data_17309 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of coronaviral stem-loop 2 (SL2) ; _BMRB_accession_number 17309 _BMRB_flat_file_name bmr17309.str _Entry_type original _Submission_date 2010-11-21 _Accession_date 2010-11-21 _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 Lee 'Chul Won' . . 2 Li Lichun . . 3 Giedroc David P. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 123 "13C chemical shifts" 35 "31P chemical shifts" 4 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2011-04-08 update BMRB 'update entry citation' 2010-12-02 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_Citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title 'The solution structure of coronaviral stem-loop 2 (SL2) reveals a canonical CUYG tetraloop fold.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 21382373 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Lee 'Chul Won' . . 2 Li Lichun . . 3 Giedroc David P. . stop_ _Journal_abbreviation 'FEBS Lett.' _Journal_name_full 'FEBS letters' _Journal_volume 585 _Journal_issue 7 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1049 _Page_last 1053 _Year 2011 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'coronavirus stem-loop 2' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'coronavirus stem-loop 2' $SL2 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_SL2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common SL2 _Molecular_mass 135.128 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 16 _Mol_residue_sequence GAUCUCUUGUAGAUCA loop_ _Residue_seq_code _Residue_label 1 G 2 A 3 U 4 C 5 U 6 C 7 U 8 U 9 G 10 U 11 A 12 G 13 A 14 U 15 C 16 A 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 _ICTVdb_decimal_code _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $SL2 coronavirus 03.019.0.01.004. 693996 virus . Alphacoronavirus Alphacoronavirus_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 $SL2 'in vitro transcription' . Escherichia coli . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_SL2_of_SARS_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $SL2 . mM 0.8 2 'natural abundance' 'potassium phosphate' 10 mM . . 'natural abundance' DSS 0.1 mM . . 'natural abundance' D2O 100 % . . 'natural abundance' stop_ save_ save_SL2_of_SARS_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $SL2 . mM 0.8 2 '[U-13C; U-15N]-Ura' 'potassium phosphate' 10 mM . . 'natural abundance' DSS 0.1 mM . . 'natural abundance' D2O 10 % . . 'natural abundance' H2O 90 % . . 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ 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 refinement stop_ _Details . save_ save_CYANA _Saveframe_category software _Name CYANA _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_NMRView _Saveframe_category software _Name NMRView _Version . loop_ _Vendor _Address _Electronic_address 'Johnson, One Moon Scientific' . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' 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_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 500 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _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 $SL2_of_SARS_1 save_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $SL2_of_SARS_1 save_ save_2D_1H-13C_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $SL2_of_SARS_1 save_ save_3D_HCCH-TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HCCH-TOCSY' _Sample_label $SL2_of_SARS_1 save_ save_2D_HNCCCH_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D HNCCCH' _Sample_label $SL2_of_SARS_1 save_ save_2D_H(CCN)H-TOCSY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D H(CCN)H-TOCSY' _Sample_label $SL2_of_SARS_1 save_ save_2D_HCN-HMQC_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D HCN-HMQC' _Sample_label $SL2_of_SARS_1 save_ save_2D_HCN-TROSY_8 _Saveframe_category NMR_applied_experiment _Experiment_name '2D HCN-TROSY' _Sample_label $SL2_of_SARS_1 save_ save_2D_HCNCH_9 _Saveframe_category NMR_applied_experiment _Experiment_name '2D HCNCH' _Sample_label $SL2_of_SARS_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.0 . pH pressure 1 . atm temperature 298 0.1 K stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.0 . pH pressure 1 . atm temperature 283 0.1 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 C 13 'methyl protons' ppm 0.00 . indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 DSS P 31 'methyl protons' ppm 0.00 . indirect . . . 0.404808636 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' '2D 1H-1H TOCSY' '3D HCCH-TOCSY' '2D HNCCCH' '2D H(CCN)H-TOCSY' '2D HCN-HMQC' '2D HCNCH' stop_ loop_ _Sample_label $SL2_of_SARS_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'coronavirus stem-loop 2' _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 12.0500 0.02 1 2 1 1 G H1' H 5.8980 0.02 1 3 1 1 G H2' H 4.9230 0.02 1 4 1 1 G H3' H 4.3340 0.02 1 5 1 1 G H4' H 4.7430 0.02 1 6 1 1 G H5' H 4.4700 0.02 2 7 1 1 G H5'' H 4.6280 0.02 2 8 1 1 G H8 H 8.1940 0.02 1 9 2 2 A H1' H 6.0280 0.02 1 10 2 2 A H2 H 7.7850 0.02 1 11 2 2 A H2' H 4.5880 0.02 1 12 2 2 A H3' H 4.6430 0.02 1 13 2 2 A H8 H 8.0360 0.02 1 14 3 3 U H1' H 5.5170 0.02 1 15 3 3 U H2' H 4.4620 0.02 1 16 3 3 U H3 H 14.1900 0.02 1 17 3 3 U H3' H 4.4380 0.02 1 18 3 3 U H4' H 4.4220 0.02 1 19 3 3 U H5 H 5.0630 0.02 1 20 3 3 U H5' H 4.5690 0.02 2 21 3 3 U H5'' H 4.0910 0.02 2 22 3 3 U H6 H 7.6130 0.02 1 23 3 3 U C1' C 93.3700 0.3 1 24 3 3 U C2' C 75.4500 0.3 1 25 3 3 U C3' C 72.4500 0.3 1 26 3 3 U C4' C 82.0100 0.3 1 27 3 3 U C5 C 102.7000 0.3 1 28 3 3 U C5' C 64.6000 0.3 1 29 4 4 C H1' H 5.3880 0.02 1 30 4 4 C H2' H 4.3250 0.02 1 31 4 4 C H3' H 4.4070 0.02 1 32 4 4 C H5 H 5.6250 0.02 1 33 4 4 C H6 H 7.7960 0.02 1 34 4 4 C H41 H 7.0270 0.02 2 35 4 4 C H42 H 8.4370 0.02 2 36 5 5 U H1' H 5.5480 0.02 1 37 5 5 U H2' H 4.2360 0.02 1 38 5 5 U H3 H 13.6400 0.02 1 39 5 5 U H3' H 4.5400 0.02 1 40 5 5 U H4' H 4.3800 0.02 1 41 5 5 U H5 H 5.3940 0.02 1 42 5 5 U H5' H 4.5860 0.02 2 43 5 5 U H5'' H 4.0920 0.02 2 44 5 5 U H6 H 7.8730 0.02 1 45 5 5 U C1' C 93.9800 0.3 1 46 5 5 U C2' C 75.4600 0.3 1 47 5 5 U C3' C 72.2900 0.3 1 48 5 5 U C4' C 82.3500 0.3 1 49 5 5 U C5 C 103.2000 0.3 1 50 5 5 U C5' C 64.3600 0.3 1 51 6 6 C H1' H 5.7450 0.02 1 52 6 6 C H2' H 4.1770 0.02 1 53 6 6 C H3' H 4.5620 0.02 1 54 6 6 C H4' H 4.4400 0.02 1 55 6 6 C H5 H 5.6790 0.02 1 56 6 6 C H5' H 4.0730 0.02 2 57 6 6 C H6 H 7.6820 0.02 1 58 6 6 C H41 H 7.2020 0.02 2 59 6 6 C H42 H 7.9920 0.02 2 60 7 7 U H1' H 5.9980 0.02 1 61 7 7 U H2' H 4.3970 0.02 1 62 7 7 U H3 H 11.2200 0.02 1 63 7 7 U H3' H 4.3960 0.02 1 64 7 7 U H4' H 4.3550 0.02 1 65 7 7 U H5 H 5.9110 0.02 1 66 7 7 U H5' H 4.1540 0.02 2 67 7 7 U H5'' H 4.0540 0.02 2 68 7 7 U H6 H 7.9420 0.02 1 69 7 7 U C1' C 89.8600 0.3 1 70 7 7 U C2' C 75.6900 0.3 1 71 7 7 U C3' C 77.9700 0.3 1 72 7 7 U C4' C 86.1400 0.3 1 73 7 7 U C5 C 105.4000 0.3 1 74 7 7 U C5' C 67.4300 0.3 1 75 7 7 U P P -3.5440 0.02 1 76 8 8 U H1' H 5.2910 0.02 1 77 8 8 U H2' H 3.9680 0.02 1 78 8 8 U H3' H 4.4330 0.02 1 79 8 8 U H4' H 3.8540 0.02 1 80 8 8 U H5 H 5.5340 0.02 1 81 8 8 U H5' H 3.9020 0.02 2 82 8 8 U H5'' H 3.8300 0.02 2 83 8 8 U H6 H 7.5020 0.02 1 84 8 8 U C1' C 88.9400 0.3 1 85 8 8 U C2' C 76.9800 0.3 1 86 8 8 U C3' C 79.3300 0.3 1 87 8 8 U C4' C 85.5000 0.3 1 88 8 8 U C5 C 104.9000 0.3 1 89 8 8 U C5' C 68.2100 0.3 1 90 8 8 U P P -4.3240 0.02 1 91 9 9 G H1' H 5.9200 0.02 1 92 9 9 G H2' H 5.0440 0.02 1 93 9 9 G H3' H 4.9190 0.02 1 94 9 9 G H4' H 4.4920 0.02 1 95 9 9 G H5' H 3.8750 0.02 2 96 9 9 G H5'' H 4.0700 0.02 2 97 9 9 G H8 H 7.8230 0.02 1 98 10 10 U H1' H 6.0630 0.02 1 99 10 10 U H2' H 4.5680 0.02 1 100 10 10 U H3' H 4.8160 0.02 1 101 10 10 U H4' H 4.5770 0.02 1 102 10 10 U H5 H 5.9690 0.02 1 103 10 10 U H5' H 4.3260 0.02 2 104 10 10 U H5'' H 4.3270 0.02 2 105 10 10 U H6 H 7.9040 0.02 1 106 10 10 U C1' C 91.7000 0.3 1 107 10 10 U C2' C 75.5700 0.3 1 108 10 10 U C3' C 76.3800 0.3 1 109 10 10 U C4' C 85.4800 0.3 1 110 10 10 U C5 C 105.4000 0.3 1 111 10 10 U C5' C 68.1000 0.3 1 112 10 10 U P P -3.6200 0.02 1 113 11 11 A H1' H 5.7380 0.02 1 114 11 11 A H2 H 7.5380 0.02 1 115 11 11 A H2' H 4.7590 0.02 1 116 11 11 A H3' H 4.5580 0.02 1 117 11 11 A H4' H 4.4880 0.02 1 118 11 11 A H5' H 4.2480 0.02 2 119 11 11 A H5'' H 4.2450 0.02 2 120 11 11 A H8 H 7.7490 0.02 1 121 11 11 A P P -5.0850 0.02 1 122 12 12 G H1 H 12.6800 0.02 1 123 12 12 G H1' H 5.7070 0.02 1 124 12 12 G H2' H 4.5960 0.02 1 125 12 12 G H3' H 4.5000 0.02 1 126 12 12 G H4' H 4.1110 0.02 1 127 12 12 G H5' H 4.1010 0.02 2 128 12 12 G H8 H 7.2340 0.02 1 129 12 12 G H21 H 6.0950 0.02 2 130 12 12 G H22 H 8.1300 0.02 2 131 13 13 A H1' H 5.9480 0.02 1 132 13 13 A H2 H 7.7950 0.02 1 133 13 13 A H2' H 4.4970 0.02 1 134 13 13 A H3' H 4.5680 0.02 1 135 13 13 A H8 H 7.7230 0.02 1 136 14 14 U H1' H 5.5060 0.02 1 137 14 14 U H2' H 4.4090 0.02 1 138 14 14 U H3 H 14.1400 0.02 1 139 14 14 U H3' H 4.3660 0.02 1 140 14 14 U H4' H 4.4340 0.02 1 141 14 14 U H5 H 4.9950 0.02 1 142 14 14 U H5' H 4.5320 0.02 2 143 14 14 U H5'' H 4.0530 0.02 2 144 14 14 U H6 H 7.5820 0.02 1 145 14 14 U C2' C 75.4500 0.3 1 146 14 14 U C3' C 72.2800 0.3 1 147 14 14 U C4' C 82.0500 0.3 1 148 14 14 U C5 C 102.6000 0.3 1 149 14 14 U C5' C 64.4300 0.3 1 150 15 15 C H1' H 5.5760 0.02 1 151 15 15 C H2' H 4.3800 0.02 1 152 15 15 C H3' H 4.4100 0.02 1 153 15 15 C H5 H 5.5060 0.02 1 154 15 15 C H5' H 4.1030 0.02 2 155 15 15 C H6 H 7.6800 0.02 1 156 15 15 C H41 H 6.9950 0.02 2 157 15 15 C H42 H 8.1820 0.02 2 158 16 16 A H1' H 5.9460 0.02 1 159 16 16 A H2 H 7.3780 0.02 1 160 16 16 A H2' H 4.2980 0.02 1 161 16 16 A H3' H 4.4120 0.02 1 162 16 16 A H8 H 8.0740 0.02 1 stop_ save_