data_50340 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Assignment of base 15N and 1H chemical shifts for 5_SL5stem ; _BMRB_accession_number 50340 _BMRB_flat_file_name bmr50340.str _Entry_type original _Submission_date 2020-06-23 _Accession_date 2020-06-23 _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 Schwalbe Harald . . 2 Richter Christian . . 3 Schlundt Andreas . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 72 "15N chemical shifts" 77 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2020-12-18 update BMRB 'update entry citation' 2020-07-10 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 50339 'chemical shifts of the 5_SL5B+C' 50341 'chemical shifts of the 3_s2m' 50342 'chemical shifts of the 3_SL1' 50343 'chemical shifts of the 2_SL3' 50344 'chemical shifts of the 5_SL2+3' 50346 'chemical shifts of the 5_SL5a' 50347 'chemical shifts of the 5_SL4' 50348 'chemical shifts of the PK (Pseudoknot)' 50349 'chemical shifts of the 5_SL1' 50350 'chemical shifts of the 3_SL3base' 50351 'chemical shifts of the 5_SL6' 50352 'chemical shifts of the 5_SL8' stop_ _Original_release_date 2020-06-25 save_ ############################# # Citation for this entry # ############################# save_citations_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 33167030 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Wacker Anna . . 2 Weigand Julia E. . 3 Akabayov Sabine R. . 4 Altincekic Nadide . . 5 'Kaur Bains' Jasleen . . 6 Banijamali Elnaz . . 7 Binas Oliver . . 8 Castillo-Martinez Jesus . . 9 Cetiner Erhan . . 10 Ceylan Betul . . 11 Chiu Liang-Yuan . . 12 Davila-Calderon Jesse . . 13 'De Jesus' Vanessa . . 14 Dhamotharan Karthikeyan . . 15 Duchardt-Ferner Elke . . 16 Ferner Jan . . 17 Frydman Lucio . . 18 Furtig Boris . . 19 Gallego Jose . . 20 Grun 'J. Tassilo' . . 21 Hacker Carolin . . 22 Haddad Christina . . 23 Hahnke Martin . . 24 Hengesbach Martin . . 25 Hiller Fabian . . 26 Hohmann Katharina F. . 27 Hymon Daniel . . 28 Jonker Henry . . 29 Keller Heiko . . 30 Knezic Bozana . . 31 Landgraf Tom . . 32 Lohr Frank . . 33 Luo Luke . . 34 Mertinkus Klara R. . 35 Muhs Christina . . 36 Novakovic Mihajlo . . 37 Oxenfarth Andreas . . 38 Palomino-Schatzlein Martina . . 39 Petzold Katja . . 40 Peter Stephen A. . 41 Pyper Dennis J. . 42 Qureshi Nusrat S. . 43 Riad Magdalena . . 44 Richter Christian . . 45 Saxena Krishna . . 46 Schamber Tatjana . . 47 Scherf Tali . . 48 Schlagnitweit Judith . . 49 Schlundt Andreas . . 50 Schnieders Robbin . . 51 Schwalbe Harald . . 52 Simba-Lahuasi Alvaro . . 53 Sreeramulu Sridhar . . 54 Stirnal Elke . . 55 Sudakov Alexey . . 56 Tants Jan-Niklas . . 57 Tolbert Blanton S. . 58 Vogele Jenny . . 59 Weiss Lena . . 60 Wirmer-Bartoschek Julia . . 61 'Wirtz Martin' Maria A. . 62 Wohnert Jens . . 63 Zetzsche Heidi . . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_name_full 'Nucleic acids research' _Journal_volume 48 _Journal_issue 22 _Journal_ISSN 1362-4962 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 12415 _Page_last 12435 _Year 2020 _Details . loop_ _Keyword "5'-untranslated region" Covid19-nmr 'RNA structure' SARS-CoV-2 stop_ save_ ################################## # Molecular system description # ################################## save_assembly_1 _Saveframe_category molecular_system _Mol_system_name 5_SL5stem _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 5_SL5stem $entity_1 stop_ _System_molecular_weight 22331 _System_physical_state native _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 . _Mol_thiol_state 'not present' loop_ _Biological_function "Sub-structure of the SARS-CoV-2 leader sequence (5'-UTR)." stop_ _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 69 _Mol_residue_sequence ; GGGAUGGAGAGCCUUGUCCC UGGUUUCAACGAUUCGUCGU UGACAGGACACGAGUAACUC GUCUAUCCC ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 -1 G 2 -2 G 3 265 G 4 266 A 5 267 U 6 268 G 7 269 G 8 270 A 9 271 G 10 272 A 11 273 G 12 274 C 13 275 C 14 276 U 15 277 U 16 278 G 17 279 U 18 280 C 19 281 C 20 282 C 21 283 U 22 284 G 23 285 G 24 286 U 25 287 U 26 288 U 27 289 C 28 290 A 29 291 A 30 292 C 31 293 G 32 294 A 33 295 U 34 . U 35 . C 36 149 G 37 150 U 38 151 C 39 152 G 40 153 U 41 154 U 42 155 G 43 156 A 44 157 C 45 158 A 46 159 G 47 160 G 48 161 A 49 162 C 50 163 A 51 164 C 52 165 G 53 166 A 54 167 G 55 168 U 56 169 A 57 170 A 58 171 C 59 172 U 60 173 C 61 174 G 62 175 U 63 176 C 64 177 U 65 178 A 66 179 U 67 180 C 68 1 C 69 2 C stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value NCBI NC_045512.2 . . . . . . stop_ save_ #################### # Natural source # #################### save_natural_source_1 _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Strain $entity_1 SARS-CoV-2 2697049 Viruses . Betacoronavirus HCoV-SARS SARS-CoV-2 stop_ save_ ######################### # Experimental source # ######################### save_experimental_source_1 _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name _Details $entity_1 'reverse transcriptase (in vitro)' . . . . . 'Self-cleaved from HDV ribozyme construct' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 671 uM [U-15N] 'potassium phosphate' 25 mM 'natural abundance' KCl 50 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name LOGS _Version 2.2 loop_ _Task collection stop_ _Details . save_ save_software_2 _Saveframe_category software _Name SPARKY _Version 3.114 loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name TOPSPIN _Version 3.6.2 loop_ _Task collection processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'Bruker Avance III HD 600 MHz' _Field_strength 600 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'Bruker Avance III HD 700 MHz' _Field_strength 700 _Details . save_ ############################# # NMR applied experiments # ############################# save_1H-ES_1 _Saveframe_category NMR_applied_experiment _Experiment_name 1H-ES _Sample_label $sample_1 save_ save_1H-JR[15N]_2 _Saveframe_category NMR_applied_experiment _Experiment_name 1H-JR[15N] _Sample_label $sample_1 save_ save_TROSY[15N]_3 _Saveframe_category NMR_applied_experiment _Experiment_name TROSY[15N] _Sample_label $sample_1 save_ save_1H-ES_4 _Saveframe_category NMR_applied_experiment _Experiment_name 1H-ES _Sample_label $sample_1 save_ save_1H-JR[15N]_5 _Saveframe_category NMR_applied_experiment _Experiment_name 1H-JR[15N] _Sample_label $sample_1 save_ save_TROSY[15N]_6 _Saveframe_category NMR_applied_experiment _Experiment_name TROSY[15N] _Sample_label $sample_1 save_ save_1H-JR[15N]_7 _Saveframe_category NMR_applied_experiment _Experiment_name 1H-JR[15N] _Sample_label $sample_1 save_ save_1H-JR[15N]_8 _Saveframe_category NMR_applied_experiment _Experiment_name 1H-JR[15N] _Sample_label $sample_1 save_ save_TROSY[15N]_9 _Saveframe_category NMR_applied_experiment _Experiment_name TROSY[15N] _Sample_label $sample_1 save_ save_HNN-COSY[15N]_10 _Saveframe_category NMR_applied_experiment _Experiment_name HNN-COSY[15N] _Sample_label $sample_1 save_ save_HSQC[15N]-2J_11 _Saveframe_category NMR_applied_experiment _Experiment_name HSQC[15N]-2J _Sample_label $sample_1 save_ save_HSQC[15N]-2J_12 _Saveframe_category NMR_applied_experiment _Experiment_name HSQC[15N]-2J _Sample_label $sample_1 save_ save_HSQC[15N]-2J_13 _Saveframe_category NMR_applied_experiment _Experiment_name HSQC[15N]-2J _Sample_label $sample_1 save_ save_NOESY[15N]-Imino_14 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY[15N]-Imino _Sample_label $sample_1 save_ save_HSQC[15N]-Amino_15 _Saveframe_category NMR_applied_experiment _Experiment_name HSQC[15N]-Amino _Sample_label $sample_1 save_ save_NOESY-JR[15N]-Amino_16 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY-JR[15N]-Amino _Sample_label $sample_1 save_ save_sfHMQC[13C]_17 _Saveframe_category NMR_applied_experiment _Experiment_name sfHMQC[13C] _Sample_label $sample_1 save_ save_1H-JR[15N]_18 _Saveframe_category NMR_applied_experiment _Experiment_name 1H-JR[15N] _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' 75 . mM pH 6.2 . pH pressure 1 . atm temperature 298 . 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' 75 . mM pH 6.2 . pH pressure 1 . atm temperature 283 . 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 DSS C 13 'methyl protons' ppm 0.00 na indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 DSS N 15 'methyl protons' ppm 0.00 na indirect . . . 0.101329118 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_ _Software_label $software_1 $software_2 $software_3 stop_ loop_ _Experiment_label TROSY[15N] 1H-JR[15N] HNN-COSY[15N] HSQC[15N]-2J NOESY[15N]-Imino HSQC[15N]-Amino NOESY-JR[15N]-Amino stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_2 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name 5_SL5stem _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 12.012 0.002 1 2 -1 1 G N1 N 147.141 0.049 1 3 -2 2 G H1 H 12.433 0.031 1 4 -2 2 G N1 N 147.613 0.044 1 5 265 3 G H1 H 12.144 0.004 1 6 265 3 G N1 N 147.462 0.013 1 7 266 4 A H2 H 7.515 0.000 1 8 266 4 A H61 H 8.236 0.000 1 9 266 4 A H62 H 6.541 0.000 1 10 266 4 A N1 N 222.705 0.003 1 11 266 4 A N3 N 212.897 0.000 1 12 266 4 A N6 N 83.415 0.013 1 13 267 5 U H3 H 13.360 0.002 1 14 267 5 U N3 N 162.663 0.011 1 15 268 6 G H1 H 10.015 0.004 1 16 268 6 G N1 N 142.507 0.004 1 17 269 7 G H1 H 12.047 0.011 1 18 269 7 G N1 N 146.702 0.024 1 19 270 8 A H2 H 7.723 0.000 1 20 270 8 A N1 N 222.659 0.009 1 21 270 8 A N3 N 213.700 0.000 1 22 271 9 G H1 H 13.137 0.004 1 23 271 9 G N1 N 148.877 0.008 1 24 272 10 A H2 H 7.310 0.001 1 25 272 10 A N1 N 220.613 0.030 1 26 272 10 A N3 N 212.595 0.000 1 27 273 11 G H1 H 12.108 0.007 1 28 273 11 G N1 N 146.536 0.009 1 29 275 13 C H41 H 8.029 0.000 1 30 275 13 C H42 H 7.092 0.002 1 31 275 13 C N3 N 198.241 0.000 1 32 275 13 C N4 N 97.406 0.040 1 33 276 14 U H3 H 13.820 0.003 1 34 276 14 U N3 N 162.167 0.030 1 35 277 15 U H3 H 11.358 0.002 1 36 277 15 U N3 N 158.264 0.043 1 37 278 16 G H1 H 12.549 0.002 1 38 278 16 G N1 N 148.186 0.011 1 39 279 17 U H3 H 14.262 0.006 1 40 279 17 U N3 N 163.114 0.410 1 41 281 19 C H41 H 8.184 0.000 1 42 281 19 C H42 H 6.820 0.000 1 43 281 19 C N3 N 196.361 0.000 1 44 281 19 C N4 N 98.094 0.029 1 45 282 20 C H41 H 8.157 0.000 1 46 282 20 C N3 N 197.406 0.000 1 47 283 21 U H3 H 13.297 0.003 1 48 283 21 U N3 N 161.983 0.018 1 49 284 22 G H1 H 12.518 0.018 1 50 284 22 G N1 N 147.333 0.018 1 51 288 26 U H3 H 11.380 0.000 1 52 288 26 U N3 N 160.391 0.002 1 53 289 27 C H41 H 8.044 0.009 1 54 289 27 C H42 H 6.742 0.010 1 55 289 27 C N3 N 197.464 0.000 1 56 289 27 C N4 N 96.679 0.010 1 57 290 28 A H2 H 6.412 0.001 1 58 290 28 A N1 N 219.796 0.008 1 59 290 28 A N3 N 212.562 0.000 1 60 291 29 A H2 H 7.373 0.001 1 61 291 29 A N1 N 221.602 0.001 1 62 291 29 A N3 N 210.872 0.000 1 63 292 30 C H41 H 8.146 0.001 1 64 292 30 C H42 H 6.718 0.000 1 65 292 30 C N3 N 196.765 0.000 1 66 292 30 C N4 N 97.475 0.051 1 67 293 31 G H1 H 11.733 0.005 1 68 293 31 G N1 N 146.235 0.012 1 69 294 32 A H2 H 7.553 0.002 1 70 294 32 A H61 H 8.184 0.000 1 71 294 32 A H62 H 6.584 0.000 1 72 294 32 A N1 N 222.248 0.019 1 73 294 32 A N3 N 213.777 0.000 1 74 294 32 A N6 N 83.420 0.000 1 75 295 33 U H3 H 11.400 0.000 1 76 149 36 G H1 H 10.143 0.000 1 77 149 36 G N1 N 144.218 0.012 1 78 150 37 U H3 H 14.313 0.003 1 79 150 37 U N3 N 163.579 0.008 1 80 151 38 C H41 H 8.134 0.005 1 81 151 38 C H42 H 6.708 0.000 1 82 151 38 C N3 N 197.860 0.000 1 83 151 38 C N4 N 96.619 0.050 1 84 152 39 G H1 H 12.567 0.006 1 85 152 39 G N1 N 147.447 0.005 1 86 153 40 U H3 H 14.098 0.004 1 87 153 40 U N3 N 162.530 0.035 1 88 154 41 U H3 H 12.940 0.003 1 89 154 41 U N3 N 162.170 0.023 1 90 155 42 G H1 H 11.558 0.006 1 91 155 42 G N1 N 146.307 0.015 1 92 157 44 C H41 H 8.109 0.006 1 93 157 44 C H42 H 6.797 0.000 1 94 157 44 C N3 N 197.891 0.000 1 95 157 44 C N4 N 97.100 0.007 1 96 158 45 A H2 H 6.768 0.000 1 97 158 45 A N1 N 219.911 0.005 1 98 158 45 A N3 N 213.276 0.000 1 99 159 46 G H1 H 12.578 0.014 1 100 159 46 G N1 N 147.256 0.026 1 101 160 47 G H1 H 12.484 0.014 1 102 160 47 G N1 N 147.683 0.084 1 103 163 50 A H61 H 7.579 0.000 1 104 163 50 A H62 H 6.421 0.000 1 105 163 50 A N1 N 222.258 0.000 1 106 163 50 A N6 N 82.630 0.007 1 107 165 52 G H1 H 9.856 0.002 1 108 165 52 G H21 H 7.415 0.000 1 109 165 52 G N1 N 142.040 0.032 1 110 166 53 A H2 H 7.390 0.001 1 111 166 53 A H61 H 7.585 0.000 1 112 166 53 A H62 H 6.479 0.000 1 113 166 53 A N1 N 219.904 0.009 1 114 166 53 A N3 N 211.615 0.000 1 115 166 53 A N6 N 82.640 0.002 1 116 167 54 G H1 H 13.271 0.006 1 117 167 54 G N1 N 148.944 0.021 1 118 171 58 C H41 H 8.204 0.015 1 119 171 58 C H42 H 6.775 0.001 1 120 171 58 C N3 N 196.647 0.000 1 121 171 58 C N4 N 97.745 0.021 1 122 172 59 U H3 H 14.078 0.007 1 123 172 59 U N3 N 162.957 0.047 1 124 173 60 C H41 H 7.963 0.011 1 125 173 60 C H42 H 6.832 0.197 1 126 173 60 C N3 N 198.558 0.000 1 127 173 60 C N4 N 97.336 0.030 1 128 175 62 U H3 H 13.703 0.012 1 129 175 62 U N3 N 162.339 0.060 1 130 176 63 C H41 H 8.206 0.028 1 131 176 63 C H42 H 6.646 0.009 1 132 176 63 C N3 N 196.959 0.000 1 133 176 63 C N4 N 96.844 0.124 1 134 177 64 U H3 H 11.421 0.001 1 135 177 64 U N3 N 157.731 0.013 1 136 178 65 A H2 H 7.111 0.000 1 137 178 65 A H61 H 7.520 0.000 1 138 178 65 A H62 H 6.583 0.000 1 139 178 65 A N1 N 222.352 0.025 1 140 178 65 A N3 N 213.289 0.000 1 141 178 65 A N6 N 82.638 0.008 1 142 179 66 U H3 H 13.748 0.003 1 143 179 66 U N3 N 162.315 0.027 1 144 180 67 C H41 H 8.246 0.000 1 145 180 67 C H42 H 6.688 0.004 1 146 180 67 C N3 N 198.010 0.000 1 147 180 67 C N4 N 97.971 0.067 1 148 1 68 C N3 N 197.459 0.000 1 149 2 69 C N3 N 197.159 0.000 1 stop_ save_