BMRB Entry 34321

Name: NMR solution structure of the C/D box snoRNA U14
Published: 2019-04-22

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PDB ID: 6hyk
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34321
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR solution structure of the C/D box snoRNA U14

Deposition date:

2018-10-22

Original release date:

2019-04-22

Authors:

Chagot, M.; Quinternet, M.; Rothe, B.; Charpentier, B.; Coutant, J.; Manival, X.; Lebars, I.

Citation:

Citation: Chagot, M.; Quinternet, M.; Rothe, B.; Charpentier, B.; Coutant, J.; Manival, X.; Lebars, I.. "The yeast C/D box snoRNA U14 adopts a "weak" K-turn like conformation recognized by the Snu13 core protein in solution." Biochimie 164, 70-82 (2019).
PubMed: 30914254

Assembly members:

Assembly members:
entity_1, polymer, 31 residues, 9998.949 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: recombinant technology

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GGCACGGUGAUGACCUUCGG GUCUGAGUGCC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	207
15N chemical shifts	77
1H chemical shifts	242
31P chemical shifts	11

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 31 residues - 9998.949 Da.

1

G

C

A

C

G

U

G

A

2

U

G

A

C

U

C

G

3

G

U

C

U

G

A

G

U

G

C

4

C

Samples:

sample_1: RNA (31-MER)_unlabel 500 uM; RNA (31-MER)_label, [U-99% 13C; U-99% 15N], 500 uM; NaCl 150 mM

sample_2: RNA (31-MER)_unlabel 500 uM; RNA (31-MER)_label, [U-99% 13C; U-99% 15N], 500 uM; NaCl 150 mM

sample_conditions_1: ionic strength: 150 mM; pH: 6.4; pressure: 1 atm; temperature: 283 K

sample_conditions_2: ionic strength: 150 mM; pH: 6.4; pressure: 1 atm; temperature: 288 K

sample_conditions_3: ionic strength: 150 mM; pH: 6.4; pressure: 1 atm; temperature: 293 K

sample_conditions_4: ionic strength: 150 mM; pH: 6.4; pressure: 1 atm; temperature: 298 K

sample_conditions_5: ionic strength: 150 mM; pH: 6.4; pressure: 1 atm; temperature: 303 K

sample_conditions_6: ionic strength: 150 mM; pH: 6.4; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_4
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_2
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_4
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_4
2D 1H-15N HSQC	sample_1	anisotropic	sample_conditions_6
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_3
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_4
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_5
2D MLEV	sample_2	isotropic	sample_conditions_3
2D MLEV	sample_2	isotropic	sample_conditions_4
2D MLEV	sample_2	isotropic	sample_conditions_5
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_3
2D HNN COSY	sample_1	isotropic	sample_conditions_1
2D HNN COSY	sample_1	isotropic	sample_conditions_2
2D HNN COSY	sample_1	isotropic	sample_conditions_3
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_4
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_5
2D 1H-13C HSQC	sample_2	anisotropic	sample_conditions_6
2D DQF-COSY	sample_2	isotropic	sample_conditions_4
2D HCN	sample_2	isotropic	sample_conditions_4
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_4
3D HCP	sample_2	isotropic	sample_conditions_4
2D HPCOSY	sample_2	isotropic	sample_conditions_4
2D HCC	sample_2	isotropic	sample_conditions_4

Software:

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

TOPSPIN, Bruker Biospin - processing

SPARKY, Goddard - chemical shift assignment

NMR spectrometers:

Bruker DRX 600 MHz
Bruker AVANCE NEO 500 MHz