BMRB Entry 50349

Name: Assignment of base 15N and 1H chemical shifts for &lt;5_SL1&gt;
Published: 2020-07-10

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR50349

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Assignment of base 15N and 1H chemical shifts for <5_SL1>

Deposition date:

2020-06-23

Original release date:

2020-07-10

Authors:

Schwalbe, Harald; Richter, Christian

Citation:

Citation: Wacker, Anna; Weigand, Julia; Akabayov, Sabine; Altincekic, Nadide; Kaur Bains, Jasleen; Banijamali, Elnaz; Binas, Oliver; Castillo-Martinez, Jesus; Cetiner, Erhan; Ceylan, Betul; Chiu, Liang-Yuan; Davila-Calderon, Jesse; De Jesus, Vanessa; Dhamotharan, Karthikeyan; Duchardt-Ferner, Elke; Ferner, Jan; Frydman, Lucio; Furtig, Boris; Gallego, Jose; Grun, J. Tassilo; Hacker, Carolin; Haddad, Christina; Hahnke, Martin; Hengesbach, Martin; Hiller, Fabian; Hohmann, Katharina; Hymon, Daniel; Jonker, Henry; Keller, Heiko; Knezic, Bozana; Landgraf, Tom; Lohr, Frank; Luo, Luke; Mertinkus, Klara; Muhs, Christina; Novakovic, Mihajlo; Oxenfarth, Andreas; Palomino-Schatzlein, Martina; Petzold, Katja; Peter, Stephen; Pyper, Dennis; Qureshi, Nusrat; Riad, Magdalena; Richter, Christian; Saxena, Krishna; Schamber, Tatjana; Scherf, Tali; Schlagnitweit, Judith; Schlundt, Andreas; Schnieders, Robbin; Schwalbe, Harald; Simba-Lahuasi, Alvaro; Sreeramulu, Sridhar; Stirnal, Elke; Sudakov, Alexey; Tants, Jan-Niklas; Tolbert, Blanton; Vogele, Jenny; Weiss, Lena; Wirmer-Bartoschek, Julia; Wirtz Martin, Maria; Wohnert, Jens; Zetzsche, Heidi. "Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy" Nucleic Acids Res. 48, 12415-12435 (2020).
PubMed: 33167030

Assembly members:

Assembly members:
entity_1, polymer, 29 residues, Formula weight is not available

Natural source:

Natural source: Common Name: SARS-CoV-2 Taxonomy ID: 2697049 Superkingdom: Viruses Kingdom: not available Genus/species: Betacoronavirus HCoV-SARS

Experimental source:

Experimental source: Production method: transcription Host organism: in vitro

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GGGUUUAUACCUUCCCAGGU AACAAACCC

Data sets:

RDCs
- RDC_list_1
assigned_chemical_shifts
- assigned_chemical_shifts_1
- assigned_chemical_shifts_2
heteronucl_NOEs
- heteronucl_NOEs_1

Data type	Count
13C chemical shifts	245
15N chemical shifts	106
1H chemical shifts	258
heteronuclear NOE values	37
residual dipolar couplings	18

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	5_SL1	1

Entities:

Entity 1, 5_SL1 29 residues - Formula weight is not available

1

G

U

A

U

A

C

2

C

U

C

A

G

U

3

A

C

A

C

Samples:

sample_1: 5_SL1 13C 15N, [U-13C; U-15N], 150 uM; potassium phosphate 25 mM; KCl 50 mM

sample_2: 5_SL1 15N, [U-15N], 150 uM; potassium phosphate 25 mM; KCl 50 mM

sample_3: 5_SL1 13C 15N, [U-13C; U-15N], 150 uM; potassium phosphate 25 mM; KCl 50 mM; Pf1 phages 10 mg/mL

sample_conditions_1: ionic strength: 75 mM; pH: 6.2; pressure: 1 atm; temperature: 283 K

sample_conditions_2: ionic strength: 75 mM; pH: 6.2; pressure: 1 atm; temperature: 298 K

sample_conditions_3: ionic strength: 75 mM; pH: 6.2; pressure: 1 atm; temperature: 288 K

Experiments:

Name	Sample	Sample state	Sample conditions
1H-JR[15N]	sample_2	isotropic	sample_conditions_3
NOESY[15N]-Imino	sample_2	isotropic	sample_conditions_3
HSQC[15N]-Amino	sample_2	isotropic	sample_conditions_3
HSQC[15N]-2J	sample_2	isotropic	sample_conditions_3
TROSY[15N]	sample_2	isotropic	sample_conditions_3
NOESY-JR[15N]-Amino	sample_2	isotropic	sample_conditions_3
TOCSY	sample_2	isotropic	sample_conditions_3
HSQC[13C]-Aromaten	sample_1	isotropic	sample_conditions_1
1H-JR[15N]	sample_1	isotropic	sample_conditions_2
NOESY[15N]-Imino	sample_1	isotropic	sample_conditions_2
HSQC[15N]-Amino	sample_1	isotropic	sample_conditions_2
HSQC[15N]-2J	sample_1	isotropic	sample_conditions_2
TROSY[15N]	sample_1	isotropic	sample_conditions_2
NOESY-JR[15N]-Amino	sample_1	isotropic	sample_conditions_2
TOCSY	sample_1	isotropic	sample_conditions_2
HSQC[13C]-Aromaten	sample_1	isotropic	sample_conditions_2
IPAP-sfHMQC [15N]	sample_3	isotropic	sample_conditions_3
IPAP-HSQC [13C]	sample_3	isotropic	sample_conditions_3
CT-HSQC-NOE [13C] interleaved	sample_1	isotropic	sample_conditions_1

Software:

LOGS v2.2 - collection

SPARKY v3.114 - chemical shift assignment, peak picking

TOPSPIN v3.6.2 - collection

TOPSPIN v2.1 - collection

NMR spectrometers:

Bruker Bruker Avance III HD 800 MHz 800 MHz
Bruker Bruker Avance III HD 700 MHz 700 MHz
Bruker Bruker Avance I 600 MHz 600 MHz