BMRB Entry 27770

Name: GA-branchsite-containing RNA duplex with pseudouridine-modified U2 snRNA site
Published: 2019-03-08

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR27770

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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:

GA-branchsite-containing RNA duplex with pseudouridine-modified U2 snRNA site

Deposition date:

2019-01-30

Original release date:

2019-03-08

Authors:

Kennedy, Scott; Kielkopf, Clara; Bauer, William

Citation:

Citation: Kennedy, Scott; Bauer, William; Wang, Wenhua; Kielkopf, Clara. "Dynamic stacking of an expected branch point adenosine in duplexes containing pseudouridine-modified or unmodified U2 snRNA sites" Biochem. Biophys. Res. Commun. 511, 416-421 (2019).
PubMed: 30797552

Assembly members:

Assembly members:
RNA_with_branchpoint_sequence, polymer, 11 residues, Formula weight is not available
RNA_with_pseudoU-modified_U2_snRNA_site, polymer, 10 residues, Formula weight is not available

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: chemical synthesis Host organism: NA Vector: NA

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA_with_branchpoint_sequence: GCUACUGACGA
RNA_with_pseudoU-modified_U2_snRNA_site: CGXAGUAGCA

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
- assigned_chem_shift_list_2

Data type	Count
13C chemical shifts	35
1H chemical shifts	186
31P chemical shifts	19

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA with branchpoint sequence	1
2	RNA with pseudoU-modified U2 snRNA site	2

Entities:

Entity 1, RNA with branchpoint sequence 11 residues - Formula weight is not available

1

G

C

U

A

C

U

G

A

C

G

2

A

Entity 2, RNA with pseudoU-modified U2 snRNA site 10 residues - Formula weight is not available

1

C

G

PSU

A

G

U

A

G

C

A

Samples:

sample_1: RNA with branchpoint sequence 1 mM; RNA with pseudoU-modified U2 snRNA site 1 mM; potassium phosphate 10 mM; EDTA 0.25 mM

sample_2: RNA with branchpoint sequence 1 mM; RNA with pseudoU-modified U2 snRNA site 1 mM; potassium phosphate 10 mM; EDTA 0.25 mM

sample_conditions_1: ionic strength: 0.017 M; pH: 6.8; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 0.017 M; pH: 6.8; pressure: 1 atm; temperature: 273 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_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_2
2D 1H-31P COSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_2

Software:

VNMR v6.1C, Varian - collection

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

SPARKY, Goddard - chemical shift assignment, data analysis, peak picking

NMR spectrometers:

Varian INOVA 600 MHz