BMRB Entry 28094

Name: Solution NMR structure of 5'UTR of Stem loop B in DENV4
Published: 2020-08-18

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PDB ID: 6w3m
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR28094
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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:

Solution NMR structure of 5'UTR of Stem loop B in DENV4

Deposition date:

2020-03-06

Original release date:

2020-08-18

Authors:

Sharma, Shrikant; Varani, Gabriele

Citation:

Citation: Sharma, Shrikant; Varani, Gabriele. "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).
PubMed: 32807496

Assembly members:

Assembly members:
DENV4, polymer, 41 residues, Formula weight is not available

Natural source:

Natural source: Common Name: Flavivirus Taxonomy ID: 11051 Superkingdom: Viruses Kingdom: not available Genus/species: Flavivirus not available

Experimental source:

Experimental source: Production method: reverse transcriptase Host organism: Dengue virus Vector: Ades

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DENV4: GGUUUGUUUGAAUAGAGAGC AGAUCUCUGGAAAAAUGAAC C

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	265
15N chemical shifts	18
1H chemical shifts	327

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	5_prime_UTR	1

Entities:

Entity 1, 5_prime_UTR 41 residues - Formula weight is not available

1

G

U

G

U

G

2

A

U

A

G

A

G

A

G

C

3

A

G

A

U

C

U

C

U

G

4

A

U

G

A

C

5

C

Samples:

sample_1: DENV4, [U-99% 13C; U-99% 15N], 0.75 mM; sodium phosphate 20 mM

sample_conditions_1: ionic strength: 20 mM; pH: 6.0; pressure: 1 atm; temperature: 293 K

Experiments:

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

Software:

SPARKY, Goddard - chemical shift assignment

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 800 MHz