data_50351 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Assignment of base 15N, 13C and 1H chemical shifts for 5_SL6 ; _BMRB_accession_number 50351 _BMRB_flat_file_name bmr50351.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" 99 "13C chemical shifts" 31 "15N chemical shifts" 51 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)' 50349 'chemical shifts of the 5_SL1' 50350 'chemical shifts of the 3_SL3base' 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_SL6 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 5_SL6 $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 46 _Mol_residue_sequence ; GGCACGUCCAACUCAGUUUG CCUGUUUUACAGGUUCGCGA CGUGCC ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 -2 G 2 -1 G 3 302 C 4 303 A 5 304 C 6 305 G 7 306 U 8 307 C 9 308 C 10 309 A 11 310 A 12 311 C 13 312 U 14 313 C 15 314 A 16 315 G 17 316 U 18 317 U 19 318 U 20 319 G 21 320 C 22 321 C 23 322 U 24 323 G 25 324 U 26 325 U 27 326 U 28 327 U 29 328 A 30 329 C 31 330 A 32 331 G 33 332 G 34 333 U 35 334 U 36 335 C 37 336 G 38 337 C 39 338 G 40 339 A 41 340 C 42 341 G 43 342 U 44 343 G 45 1 C 46 2 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 'reverse transcriptase' . . . . . 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_1 600 uM '[15N (AC) 15N13C (GU)]' '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_1 600 uM '[15N (AC) 15N13C (GU)]' '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 4.0.8 loop_ _Task collection stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'Bruker Avance neo 900 MHz' _Field_strength 900 _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_HSQC[13C]-Aromaten_1 _Saveframe_category NMR_applied_experiment _Experiment_name HSQC[13C]-Aromaten _Sample_label $sample_2 save_ save_HCCNH[13C]_2 _Saveframe_category NMR_applied_experiment _Experiment_name HCCNH[13C] _Sample_label $sample_2 save_ save_2D_DARR_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DARR' _Sample_label $sample_2 save_ save_HSQC[15N]-Amino_4 _Saveframe_category NMR_applied_experiment _Experiment_name HSQC[15N]-Amino _Sample_label $sample_2 save_ save_3D_1H-13C_NOESY_aromatic_5 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-13C NOESY aromatic' _Sample_label $sample_2 save_ save_TROSY[15N]_6 _Saveframe_category NMR_applied_experiment _Experiment_name TROSY[15N] _Sample_label $sample_2 save_ save_1H-JR[15N]_7 _Saveframe_category NMR_applied_experiment _Experiment_name 1H-JR[15N] _Sample_label $sample_2 save_ save_HSQC[15N]-2J_8 _Saveframe_category NMR_applied_experiment _Experiment_name HSQC[15N]-2J _Sample_label $sample_2 save_ save_2D_1H-13C_HSQC_aliphatic_9 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aliphatic' _Sample_label $sample_2 save_ save_1H-ES_10 _Saveframe_category NMR_applied_experiment _Experiment_name 1H-ES _Sample_label $sample_2 save_ save_NOESY[15N]CPMG_11 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY[15N]CPMG _Sample_label $sample_2 save_ save_NOESY[15N]-Imino_12 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY[15N]-Imino _Sample_label $sample_2 save_ save_HNN-COSY[15N]_13 _Saveframe_category NMR_applied_experiment _Experiment_name HNN-COSY[15N] _Sample_label $sample_2 save_ save_2D_1H-13C_HSQC_aromatic_14 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aromatic' _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 298 . 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 HSQC[13C]-Aromaten HCCNH[13C] '2D DARR' HSQC[15N]-Amino '3D 1H-13C NOESY aromatic' TROSY[15N] 1H-JR[15N] HSQC[15N]-2J '2D 1H-13C HSQC aliphatic' 1H-ES NOESY[15N]CPMG NOESY[15N]-Imino HNN-COSY[15N] '2D 1H-13C HSQC aromatic' stop_ loop_ _Sample_label $sample_2 $sample_1 stop_ _Sample_conditions_label $sample_conditions_2 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name 5_SL6 _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 -2 1 G H1' H 5.8225 . 1 2 -2 1 G H8 H 8.13033 . 1 3 -2 1 G C8 C 139.005 . 1 4 -2 1 G N9 N 168.507 . 1 5 -1 2 G H1 H 13.2962 . 1 6 -1 2 G H1' H 5.91067 . 1 7 -1 2 G H8 H 7.61175 . 1 8 -1 2 G C1' C 92.998 . 1 9 -1 2 G C8 C 136.812 . 1 10 -1 2 G N1 N 148.439 . 1 11 -1 2 G N9 N 169.31 . 1 12 302 3 C H1' H 5.53275 . 1 13 302 3 C H5 H 5.288 . 1 14 302 3 C H6 H 7.69967 . 1 15 302 3 C H41 H 8.52025 . 1 16 302 3 C H42 H 6.84867 . 1 17 302 3 C N3 N 197.129 . 1 18 302 3 C N4 N 98.1474 . 1 19 303 4 A H1' H 5.95875 . 1 20 303 4 A H2 H 7.34911 . 1 21 303 4 A H8 H 8.028 . 1 22 303 4 A N1 N 222.396 . 1 23 303 4 A N3 N 213.339 . 1 24 304 5 C H1' H 5.39533 . 1 25 304 5 C H5 H 5.2034 . 1 26 304 5 C H6 H 7.44989 . 1 27 304 5 C H41 H 8.26167 . 1 28 304 5 C H42 H 6.86067 . 1 29 304 5 C N3 N 197.536 . 1 30 304 5 C N4 N 97.8876 . 1 31 305 6 G H1 H 12.9881 . 1 32 305 6 G H1' H 5.71575 . 1 33 305 6 G H8 H 7.5438 . 1 34 305 6 G C1' C 93.142 . 1 35 305 6 G C8 C 136.248 . 1 36 305 6 G N1 N 147.554 . 1 37 305 6 G N9 N 168.887 . 1 38 306 7 U H1' H 5.5505 . 1 39 306 7 U H3 H 14.336 . 1 40 306 7 U H5 H 5.041 . 1 41 306 7 U H6 H 7.814 . 1 42 306 7 U C1' C 93.774 . 1 43 306 7 U C5 C 102.426 . 1 44 306 7 U C6 C 141.929 . 1 45 306 7 U N1 N 146.748 . 1 46 306 7 U N3 N 162.724 . 1 47 307 8 C H5 H 5.596 . 1 48 307 8 C H6 H 7.81167 . 1 49 307 8 C H41 H 8.4575 . 1 50 307 8 C H42 H 6.92 . 1 51 307 8 C N3 N 198.001 . 1 52 307 8 C N4 N 98.7343 . 1 53 320 21 C H5 H 5.491 . 1 54 320 21 C H6 H 7.82267 . 1 55 320 21 C H41 H 8.554 . 1 56 320 21 C H42 H 6.98733 . 1 57 320 21 C N3 N 197.825 . 1 58 320 21 C N4 N 99.3 . 1 59 321 22 C H5 H 5.54133 . 1 60 321 22 C H6 H 7.82667 . 1 61 321 22 C H41 H 8.4364 . 1 62 321 22 C H42 H 6.94067 . 1 63 321 22 C N3 N 196.779 . 1 64 321 22 C N4 N 98.2448 . 1 65 322 23 U H1' H 5.52525 . 1 66 322 23 U H3 H 13.4929 . 1 67 322 23 U H5 H 5.4395 . 1 68 322 23 U H6 H 7.873 . 1 69 322 23 U C1' C 93.739 . 1 70 322 23 U C5 C 103.476 . 1 71 322 23 U C6 C 141.869 . 1 72 322 23 U N1 N 145.89 . 1 73 322 23 U N3 N 161.948 . 1 74 323 24 G H1 H 12.5177 . 1 75 323 24 G H1' H 5.785 . 1 76 323 24 G H8 H 7.7118 . 1 77 323 24 G C1' C 93.027 . 1 78 323 24 G C8 C 136.552 . 1 79 323 24 G N1 N 147.115 . 1 80 323 24 G N9 N 169.631 . 1 81 324 25 U H1' H 5.73433 . 1 82 324 25 U H3 H 14.001 . 1 83 324 25 U H5 H 5.19875 . 1 84 324 25 U H6 H 7.48914 . 1 85 324 25 U C1' C 90.841 . 1 86 324 25 U C5 C 104.321 . 1 87 324 25 U C6 C 141.509 . 1 88 324 25 U N1 N 143.742 . 1 89 324 25 U N3 N 161.754 . 1 90 328 29 A H1' H 5.86617 . 1 91 328 29 A H2 H 7.965 . 1 92 328 29 A H8 H 8.4532 . 1 93 328 29 A N1 N 224.173 . 1 94 328 29 A N3 N 214.374 . 1 95 329 30 C H1' H 5.714 . 1 96 329 30 C H5 H 5.2544 . 1 97 329 30 C H6 H 7.6026 . 1 98 329 30 C H41 H 8.256 . 1 99 329 30 C H42 H 6.71513 . 1 100 329 30 C N3 N 197.452 . 1 101 329 30 C N4 N 96.7195 . 1 102 330 31 A H1' H 5.9925 . 1 103 330 31 A H2 H 7.06614 . 1 104 330 31 A H8 H 8.018 . 1 105 330 31 A N1 N 220.261 . 1 106 330 31 A N3 N 213.58 . 1 107 331 32 G H1 H 12.9202 . 1 108 331 32 G H1' H 5.57983 . 1 109 331 32 G H8 H 7.14 . 1 110 331 32 G C1' C 92.511 . 1 111 331 32 G C8 C 135.579 . 1 112 331 32 G N1 N 147.358 . 1 113 331 32 G N9 N 169.118 . 1 114 332 33 G H1 H 13.4465 . 1 115 332 33 G H1' H 5.71 . 1 116 332 33 G H8 H 7.065 . 1 117 332 33 G C1' C 93.177 . 1 118 332 33 G C8 C 135.721 . 1 119 332 33 G N1 N 148.681 . 1 120 332 33 G N9 N 169.45 . 1 121 333 34 U H1' H 5.6495 . 1 122 333 34 U H3 H 12.0985 . 1 123 333 34 U H5 H 5.3588 . 1 124 333 34 U H6 H 7.603 . 1 125 333 34 U C1' C 93.33 . 1 126 333 34 U C5 C 104.169 . 1 127 333 34 U C6 C 140.716 . 1 128 333 34 U N1 N 145.793 . 1 129 333 34 U N3 N 158.882 . 1 130 338 39 G H1 H 12.4016 . 1 131 338 39 G H8 H 7.521 . 1 132 338 39 G C8 C 137.277 . 1 133 338 39 G N1 N 147.108 . 1 134 339 40 A H1' H 6.0092 . 1 135 339 40 A H2 H 7.756 . 1 136 339 40 A N1 N 222.646 . 1 137 339 40 A N3 N 212.288 . 1 138 340 41 C H1' H 5.3925 . 1 139 340 41 C H5 H 5.24933 . 1 140 340 41 C H6 H 7.3685 . 1 141 340 41 C H41 H 8.2575 . 1 142 340 41 C H42 H 6.84533 . 1 143 340 41 C N3 N 197.156 . 1 144 340 41 C N4 N 98.209 . 1 145 341 42 G H1 H 12.8978 . 1 146 341 42 G H1' H 5.72075 . 1 147 341 42 G H8 H 7.51075 . 1 148 341 42 G C1' C 93.145 . 1 149 341 42 G C8 C 136.283 . 1 150 341 42 G N1 N 147.524 . 1 151 341 42 G N9 N 168.937 . 1 152 342 43 U H1' H 5.5375 . 1 153 342 43 U H3 H 13.6288 . 1 154 342 43 U H5 H 5.0765 . 1 155 342 43 U H6 H 7.7408 . 1 156 342 43 U C1' C 93.519 . 1 157 342 43 U C5 C 103 . 1 158 342 43 U C6 C 141.239 . 1 159 342 43 U N1 N 145.666 . 1 160 342 43 U N3 N 162.112 . 1 161 343 44 G H1 H 12.5891 . 1 162 343 44 G H1' H 5.79917 . 1 163 343 44 G H8 H 7.7128 . 1 164 343 44 G C1' C 92.907 . 1 165 343 44 G C8 C 136.105 . 1 166 343 44 G N1 N 147.914 . 1 167 343 44 G N9 N 169.439 . 1 168 1 45 C H1' H 5.479 . 1 169 1 45 C H5 H 5.23667 . 1 170 1 45 C H6 H 7.64871 . 1 171 1 45 C H41 H 8.5065 . 1 172 1 45 C H42 H 6.87433 . 1 173 1 45 C N3 N 198.255 . 1 174 1 45 C N4 N 99.1672 . 1 175 2 46 C H1' H 6.105 . 1 176 2 46 C H3' H 4.947 . 1 177 2 46 C H5 H 5.546 . 1 178 2 46 C H6 H 7.47582 . 1 179 2 46 C H41 H 8.518 . 1 180 2 46 C H42 H 7.06175 . 1 181 2 46 C N4 N 99.2467 . 1 stop_ save_