data_17083 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of a conserved retroviral RNA packaging element by NMR spectroscopy and cryo-electron tomography ; _BMRB_accession_number 17083 _BMRB_flat_file_name bmr17083.str _Entry_type original _Submission_date 2010-07-28 _Accession_date 2010-07-28 _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 Summers Michael F. . 2 Irobalieva Rossitza N. . 3 Tolbert Blanton . . 4 Smalls-Manty Adjoa . . 5 Iyalla Kilali . . 6 Loeliger Kelsey . . 7 D'Souza Victoria . . 8 Khant Htet . . 9 Schmid Michael . . 10 Garcia Eric . . 11 Telesnitsky Alice . . 12 Chiu Wah . . 13 Miyazaki Yasuyuki . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 208 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-12-01 update BMRB 'update entry citation' 2010-10-14 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structure of a conserved retroviral RNA packaging element by NMR spectroscopy and cryo-electron tomography.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 20933521 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Miyazaki Yasuyuki . . 2 Irobalieva Rossitza N. . 3 Tolbert Blanton S. . 4 Smalls-Mantey Adjoa . . 5 Iyalla Kilali . . 6 Loeliger Kelsey . . 7 Khant Victoria . . 8 Schmid Htet . . 9 Garcia Michael F. . 10 Telesnitsky Eric L. . 11 Chiu Alice . . 12 Summers Wah . . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_name_full 'Journal of molecular biology' _Journal_volume 404 _Journal_issue 5 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 751 _Page_last 772 _Year 2010 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 65-MER _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'RNA (65-MER)' $RNA_(65-MER) 'RNA (66-MER)' $RNA_(66-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_(65-MER) _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_(65-MER) _Molecular_mass 21071.766 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 65 _Mol_residue_sequence ; GGCGGACCCGUGGUGGAACA GACGUGUUCGGAACACCCGG CCGCAACCCUGGGAGACGUC CCAGG ; loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 C 4 G 5 G 6 A 7 C 8 C 9 C 10 G 11 U 12 G 13 G 14 U 15 G 16 G 17 A 18 A 19 C 20 A 21 G 22 A 23 C 24 G 25 U 26 G 27 U 28 U 29 C 30 G 31 G 32 A 33 A 34 C 35 A 36 C 37 C 38 C 39 G 40 G 41 C 42 C 43 G 44 C 45 A 46 A 47 C 48 C 49 C 50 U 51 G 52 G 53 G 54 A 55 G 56 A 57 C 58 G 59 U 60 C 61 C 62 C 63 A 64 G 65 G stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_RNA_(66-MER) _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_(66-MER) _Molecular_mass 21416.973 _Mol_thiol_state 'not present' _Details . _Residue_count 66 _Mol_residue_sequence ; GGCGGACCCGUGGUGGAACA GACGUGUUCGGAACACCCGG CCGCAACCCUGGGAGACGUC CCAGGG ; loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 C 4 G 5 G 6 A 7 C 8 C 9 C 10 G 11 U 12 G 13 G 14 U 15 G 16 G 17 A 18 A 19 C 20 A 21 G 22 A 23 C 24 G 25 U 26 G 27 U 28 U 29 C 30 G 31 G 32 A 33 A 34 C 35 A 36 C 37 C 38 C 39 G 40 G 41 C 42 C 43 G 44 C 45 A 46 A 47 C 48 C 49 C 50 U 51 G 52 G 53 G 54 A 55 G 56 A 57 C 58 G 59 U 60 C 61 C 62 C 63 A 64 G 65 G 66 G 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 _Organism_acronym _ICTVdb_decimal_code _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $RNA_(65-MER) 'Moloney Murine Leukemia Virus' MoMLV 00.061.1.02.014.00.001. 11801 Virus . Gammaretrovirus . $RNA_(66-MER) 'Moloney Murine Leukemia Virus' MoMLV 00.061.1.02.014.00.001. 11801 Virus . Gammaretrovirus . 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 $RNA_(65-MER) 'recombinant technology' . Moloney "Murine Leukemia Virus" . pMoMuLV-SL-CD-HDV ; pMoMuLV-SL-CD-HDV was generated by PCR on pMoMuLV-SL-BCD-HDV, which contains the proviral DNA of MoMuLV. DNA fragments were amplified with oligonucleotide MoMuLV-309f (5′-CCAGTGAATTCTAATACGACTCACTATAGGCGG-ACCCGTGGTGGAACTGACGAGTTCGGAACAC-3′), carrying an Eco RI site and a T7 RNA polymerase promoter, and oligonucleotide M13r. The amplified product was inserted in the pUC19 plasmid after EcoR I and Hind III digestions (New England Biolabs). ; $RNA_(66-MER) 'recombinant technology' . Moloney "Murine Leukemia Virus" . pMoMuLV-SL-CD-HDV ; pMoMuLV-SL-CD-HDV was generated by PCR on pMoMuLV-SL-BCD-HDV, which contains the proviral DNA of MoMuLV. DNA fragments were amplified with oligonucleotide MoMuLV-309f (5′-CCAGTGAATTCTAATACGACTCACTATAGGCGG-ACCCGTGGTGGAACTGACGAGTTCGGAACAC-3′), carrying an Eco RI site and a T7 RNA polymerase promoter, and oligonucleotide M13r. The amplified product was inserted in the pUC19 plasmid after EcoR I and Hind III digestions (New England Biolabs). ; stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details 'A series of RNAs containing different isotopic labelings were used, as described in the associated paper.' loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $RNA_(65-MER) . uM 400 800 [U-2H] D2O 100 % . . 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CYANA _Saveframe_category software _Name CYANA _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 800 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_1 save_ save_2D_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 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' 80 5 mM pH 7.0 0.1 pH pressure 1 . atm temperature 273 . 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 4.776 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_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D NOESY' 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 'RNA (66-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 6.0231 . 1 2 1 1 G H2' H 4.9414 . 1 3 1 1 G H3' H 4.9116 . 1 4 1 1 G H8 H 8.1912 . 1 5 2 2 G H1' H 5.8502 . 1 6 2 2 G H3' H 4.8124 . 1 7 2 2 G H8 H 7.9551 . 1 8 3 3 C H1' H 5.5538 . 1 9 3 3 C H2' H 4.4825 . 1 10 3 3 C H3' H 4.6814 . 1 11 3 3 C H5 H 5.1824 . 1 12 3 3 C H6 H 7.6468 . 1 13 4 4 G H1' H 5.6486 . 1 14 4 4 G H8 H 7.3760 . 1 15 5 5 G H1' H 5.6382 . 1 16 5 5 G H2' H 4.3107 . 1 17 5 5 G H8 H 7.1580 . 1 18 6 6 A H1' H 5.9570 . 1 19 6 6 A H2 H 8.0468 . 1 20 6 6 A H2' H 4.7277 . 1 21 6 6 A H3' H 4.4414 . 1 22 6 6 A H8 H 7.1580 . 1 23 7 7 C H1' H 5.8656 . 1 24 7 7 C H2' H 4.2733 . 1 25 7 7 C H5 H 5.6983 . 1 26 7 7 C H6 H 7.6091 . 1 27 8 8 C H1' H 5.7701 . 1 28 8 8 C H2' H 4.4673 . 1 29 8 8 C H5 H 5.6435 . 1 30 8 8 C H6 H 7.7130 . 1 31 10 10 G H1' H 5.9007 . 1 32 10 10 G H2' H 4.5028 . 1 33 10 10 G H3' H 4.8045 . 1 34 10 10 G H8 H 7.7319 . 1 35 11 11 U H1' H 6.0063 . 1 36 11 11 U H2' H 4.4860 . 1 37 11 11 U H3' H 4.7524 . 1 38 11 11 U H5 H 5.9584 . 1 39 11 11 U H6 H 7.9006 . 1 40 12 12 G H1' H 5.8119 . 1 41 12 12 G H2' H 4.9194 . 1 42 12 12 G H3' H 4.5887 . 1 43 12 12 G H8 H 7.5578 . 1 44 13 13 G H1' H 5.8183 . 1 45 13 13 G H3' H 4.5966 . 1 46 13 13 G H8 H 7.3563 . 1 47 14 14 U H1' H 5.6207 . 1 48 14 14 U H5 H 5.1128 . 1 49 14 14 U H6 H 7.7193 . 1 50 15 15 G H1' H 6.0378 . 1 51 15 15 G H3' H 4.8244 . 1 52 15 15 G H8 H 7.7928 . 1 53 16 16 G H1' H 5.6982 . 1 54 16 16 G H2' H 4.8186 . 1 55 16 16 G H8 H 7.8280 . 1 56 17 17 A H1' H 5.9266 . 1 57 17 17 A H2 H 7.0798 . 1 58 17 17 A H2' H 4.7164 . 1 59 17 17 A H3' H 4.5964 . 1 60 17 17 A H8 H 7.8387 . 1 61 18 18 A H1' H 5.8729 . 1 62 18 18 A H2 H 7.6377 . 1 63 18 18 A H2' H 4.5930 . 1 64 18 18 A H8 H 7.7719 . 1 65 19 19 C H1' H 5.3127 . 1 66 19 19 C H2' H 4.2981 . 1 67 19 19 C H3' H 4.3757 . 1 68 19 19 C H5 H 5.1615 . 1 69 19 19 C H6 H 7.3348 . 1 70 20 20 A H1' H 6.0144 . 1 71 20 20 A H2 H 7.2762 . 1 72 20 20 A H2' H 4.8181 . 1 73 20 20 A H8 H 7.9490 . 1 74 21 21 G H1' H 5.3104 . 1 75 21 21 G H2' H 4.0939 . 1 76 21 21 G H3' H 4.7084 . 1 77 21 21 G H8 H 7.0151 . 1 78 22 22 A H1' H 5.9014 . 1 79 22 22 A H2 H 8.0472 . 1 80 22 22 A H3' H 4.6141 . 1 81 22 22 A H8 H 8.5937 . 1 82 23 23 C H1' H 5.6367 . 1 83 23 23 C H5 H 5.5574 . 1 84 23 23 C H6 H 8.0954 . 1 85 24 24 G H1' H 5.9499 . 1 86 24 24 G H2' H 4.7732 . 1 87 24 24 G H3' H 4.6575 . 1 88 24 24 G H8 H 7.6802 . 1 89 25 25 U H1' H 3.8665 . 1 90 25 25 U H2' H 4.8520 . 1 91 25 25 U H3' H 4.3357 . 1 92 25 25 U H5 H 5.8894 . 1 93 25 25 U H6 H 8.2432 . 1 94 26 26 G H1' H 5.8218 . 1 95 26 26 G H2' H 4.3088 . 1 96 26 26 G H3' H 4.0656 . 1 97 26 26 G H4' H 2.7904 . 1 98 26 26 G H8 H 7.6096 . 1 99 27 27 U H1' H 5.5093 . 1 100 27 27 U H6 H 7.8127 . 1 101 28 28 U H1' H 5.3607 . 1 102 28 28 U H5 H 5.1092 . 1 103 28 28 U H6 H 7.7123 . 1 104 29 29 C H1' H 5.4070 . 1 105 29 29 C H5 H 5.4948 . 1 106 29 29 C H6 H 7.6322 . 1 107 30 30 G H1' H 5.1808 . 1 108 30 30 G H2' H 3.9167 . 1 109 30 30 G H3' H 4.4457 . 1 110 30 30 G H8 H 7.3182 . 1 111 31 31 G H1' H 5.3854 . 1 112 31 31 G H2' H 4.5363 . 1 113 31 31 G H3' H 4.5838 . 1 114 31 31 G H8 H 7.4980 . 1 115 32 32 A H1' H 5.7731 . 1 116 32 32 A H2 H 7.7568 . 1 117 32 32 A H2' H 4.6570 . 1 118 32 32 A H8 H 8.0874 . 1 119 33 33 A H1' H 5.7731 . 1 120 33 33 A H2 H 8.0456 . 1 121 33 33 A H8 H 8.1253 . 1 122 34 34 C H1' H 5.2386 . 1 123 34 34 C H2' H 4.2931 . 1 124 34 34 C H3' H 4.6072 . 1 125 34 34 C H5 H 5.6418 . 1 126 34 34 C H6 H 7.7740 . 1 127 35 35 A H1' H 5.9626 . 1 128 35 35 A H2 H 7.6545 . 1 129 35 35 A H2' H 4.4905 . 1 130 35 35 A H3' H 4.6866 . 1 131 35 35 A H8 H 8.1495 . 1 132 36 36 C H1' H 5.4477 . 1 133 36 36 C H5 H 5.3041 . 1 134 36 36 C H6 H 7.5497 . 1 135 37 37 C H1' H 5.5044 . 1 136 37 37 C H5 H 5.4419 . 1 137 37 37 C H6 H 7.5848 . 1 138 38 38 C H1' H 5.4600 . 1 139 38 38 C H5 H 5.4616 . 1 140 38 38 C H6 H 7.7496 . 1 141 39 39 G H1' H 5.6538 . 1 142 39 39 G H2' H 4.6818 . 1 143 39 39 G H8 H 7.4752 . 1 144 40 40 G H1' H 5.6932 . 1 145 40 40 G H8 H 7.1151 . 1 146 41 41 C H5 H 5.3205 . 1 147 41 41 C H6 H 7.5315 . 1 148 42 42 C H1' H 5.4056 . 1 149 43 43 G H1' H 5.6118 . 1 150 43 43 G H8 H 7.4220 . 1 151 44 44 C H1' H 5.4419 . 1 152 44 44 C H5 H 5.0401 . 1 153 44 44 C H6 H 6.9160 . 1 154 45 45 A H1' H 5.8225 . 1 155 45 45 A H2 H 7.0680 . 1 156 45 45 A H8 H 7.8454 . 1 157 46 46 A H1' H 5.3569 . 1 158 46 46 A H2 H 7.8959 . 1 159 46 46 A H2' H 4.4504 . 1 160 46 46 A H8 H 7.6511 . 1 161 51 51 G H1' H 5.7745 . 1 162 51 51 G H2' H 4.5832 . 1 163 51 51 G H3' H 4.5974 . 1 164 51 51 G H8 H 7.7134 . 1 165 52 52 G H1' H 5.6524 . 1 166 52 52 G H2' H 4.6761 . 1 167 52 52 G H8 H 7.1528 . 1 168 53 53 G H1' H 5.6902 . 1 169 53 53 G H8 H 7.0561 . 1 170 54 54 A H1' H 6.0389 . 1 171 54 54 A H2 H 7.8688 . 1 172 54 54 A H8 H 7.0732 . 1 173 55 55 G H1' H 5.3442 . 1 174 55 55 G H2' H 4.1123 . 1 175 55 55 G H3' H 4.7077 . 1 176 55 55 G H8 H 7.0180 . 1 177 56 56 A H1' H 5.9079 . 1 178 56 56 A H2 H 7.9908 . 1 179 56 56 A H8 H 8.5838 . 1 180 57 57 C H1' H 5.6634 . 1 181 57 57 C H5 H 5.6113 . 1 182 57 57 C H6 H 8.1494 . 1 183 58 58 G H1' H 5.9506 . 1 184 58 58 G H2' H 4.7732 . 1 185 58 58 G H3' H 4.6700 . 1 186 58 58 G H8 H 7.6511 . 1 187 59 59 U H3' H 4.3375 . 1 188 59 59 U H5 H 5.8894 . 1 189 59 59 U H6 H 8.2717 . 1 190 60 60 C H1' H 5.3090 . 1 191 60 60 C H4' H 2.7614 . 1 192 60 60 C H5 H 5.4980 . 1 193 60 60 C H6 H 7.7670 . 1 194 62 62 C H1' H 5.6570 . 1 195 63 63 A H1' H 5.8692 . 1 196 63 63 A H2 H 6.9221 . 1 197 63 63 A H2' H 4.6194 . 1 198 63 63 A H3' H 4.5553 . 1 199 63 63 A H8 H 7.9498 . 1 200 64 64 G H1' H 5.5785 . 1 201 64 64 G H2' H 4.5232 . 1 202 64 64 G H3' H 4.4106 . 1 203 64 64 G H8 H 7.1018 . 1 204 65 65 G H1' H 5.6613 . 1 205 65 65 G H8 H 7.0881 . 1 206 66 66 G H1' H 6.1145 . 1 207 66 66 G H3' H 4.6467 . 1 208 66 66 G H8 H 7.1880 . 1 stop_ save_