BMRB Entry 30665

Name: NMR assignment and RNA structure of 5' UTR region stem loop from West Nile Virus
Published: 2020-08-18

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PDB ID: 6u79
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30665
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: NMR assignment and RNA structure of 5' UTR region stem loop from West Nile Virus PubMed: 32807496

Deposition date: 2019-09-01 Original release date: 2020-08-18

Authors: Sharma, S.; Varani, G.

Citation: Sharma, S.; Varani, G.. "NMR structure of Dengue West Nile viruses stem-loop B: A key cis-acting element for flavivirus replication" Biochem. Biophys. Res. Commun. 531, 522-527 (2020).

Assembly members:
entity_1, polymer, 37 residues, 11841.064 Da.

Natural source: Common Name: West Nile virus Taxonomy ID: 11082 Superkingdom: Viruses Kingdom: not available Genus/species: Flavivirus West Nile virus

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):
entity_1: GGUUUCUUAGCACGAAGAUC UCGAUGUCUAAGAAACC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	215
15N chemical shifts	13
1H chemical shifts	277

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 37 residues - 11841.064 Da.

1

G

U

C

U

A

G

2

C

A

C

G

A

G

A

U

C

3

U

C

G

A

U

G

U

C

U

A

4

A

G

A

C

Samples:

sample_1: entity_1, [U-99% 13C; U-99% 15N], 0.5 ± 0.1 mM; sodium phosphate 20 mM

sample_conditions_1: ionic strength: 20 mM; pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
1H proton	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1

Software:

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation

Sparky, Goddard - chemical shift assignment, peak picking

NMR spectrometers:

Bruker AVANCE II 600 MHz
Bruker AVANCE II 800 MHz