BMRB Entry 50346

Name: Assignment of base 15N and 1H chemical shifts for 5_SL5a
Published: 2020-07-10

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PDB ID: 9fo9
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR50346
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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_SL5a

Deposition date:

2020-06-23

Original release date:

2020-07-10

Authors:

Schwalbe, Harald; Richter, Christian; Schnieders, Robbin

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, 33 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: GGGCUGCUUACGGUUUCGUC CGUGUUGCAGCCC

Data sets:

assigned_chemical_shifts

Data type	Count
13C chemical shifts	319
15N chemical shifts	119
1H chemical shifts	334

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	5_SL5A	1

Entities:

Entity 1, 5_SL5A 33 residues - Formula weight is not available

1

G

C

U

G

C

U

A

2

C

G

U

C

G

U

C

3

C

G

U

G

U

G

C

A

G

4

C

Samples:

sample_1: 5_SL5A, [U-15N], 807 uM; potassium phosphate 25 mM; KCl 50 mM

sample_conditions_1: ionic strength: 75 mM; pH: 6.2; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 75 mM; pH: 6.2; pressure: 1 atm; temperature: 283 K

sample_conditions_3: ionic strength: 75 mM; pH: 6.2; pressure: 1 atm; temperature: 278 K

Experiments:

Name	Sample	Sample state	Sample conditions
NOESY-JR[15N]-Amino	sample_1	isotropic	sample_conditions_1
HSQC[15N]	sample_1	isotropic	sample_conditions_1
HSQC[15N]-2J	sample_1	isotropic	sample_conditions_1
HSQC[15N]-2J	sample_1	isotropic	sample_conditions_1
TROSY[15N]	sample_1	isotropic	sample_conditions_1
HNN-COSY[15N]	sample_1	isotropic	sample_conditions_1
HSQC[15N]-Amino	sample_1	isotropic	sample_conditions_1
TOCSY	sample_1	isotropic	sample_conditions_1
HNN-COSY[15N]	sample_1	isotropic	sample_conditions_1
2D HSQC HC	sample_1	isotropic	sample_conditions_1
NOESY[15N]-Imino	sample_1	isotropic	sample_conditions_1
NOESY-JR[15N]-Amino	sample_1	isotropic	sample_conditions_2
HSQC[15N]	sample_1	isotropic	sample_conditions_2
HSQC[15N]-2J	sample_1	isotropic	sample_conditions_2
HSQC[15N]-2J	sample_1	isotropic	sample_conditions_2
TROSY[15N]	sample_1	isotropic	sample_conditions_2
HNN-COSY[15N]	sample_1	isotropic	sample_conditions_2
HSQC[15N]-Amino	sample_1	isotropic	sample_conditions_2
TOCSY	sample_1	isotropic	sample_conditions_2
HNN-COSY[15N]	sample_1	isotropic	sample_conditions_2
2D HSQC HC	sample_1	isotropic	sample_conditions_2
NOESY[15N]-Imino	sample_1	isotropic	sample_conditions_2
3D-fw-TOCSY-C12	sample_1	isotropic	sample_conditions_1
3D-fw-TOCSY-C15	sample_1	isotropic	sample_conditions_1
CN-HSQC	sample_1	isotropic	sample_conditions_1
CT-HSQC[13C]	sample_1	isotropic	sample_conditions_1
H(N)CO	sample_1	isotropic	sample_conditions_1
3D-HCN	sample_1	isotropic	sample_conditions_1
H5C5C4N3N1	sample_1	isotropic	sample_conditions_1
H68C68N19C42	sample_1	isotropic	sample_conditions_1
3D-NOESY-HSQC	sample_1	isotropic	sample_conditions_1
HCCNH	sample_1	isotropic	sample_conditions_1
xf-NOESY	sample_1	isotropic	sample_conditions_1
lr-HNN-COSY	sample_1	isotropic	sample_conditions_1
TROSY[15N]	sample_1	isotropic	sample_conditions_1

Software:

LOGS v2.2 - collection

SPARKY v3.114 - chemical shift assignment, peak picking

TOPSPIN v3.6.2 - collection

NMR spectrometers:

Bruker AVIII 600 MHz