data_50352 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Assignment of base 15N and 1H chemical shifts for 5_SL8 ; _BMRB_accession_number 50352 _BMRB_flat_file_name bmr50352.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" 28 "15N chemical shifts" 34 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' 50351 'chemical shifts of the 5_SL6' 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_SL8 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 5_SL8 $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 63 _Mol_residue_sequence ; GGACUUGUGGCUUAGUAGAA GUUGAAAAAGGCGUUUUGCC UCAACUUGAACAGCCCUAUG UCC ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 -1 G 2 -2 G 3 413 A 4 414 C 5 415 U 6 416 U 7 417 G 8 418 U 9 419 G 10 420 G 11 421 C 12 422 U 13 423 U 14 424 A 15 425 G 16 426 U 17 427 A 18 428 G 19 429 A 20 430 A 21 431 G 22 432 U 23 433 U 24 434 G 25 435 A 26 436 A 27 437 A 28 438 A 29 439 A 30 440 G 31 441 G 32 442 C 33 443 G 34 444 U 35 445 U 36 446 U 37 447 U 38 448 G 39 449 C 40 450 C 41 451 U 42 452 C 43 453 A 44 454 A 45 455 C 46 456 U 47 457 U 48 458 G 49 459 A 50 460 A 51 461 C 52 462 A 53 463 G 54 464 C 55 465 C 56 466 C 57 467 U 58 468 A 59 469 U 60 470 G 61 471 U 62 1 C 63 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_1 800 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 4.0.7 loop_ _Task collection stop_ _Details . save_ save_software_4 _Saveframe_category software _Name TOPSPIN _Version 4.0.9.b.21 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 1000 MHz' _Field_strength 1000 _Details . save_ ############################# # NMR applied experiments # ############################# save_TROSY[15N]_1 _Saveframe_category NMR_applied_experiment _Experiment_name TROSY[15N] _Sample_label $sample_1 save_ save_HSQC[15N]-Amino_2 _Saveframe_category NMR_applied_experiment _Experiment_name HSQC[15N]-Amino _Sample_label $sample_1 save_ save_NOESY-JR[15N]-Amino_3 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY-JR[15N]-Amino _Sample_label $sample_1 save_ save_HSQC[15N]-2J_4 _Saveframe_category NMR_applied_experiment _Experiment_name HSQC[15N]-2J _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_NOESY[15N]-Imino_6 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY[15N]-Imino _Sample_label $sample_1 save_ save_HNN-COSY[15N]_7 _Saveframe_category NMR_applied_experiment _Experiment_name HNN-COSY[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 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 TROSY[15N] HSQC[15N]-Amino NOESY-JR[15N]-Amino HSQC[15N]-2J 1H-JR[15N] NOESY[15N]-Imino HNN-COSY[15N] stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name 5_SL8 _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 12.5993 . 1 2 -1 1 G N1 N 147.234 . 1 3 -2 2 G H1 H 12.7907 . 1 4 -2 2 G N1 N 147.322 . 1 5 413 3 A H2 H 7.82433 . 1 6 413 3 A N1 N 222.914 . 1 7 413 3 A N3 N 212.156 . 1 8 414 4 C H41 H 8.385 . 1 9 414 4 C H42 H 7.1235 . 1 10 414 4 C N3 N 197.421 . 1 11 414 4 C N4 N 98.7665 . 1 12 419 9 G H1 H 13.0405 . 1 13 419 9 G N1 N 148.478 . 1 14 420 10 G H1 H 13.4113 . 1 15 420 10 G N1 N 148.628 . 1 16 421 11 C N3 N 196.898 . 1 17 431 21 G H1 H 13.2828 . 1 18 431 21 G N1 N 148.039 . 1 19 432 22 U H3 H 14.2813 . 1 20 432 22 U N1 N 163.265 . 1 21 432 22 U N3 N 162.512 . 1 22 433 23 U H3 H 13.1056 . 1 23 433 23 U N3 N 162.195 . 1 24 434 24 G H1 H 11.6946 . 1 25 434 24 G N1 N 146.293 . 1 26 452 42 C H41 H 8.24267 . 1 27 452 42 C H42 H 6.938 . 1 28 452 42 C N3 N 197.415 . 1 29 452 42 C N4 N 96.3055 . 1 30 453 43 A H2 H 6.6352 . 1 31 453 43 A N1 N 219.928 . 1 32 453 43 A N3 N 212.602 . 1 33 454 44 A H2 H 7.65329 . 1 34 454 44 A N1 N 221.891 . 1 35 454 44 A N3 N 211.027 . 1 36 455 45 C H41 H 8.20633 . 1 37 455 45 C H42 H 7.00667 . 1 38 455 45 C N3 N 196.897 . 1 39 455 45 C N4 N 98.839 . 1 40 456 46 U H3 H 14.032 . 1 41 456 46 U N3 N 162.487 . 1 42 457 47 U H3 H 13.6165 . 1 43 457 47 U N3 N 161.741 . 1 44 463 53 G H1 H 12.94 . 1 45 463 53 G N1 N 147.49 . 1 46 464 54 C H41 H 8.7645 . 1 47 464 54 C H42 H 6.972 . 1 48 464 54 C N3 N 198.043 . 1 49 464 54 C N4 N 98.7565 . 1 50 465 55 C N3 N 197.236 . 1 51 470 60 G H1 H 13.3997 . 1 52 470 60 G N1 N 148.456 . 1 53 471 61 U H3 H 14.4803 . 1 54 471 61 U N3 N 163.178 . 1 55 1 62 C H41 H 8.4825 . 1 56 1 62 C H42 H 7.076 . 1 57 1 62 C N3 N 198.67 . 1 58 1 62 C N4 N 98.642 . 1 59 2 63 C H41 H 8.4875 . 1 60 2 63 C H42 H 7.1575 . 1 61 2 63 C N3 N 196.202 . 1 62 2 63 C N4 N 99.173 . 1 stop_ save_