data_50349 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Assignment of base 15N and 1H chemical shifts for <5_SL1> ; _BMRB_accession_number 50349 _BMRB_flat_file_name bmr50349.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 . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 104 "13C chemical shifts" 15 "15N chemical shifts" 49 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' 50340 'chemical shifts of the 5_SL5stem' 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)' 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 2020-06-23 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 . save_ ################################## # Molecular system description # ################################## save_assembly_1 _Saveframe_category molecular_system _Mol_system_name 5_SL1 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 5_SL1 $entity_1 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_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common entity_1 _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 29 _Mol_residue_sequence ; GGGUUUAUACCUUCCCAGGU AACAAACCC ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 -1 G 2 7 G 3 8 G 4 9 U 5 10 U 6 11 U 7 12 A 8 13 U 9 14 A 10 15 C 11 16 C 12 17 U 13 18 U 14 19 C 15 20 C 16 21 C 17 22 A 18 23 G 19 24 G 20 25 U 21 26 A 22 27 A 23 28 C 24 29 A 25 30 A 26 31 A 27 32 C 28 33 C 29 1 C stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . 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 $entity_1 transcription . . . . . 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_1 150 uM '[U-13C; U-15N]' 'potassium phosphate' 25 mM 'natural abundance' KCl 50 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 150 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 stop_ _Details . save_ save_software_4 _Saveframe_category software _Name TOPSPIN _Version 2.1 loop_ _Task collection stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'Bruker Avance III HD 800 MHz' _Field_strength 800 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'Bruker Avance III HD 700 MHz' _Field_strength 700 _Details . save_ save_NMR_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'Bruker Avance I 600 MHz' _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_1H-JR[15N]_1 _Saveframe_category NMR_applied_experiment _Experiment_name 1H-JR[15N] _Sample_label $sample_2 save_ save_NOESY[15N]-Imino_2 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY[15N]-Imino _Sample_label $sample_2 save_ save_HSQC[15N]-Amino_3 _Saveframe_category NMR_applied_experiment _Experiment_name HSQC[15N]-Amino _Sample_label $sample_2 save_ save_HSQC[15N]-2J_4 _Saveframe_category NMR_applied_experiment _Experiment_name HSQC[15N]-2J _Sample_label $sample_2 save_ save_TROSY[15N]_5 _Saveframe_category NMR_applied_experiment _Experiment_name TROSY[15N] _Sample_label $sample_2 save_ save_NOESY-JR[15N]-Amino_6 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY-JR[15N]-Amino _Sample_label $sample_2 save_ save_TOCSY_7 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _Sample_label $sample_2 save_ save_HSQC[13C]-Aromaten_8 _Saveframe_category NMR_applied_experiment _Experiment_name HSQC[13C]-Aromaten _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 283 . 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 298 . K stop_ save_ save_sample_conditions_3 _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_2 stop_ loop_ _Experiment_label 1H-JR[15N] NOESY[15N]-Imino HSQC[15N]-Amino HSQC[15N]-2J TROSY[15N] NOESY-JR[15N]-Amino TOCSY HSQC[13C]-Aromaten stop_ loop_ _Sample_label $sample_2 $sample_1 stop_ _Sample_conditions_label $sample_conditions_3 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name 5_SL1 _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 12.7932 . 1 2 -1 1 G H1' H 5.843 . 1 3 -1 1 G H8 H 8.16033 . 1 4 -1 1 G N7 N 231.345 . 1 5 -1 1 G N9 N 169.257 . 1 6 7 2 G H1 H 12.8791 . 1 7 7 2 G H1' H 5.96833 . 1 8 7 2 G H8 H 7.53957 . 1 9 7 2 G N1 N 147.72 . 1 10 7 2 G N7 N 233.795 . 1 11 7 2 G N9 N 169.986 . 1 12 8 3 G H1 H 13.2872 . 1 13 8 3 G H1' H 5.8105 . 1 14 8 3 G H8 H 7.19413 . 1 15 8 3 G N1 N 148.64 . 1 16 8 3 G N7 N 234.79 . 1 17 8 3 G N9 N 169.515 . 1 18 9 4 U H3 H 14.3042 . 1 19 9 4 U H5 H 5.0866 . 1 20 9 4 U H6 H 7.74871 . 1 21 9 4 U N3 N 162.484 . 1 22 10 5 U H1' H 5.66425 . 1 23 10 5 U H3 H 13.7965 . 1 24 10 5 U H5 H 5.603 . 1 25 10 5 U H6 H 7.96562 . 1 26 10 5 U N3 N 162.694 . 1 27 11 6 U H1' H 5.6298 . 1 28 11 6 U H3 H 13.0796 . 1 29 11 6 U H5 H 5.62 . 1 30 11 6 U H6 H 7.89413 . 1 31 11 6 U N3 N 161.86 . 1 32 12 7 A H1' H 5.905 . 1 33 12 7 A H2 H 7.33191 . 1 34 12 7 A H8 H 8.15657 . 1 35 12 7 A C2 C 152.722 . 1 36 12 7 A N3 N 216.164 . 1 37 12 7 A N7 N 233.307 . 1 38 12 7 A N9 N 171.642 . 1 39 13 8 U H1' H 5.409 . 1 40 13 8 U H5 H 5.45833 . 1 41 13 8 U H6 H 7.60667 . 1 42 14 9 A H1' H 5.955 . 1 43 14 9 A H2 H 7.15621 . 1 44 14 9 A H8 H 8.2221 . 1 45 14 9 A H61 H 7.871 . 1 46 14 9 A H62 H 6.534 . 1 47 14 9 A C2 C 153.225 . 1 48 14 9 A N1 N 222.75 . 1 49 14 9 A N3 N 212.02 . 1 50 14 9 A N7 N 229.715 . 1 51 14 9 A N9 N 171.238 . 1 52 15 10 C H1' H 5.34 . 1 53 15 10 C H5 H 5.19912 . 1 54 15 10 C H6 H 7.50075 . 1 55 15 10 C H41 H 8.3835 . 1 56 15 10 C H42 H 6.964 . 1 57 15 10 C C6 C 139.104 . 1 58 16 11 C H1' H 5.392 . 1 59 16 11 C H5 H 5.383 . 1 60 16 11 C H6 H 7.61509 . 1 61 16 11 C H41 H 8.423 . 1 62 16 11 C H42 H 6.8926 . 1 63 16 11 C C6 C 139.728 . 1 64 17 12 U H5 H 5.4815 . 1 65 17 12 U H6 H 7.68833 . 1 66 18 13 U H5 H 5.747 . 1 67 18 13 U H6 H 7.827 . 1 68 19 14 C H5 H 5.7735 . 1 69 19 14 C H6 H 7.8435 . 1 70 20 15 C H1' H 5.604 . 1 71 20 15 C H5 H 5.523 . 1 72 20 15 C H6 H 7.6285 . 1 73 20 15 C H42 H 7.021 . 1 74 21 16 C H5 H 5.5635 . 1 75 21 16 C H6 H 7.76125 . 1 76 22 17 A H1' H 5.553 . 1 77 22 17 A H2 H 7.81733 . 1 78 22 17 A H8 H 8.26983 . 1 79 22 17 A C2 C 153.705 . 1 80 22 17 A N1 N 222.747 . 1 81 22 17 A N3 N 214.521 . 1 82 22 17 A N7 N 231.169 . 1 83 22 17 A N9 N 170.724 . 1 84 23 18 G H1 H 12.7647 . 1 85 23 18 G H1' H 5.8025 . 1 86 23 18 G H8 H 7.198 . 1 87 23 18 G N1 N 147.558 . 1 88 23 18 G N7 N 233.7 . 1 89 23 18 G N9 N 169.19 . 1 90 24 19 G H1 H 13.2142 . 1 91 24 19 G H1' H 5.821 . 1 92 24 19 G H8 H 7.22257 . 1 93 24 19 G N1 N 148.367 . 1 94 24 19 G N7 N 234.383 . 1 95 24 19 G N9 N 169.377 . 1 96 25 20 U H1' H 5.551 . 1 97 25 20 U H3 H 13.4559 . 1 98 25 20 U H5 H 5.122 . 1 99 25 20 U H6 H 7.66225 . 1 100 25 20 U N3 N 161.668 . 1 101 26 21 A H1' H 5.92833 . 1 102 26 21 A H2 H 6.85575 . 1 103 26 21 A H8 H 8.07356 . 1 104 26 21 A C2 C 153.16 . 1 105 26 21 A N1 N 223.213 . 1 106 26 21 A N3 N 213.694 . 1 107 26 21 A N7 N 231.909 . 1 108 26 21 A N9 N 169.894 . 1 109 27 22 A H1' H 5.528 . 1 110 27 22 A H2 H 7.68611 . 1 111 27 22 A H8 H 7.9055 . 1 112 27 22 A C2 C 154.664 . 1 113 27 22 A N1 N 225.663 . 1 114 27 22 A N3 N 214.96 . 1 115 27 22 A N7 N 231.304 . 1 116 27 22 A N9 N 168.659 . 1 117 28 23 C H1' H 5.63725 . 1 118 28 23 C H5 H 5.531 . 1 119 28 23 C H6 H 7.59078 . 1 120 29 24 A H1' H 5.86975 . 1 121 29 24 A H2 H 6.61831 . 1 122 29 24 A H8 H 8.275 . 1 123 29 24 A H61 H 8.275 . 1 124 29 24 A H62 H 8.275 . 1 125 29 24 A C2 C 152.026 . 1 126 29 24 A N1 N 221.167 . 1 127 29 24 A N3 N 212.955 . 1 128 29 24 A N7 N 230.53 . 1 129 29 24 A N9 N 169.289 . 1 130 30 25 A H1' H 5.846 . 1 131 30 25 A H2 H 7.08912 . 1 132 30 25 A H8 H 7.85517 . 1 133 30 25 A H61 H 7.927 . 1 134 30 25 A H62 H 6.62 . 1 135 30 25 A C1' C 89.155 . 1 136 30 25 A C2 C 152.789 . 1 137 30 25 A N1 N 220.655 . 1 138 30 25 A N3 N 211.442 . 1 139 30 25 A N7 N 229.387 . 1 140 30 25 A N9 N 170.327 . 1 141 31 26 A H1' H 5.934 . 1 142 31 26 A H2 H 7.76863 . 1 143 31 26 A H8 H 7.85688 . 1 144 31 26 A H61 H 8.227 . 1 145 31 26 A H62 H 6.656 . 1 146 31 26 A C2 C 154.087 . 1 147 31 26 A N1 N 222.173 . 1 148 31 26 A N3 N 211.148 . 1 149 31 26 A N7 N 230.026 . 1 150 31 26 A N9 N 171.288 . 1 151 32 27 C H1' H 5.376 . 1 152 32 27 C H5 H 5.18583 . 1 153 32 27 C H6 H 7.4863 . 1 154 32 27 C H41 H 8.428 . 1 155 32 27 C H42 H 6.99314 . 1 156 32 27 C C6 C 137.938 . 1 157 33 28 C H5 H 5.43344 . 1 158 33 28 C H6 H 7.74838 . 1 159 33 28 C H41 H 8.4812 . 1 160 33 28 C H42 H 6.885 . 1 161 33 28 C C6 C 140.247 . 1 162 1 29 C H1' H 6.1205 . 1 163 1 29 C H5 H 5.5136 . 1 164 1 29 C H6 H 7.49511 . 1 165 1 29 C H41 H 8.47833 . 1 166 1 29 C H42 H 7.11988 . 1 167 1 29 C C1' C 89.322 . 1 168 1 29 C C6 C 138.097 . 1 stop_ save_