BMRB Entry 34100

Name: NMR solution structure of the TSL2 RNA hairpin
Published: 2018-03-06

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PDB ID: 5n5c
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34100
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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:

NMR solution structure of the TSL2 RNA hairpin

Deposition date:

2017-02-13

Original release date:

2018-03-06

Authors:

Garcia-Lopez, A.; Wacker, A.; Tessaro, F.; Jonker, H.; Richter, C.; Comte, A.; Berntenis, N.; Schmucki, R.; Hatje, K.; Sciarra, D.; Konieczny, P.; Fournet, G.; Faustino, I.; Orozco, M.; Artero, R.; Goekjian, P.; Metzger, F.; Ebeling, M.; Joseph, B.; Schwalbe, H.; Scapozza, L.

Citation:

Citation: Garcia-Lopez, Amparo; Tessaro, Francesca; Jonker, Hendrik; Wacker, Anna; Richter, Christian; Comte, Arnaud; Berntenis, Nikolaos; Schmucki, Roland; Hatje, Klas; Petermann, Olivier; Chiriano, Gianpaolo; Perozzo, Remo; Sciarra, Daniel; Konieczny, Piotr; Faustino, Ignacio; Fournet, Guy; Orozco, Modesto; Artero, Ruben; Metzger, Friedrich; Ebeling, Martin; Goekjian, Peter; Joseph, Benoit; Schwalbe, Harald; Scapozza, Leonardo. "Targeting RNA structure in SMN2 reverses spinal muscular atrophy molecular phenotypes" Nat. Commun. 9, 2032-2032 (2018).
PubMed: 29795225

Assembly members:

Assembly members:
entity_1, polymer, 19 residues, 6048.626 Da.

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: AUUCCUUAAAUUAAGGAGU

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	67
15N chemical shifts	4
1H chemical shifts	150

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 19 residues - 6048.626 Da.

1

A

U

C

U

A

2

U

A

G

A

G

U

Samples:

sample_1: EDTA 0.1 mM; RNA (19-MER) 0.6 mM; sodium phosphate 50 mM

sample_2: EDTA 0.1 mM; RNA (19-MER) 0.6 mM; sodium phosphate 50 mM

sample_3: EDTA 0.1 mM; RNA (19-MER), [U-98% 13C; U-96-98% 15N]-ADE, 0.6 mM; sodium phosphate 50 mM

sample_conditions_1: ionic strength: 74 mM; pH: 6.4; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 71 mM; pH: 6.4; pressure: 1 atm; temperature: 278 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_2
3D 1H-13C NOESY	sample_3	isotropic	sample_conditions_1
2D 12C-filtered 1H-1H NOESY	sample_3	isotropic	sample_conditions_1
2D 13C-editted 1H-1H NOESY	sample_3	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1
2D 1H-1H COSY	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC sugar	sample_3	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_3	isotropic	sample_conditions_1

Software:

ARIA v1.2 HJ development version, Linge, O'Donoghue and Nilges - refinement

CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - structure calculation

SPARKY v3.114, Kneller and Goddard - chemical shift assignment, data analysis, peak picking

TOPSPIN, Bruker Biospin - processing

TOPSPIN v3.2, Bruker Biospin - collection

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 800 MHz
Bruker Avance 900 MHz