36 0.01 1 13 2 2 G H8 H 7.61 0.01 1 14 2 2 G H21 H 6.28 0.01 2 15 2 2 G H22 H 6.28 0.01 2 16 3 3 A H1' H 6.05 0.01 1 17 3 3 A H2 H 7.74 0.01 1 18 3 3 A H2' H 4.86 0.01 1 19 3 3 A H3' H 4.45 0.01 1 20 3 3 A H4' H 4.31 0.01 1 21 3 3 A H8 H 7.84 0.01 1 22 4 4 U H1' H 5.52 0.01 1 23 4 4 U H2' H 4.64 0.01 1 24 4 4 U H3 H 13.14 0.01 1 25 4 4 U H3' H 4.58 0.01 1 26 4 4 U H4' H 4.47 0.01 1 27 4 4 U H5 H 5.09 0.01 1 28 4 4 U H5' H 4.13 0.01 2 29 4 4 U H5'' H 4.13 0.01 2 30 4 4 U H6 H 7.51 0.01 1 31 5 5 G H1 H 11.92 0.01 1 32 5 5 G H1' H 5.53 0.01 1 33 5 5 G H2' H 4.41 0.01 1 34 5 5 G H3' H 4.17 0.01 1 35 5 5 G H4' H 4.04 0.01 1 36 5 5 G H5' H 4.01 0.01 2 37 5 5 G H5'' H 4.01 0.01 2 38 5 5 G H8 H 7.7 0.01 1 39 5 5 G H21 H 6.85 0.01 2 40 5 5 G H22 H 5.86 0.01 2 41 6 6 G H1 H 13.21 0.01 1 42 6 6 G H1' H 5.96 0.01 1 43 6 6 G H2' H 4.48 0.01 1 44 6 6 G H3' H 4.36 0.01 1 45 6 6 G H4' H 4.21 0.01 1 46 6 6 G H5' H 4.14 0.01 2 47 6 6 G H5'' H 4.14 0.01 2 48 6 6 G H8 H 8.11 0.01 1 49 6 6 G H21 H 6.23 0.01 2 50 6 6 G H22 H 5.47 0.01 2 51 7 7 U H1' H 5.62 0.01 1 52 7 7 U H2' H 4.4 0.01 1 53 7 7 U H3 H 11.72 0.01 1 54 7 7 U H3' H 4.35 0.01 1 55 7 7 U H4' H 4.41 0.01 1 56 7 7 U H5 H 5.07 0.01 1 57 7 7 U H6 H 7.72 0.01 1 58 8 8 U H1' H 5.74 0.01 1 59 8 8 U H2' H 4.52 0.01 1 60 8 8 U H3 H 13.95 0.01 1 61 8 8 U H3' H 4.41 0.01 1 62 8 8 U H4' H 4.21 0.01 1 63 8 8 U H5 H 5.57 0.01 1 64 8 8 U H5' H 4.14 0.01 2 65 8 8 U H5'' H 4.14 0.01 2 66 8 8 U H6 H 7.89 0.01 1 67 9 9 G H1 H 13.35 0.01 1 68 9 9 G H1' H 5.57 0.01 1 69 9 9 G H2' H 4.57 0.01 1 70 9 9 G H3' H 4.39 0.01 1 71 9 9 G H4' H 4.25 0.01 1 72 9 9 G H8 H 7.64 0.01 1 73 10 10 G H1 H 13.05 0.01 1 74 10 10 G H1' H 5.51 0.01 1 75 10 10 G H2' H 4.06 0.01 1 76 10 10 G H3' H 4.34 0.01 1 77 10 10 G H4' H 4.27 0.01 1 78 10 10 G H5' H 4.12 0.01 2 79 10 10 G H5'' H 4.12 0.01 2 80 10 10 G H8 H 7.57 0.01 1 81 11 11 G H1' H 5.66 0.01 1 82 11 11 G H2' H 4.53 0.01 1 83 11 11 G H3' H 4.37 0.01 1 84 11 11 G H4' H 4.21 0.01 1 85 11 11 G H5' H 4.06 0.01 2 86 11 11 G H5'' H 4.06 0.01 2 87 11 11 G H8 H 7.93 0.01 1 88 12 12 G H1' H 5.46 0.01 1 89 12 12 G H2' H 4.55 0.01 1 90 12 12 G H3' H 4.15 0.01 1 91 12 12 G H4' H 4.06 0.01 1 92 12 12 G H8 H 7.76 0.01 1 93 13 13 U H2' H 4.48 0.01 1 94 13 13 U H3' H 4.29 0.01 1 95 13 13 U H4' H 4.21 0.01 1 96 13 13 U H5 H 5.96 0.01 1 97 13 13 U H5' H 4.15 0.01 2 98 13 13 U H5'' H 4.15 0.01 2 99 13 13 U H6 H 7.84 0.01 1 100 14 14 U H1' H 5.86 0.01 1 101 14 14 U H2' H 4.87 0.01 1 102 14 14 U H3 H 14.24 0.01 1 103 14 14 U H3' H 4.65 0.01 1 104 14 14 U H4' H 4.25 0.01 1 105 14 14 U H5 H 5.88 0.01 1 106 14 14 U H5' H 4.12 0.01 2 107 14 14 U H5'' H 4.15 0.01 2 108 14 14 U H6 H 7.94 0.01 1 109 15 15 A H1' H 6.09 0.01 1 110 15 15 A H2 H 7.24 0.01 1 111 15 15 A H2' H 4.65 0.01 1 112 15 15 A H3' H 4.51 0.01 1 113 15 15 A H4' H 4.37 0.01 1 114 15 15 A H5' H 4.29 0.01 2 115 15 15 A H5'' H 4.25 0.01 2 116 15 15 A H8 H 8.46 0.01 1 117 16 16 G H1 H 11.41 0.01 1 118 16 16 G H1' H 5.72 0.01 1 119 16 16 G H2' H 4.57 0.01 1 120 16 16 G H3' H 4.48 0.01 1 121 16 16 G H4' H 4.35 0.01 1 122 16 16 G H5' H 4.21 0.01 2 123 16 16 G H5'' H 4.18 0.01 2 124 16 16 G H8 H 7.29 0.01 1 125 17 17 C H1' H 5.61 0.01 1 126 17 17 C H2' H 4.34 0.01 1 127 17 17 C H3' H 4.55 0.01 1 128 17 17 C H4' H 4.23 0.01 1 129 17 17 C H5 H 5.35 0.01 1 130 17 17 C H5' H 4.13 0.01 2 131 17 17 C H5'' H 4.12 0.01 2 132 17 17 C H6 H 7.71 0.01 1 133 17 17 C H41 H 8.51 0.01 2 134 17 17 C H42 H 6.86 0.01 2 135 18 18 C H1' H 5.56 0.01 1 136 18 18 C H2' H 4.61 0.01 1 137 18 18 C H3' H 4.47 0.01 1 138 18 18 C H4' H 4.34 0.01 1 139 18 18 C H5 H 5.58 0.01 1 140 18 18 C H6 H 7.77 0.01 1 141 18 18 C H41 H 8.48 0.01 2 142 18 18 C H42 H 6.88 0.01 2 143 19 19 A H1' H 5.73 0.01 1 144 19 19 A H2 H 7.36 0.01 1 145 19 19 A H2' H 4.7 0.01 1 146 19 19 A H3' H 4.61 0.01 1 147 19 19 A H4' H 4.53 0.01 1 148 19 19 A H5' H 4.37 0.01 2 149 19 19 A H5'' H 4.13 0.01 2 150 19 19 A H8 H 7.25 0.01 1 151 19 19 A H61 H 7.81 0.01 2 152 19 19 A H62 H 7.81 0.01 2 153 20 20 U H1' H 5.48 0.01 1 154 20 20 U H2' H 4.56 0.01 1 155 20 20 U H3 H 14.2 0.01 1 156 20 20 U H3' H 4.38 0.01 1 157 20 20 U H4' H 4.44 0.01 1 158 20 20 U H5 H 5.44 0.01 1 159 20 20 U H5' H 4.24 0.01 2 160 20 20 U H5'' H 4.11 0.01 2 161 20 20 U H6 H 7.66 0.01 1 162 21 21 C H1' H 5.85 0.01 1 163 21 21 C H2' H 4.39 0.01 1 164 21 21 C H3' H 4.11 0.01 1 165 21 21 C H4' H 4.15 0.01 1 166 21 21 C H5 H 5.62 0.01 1 167 21 21 C H6 H 7.87 0.01 1 168 21 21 C H41 H 8.56 0.01 2 169 21 21 C H42 H 7.02 0.01 2 170 22 22 C H1' H 5.79 0.01 1 171 22 22 C H2' H 4.64 0.01 1 172 22 22 C H3' H 4.41 0.01 1 173 22 22 C H4' H 4.21 0.01 1 174 22 22 C H5 H 5.54 0.01 1 175 22 22 C H5' H 4.04 0.01 2 176 22 22 C H5'' H 4.04 0.01 2 177 22 22 C H6 H 7.67 0.01 1 178 22 22 C H41 H 8.34 0.01 2 179 22 22 C H42 H 7.06 0.01 2 stop_ save_