BMRB Entry 15080

Name: U2 snRNA stem I from S. cerevisiae
Published: 2007-02-02

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PDB ID: 2o32
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR15080
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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:

U2 snRNA stem I from S. cerevisiae

Deposition date:

2006-12-15

Original release date:

2007-02-02

Authors:

Sashital, Dipali; Venditti, Vincenzo; Angers, Cortney; Cornilescu, Gabriel; Butcher, Samuel

Citation:

Citation: Sashital, Dipali; Venditti, Vincenzo; Angers, Cortney; Cornilescu, Gabriel; Butcher, Samuel. "Structure and thermodynamics of a conserved U2 snRNA domain from yeast and human" RNA 13, 328-338 (2007).
PubMed: 17242306

Assembly members:

Assembly members:
Yeast_U2_Stem_I, polymer, 20 residues, Formula weight is not available

Natural source:

Natural source: Common Name: Yeast Taxonomy ID: 4932 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Saccharomyces cerevisiae

Experimental source:

Experimental source: Production method: enzymatic semisynthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Yeast_U2_Stem_I: GGUUUGCCUUUUGGCUUACC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	133
1H chemical shifts	177

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Yeast U2 stem I	1

Entities:

Entity 1, Yeast U2 stem I 20 residues - Formula weight is not available

1		G	G	U	U	U	G	C	C	U	U
2		U	U	G	G	C	U	U	A	C	C

Samples:

sample_1: Yeast U2 Stem I 0.5 mM; H2O 90%; sodium chloride 50 mM; D2O 10%

sample_2: Yeast U2 Stem I 0.5 mM; D2O 99.99%; sodium chloride 50 mM

sample_3: Yeast U2 Stem I, [U-100% 13C; U-100% 15N], 0.4 mM; D2O 99.99%; sodium chloride 50 mM

sample_4: Yeast U2 Stem I, [U-100% 13C; U-100% 15N], 0.4 mM; D2O 99.99%; sodium chloride 50 mM; potassium chloride 10 mM; Pf1 phage 17 w/v

sample_conditions_1: ionic strength: 50 mM; pH: 7; pressure: 1 bar; temperature: 283 K

sample_conditions_2: pH: 7.0; temperature: 303 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 TOCSY	sample_2	isotropic	sample_conditions_2
2D 1H-1H COSY	sample_3	isotropic	sample_conditions_2
3D HCCH-TOCSY	sample_3	isotropic	sample_conditions_2
2D HNCO	sample_3	isotropic	sample_conditions_2
2D J-modulated CT HSQC	sample_3	isotropic	sample_conditions_2
2D hd-ECOSY-TROSY	sample_3	isotropic	sample_conditions_2
2D J-modulated CT HSQC	sample_4	anisotropic	sample_conditions_2
2D hd-ECOSY-TROSY	sample_4	anisotropic	sample_conditions_2

Software:

xwinnmr, Bruker Biospin - collection, processing

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY, Goddard - chemical shift assignment, data analysis

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

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

NMR spectrometers:

Bruker DMX 750 MHz
Varian INOVA 900 MHz