BMRB Entry 25811

Name: NMR-SAXS/WAXS Structure of the core of the U4/U6 di-snRNA
Published: 2015-12-28

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PDB ID: 2n7m
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25811
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: NMR-SAXS/WAXS Structure of the core of the U4/U6 di-snRNA PubMed: 26655855

Deposition date: 2015-09-14 Original release date: 2015-12-28

Authors: Cornilescu, Gabriel; Didychuk, Allison; Rodgers, Margaret; Michael, Lauren; Burke, Jordan; Montemayor, Eric; Hoskins, Aaron; Butcher, Samuel; Tonelli, Marco

Citation: Cornilescu, Gabriel; Didychuk, Allison; Rodgers, Margaret; Michael, Lauren; Burke, Jordan; Montemayor, Eric; Hoskins, Aaron; Butcher, Samuel. "Structural analysis of multi-helical RNAs by NMR-SAXS/WAXS: Application to the U4/U6 di-snRNA" J. Mol. Biol. 428, 777-789 (2015).

Assembly members:
RNA_(92-MER), polymer, 92 residues, 29563.637 Da.

Natural source: Common Name: baker's yeast Taxonomy ID: 4932 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Saccharomyces cerevisiae

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):
RNA_(92-MER): GGCCUUAUGCACGGGAAAUA CGCAUAUCAGUGAGGAUUCG UCCGAGAUUGUGUUUUUGCU GGUGUAAAUCAGCAGUUCCC CUGCAUAAGGCU

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	5
15N chemical shifts	25
1H chemical shifts	30

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (92-MER)	1

Entities:

Entity 1, RNA (92-MER) 92 residues - 29563.637 Da.

Contains two G nucleotides for transcription, then snRNA U4 nucleotides 3-63, a GUAA linker, U6 snRNA nucleotides 56-80 with an A79C mutation.

1

G

C

U

A

U

G

C

2

A

C

G

A

U

A

3

C

G

C

A

U

A

U

C

A

G

4

U

G

A

G

A

U

C

G

5

U

C

G

A

G

A

U

G

6

U

G

U

G

C

U

7

G

U

G

U

A

U

C

8

A

G

C

A

G

U

C

9

C

U

G

C

A

U

A

G

10

C

U

Samples:

sample_1A: RNA (92-MER), [U-13C; U-15N]-Gua, -Ura, 0.6 mM; potassium chloride 0.02 mM; potassium phosphate 0.02 mM

sample_2A: RNA (92-MER), [U-13C; U-15N]-Ade, 0.7 mM; potassium chloride 0.02 mM; potassium phosphate 0.02 mM

sample_1B: RNA (92-MER), [U-13C; U-15N]-Gua, -Ura, 0.6 mM; potassium chloride 0.02 mM; potassium phosphate 0.02 mM; Pf1 phage 5 mg/mL

sample_2B: RNA (92-MER), [U-13C; U-15N]-Ade, 0.7 mM; potassium chloride 0.02 mM; potassium phosphate 0.02 mM; Pf1 phage 5 mg/mL

sample_conditions_1: ionic strength: 58.5 mM; pH: 7.0; pressure: 1 atm; temperature: 273 K

sample_conditions_2: ionic strength: 58.5 mM; pH: 7.0; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1A	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1B	anisotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2A	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_2B	anisotropic	sample_conditions_2

Software:

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

X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

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

NMR spectrometers:

Agilent INOVA 900 MHz
Agilent INOVA 800 MHz
Bruker DMX 750 MHz
Bruker Avance 600 MHz
Bruker Avance 500 MHz