data_30723 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Cap3G-TAR-F1 ; _BMRB_accession_number 30723 _BMRB_flat_file_name bmr30723.str _Entry_type original _Submission_date 2020-02-14 _Accession_date 2020-02-14 _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 Summers M. F. . 2 Brown J. D. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 160 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2020-04-27 original BMRB . stop_ _Original_release_date 2020-04-07 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structural Basis for Transcriptional Start Site Control of HIV-1 RNA Fate ; _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 Summers M. F. . 2 Brown J. D. . stop_ _Journal_abbreviation . _Journal_volume . _Journal_issue . _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'RNA (34-MER)' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity_1 stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common entity_1 _Molecular_mass 11041.558 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 34 _Mol_residue_sequence ; XGGGUCUCUCUUGUCGAGAG GCAAGGAACCCACU ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 0 8NK 2 1 G 3 2 G 4 3 G 5 4 U 6 5 C 7 6 U 8 7 C 9 8 U 10 9 C 11 10 U 12 11 U 13 12 G 14 13 U 15 14 C 16 15 G 17 16 A 18 17 G 19 18 A 20 19 G 21 47 G 22 48 C 23 49 A 24 50 A 25 51 G 26 52 G 27 53 A 28 54 A 29 55 C 30 56 C 31 57 C 32 58 A 33 59 C 34 60 U stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_8NK _Saveframe_category polymer_residue _Mol_type NON-POLYMER _Name_common "7-methylguanosine 5'-diphosphate" _BMRB_code 8NK _PDB_code 8NK _Standard_residue_derivative . _Molecular_mass 458.235 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons PA PA P . 0 . ? O1A O1A O . 0 . ? O2A O2A O . 0 . ? O3A O3A O . 0 . ? O5' O5' O . 0 . ? PB PB P . 0 . ? O1B O1B O . 0 . ? O2B O2B O . 0 . ? O3B O3B O . 0 . ? C5' C5' C . 0 . ? C4' C4' C . 0 . ? O4' O4' O . 0 . ? C3' C3' C . 0 . ? O3' O3' O . 0 . ? C2' C2' C . 0 . ? O2' O2' O . 0 . ? C1' C1' C . 0 . ? N9 N9 N . 0 . ? C8 C8 C . 0 . ? N7 N7 N . 1 . ? CM7 CM7 C . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? O6 O6 O . 0 . ? N1 N1 N . 0 . ? C2 C2 C . 0 . ? N2 N2 N . 0 . ? N3 N3 N . 0 . ? C4 C4 C . 0 . ? H1 H1 H . 0 . ? H2 H2 H . 0 . ? H3 H3 H . 0 . ? H4 H4 H . 0 . ? H5 H5 H . 0 . ? H6 H6 H . 0 . ? H7 H7 H . 0 . ? H8 H8 H . 0 . ? H9 H9 H . 0 . ? H10 H10 H . 0 . ? H11 H11 H . 0 . ? H12 H12 H . 0 . ? H13 H13 H . 0 . ? H14 H14 H . 0 . ? H15 H15 H . 0 . ? H16 H16 H . 0 . ? H17 H17 H . 0 . ? H18 H18 H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING O2' C2' ? ? SING O3' C3' ? ? SING N2 C2 ? ? SING C2' C3' ? ? SING C2' C1' ? ? DOUB N3 C2 ? ? SING N3 C4 ? ? SING C2 N1 ? ? SING C3' C4' ? ? SING C1' O4' ? ? SING C1' N9 ? ? SING C4' O4' ? ? SING C4' C5' ? ? SING N1 C6 ? ? SING C4 N9 ? ? DOUB C4 C5 ? ? SING N9 C8 ? ? SING C5' O5' ? ? SING C5 C6 ? ? SING C5 N7 ? ? DOUB C6 O6 ? ? DOUB C8 N7 ? ? SING O5' PA ? ? SING N7 CM7 ? ? SING PA O3A ? ? DOUB PA O1A ? ? SING PA O2A ? ? SING O3A PB ? ? DOUB O1B PB ? ? SING PB O2B ? ? SING PB O3B ? ? SING O2A H1 ? ? SING O2B H2 ? ? SING O3B H3 ? ? SING C5' H4 ? ? SING C5' H5 ? ? SING C4' H6 ? ? SING C3' H7 ? ? SING O3' H8 ? ? SING C2' H9 ? ? SING O2' H10 ? ? SING C1' H11 ? ? SING C8 H12 ? ? SING CM7 H13 ? ? SING CM7 H14 ? ? SING CM7 H15 ? ? SING N1 H16 ? ? SING N2 H17 ? ? SING N2 H18 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity_1 HIV-1 11676 Viruses . Lentivirus HIV-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 $entity_1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '150 uM Fully protonated Cap3G-TAR-F1, 10 mM Deuterated KH2PO4, 100% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 150 uM 'Fully protonated' KH2PO4 10 mM Deuterated stop_ save_ ############################ # Computer software used # ############################ save_software_1 _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_software_2 _Saveframe_category software _Name CYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name NMRView _Version . loop_ _Vendor _Address _Electronic_address 'Johnson, One Moon Scientific' . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' 'peak picking' stop_ _Details . save_ save_software_4 _Saveframe_category software _Name NMRFx _Version . loop_ _Vendor _Address _Electronic_address 'Johnson, One Moon Scientific' . . stop_ loop_ _Task processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AVANCE _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-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _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' 10 . mM pH 7.4 . pD pressure 1 . atm temperature 308 . 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' 10 . mM pH 7.4 . pH pressure 1 . atm temperature 308 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_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 4.78 internal direct . . . 1.0 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_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name entity_1 _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 0 1 8NK H9 H 4.4594 0.0080 1 2 0 1 8NK H11 H 5.9156 0.0000 1 3 0 1 8NK H12 H 9.0606 0.0095 1 4 0 1 8NK H13 H 4.1155 0.0000 1 5 1 2 G H1' H 5.5184 0.0047 1 6 1 2 G H2' H 4.7222 0.0141 1 7 1 2 G H3' H 4.5285 0.0141 1 8 1 2 G H8 H 7.5930 0.0000 1 9 2 3 G H1' H 5.7632 0.0094 1 10 2 3 G H2' H 4.6547 0.0141 1 11 2 3 G H3' H 4.4593 0.0141 1 12 2 3 G H8 H 7.2767 0.0094 1 13 3 4 G H1' H 5.7188 0.0094 1 14 3 4 G H2' H 4.4634 0.0092 1 15 3 4 G H3' H 4.3666 0.0141 1 16 3 4 G H8 H 7.1084 0.0073 1 17 4 5 U H1' H 5.8262 0.0094 1 18 4 5 U H2' H 4.2836 0.0141 1 19 4 5 U H3' H 4.4355 0.0141 1 20 4 5 U H5 H 5.1220 0.0225 1 21 4 5 U H6 H 7.5815 0.0134 1 22 5 6 C H1' H 5.9506 0.0076 1 23 5 6 C H2' H 4.4667 0.0141 1 24 5 6 C H3' H 4.4063 0.0141 1 25 5 6 C H5 H 5.9774 0.0150 1 26 5 6 C H6 H 7.8944 0.0120 1 27 6 7 U H1' H 5.6570 0.0094 1 28 6 7 U H2' H 4.4267 0.0141 1 29 6 7 U H3' H 4.4406 0.0141 1 30 6 7 U H5 H 5.6800 0.0150 1 31 6 7 U H6 H 7.8726 0.0225 1 32 7 8 C H1' H 5.9573 0.0094 1 33 7 8 C H2' H 4.2874 0.0141 1 34 7 8 C H3' H 4.4554 0.0141 1 35 7 8 C H5 H 5.7726 0.0131 1 36 7 8 C H6 H 7.7453 0.0137 1 37 8 9 U H1' H 5.5337 0.0094 1 38 8 9 U H2' H 4.4955 0.0141 1 39 8 9 U H3' H 4.4383 0.0141 1 40 8 9 U H5 H 5.8985 0.0105 1 41 8 9 U H6 H 7.8719 0.0225 1 42 9 10 C H1' H 5.5347 0.0094 1 43 9 10 C H2' H 4.4899 0.0141 1 44 9 10 C H3' H 4.5227 0.0141 1 45 9 10 C H5 H 5.6956 0.0225 1 46 9 10 C H6 H 7.7397 0.0150 1 47 10 11 U H1' H 5.5598 0.0094 1 48 10 11 U H2' H 4.5293 0.0141 1 49 10 11 U H3' H 4.5555 0.0141 1 50 10 11 U H5 H 5.4182 0.0146 1 51 10 11 U H6 H 7.9383 0.0132 1 52 11 12 U H1' H 5.6285 0.0094 1 53 11 12 U H2' H 4.6055 0.0197 1 54 11 12 U H3' H 4.6086 0.0141 1 55 11 12 U H5 H 5.5863 0.0225 1 56 11 12 U H6 H 7.9419 0.0150 1 57 12 13 G H1' H 5.7429 0.0049 1 58 12 13 G H2' H 4.5449 0.0119 1 59 12 13 G H3' H 4.4674 0.0141 1 60 12 13 G H8 H 7.6809 0.0141 1 61 13 14 U H1' H 5.4043 0.0094 1 62 13 14 U H2' H 4.5201 0.0084 1 63 13 14 U H3' H 4.4615 0.0141 1 64 13 14 U H5 H 5.3953 0.0225 1 65 13 14 U H6 H 7.7381 0.0150 1 66 14 15 C H1' H 5.5321 0.0141 1 67 14 15 C H2' H 4.4150 0.0141 1 68 14 15 C H3' H 4.4660 0.0141 1 69 14 15 C H5 H 5.5044 0.0225 1 70 14 15 C H6 H 7.7462 0.0150 1 71 15 16 G H1' H 5.5883 0.0094 1 72 15 16 G H2' H 4.3735 0.0141 1 73 15 16 G H3' H 4.5160 0.0141 1 74 15 16 G H8 H 7.4664 0.0094 1 75 16 17 A H1' H 5.7091 0.0094 1 76 16 17 A H2 H 7.9538 0.0061 1 77 16 17 A H2' H 4.5823 0.0141 1 78 16 17 A H3' H 4.4167 0.0141 1 79 16 17 A H8 H 8.1924 0.0063 1 80 17 18 G H1' H 5.3014 0.0094 1 81 17 18 G H2' H 4.3014 0.0141 1 82 17 18 G H3' H 4.5439 0.0141 1 83 17 18 G H8 H 7.6326 0.0065 1 84 18 19 A H1' H 6.0959 0.0094 1 85 18 19 A H2 H 8.1458 0.0047 1 86 18 19 A H2' H 4.6486 0.0141 1 87 18 19 A H3' H 5.0643 0.0141 1 88 18 19 A H8 H 8.1839 0.0077 1 89 19 20 G H1' H 4.5383 0.0141 1 90 19 20 G H2' H 4.4188 0.0141 1 91 19 20 G H3' H 4.2451 0.0141 1 92 19 20 G H8 H 7.9331 0.0094 1 93 47 21 G H1' H 5.7415 0.0094 1 94 47 21 G H2' H 4.5983 0.0141 1 95 47 21 G H3' H 4.3129 0.0141 1 96 47 21 G H8 H 7.2009 0.0094 1 97 48 22 C H1' H 5.4373 0.0094 1 98 48 22 C H2' H 4.4114 0.0141 1 99 48 22 C H3' H 4.4680 0.0141 1 100 48 22 C H5 H 5.3190 0.0225 1 101 48 22 C H6 H 7.5866 0.0150 1 102 49 23 A H1' H 5.8498 0.0094 1 103 49 23 A H2 H 6.6653 0.0047 1 104 49 23 A H2' H 4.5628 0.0141 1 105 49 23 A H3' H 4.6540 0.0141 1 106 49 23 A H8 H 7.8496 0.0094 1 107 50 24 A H1' H 5.8322 0.0094 1 108 50 24 A H2 H 7.4480 0.0078 1 109 50 24 A H2' H 4.5937 0.0141 1 110 50 24 A H3' H 4.5204 0.0141 1 111 50 24 A H8 H 7.6339 0.0141 1 112 51 25 G H1' H 5.4411 0.0094 1 113 51 25 G H2' H 4.5300 0.0141 1 114 51 25 G H3' H 4.2821 0.0141 1 115 51 25 G H8 H 6.8373 0.0094 1 116 52 26 G H1' H 5.6627 0.0131 1 117 52 26 G H2' H 4.5255 0.0141 1 118 52 26 G H3' H 4.6475 0.0141 1 119 52 26 G H8 H 7.1623 0.0094 1 120 53 27 A H1' H 5.8902 0.0094 1 121 53 27 A H2 H 7.5457 0.0070 1 122 53 27 A H2' H 4.6660 0.0172 1 123 53 27 A H3' H 4.5826 0.0141 1 124 53 27 A H8 H 7.6782 0.0094 1 125 54 28 A H1' H 5.6881 0.0094 1 126 54 28 A H2 H 7.8056 0.0042 1 127 54 28 A H2' H 4.4161 0.0141 1 128 54 28 A H3' H 4.5593 0.0141 1 129 54 28 A H8 H 7.6975 0.0078 1 130 55 29 C H1' H 5.3805 0.0081 1 131 55 29 C H2' H 4.1337 0.0138 1 132 55 29 C H3' H 4.3664 0.0141 1 133 55 29 C H5 H 5.2193 0.0225 1 134 55 29 C H5'' H 4.1106 0.0289 2 135 55 29 C H6 H 7.5451 0.0150 1 136 56 30 C H1' H 5.4572 0.0094 1 137 56 30 C H2' H 4.3097 0.0141 1 138 56 30 C H3' H 4.4588 0.0141 1 139 56 30 C H5 H 5.3722 0.0150 1 140 56 30 C H6 H 7.7326 0.0150 1 141 57 31 C H1' H 5.4689 0.0094 1 142 57 31 C H2' H 4.5702 0.0141 1 143 57 31 C H3' H 4.4401 0.0141 1 144 57 31 C H5 H 5.3785 0.0225 1 145 57 31 C H6 H 7.6200 0.0150 1 146 58 32 A H1' H 5.8133 0.0094 1 147 58 32 A H2 H 7.4888 0.0094 1 148 58 32 A H2' H 4.3800 0.0141 1 149 58 32 A H3' H 4.4854 0.0141 1 150 58 32 A H8 H 7.9720 0.0094 1 151 59 33 C H1' H 5.3243 0.0094 1 152 59 33 C H2' H 3.9965 0.0141 1 153 59 33 C H3' H 4.2411 0.0141 1 154 59 33 C H5 H 5.3183 0.0225 1 155 59 33 C H6 H 7.3718 0.0150 1 156 60 34 U H1' H 5.8160 0.0094 1 157 60 34 U H2' H 4.1818 0.0141 1 158 60 34 U H3' H 4.0735 0.0141 1 159 60 34 U H5 H 5.6551 0.0225 1 160 60 34 U H6 H 7.7182 0.0150 1 stop_ save_