BMRB Entry 50348

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

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR50348

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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 imino 1H and 15N chemical shifts for PK

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, 69 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: reverse transcriptase

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GGCGGUGUAAGUGCAGCCCG UCUUACACCGUGCGGCACAG GCACUAGUACUGAUGUCGUA UACAGGGCU

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
15N chemical shifts	25
1H chemical shifts	25

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Pseudoknot	1

Entities:

Entity 1, Pseudoknot 69 residues - Formula weight is not available

1

G

C

G

U

G

U

A

2

G

U

G

C

A

G

C

G

3

U

C

U

A

C

A

C

G

4

U

G

C

G

C

A

C

A

G

5

G

C

A

C

U

A

G

U

A

C

6

U

G

A

U

G

U

C

G

U

A

7

U

A

C

A

G

C

U

Samples:

sample_1: PK, [U-15N], 790 uM; Kpi 25 mM; KCl 50 mM

sample_2: PK 637 uM; Kpi 25 mM; KCl 50 mM

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: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
NOESY	sample_2	isotropic	sample_conditions_2
TROSY[15N]	sample_1	isotropic	sample_conditions_1
HNN-COSY[15N]	sample_1	isotropic	sample_conditions_1

Software:

LOGS v2.2 - collection

CARA v1.9.1.7 - chemical shift assignment, peak picking

TOPSPIN v2.1 - collection

TOPSPIN v3.6.2 - collection

NMR spectrometers:

Bruker Bruker Avance III 800 MHz 800 MHz
Bruker Bruker Avance I 600 MHz 600 MHz