data_17408 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Chemical probe bound to HIV TAR RNA ; _BMRB_accession_number 17408 _BMRB_flat_file_name bmr17408.str _Entry_type original _Submission_date 2011-01-12 _Accession_date 2011-01-12 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'fragment based ligand design for HIV-1 TAR' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Davidson Amy . . 2 Begley Darren . . 3 Lau Carmen . . 4 Varani Gabriele . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 177 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-08-14 original author . stop_ save_ ############################# # Citation for this entry # ############################# save_citations _Saveframe_category entry_citation _Citation_full . _Citation_title 'A small-molecule probe induces a conformation in HIV TAR RNA capable of binding drug-like fragments' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 21763501 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Davidson Amy . . 2 Begley Darren . . 3 Lau Carmen . . 4 Varani Gabriele . . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_volume 410 _Journal_issue 5 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 984 _Page_last 996 _Year 2011 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'HIV TAR RNA' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'HIV TAR RNA' $HIV_TAR_RNA ARGININE $ARG 4-METHOXYNAPHTHALEN-2-AMINE $L8H 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_HIV_TAR_RNA _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common HIV_TAR_RNA _Molecular_mass 132.116 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 29 _Mol_residue_sequence ; GGCAGAUCUGAGCCUGGGAG CUCUCUGCC ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 17 G 2 18 G 3 19 C 4 20 A 5 21 G 6 22 A 7 23 U 8 24 C 9 25 U 10 26 G 11 27 A 12 28 G 13 29 C 14 30 C 15 31 U 16 32 G 17 33 G 18 34 G 19 35 A 20 36 G 21 37 C 22 38 U 23 39 C 24 40 U 25 41 C 26 42 U 27 43 G 28 44 C 29 45 C stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ############# # Ligands # ############# save_ARG _Saveframe_category ligand _Mol_type "non-polymer (L-peptide linking)" _Name_common "ARG (ARGININE)" _BMRB_code . _PDB_code ARG _Molecular_mass 175.209 _Mol_charge 1 _Mol_paramagnetic . _Mol_aromatic no _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Thu Feb 17 14:03:25 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? CA CA C . 0 . ? C C C . 0 . ? O O O . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? CD CD C . 0 . ? NE NE N . 0 . ? CZ CZ C . 0 . ? NH1 NH1 N . 0 . ? NH2 NH2 N . 1 . ? OXT OXT O . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG2 HG2 H . 0 . ? HG3 HG3 H . 0 . ? HD2 HD2 H . 0 . ? HD3 HD3 H . 0 . ? HE HE H . 0 . ? HH11 HH11 H . 0 . ? HH12 HH12 H . 0 . ? HH21 HH21 H . 0 . ? HH22 HH22 H . 0 . ? HXT HXT 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 N CA ? ? SING N H ? ? SING N H2 ? ? SING CA C ? ? SING CA CB ? ? SING CA HA ? ? DOUB C O ? ? SING C OXT ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG CD ? ? SING CG HG2 ? ? SING CG HG3 ? ? SING CD NE ? ? SING CD HD2 ? ? SING CD HD3 ? ? SING NE CZ ? ? SING NE HE ? ? SING CZ NH1 ? ? DOUB CZ NH2 ? ? SING NH1 HH11 ? ? SING NH1 HH12 ? ? SING NH2 HH21 ? ? SING NH2 HH22 ? ? SING OXT HXT ? ? stop_ _Mol_thiol_state . _Sequence_homology_query_date . save_ save_L8H _Saveframe_category ligand _Mol_type non-polymer _Name_common "L8H (4-methoxynaphthalen-2-amine)" _BMRB_code . _PDB_code L8H _Molecular_mass 173.211 _Mol_charge 0 _Mol_paramagnetic . _Mol_aromatic yes _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Thu Feb 17 14:26:53 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? CAA CAA C . 0 . ? CAF CAF C . 0 . ? CAG CAG C . 0 . ? CAH CAH C . 0 . ? CAI CAI C . 0 . ? CAJ CAJ C . 0 . ? CAK CAK C . 0 . ? OAQ OAQ O . 0 . ? CAT CAT C . 0 . ? CAU CAU C . 0 . ? CAV CAV C . 0 . ? CAW CAW C . 0 . ? HN HN H . 0 . ? HAA HAA H . 0 . ? HAAA HAAA H . 0 . ? HAAB HAAB H . 0 . ? HAF HAF H . 0 . ? HAG HAG H . 0 . ? HAH HAH H . 0 . ? HAI HAI H . 0 . ? HAJ HAJ H . 0 . ? HAK HAK H . 0 . ? H11 H11 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 N CAT ? ? SING N HN ? ? SING CAA OAQ ? ? SING CAA HAA ? ? SING CAA HAAA ? ? SING CAA HAAB ? ? DOUB CAF CAG ? ? SING CAF CAH ? ? SING CAF HAF ? ? SING CAG CAI ? ? SING CAG HAG ? ? DOUB CAH CAV ? ? SING CAH HAH ? ? DOUB CAI CAW ? ? SING CAI HAI ? ? SING CAJ CAT ? ? DOUB CAJ CAU ? ? SING CAJ HAJ ? ? DOUB CAK CAT ? ? SING CAK CAV ? ? SING CAK HAK ? ? SING OAQ CAU ? ? SING CAU CAW ? ? SING CAV CAW ? ? SING N H11 ? ? stop_ _Mol_thiol_state . _Sequence_homology_query_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $HIV_TAR_RNA 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 _Details $HIV_TAR_RNA 'enzymatic semisynthesis' . . . . . 'in vitro transcription using T7 polymerase' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '10 mM phosphate buffer, 99.99% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $HIV_TAR_RNA 1 mM 'natural abundance' $ARG 4 mM 'natural abundance' $L8H 4 mM 'natural abundance' 'potassium phosphate' 10 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '10 mM phosphate buffer, 90% H2O, 10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $HIV_TAR_RNA 1 mM 'natural abundance' $ARG 4 mM 'natural abundance' $L8H 4 mM 'natural abundance' 'potassium phosphate' 10 mM 'natural abundance' stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type solution _Details '10 mM phosphate buffer, 99.99% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $HIV_TAR_RNA 1 mM '[U-100% 13C; U-100% 15N]' $ARG 4 mM 'natural abundance' $L8H 4 mM 'natural abundance' 'potassium phosphate' 10 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_X-PLOR _Saveframe_category software _Name X-PLOR _Version . loop_ _Vendor _Address _Electronic_address 'Brunger A. T. et.al.' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 500 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DMX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H NOESY' _Sample_label $sample_1 save_ save_1H-1H_NOESY_with_WATERGATE_2 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H NOESY with WATERGATE' _Sample_label $sample_2 save_ save_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H TOCSY' _Sample_label $sample_1 save_ save_HCCH-COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name HCCH-COSY _Sample_label $sample_3 save_ save_13C_HSQC-NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '13C HSQC-NOESY' _Sample_label $sample_3 save_ ####################### # Sample conditions # ####################### 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 6.6 . pH pressure 1 . atm temperature 277 . K stop_ save_ 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 6.6 . 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 water H 1 protons ppm 4.70 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 '1H-1H NOESY' '1H-1H TOCSY' HCCH-COSY '13C HSQC-NOESY' stop_ loop_ _Sample_label $sample_1 $sample_3 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'HIV TAR RNA' _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 17 1 G H1 H 12.179 0.006 . 2 17 1 G H1' H 5.649 0.007 . 3 17 1 G H2' H 4.787 0.002 . 4 17 1 G H4' H 4.542 0.000 . 5 17 1 G H8 H 8.067 0.034 . 6 18 2 G H1 H 13.191 0.011 . 7 18 2 G H1' H 5.737 0.008 . 8 18 2 G H2' H 4.474 0.005 . 9 18 2 G H3' H 4.623 0.000 . 10 18 2 G H4' H 4.458 0.020 . 11 18 2 G H8 H 7.472 0.024 . 12 19 3 C H1' H 5.454 0.011 . 13 19 3 C H2' H 4.529 0.006 . 14 19 3 C H3' H 4.492 0.002 . 15 19 3 C H4' H 4.388 0.000 . 16 19 3 C H5 H 5.181 0.009 . 17 19 3 C H6 H 7.606 0.015 . 18 19 3 C H41 H 6.881 0.000 . 19 19 3 C H42 H 8.374 0.001 . 20 20 4 A H1' H 5.906 0.006 . 21 20 4 A H2 H 6.885 0.007 . 22 20 4 A H2' H 4.678 0.012 . 23 20 4 A H3' H 4.642 0.001 . 24 20 4 A H4' H 4.480 0.000 . 25 20 4 A H8 H 7.901 0.006 . 26 21 5 G H1 H 12.538 0.005 . 27 21 5 G H1' H 5.484 0.010 . 28 21 5 G H2' H 4.396 0.010 . 29 21 5 G H3' H 4.452 0.003 . 30 21 5 G H8 H 7.054 0.009 . 31 22 6 A H1' H 5.791 0.363 . 32 22 6 A H2 H 7.051 0.002 . 33 22 6 A H2' H 4.165 0.007 . 34 22 6 A H3' H 4.636 0.001 . 35 22 6 A H8 H 7.789 0.018 . 36 23 7 U H1' H 5.538 0.014 . 37 23 7 U H3 H 14.361 0.007 . 38 23 7 U H4' H 4.133 0.005 . 39 24 8 C H1' H 5.944 0.011 . 40 24 8 C H2' H 4.331 0.019 . 41 24 8 C H3' H 4.542 0.017 . 42 24 8 C H4' H 4.321 0.000 . 43 24 8 C H5 H 5.989 0.022 . 44 24 8 C H5' H 4.242 0.000 . 45 24 8 C H5'' H 4.108 0.000 . 46 24 8 C H6 H 7.841 0.017 . 47 25 9 U H1' H 5.962 0.013 . 48 25 9 U H2' H 4.341 0.009 . 49 25 9 U H3' H 4.612 0.013 . 50 25 9 U H4' H 4.377 0.000 . 51 25 9 U H5 H 5.795 0.017 . 52 25 9 U H6 H 7.802 0.039 . 53 26 10 G H1 H 12.533 0.003 . 54 26 10 G H1' H 5.764 0.006 . 55 26 10 G H2' H 4.472 0.015 . 56 26 10 G H3' H 4.894 0.001 . 57 26 10 G H4' H 4.589 0.000 . 58 26 10 G H8 H 7.557 0.007 . 59 27 11 A H1' H 5.921 0.007 . 60 27 11 A H2 H 7.341 0.017 . 61 27 11 A H2' H 4.744 0.006 . 62 27 11 A H3' H 4.749 0.000 . 63 27 11 A H4' H 4.557 0.000 . 64 27 11 A H8 H 7.664 0.011 . 65 27 11 A H61 H 8.432 0.000 . 66 27 11 A H62 H 7.986 0.006 . 67 28 12 G H1 H 13.745 0.005 . 68 28 12 G H1' H 5.827 0.011 . 69 28 12 G H2' H 4.500 0.007 . 70 28 12 G H3' H 4.580 0.003 . 71 28 12 G H8 H 7.704 0.008 . 72 28 12 G H21 H 7.049 0.000 . 73 28 12 G H22 H 9.055 0.004 . 74 29 13 C H1' H 5.494 0.007 . 75 29 13 C H2' H 4.010 0.008 . 76 29 13 C H3' H 4.481 0.009 . 77 29 13 C H4' H 4.333 0.000 . 78 29 13 C H5 H 5.126 0.011 . 79 29 13 C H6 H 7.631 0.012 . 80 29 13 C H41 H 7.024 0.002 . 81 29 13 C H42 H 8.498 0.006 . 82 30 14 C H1' H 5.953 0.017 . 83 30 14 C H2' H 4.348 0.007 . 84 30 14 C H3' H 4.631 0.000 . 85 30 14 C H4' H 4.486 0.018 . 86 30 14 C H5 H 5.427 0.012 . 87 30 14 C H6 H 7.524 0.009 . 88 31 15 U H1' H 5.871 0.067 . 89 31 15 U H2' H 4.268 0.018 . 90 31 15 U H3' H 4.515 0.000 . 91 31 15 U H4' H 4.215 0.019 . 92 31 15 U H5 H 5.808 0.022 . 93 31 15 U H6 H 7.780 0.033 . 94 32 16 G H1' H 5.423 0.014 . 95 32 16 G H2' H 4.585 0.051 . 96 32 16 G H3' H 4.589 0.000 . 97 32 16 G H4' H 4.098 0.000 . 98 32 16 G H8 H 7.737 0.013 . 99 33 17 G H1' H 5.354 0.009 . 100 33 17 G H2' H 4.413 0.116 . 101 33 17 G H3' H 4.155 0.165 . 102 33 17 G H4' H 3.903 0.018 . 103 33 17 G H8 H 7.574 0.011 . 104 34 18 G H1' H 5.658 0.011 . 105 34 18 G H2' H 4.948 0.025 . 106 34 18 G H3' H 4.308 0.092 . 107 34 18 G H4' H 4.369 0.028 . 108 34 18 G H8 H 7.730 0.010 . 109 35 19 A H1' H 5.951 0.008 . 110 35 19 A H2 H 7.478 0.000 . 111 35 19 A H2' H 4.708 0.000 . 112 36 20 G H1 H 13.203 0.014 . 113 36 20 G H1' H 5.540 0.008 . 114 36 20 G H2' H 4.511 0.003 . 115 36 20 G H3' H 4.697 0.003 . 116 36 20 G H8 H 7.378 0.017 . 117 37 21 C H1' H 5.558 0.010 . 118 37 21 C H2' H 4.439 0.006 . 119 37 21 C H5 H 5.284 0.009 . 120 37 21 C H6 H 7.964 0.010 . 121 37 21 C H41 H 7.056 0.009 . 122 37 21 C H42 H 9.057 0.007 . 123 38 22 U H1' H 5.630 0.009 . 124 38 22 U H2' H 4.718 0.005 . 125 38 22 U H3 H 14.502 0.005 . 126 38 22 U H3' H 4.487 0.001 . 127 38 22 U H4' H 4.380 0.000 . 128 38 22 U H5 H 5.525 0.010 . 129 38 22 U H6 H 7.929 0.007 . 130 39 23 C H1' H 5.194 0.031 . 131 39 23 C H2' H 4.441 0.002 . 132 39 23 C H5 H 5.524 0.011 . 133 39 23 C H6 H 7.463 0.011 . 134 39 23 C H41 H 7.290 0.006 . 135 39 23 C H42 H 8.414 0.001 . 136 40 24 U H1' H 5.421 0.003 . 137 40 24 U H2' H 4.309 0.006 . 138 40 24 U H3' H 4.448 0.000 . 139 40 24 U H5 H 5.425 0.008 . 140 40 24 U H6 H 7.962 0.008 . 141 41 25 C H1' H 5.419 0.002 . 142 41 25 C H2' H 4.175 0.024 . 143 41 25 C H3' H 4.483 0.000 . 144 41 25 C H5 H 5.637 0.008 . 145 41 25 C H6 H 7.882 0.012 . 146 41 25 C H41 H 7.085 0.017 . 147 41 25 C H42 H 8.355 0.008 . 148 42 26 U H1' H 5.407 0.007 . 149 42 26 U H2' H 4.519 0.007 . 150 42 26 U H3 H 13.378 0.010 . 151 42 26 U H3' H 4.566 0.011 . 152 42 26 U H4' H 4.381 0.000 . 153 42 26 U H5 H 5.288 0.007 . 154 42 26 U H6 H 7.822 0.011 . 155 43 27 G H1 H 12.441 0.008 . 156 43 27 G H1' H 5.733 0.006 . 157 43 27 G H2' H 4.425 0.008 . 158 43 27 G H3' H 4.594 0.003 . 159 43 27 G H4' H 4.474 0.000 . 160 43 27 G H8 H 7.731 0.005 . 161 43 27 G H22 H 8.374 0.009 . 162 44 28 C H1' H 5.436 0.006 . 163 44 28 C H2' H 4.158 0.013 . 164 44 28 C H3' H 4.434 0.000 . 165 44 28 C H4' H 4.348 0.002 . 166 44 28 C H5 H 5.153 0.006 . 167 44 28 C H6 H 7.671 0.006 . 168 44 28 C H41 H 6.860 0.002 . 169 44 28 C H42 H 8.486 0.006 . 170 45 29 C H1' H 5.671 0.014 . 171 45 29 C H2' H 3.981 0.023 . 172 45 29 C H3' H 4.200 0.000 . 173 45 29 C H4' H 4.117 0.021 . 174 45 29 C H5 H 5.412 0.011 . 175 45 29 C H6 H 7.611 0.005 . 176 45 29 C H41 H 6.907 0.015 . 177 45 29 C H42 H 8.262 0.004 . stop_ save_