data_27289 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR and Molecular Dynamics Approach ; _BMRB_accession_number 27289 _BMRB_flat_file_name bmr27289.str _Entry_type original _Submission_date 2017-10-23 _Accession_date 2017-10-23 _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 Keane Sarah C. . 2 Summers Michael F. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 214 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2018-02-08 original BMRB . stop_ _Original_release_date 2017-10-24 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR, and Molecular Dynamics Approach ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 29398526 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Zhang Kaiming . . 2 Keane Sarah C. . 3 Zhaoming Su . . 4 Irobalieva Rossitza N. . 5 Chen Muyuan . . 6 Van Verna . . 7 Sciandra Carly A. . 8 Marchant Jan . . 9 Heng Xiao . . 10 Schmid Michael F. . 11 Case David A. . 12 Ludtke Steven J. . 13 Summers Michael F. . 14 Chiu Wah . . stop_ _Journal_abbreviation Structure _Journal_volume S0969-2126 _Journal_issue 18 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 30001 _Page_last 30007 _Year 2018 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name DIS _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label DIS $DIS 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_DIS _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common DIS _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 47 _Mol_residue_sequence ; GGCAGGACUCGGCUUGCUGA AGCGCGCACGGCAAGAGGCG AGGGGCC ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 G 2 237 G 3 238 C 4 239 A 5 240 G 6 241 G 7 242 A 8 243 C 9 244 U 10 245 C 11 246 G 12 247 G 13 248 C 14 249 U 15 250 U 16 251 G 17 252 C 18 253 U 19 254 G 20 255 A 21 256 A 22 257 G 23 258 C 24 259 G 25 260 C 26 261 G 27 262 C 28 263 A 29 264 C 30 265 G 31 266 G 32 267 C 33 268 A 34 269 A 35 270 G 36 271 A 37 272 G 38 273 G 39 274 C 40 275 G 41 276 A 42 277 G 43 278 G 44 279 G 45 280 G 46 281 C 47 282 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 $DIS 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_type _Vector_name $DIS 'recombinant technology' . . . . n/a n/a stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_DIS_H _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DIS 300 uM 'natural abundance' TRIS 20 mM [U-2H] stop_ save_ save_DIS_A2rGr _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DIS 300 uM A2rGr TRIS 20 mM [U-2H] stop_ save_ save_DIS_A28GH _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DIS 300 uM A28GH TRIS 20 mM [U-2H] stop_ save_ save_DIS_G8C6r _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DIS 300 uM G8C6r TRIS 20 mM [U-2H] stop_ save_ ############################ # Computer software used # ############################ save_NMRView _Saveframe_category software _Name NMRView _Version . loop_ _Vendor _Address _Electronic_address 'Johnson, One Moon Scientific' . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' processing 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_CYANA _Saveframe_category software _Name CYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'geometry optimization' 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 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 $DIS_H save_ save_2D_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $DIS_A2rGr save_ save_2D_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $DIS_A28GH save_ save_2D_1H-1H_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $DIS_G8C6r save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7.5 . pH pressure 1 . atm temperature 308 . 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 4.6588 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 1H-1H NOESY' stop_ loop_ _Sample_label $DIS_H $DIS_A2rGr $DIS_A28GH $DIS_G8C6r stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name DIS _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 5.8120 0.0330 1 2 1 1 G H2' H 4.9080 0.0140 1 3 1 1 G H3' H 4.7296 0.0139 1 4 1 1 G H8 H 8.1153 0.0103 1 5 237 2 G H1' H 5.8915 0.0068 1 6 237 2 G H2' H 4.5829 0.0000 1 7 237 2 G H3' H 4.4961 0.0268 1 8 237 2 G H8 H 7.6073 0.0085 1 9 238 3 C H1' H 5.4501 0.0127 1 10 238 3 C H2' H 4.5115 0.0000 1 11 238 3 C H3' H 4.3765 0.0000 1 12 238 3 C H5 H 5.1653 0.0132 1 13 238 3 C H6 H 7.4190 0.0255 1 14 239 4 A H1' H 5.8778 0.0057 1 15 239 4 A H2 H 7.1988 0.0095 1 16 239 4 A H2' H 4.1943 0.0000 1 17 239 4 A H3' H 4.5329 0.0000 1 18 239 4 A H8 H 7.8910 0.0094 1 19 240 5 G H1' H 5.2352 0.0243 1 20 240 5 G H2' H 4.2334 0.0272 1 21 240 5 G H3' H 4.6697 0.0310 1 22 240 5 G H8 H 7.5854 0.0123 1 23 241 6 G H1' H 5.8527 0.0387 1 24 241 6 G H2' H 4.8038 0.0163 1 25 241 6 G H3' H 4.7678 0.0163 1 26 241 6 G H8 H 7.9539 0.0078 1 27 242 7 A H1' H 5.9193 0.0075 1 28 242 7 A H2 H 7.9606 0.0110 1 29 242 7 A H2' H 4.8198 0.0165 1 30 242 7 A H3' H 4.5562 0.0000 1 31 242 7 A H8 H 8.2362 0.0145 1 32 243 8 C H1' H 5.2069 0.0178 1 33 243 8 C H2' H 4.2386 0.0000 1 34 243 8 C H3' H 4.4233 0.0000 1 35 243 8 C H5 H 5.5470 0.0203 1 36 243 8 C H6 H 7.6506 0.0135 1 37 244 9 U H1' H 5.5109 0.0117 1 38 244 9 U H2' H 4.2561 0.0000 1 39 244 9 U H3' H 4.4260 0.0000 1 40 244 9 U H5 H 5.4040 0.0109 1 41 244 9 U H6 H 7.9312 0.0082 1 42 245 10 C H1' H 5.5482 0.0191 1 43 245 10 C H2' H 4.4509 0.0000 1 44 245 10 C H3' H 4.5030 0.0000 1 45 245 10 C H5 H 5.6120 0.0000 1 46 245 10 C H6 H 7.7974 0.0000 1 47 246 11 G H1' H 5.6481 0.0052 1 48 246 11 G H2' H 4.6484 0.0103 1 49 246 11 G H3' H 4.5443 0.0169 1 50 246 11 G H8 H 7.4965 0.0049 1 51 247 12 G H1' H 5.7335 0.0161 1 52 247 12 G H2' H 4.5982 0.0000 1 53 247 12 G H3' H 4.5017 0.0160 1 54 247 12 G H8 H 7.4590 0.0075 1 55 248 13 C H1' H 5.4861 0.0000 1 56 248 13 C H2' H 4.3477 0.0000 1 57 248 13 C H3' H 4.4424 0.0000 1 58 248 13 C H5 H 5.3700 0.0000 1 59 248 13 C H6 H 7.6444 0.0000 1 60 249 14 U H1' H 5.9078 0.0000 1 61 249 14 U H2' H 4.5119 0.0000 1 62 249 14 U H3' H 4.4333 0.0000 1 63 249 14 U H5 H 5.3980 0.0000 1 64 249 14 U H6 H 7.8979 0.0000 1 65 250 15 U H1' H 5.6107 0.0000 1 66 250 15 U H2' H 4.5139 0.0000 1 67 250 15 U H3' H 4.4249 0.0000 1 68 250 15 U H5 H 5.5538 0.0000 1 69 250 15 U H6 H 7.9020 0.0000 1 70 251 16 G H1' H 5.7298 0.0237 1 71 251 16 G H2' H 4.4913 0.0000 1 72 251 16 G H3' H 4.4906 0.0000 1 73 251 16 G H8 H 7.7410 0.0113 1 74 252 17 C H1' H 5.4083 0.0000 1 75 252 17 C H2' H 4.5235 0.0000 1 76 252 17 C H3' H 4.2389 0.0000 1 77 252 17 C H5 H 5.0945 0.0000 1 78 252 17 C H6 H 7.4638 0.0000 1 79 253 18 U H1' H 5.5693 0.0000 1 80 253 18 U H2' H 4.2894 0.0000 1 81 253 18 U H3' H 4.5313 0.0000 1 82 253 18 U H5 H 5.6039 0.0000 1 83 253 18 U H6 H 7.6568 0.0000 1 84 254 19 G H1' H 5.6322 0.0285 1 85 254 19 G H2' H 4.3557 0.0204 1 86 254 19 G H3' H 4.6175 0.0204 1 87 254 19 G H8 H 7.7440 0.0102 1 88 255 20 A H1' H 5.7772 0.0036 1 89 255 20 A H2 H 7.7799 0.0087 1 90 255 20 A H2' H 4.4443 0.0000 1 91 255 20 A H3' H 4.6280 0.0112 1 92 255 20 A H8 H 8.0199 0.0088 1 93 256 21 A H1' H 5.8710 0.0082 1 94 256 21 A H2 H 8.0425 0.0097 1 95 256 21 A H2' H 4.6142 0.0000 1 96 256 21 A H3' H 4.6991 0.0000 1 97 256 21 A H8 H 8.1822 0.0073 1 98 257 22 G H1' H 5.5879 0.0206 1 99 257 22 G H2' H 4.6484 0.0000 1 100 257 22 G H3' H 4.4916 0.0188 1 101 257 22 G H8 H 7.6899 0.0092 1 102 258 23 C H1' H 5.5185 0.0000 1 103 258 23 C H2' H 4.4956 0.0000 1 104 258 23 C H3' H 4.4555 0.0000 1 105 258 23 C H5 H 5.1544 0.0000 1 106 258 23 C H6 H 7.5780 0.0000 1 107 259 24 G H1' H 5.6905 0.0093 1 108 259 24 G H2' H 4.4963 0.0000 1 109 259 24 G H3' H 4.4619 0.0000 1 110 259 24 G H8 H 7.4854 0.0105 1 111 260 25 C H1' H 5.4608 0.0000 1 112 260 25 C H2' H 4.5105 0.0000 1 113 260 25 C H3' H 4.4521 0.0000 1 114 260 25 C H5 H 5.1448 0.0000 1 115 260 25 C H6 H 7.5461 0.0000 1 116 261 26 G H1' H 5.7002 0.0230 1 117 261 26 G H2' H 4.4602 0.0000 1 118 261 26 G H3' H 4.5006 0.0000 1 119 261 26 G H8 H 7.4861 0.0054 1 120 262 27 C H1' H 5.4774 0.0000 1 121 262 27 C H2' H 4.4605 0.0000 1 122 262 27 C H3' H 4.4412 0.0000 1 123 262 27 C H5 H 5.1414 0.0000 1 124 262 27 C H6 H 7.4492 0.0000 1 125 263 28 A H1' H 5.9210 0.0233 1 126 263 28 A H2 H 7.5776 0.0116 1 127 263 28 A H2' H 4.4646 0.0270 1 128 263 28 A H3' H 4.6283 0.0000 1 129 263 28 A H8 H 7.9870 0.0000 1 130 264 29 C H1' H 5.3795 0.0000 1 131 264 29 C H2' H 4.4132 0.0000 1 132 264 29 C H3' H 4.0816 0.0000 1 133 264 29 C H5 H 5.3642 0.0000 1 134 264 29 C H6 H 7.5184 0.0000 1 135 265 30 G H1' H 5.6220 0.0078 1 136 265 30 G H2' H 4.6839 0.0000 1 137 265 30 G H3' H 4.4677 0.0178 1 138 265 30 G H8 H 7.5695 0.0118 1 139 266 31 G H1' H 5.6513 0.0340 1 140 266 31 G H2' H 4.4597 0.0000 1 141 266 31 G H3' H 4.4627 0.0000 1 142 266 31 G H8 H 7.1941 0.0096 1 143 267 32 C H1' H 5.4562 0.0000 1 144 267 32 C H2' H 4.5093 0.0000 1 145 267 32 C H3' H 4.4443 0.0000 1 146 267 32 C H5 H 5.1621 0.0000 1 147 267 32 C H6 H 7.4881 0.0000 1 148 268 33 A H1' H 5.8332 0.0143 1 149 268 33 A H2 H 6.6990 0.0147 1 150 268 33 A H2' H 4.4356 0.0000 1 151 268 33 A H3' H 4.5249 0.0000 1 152 268 33 A H8 H 7.9028 0.0000 1 153 269 34 A H1' H 5.7230 0.0305 1 154 269 34 A H2 H 7.3872 0.0104 1 155 269 34 A H2' H 4.4281 0.0000 1 156 269 34 A H3' H 4.5144 0.0092 1 157 269 34 A H8 H 7.6538 0.0000 1 158 270 35 G H1' H 5.4488 0.0149 1 159 270 35 G H2' H 4.2412 0.0145 1 160 270 35 G H3' H 4.4608 0.0122 1 161 270 35 G H8 H 7.1314 0.0138 1 162 271 36 A H1' H 5.8127 0.0182 1 163 271 36 A H2 H 7.6896 0.0060 1 164 271 36 A H2' H 4.3617 0.0000 1 165 271 36 A H3' H 4.5303 0.0000 1 166 271 36 A H8 H 7.8369 0.0069 1 167 272 37 G H1' H 5.5870 0.0249 1 168 272 37 G H2' H 4.5669 0.0000 1 169 272 37 G H3' H 4.4008 0.0000 1 170 272 37 G H8 H 7.5939 0.0609 1 171 273 38 G H1' H 5.7874 0.0058 1 172 273 38 G H2' H 4.5684 0.0279 1 173 273 38 G H3' H 4.7588 0.0097 1 174 273 38 G H8 H 7.8443 0.0063 1 175 274 39 C H1' H 5.6343 0.0000 1 176 274 39 C H2' H 4.5603 0.0000 1 177 274 39 C H3' H 4.4833 0.0000 1 178 274 39 C H5 H 5.7698 0.0000 1 179 274 39 C H6 H 7.6965 0.0000 1 180 275 40 G H1' H 5.7360 0.0181 1 181 275 40 G H2' H 4.6985 0.0000 1 182 275 40 G H3' H 4.6509 0.0188 1 183 275 40 G H8 H 7.6494 0.0036 1 184 276 41 A H1' H 5.8882 0.0068 1 185 276 41 A H2 H 7.4153 0.0104 1 186 276 41 A H2' H 4.6592 0.0000 1 187 276 41 A H3' H 4.4859 0.0000 1 188 276 41 A H8 H 7.7480 0.0071 1 189 277 42 G H1' H 5.4927 0.0143 1 190 277 42 G H2' H 4.3035 0.0000 1 191 277 42 G H3' H 4.4335 0.0000 1 192 277 42 G H8 H 7.0506 0.0150 1 193 278 43 G H1' H 5.7063 0.0054 1 194 278 43 G H2' H 4.4060 0.0231 1 195 278 43 G H3' H 4.6704 0.0000 1 196 278 43 G H8 H 7.5971 0.0146 1 197 279 44 G H1' H 5.7834 0.0075 1 198 279 44 G H2' H 4.8962 0.0243 1 199 279 44 G H3' H 4.7383 0.0134 1 200 279 44 G H8 H 7.7220 0.0155 1 201 280 45 G H1' H 5.8423 0.0045 1 202 280 45 G H2' H 4.7139 0.0178 1 203 280 45 G H3' H 4.6061 0.0110 1 204 280 45 G H8 H 7.9179 0.0078 1 205 281 46 C H1' H 5.5278 0.0045 1 206 281 46 C H2' H 4.2888 0.0000 1 207 281 46 C H3' H 4.4739 0.0000 1 208 281 46 C H5 H 5.2581 0.0170 1 209 281 46 C H6 H 7.7238 0.0131 1 210 282 47 C H1' H 5.7767 0.0000 1 211 282 47 C H2' H 4.0072 0.0000 1 212 282 47 C H3' H 4.1773 0.0000 1 213 282 47 C H5 H 5.5327 0.0000 1 214 282 47 C H6 H 7.6682 0.0000 1 stop_ save_