BMRB Entry 31171

Name: ;
Published: 2024-11-21

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PDB ID: 9blm
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31171
MolProbity Validation Chart

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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:

;

Deposition date:

Original release date:

2024-11-21

Authors:

,

Citation:

Citation: Zhu, Ying; Chaubey, Bhawna; Olsen, Gregory; Varani, Gabriele. "Structure of Essential RNA Regulatory Elements in the West Nile Virus 3'-Terminal Stem Loop" J. Mol. Biol. 436, 168767-168767 (2024).
PubMed: 39214284

Assembly members:

Assembly members:
entity_1, polymer, 68 residues, 21948.059 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GGCCUGGGAUAGACUAGGAG AUCUUCUGCUCUGCACAACC UUCGGGUGGUGCGAGAXCAC AGGAUACU

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	171
15N chemical shifts	33
1H chemical shifts	401

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 68 residues - 21948.059 Da.

1

G

C

U

G

A

U

2

A

G

A

C

U

A

G

A

G

3

A

U

C

U

C

U

G

C

U

4

C

U

G

C

A

C

A

C

5

U

C

G

U

G

U

6

G

C

G

A

G

A

AP7

C

A

C

7

A

G

A

U

A

C

U

Samples:

sample_1: RNA (68-MER) 1 ± 0.1 mM

sample_2: RNA (68-MER) 1 ± 0.1 mM

sample_3: RNA (68-MER), [U-99% 13C; U-99% 15N], 0.8 ± 0.1 mM

sample_4: RNA (68-MER), [U-99% 13C; U-99% 15N], 0.8 ± 0.1 mM

sample_5: RNA (68-MER), [U-2H], 0.8 ± 0.1 mM

sample_conditions_1: ionic strength: 20 mM; pH: 6.4; pressure: 1 atm; temperature: 310 K

sample_conditions_2: ionic strength: 20 mM; pH: 6.4; pressure: 1 atm; temperature: 288 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_4	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_5	isotropic	sample_conditions_1

Software:

TopSpin, Bruker Biospin - processing

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

NMRFAM-SPARKY, Woonghee Lee, John L. Markley - chemical shift assignment

NMR spectrometers:

Bruker AVANCE II 600 MHz
Bruker AVANCE II 800 MHz