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_