BMRB Entry 25996

Name: Solution structure of the J-K region of EMCV IRES
Published: 2016-08-08

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PDB ID: 2nbx
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25996
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Solution structure of the J-K region of EMCV IRES PubMed: 27525590

Deposition date: 2016-03-16 Original release date: 2016-08-08

Authors: Imai, Shunsuke; D'Souza, Victoria; Wagner, Gerhard

Citation: Imai, Shunsuke; Hellen, Christopher; D'Souza, Victoria; Wagner, Gerhard. "An accurately preorganized IRES RNA structure enables eIF4G capture for initiation of viral translation" Nat. Struct. Mol. Biol. 23, 859-864 (2016).

Assembly members:
RNA_(108-MER), polymer, 108 residues, 34838.840 Da.

Natural source: Common Name: Encephalomyocarditis virus Taxonomy ID: 12104 Superkingdom: Viruses Kingdom: not available Genus/species: Cardiovirus Cardiovirus A

Experimental source: Production method: enzymatic semisynthesis

Entity Sequences (FASTA):
RNA_(108-MER): GGGGCUGAAGGAUGCCCAGA AGGUACCCCAUUGUAUGGGA UCUGAUCUGGGGCCUCGGUG CACAUGCUUUACAUGUGUUU AGUCGAGGUUAAAAAACGUC UAGGCCCC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	90

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (108-MER)	1

Entities:

Entity 1, RNA (108-MER) 108 residues - 34838.840 Da.

1

G

C

U

G

A

G

2

G

A

U

G

C

A

G

A

3

A

G

U

A

C

A

4

U

G

U

A

U

G

A

5

U

C

U

G

A

U

C

U

G

6

G

C

U

C

G

U

G

7

C

A

C

A

U

G

C

U

8

A

C

A

U

G

U

G

U

9

A

G

U

C

G

A

G

U

10

A

C

G

U

C

11

U

A

G

C

Samples:

sample_1: RNA (108-MER) 0.5 mM; potassium phosphate 10 mM; sodium chloride 10 mM; D2O, [U-2H], 100%

sample_2: RNA (108-MER), [U-2H, {H1',H2',H2,H8}-Ade], 0.5 mM; potassium phosphate 10 mM; sodium chloride 10 mM; D2O, [U-2H], 100%

sample_conditions_1: ionic strength: 20 mM; pH: 6.5; pressure: 1 atm; temperature: 308 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1

Software:

CARA, Keller and Wuthrich - chemical shift assignment

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

Bruker Avance 800 MHz
Bruker Avance 700 MHz