BMRB Entry 15417

Name: Solution Structure of the Frameshift-Inducing RNA Stem-Loop in SIV
Published: 2007-09-18

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PDB ID: 2jtp
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR15417
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Solution Structure of the Frameshift-Inducing RNA Stem-Loop in SIV PubMed: 17868691

Deposition date: 2007-08-04 Original release date: 2007-09-18

Authors: Marcheschi, Ryan; Staple, David; Butcher, Samuel

Citation: Marcheschi, Ryan; Staple, David; Butcher, Samuel. "Programmed Ribosomal Frameshifting in SIV is Induced by a Highly Structured RNA Stem-Loop" J. Mol. Biol. 373, 652-663 (2007).

Assembly members:
SIV_RNA_(34-MER), polymer, 34 residues, Formula weight is not available

Natural source: Common Name: not available Taxonomy ID: not available Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source: Production method: enzymatic semisynthesis

Entity Sequences (FASTA):
SIV_RNA_(34-MER): GGAUGGGGAAAGAAGCCCCG CAAUUUCCCCAUCC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	137
15N chemical shifts	11
1H chemical shifts	249

Time Domain Data

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA	1

Entities:

Entity 1, RNA 34 residues - Formula weight is not available

1

G

A

U

G

A

2

A

G

A

G

C

G

3

C

A

U

C

4

A

U

C

Samples:

sample_1: SIV17-50 RNA (34-MER) 1 mM; H2O 90%; D2O 10%

sample_2: SIV17-50 RNA (34-MER) 1 mM; H2O 90%; D2O 10%

sample_3: SIV17-50 RNA (34-MER), [U-100% 13C; U-100% 15N], 1 mM; H2O 90%; D2O 10%

sample_4: SIV17-50 RNA (34-MER), [U-100% 13C; U-100% 15N], 1 mM; H2O 90%; D2O 10%

sample_conditions_1: pH: 7.0; pressure: 1 atm; temperature: 277 K

sample_conditions_2: pH: 7.0; pressure: 1 atm; temperature: 283 K

sample_conditions_3: pH: 7.0; pressure: 1 atm; temperature: 303 K

sample_conditions_4: pH: 7.0; pressure: 1 atm; temperature: 308 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H COSY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_4	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_4	isotropic	sample_conditions_1
3D 1H-13C-1H HCCH-TOCSY	sample_4	isotropic	sample_conditions_1
3D NOESY-HMQC	sample_4	isotropic	sample_conditions_1
J-MODULATED 1H-13C CT-HSQC	sample_3	isotropic	sample_conditions_1
J-MODULATED 1H-13C CT-HSQC	sample_3	anisotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1

Software:

xwinnmr v3.5, Bruker Biospin - collection, processing

SPARKY v3.111, Goddard - data analysis, peak picking

CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

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

VNMR, Varian - collection

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis, peak picking, processing

NMR spectrometers:

Bruker DMX 750 MHz
Bruker DMX 600 MHz
Varian INOVA 600 MHz
Varian INOVA 800 MHz
Bruker DMX 500 MHz
Varian INOVA 900 MHz