BMRB Entry 30026

Name: NMR structure of the 5'-terminal hairpin of the 7SK snRNA
Published: 2016-10-28

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PDB ID: 5iem
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30026
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: NMR structure of the 5'-terminal hairpin of the 7SK snRNA PubMed: 27852926

Deposition date: 2016-02-25 Original release date: 2016-10-28

Authors: Bourbigot, S.; Dock-Bregeon, A.C.; Coutant, J.; Kieffer, B.; Lebars, I.

Citation: Bourbigot, S.; Dock-Bregeon, A.C.; Eberling, P.; Coutant, J.; Kieffer, B.; Lebars, I.. "Solution structure of the 5'-terminal hairpin of the 7SK small nuclear RNA" RNA 22, 1844-1858 (2016).

Assembly members:
RNA (57-MER), polymer, 57 residues, 18268.777 Da.

Natural source: Common Name: not available Taxonomy ID: 32630 Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):
RNA (57-MER): GGGAUCUGUCACCCCAUUGA UCGCCUUCGGGCUGAUCUGG CUGGCUAGGCGGGUCCC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	68
15N chemical shifts	23
1H chemical shifts	256

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 57 residues - 18268.777 Da.

1

G

A

U

C

U

G

U

C

2

A

C

A

U

G

A

3

U

C

G

C

U

C

G

4

G

C

U

G

A

U

C

U

G

5

C

U

G

C

U

A

G

C

6

G

U

C

Samples:

sample_1: HPI 0.8 mM; HPI, [U-99% 13C; U-99% 15N], 0.4 mM; HPI, [U-13C; U-15N]-Ade, 0.4 mM; HPI, [U-13C; U-15N]-Cyt, 0.4 mM; HPI, [U-13C; U-15N]-Gua, 0.4 mM; HPI, [U-13C; U-15N]-Ura, 0.4 mM; H2O 90%; D2O 10%

sample_2: HPI 0.8 mM; HPI, [U-99% 13C; U-99% 15N], 0.4 mM; HPI, [U-13C; U-15N]-Ade, 0.4 mM; HPI, [U-13C; U-15N]-Cyt, 0.4 mM; HPI, [U-13C; U-15N]-Gua, 0.4 mM; HPI, [U-13C; U-15N]-Ura, 0.4 mM; D2O 100%

sample_3: HPI, [U-13C; U-15N]-Ade, 0.4 mM; HPI, [U-13C; U-15N]-Gua, 0.4 mM; HPI, [U-13C; U-15N]-Ura, 0.4 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 50 mM; pH: 6.4; pressure: 101325 Pa; temperature: 288 K

sample_conditions_2: ionic strength: 50 mM; pH: 6.4; pressure: 101325 Pa; temperature: 303 K

sample_conditions_3: ionic strength: 50 mM; pH: 6.4; pressure: 101325 Pa; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_3	anisotropic	sample_conditions_3
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_2
2D DQF-COSY	sample_2	isotropic	sample_conditions_2
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_2
2D 1H-15N HSQC	sample_3	anisotropic	sample_conditions_3
3D HCP	sample_2	isotropic	sample_conditions_2
2D HPCOSY	sample_2	isotropic	sample_conditions_2
2D HCN	sample_2	isotropic	sample_conditions_2

Software:

CNS, Brunger A. T. et.al., Brunger, Adams, Clore, Gros, Nilges and Read - refinement, structure calculation

SPARKY, Goddard - chemical shift assignment, peak picking

NMR spectrometers:

Bruker AvanceIII 500 MHz
Bruker AvanceIII 700 MHz
Bruker DRX 600 MHz