BMRB Entry 17941

Name: the structure of subdomain IV-B from the CVB-3 IRES
Published: 2012-09-17

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PDB ID: 2ljj
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17941
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

the structure of subdomain IV-B from the CVB-3 IRES

Deposition date:

2011-09-15

Original release date:

2012-09-17

Authors:

Ihle, Yvonne; Zell, Roland; Goerlach, Matthias

Citation:

Citation: Ihle, Yvonne. "The Structure of Subdomain IV-B from the CVB-3 IRES" .

Assembly members:

Assembly members:
IV-B_RNA, polymer, 27 residues, 8600.216 Da.

Natural source:

Natural source: Common Name: Coxsackievirus B3 Taxonomy ID: 12072 Superkingdom: Viruses Kingdom: not available Genus/species: Enterovirus Human enterovirus B

Experimental source:

Experimental source: Production method: enzymatic semisynthesis Vector: pUC19

Entity Sequences (FASTA):

Entity Sequences (FASTA):
IV-B_RNA: GGCCUCAGCACUACCCCAGU GUAGGUC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	179
15N chemical shifts	47
1H chemical shifts	243
31P chemical shifts	2

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	IV-B_RNA	1

Entities:

Entity 1, IV-B_RNA 27 residues - 8600.216 Da.

Residues 290-292 and 314-316 are non-native and were attached facilitating transcription and purification.

1

G

C

U

C

A

G

C

A

2

C

U

A

C

A

G

U

3

G

U

A

G

U

C

Samples:

15N-IVB: IV-B RNA, [U-100% 15N], 1 mM; potassium phosphate 10 mM; potassium chloride 40 mM; EDTA 200 uM; H2O 90%; D2O 10%

13C_15N-IVB: IV-B RNA, [U-100% 13C; U-100% 15N], 1 mM; potassium phosphate 10 mM; potassium chloride 40 mM; EDTA 200 uM; D2O 100%

(C_A-13C_15N)-IVB: IV-B RNA, [U-13C; U-15N]-Ade,Cyt, 1 mM; potassium phosphate 10 mM; potassium chloride 40 mM; EDTA 200 uM; D2O 100%

(G_U-13C_15N)-IVB: IV-B RNA, [U-13C; U-15N]-Gua,Ura, 1 mM; potassium phosphate 10 mM; potassium chloride 40 mM; EDTA 200 uM; D2O 100%

sample_conditions_1: ionic strength: 50 mM; pH: 6.2; pressure: 1 atm; temperature: 273 K

sample_conditions_2: pH: 6.2; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	15N-IVB	isotropic	sample_conditions_1

Software:

CYANA v1.1, Guntert, Mumenthaler and Wuthrich - structure solution

TOPSPIN v2.1, Bruker Biospin - collection, processing

CARA v1.5.5, Rochus Keller - chemical shift assignment, peak picking

CNS v1.3, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 750 MHz