BMRB Entry 26000

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

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PDB ID: 2nc1
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR26000
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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 structure of the delta-J-delta-K domain of EMCV IRES

Deposition date:

2016-03-16

Original release date:

2016-08-08

Authors:

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

Citation:

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).
PubMed: 27525590

Assembly members:

Assembly members:
RNA_(67-MER), polymer, 67 residues, 21821.207 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: enzymatic semisynthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA_(67-MER): GGGGCUGAAGGAUGCCCAGA GAGAUCUGGGGCCUCGGGAG AUCGAGGUUAAAAAACGUCU AGGCCCC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	274

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (67-MER)	1

Entities:

Entity 1, RNA (67-MER) 67 residues - 21821.207 Da.

1

G

C

U

G

A

G

2

G

A

U

G

C

A

G

A

3

G

A

G

A

U

C

U

G

4

G

C

U

C

G

A

G

5

A

U

C

G

A

G

U

A

6

A

C

G

U

C

U

7

A

G

C

Samples:

sample_1: RNA (67-MER) 0.5 mM; potassium phosphate 10 mM; sodium chloride 10 mM; D2O, [U-2H], 100%

sample_2: RNA (67-MER) 0.5 mM; potassium phosphate 10 mM; sodium chloride 10 mM; H2O 90%; D2O, [U-2H], 10%

sample_3: RNA (67-MER), [U-2H, {H1',H2',H2,H8}-Ade], 0.5 mM; potassium phosphate 10 mM; sodium chloride 10 mM; D2O, [U-2H], 100%

sample_4: RNA (67-MER), [U-2H]-Cyt, [U-2H]-Ura, 0.5 mM; potassium phosphate 10 mM; sodium chloride 10 mM; D2O, [U-2H], 100%

sample_5: RNA (67-MER), [U-2H]-Gua, [U-2H]-Ura, 0.5 mM; potassium phosphate 10 mM; sodium chloride 10 mM; D2O, [U-2H], 100%

sample_6: RNA (67-MER), [U-2H, {H1',H2',H2,H8}-Ade], 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_3	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_4	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_5	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-1H NOESY	sample_6	isotropic	sample_conditions_2
2D 1H-1H NOESY	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