BMRB Entry 25997

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

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PDB ID: 2nby
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25997
MolProbity Validation Chart

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Nicholas Rego and David Koes
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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 domain 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_(39-MER), polymer, 39 residues, 12538.552 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_(39-MER): GGGCAGAAGGUACCCCAUUG UAUGGGAUCUGAUCUGCCC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	143
1H chemical shifts	154

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (39-MER)	1

Entities:

Entity 1, RNA (39-MER) 39 residues - 12538.552 Da.

1

G

C

A

G

A

G

2

U

A

C

A

U

G

3

U

A

U

G

A

U

C

U

4

G

A

U

C

U

G

C

Samples:

sample_1: RNA (39-MER) 0.5 mM; potassium phosphate 10 mM; sodium chloride 10 mM; D2O, [U-2H], 100%

sample_2: RNA (39-MER) 0.5 mM; potassium phosphate 10 mM; sodium chloride 10 mM; H2O 90%; D2O, [U-2H], 10%

sample_3: RNA (39-MER), [U-13C; U-15N]-Ade, [U-13C; U-15N]-Cyt, 0.5 mM; potassium phosphate 10 mM; sodium chloride 10 mM; D2O, [U-2H], 100%

sample_4: RNA (39-MER), [U-13C; U-15N]-Gua, [U-13C; U-15N]-Ura, 0.5 mM; potassium phosphate 10 mM; sodium chloride 10 mM; D2O, [U-2H], 100%

sample_5: RNA (39-MER), [U-13C; U-15N]-Ade, [U-13C; U-15N]-Cyt, 0.5 mM; potassium phosphate 10 mM; sodium chloride 10 mM; H2O 90%; D2O, [U-2H], 10%

sample_6: RNA (39-MER), [U-13C; U-15N]-Gua, [U-13C; U-15N]-Ura, 0.5 mM; potassium phosphate 10 mM; sodium chloride 10 mM; H2O 90%; D2O, [U-2H], 10%

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

sample_conditions_2: ionic strength: 20 mM; pH: 6.5; pressure: 1 atm; temperature: 283 K

sample_conditions_3: ionic strength: 20 mM; pH: 5.5; pressure: 1 atm; temperature: 283 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_2
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_3
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_4	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_4	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_5	isotropic	sample_conditions_2
2D 1H-15N HSQC	sample_5	isotropic	sample_conditions_3
2D 1H-15N HSQC	sample_6	isotropic	sample_conditions_2
2D 1H-15N HSQC	sample_6	isotropic	sample_conditions_3

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