data_50339
#######################
# Entry information #
#######################
save_entry_information
_Saveframe_category entry_information
_Entry_title
;
Assignment of base 15N and 1H chemical shifts for <5_SL5B+C>
;
_BMRB_accession_number 50339
_BMRB_flat_file_name bmr50339.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" 14
"15N chemical shifts" 15
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
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'
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_SL5B+C
_Enzyme_commission_number .
loop_
_Mol_system_component_name
_Mol_label
5_SL5B+C $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 37
_Mol_residue_sequence
;
GCACAUCUAGGUUUCGUCCG
GGUGUGACCGAAAGGUA
;
loop_
_Residue_seq_code
_Residue_author_seq_code
_Residue_label
1 227 G 2 228 C 3 229 A 4 230 C 5 231 A
6 232 U 7 233 C 8 234 U 9 235 A 10 236 G
11 237 G 12 238 U 13 239 U 14 240 U 15 241 C
16 242 G 17 243 U 18 244 C 19 245 C 20 246 G
21 247 G 22 248 G 23 249 U 24 250 G 25 251 U
26 252 G 27 253 A 28 254 C 29 255 C 30 256 G
31 257 A 32 258 A 33 259 A 34 260 G 35 261 G
36 262 U 37 263 A
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_1 350 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_
#########################
# Experimental detail #
#########################
##################################
# NMR Spectrometer definitions #
##################################
save_NMR_spectrometer_1
_Saveframe_category NMR_spectrometer
_Manufacturer Bruker
_Model 'Bruker Avance neo 600 MHz'
_Field_strength 600
_Details .
save_
save_NMR_spectrometer_2
_Saveframe_category NMR_spectrometer
_Manufacturer Bruker
_Model 'Bruker Avance neo 1000 MHz'
_Field_strength 1000
_Details .
save_
#############################
# NMR applied experiments #
#############################
save_P_TROSY[15N]_1
_Saveframe_category NMR_applied_experiment
_Experiment_name P_TROSY[15N]
_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_HNN-COSY[15N]_3
_Saveframe_category NMR_applied_experiment
_Experiment_name HNN-COSY[15N]
_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_NOESY-JR[15N]-Amino_5
_Saveframe_category NMR_applied_experiment
_Experiment_name NOESY-JR[15N]-Amino
_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_
#######################
# 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
P_TROSY[15N]
1H-JR[15N]
HNN-COSY[15N]
HSQC[15N]-2J
NOESY-JR[15N]-Amino
NOESY[15N]-Imino
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_SL5B+C
_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
1 229 3 A H2 H 7.50886 . 1
2 229 3 A N1 N 221.551 . 1
3 229 3 A N3 N 212.102 . 1
4 230 4 C H41 H 8.308 . 1
5 230 4 C H42 H 6.99267 . 1
6 230 4 C N4 N 98.216 . 1
7 231 5 A H2 H 7.39618 . 1
8 231 5 A N1 N 220.674 . 1
9 231 5 A N3 N 213.859 . 1
10 232 6 U H3 H 11.9748 . 1
11 232 6 U N3 N 158.387 . 1
12 233 7 C H41 H 8.416 . 1
13 233 7 C H42 H 6.8476 . 1
14 233 7 C N3 N 195.631 . 1
15 233 7 C N4 N 98.1205 . 1
16 234 8 U H3 H 11.9794 . 1
17 234 8 U N3 N 157.674 . 1
18 246 20 G H1 H 10.5388 . 1
19 246 20 G N1 N 143.769 . 1
20 247 21 G H1 H 12.8844 . 1
21 247 21 G N1 N 148.108 . 1
22 248 22 G H1 H 11.5384 . 1
23 248 22 G N1 N 144.754 . 1
24 249 23 U H3 H 13.6816 . 1
25 249 23 U N3 N 162.594 . 1
26 250 24 G H1 H 12.5534 . 1
27 250 24 G N1 N 147.309 . 1
28 251 25 U H3 H 13.9372 . 1
29 251 25 U N3 N 162.217 . 1
stop_
save_