data_25671 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; 1H Chemical Shift Assignments of the HIV ISS element ; _BMRB_accession_number 25671 _BMRB_flat_file_name bmr25671.str _Entry_type original _Submission_date 2015-06-23 _Accession_date 2015-06-23 _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 Tolbert Blanton S. . 2 Jain Niyati . . 3 Morgan Christopher E. . 4 Rife Brittany D. . 5 Salemi Marco . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 172 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2016-08-12 update BMRB 'update entry citation' 2015-11-30 original author 'original release' stop_ _Original_release_date 2015-11-30 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Solution Structure of the HIV-1 Intron Splicing Silencer and Its Interactions with the UP1 Domain of Heterogeneous Nuclear Ribonucleoprotein (hnRNP) A1 ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 26607354 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Jain Niyati . . 2 Morgan Christopher E. . 3 Rife Brittany D. . 4 Salemi Marco . . 5 Tolbert Blanton S. . stop_ _Journal_abbreviation 'J. Biol. Chem.' _Journal_volume 291 _Journal_issue 5 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 2331 _Page_last 2344 _Year 2016 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'HIV ISS element' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'RNA (53-MER)' $RNA_(53-MER) 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_RNA_(53-MER) _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_(53-MER) _Molecular_mass 17006.127 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 53 _Mol_residue_sequence ; GGAAUAUUUUUGCUGUACUU UCUAUAGUGAAUAGAGUUAG GCAGGGAUAUUCC ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 G 2 2 G 3 3 A 4 4 A 5 5 U 6 6 A 7 7 U 8 8 U 9 9 U 10 10 U 11 11 U 12 12 G 13 13 C 14 14 U 15 15 G 16 16 U 17 17 A 18 18 C 19 19 U 20 20 U 21 21 U 22 22 C 23 23 U 24 24 A 25 25 U 26 26 A 27 27 G 28 28 U 29 29 G 30 30 A 31 31 A 32 32 U 33 33 A 34 34 G 35 35 A 36 36 G 37 37 U 38 38 U 39 39 A 40 40 G 41 41 G 42 42 C 43 43 A 44 44 G 45 45 G 46 46 G 47 47 A 48 48 U 49 49 A 50 50 U 51 51 U 52 52 C 53 53 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 $RNA_(53-MER) HIV 11676 Viruses . Lentivirus 'Human immunodeficiency virus 1' 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 $RNA_(53-MER) 'In vitro transcription' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_ISS_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $RNA_(53-MER) . uM 80 120 [U-2H] D2O 100 % . . 'natural abunance' stop_ save_ save_ISS_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $RNA_(53-MER) . uM 80 120 [U-2H] D2O 100 % . . 'natural abunance' stop_ save_ save_ISS_3 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $RNA_(53-MER) . uM 80 120 '[U-100% 13C]' D2O 100 % . . 'natural abunance' stop_ save_ ############################ # Computer software used # ############################ save_NMRDraw _Saveframe_category software _Name NMRDraw _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing 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_X-PLOR_NIH _Saveframe_category software _Name X-PLOR_NIH _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection stop_ _Details . save_ 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_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 900 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _Details . save_ save_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _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 $ISS_1 save_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $ISS_2 save_ save_2D_1H-13C_HMQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HMQC' _Sample_label $ISS_3 save_ ####################### # Sample conditions # ####################### save_ISS_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 10 . mM pH 6.5 . pH pressure 1 . atm temperature 298 . 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 $ISS_1 stop_ _Sample_conditions_label $ISS_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'RNA (53-MER)' _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 5.7 . . 2 1 1 G H2' H 4.82 . . 3 1 1 G H8 H 8.07 . . 4 2 2 G H1' H 5.78 . . 5 2 2 G H2' H 4.54 . . 6 2 2 G H8 H 7.47 . . 7 3 3 A H1' H 5.8 . . 8 3 3 A H2 H 7.06 . . 9 3 3 A H2' H 4.5 . . 10 3 3 A H8 H 7.63 . . 11 4 4 A H1' H 5.76 . . 12 4 4 A H2 H 7.57 . . 13 4 4 A H2' H 4.28 . . 14 4 4 A H8 H 7.62 . . 15 5 5 U H1' H 5.3 . . 16 5 5 U H2' H 4.29 . . 17 5 5 U H6 H 7.44 . . 18 6 6 A H1' H 5.87 . . 19 6 6 A H2 H 6.96 . . 20 6 6 A H2' H 4.35 . . 21 6 6 A H8 H 7.99 . . 22 7 7 U H1' H 5.29 . . 23 7 7 U H2' H 4.36 . . 24 7 7 U H6 H 7.38 . . 25 8 8 U H1' H 5.34 . . 26 8 8 U H2' H 4.11 . . 27 8 8 U H6 H 7.8 . . 28 9 9 U H1' H 5.38 . . 29 9 9 U H2' H 4.09 . . 30 9 9 U H6 H 7.94 . . 31 10 10 U H1' H 5.43 . . 32 10 10 U H2' H 3.98 . . 33 10 10 U H6 H 7.9 . . 34 11 11 U H1' H 5.39 . . 35 11 11 U H2' H 4.44 . . 36 11 11 U H6 H 7.82 . . 37 12 12 G H1' H 5.62 . . 38 12 12 G H2' H 4.42 . . 39 12 12 G H8 H 7.6 . . 40 13 13 C H1' H 5.28 . . 41 13 13 C H2' H 4.41 . . 42 13 13 C H6 H 7.39 . . 43 14 14 U H1' H 5.36 . . 44 14 14 U H2' H 4.23 . . 45 14 14 U H6 H 7.41 . . 46 15 15 G H1' H 5.33 . . 47 15 15 G H2' H 4.31 . . 48 15 15 G H8 H 7.93 . . 49 16 16 U H1' H 5.34 . . 50 16 16 U H2' H 4.13 . . 51 16 16 U H6 H 7.62 . . 52 17 17 A H1' H 5.72 . . 53 17 17 A H2 H 7.85 . . 54 17 17 A H2' H 4.35 . . 55 17 17 A H8 H 7.95 . . 56 18 18 C H1' H 5.46 . . 57 18 18 C H2' H 4.07 . . 58 18 18 C H6 H 7.28 . . 59 19 19 U H1' H 5.78 . . 60 19 19 U H2' H 4.27 . . 61 19 19 U H6 H 7.69 . . 62 20 20 U H1' H 5.87 . . 63 20 20 U H2' H 4.45 . . 64 20 20 U H6 H 7.78 . . 65 21 21 U H1' H 5.7 . . 66 21 21 U H2' H 4.31 . . 67 21 21 U H6 H 7.85 . . 68 22 22 C H1' H 5.5 . . 69 22 22 C H2' H 4.44 . . 70 22 22 C H6 H 7.83 . . 71 23 23 U H1' H 5.37 . . 72 23 23 U H2' H 4.39 . . 73 23 23 U H6 H 7.78 . . 74 24 24 A H1' H 5.84 . . 75 24 24 A H2 H 7.39 . . 76 24 24 A H2' H 4.31 . . 77 24 24 A H8 H 8.04 . . 78 25 25 U H1' H 5.3 . . 79 25 25 U H2' H 4.18 . . 80 25 25 U H6 H 7.29 . . 81 26 26 A H1' H 5.57 . . 82 26 26 A H2 H 7.52 . . 83 26 26 A H2' H 4.25 . . 84 26 26 A H8 H 7.86 . . 85 27 27 G H1' H 5.54 . . 86 27 27 G H2' H 3.84 . . 87 27 27 G H8 H 7.53 . . 88 28 28 U H1' H 5.72 . . 89 28 28 U H2' H 4.11 . . 90 28 28 U H6 H 7.54 . . 91 29 29 G H1' H 5.39 . . 92 29 29 G H2' H 4.54 . . 93 29 29 G H8 H 7.61 . . 94 30 30 A H1' H 5.84 . . 95 30 30 A H2 H 7.86 . . 96 30 30 A H2' H 4.52 . . 97 30 30 A H8 H 8.07 . . 98 31 31 A H1' H 5.6 . . 99 31 31 A H2 H 7.5 . . 100 31 31 A H2' H 4.29 . . 101 31 31 A H8 H 8.09 . . 102 32 32 U H1' H 5.42 . . 103 32 32 U H2' H 4.47 . . 104 32 32 U H6 H 7.48 . . 105 33 33 A H1' H 5.83 . . 106 33 33 A H2 H 6.66 . . 107 33 33 A H2' H 4.48 . . 108 33 33 A H8 H 7.92 . . 109 34 34 G H1' H 5.36 . . 110 34 34 G H2' H 4.47 . . 111 34 34 G H8 H 6.96 . . 112 35 35 A H1' H 5.68 . . 113 35 35 A H2 H 7.47 . . 114 35 35 A H2' H 4.48 . . 115 35 35 A H8 H 7.45 . . 116 36 36 G H1' H 5.36 . . 117 36 36 G H2' H 4.18 . . 118 36 36 G H8 H 7.08 . . 119 37 37 U H1' H 5.44 . . 120 37 37 U H2' H 4.31 . . 121 37 37 U H6 H 7.45 . . 122 38 38 U H1' H 5.27 . . 123 38 38 U H2' H 4.09 . . 124 38 38 U H6 H 7.65 . . 125 39 39 A H1' H 5.81 . . 126 39 39 A H2 H 7.88 . . 127 39 39 A H2' H 4.76 . . 128 39 39 A H8 H 7.75 . . 129 40 40 G H1' H 5.03 . . 130 40 40 G H2' H 4.44 . . 131 40 40 G H8 H 7.3 . . 132 41 41 G H1' H 5.56 . . 133 41 41 G H2' H 4.44 . . 134 41 41 G H8 H 7.02 . . 135 42 42 C H1' H 5.37 . . 136 42 42 C H2' H 4.37 . . 137 42 42 C H6 H 7.53 . . 138 43 43 A H1' H 5.86 . . 139 43 43 A H2 H 6.71 . . 140 43 43 A H2' H 4.47 . . 141 43 43 A H8 H 7.92 . . 142 44 44 G H1' H 5.59 . . 143 44 44 G H2' H 4.4 . . 144 44 44 G H8 H 6.94 . . 145 45 45 G H1' H 5.65 . . 146 45 45 G H2' H 4.47 . . 147 45 45 G H8 H 6.92 . . 148 46 46 G H1' H 5.63 . . 149 46 46 G H2' H 4.64 . . 150 46 46 G H8 H 6.9 . . 151 47 47 A H1' H 5.83 . . 152 47 47 A H2 H 7.71 . . 153 47 47 A H2' H 4.35 . . 154 47 47 A H8 H 7.68 . . 155 48 48 U H1' H 5.36 . . 156 48 48 U H2' H 4.32 . . 157 48 48 U H6 H 7.54 . . 158 49 49 A H1' H 5.89 . . 159 49 49 A H2 H 7 . . 160 49 49 A H2' H 4.34 . . 161 49 49 A H8 H 8.04 . . 162 50 50 U H1' H 5.35 . . 163 50 50 U H2' H 4.17 . . 164 50 50 U H6 H 7.58 . . 165 51 51 U H1' H 5.52 . . 166 51 51 U H2' H 4.31 . . 167 51 51 U H6 H 7.89 . . 168 52 52 C H1' H 5.41 . . 169 52 52 C H2' H 4.06 . . 170 52 52 C H6 H 7.77 . . 171 53 53 C H1' H 5.41 . . 172 53 53 C H6 H 7.53 . . stop_ save_