BMRB Entry 18894

Name: NMR solution structure of the d3&#039;-hairpin including the exon binding site 1 (EBS1) of the group II intron Sc.ai5gamma
Published: 2013-12-16

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PDB ID: 2m24
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR18894
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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 d3'-hairpin including the exon binding site 1 (EBS1) of the group II intron Sc.ai5gamma

Deposition date:

2012-12-12

Original release date:

2013-12-16

Authors:

Kruschel, Daniela; Skilandat, Miriam; Sigel, Roland

Citation:

Citation: Kruschel, Daniela; Skilandat, Miriam; Sigel, Roland. "NMR structure of the 5'-splice site in the group IIB intron Sc.ai5--conformational requirements for exon-intron recognition." RNA ., .-. (2014).
PubMed: 24448450

Assembly members:

Assembly members:
RNA_(29-MER), polymer, 29 residues, 9301.611 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: cell free synthesis Host organism: not applicable Vector: not applicable

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA_(29-MER): GGAGUAUGUAUUGGCACUGA GCAUACUCC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	102
15N chemical shifts	18
1H chemical shifts	223

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (29-MER)	1

Entities:

Entity 1, RNA (29-MER) 29 residues - 9301.611 Da.

part of intron domain one; postion 5-25 correspond to 315-335 on intron (25657-25677 on gene); extended by 4 nt on each side

1

G

A

G

U

A

U

G

U

A

2

U

G

C

A

C

U

G

A

3

G

C

A

U

A

C

U

C

Samples:

unlabelled_d2o: RNA (29-MER)0.4 – 1.2 mM; potassium chloride 10 mM; EDTA 10 uM; D2O 100%

unlabelled_h2o: RNA (29-MER)0.4 – 1.2 mM; potassium chloride 10 mM; EDTA 10 uM; D2O 10%; H2O 90%

labelled_h2o: RNA (29-MER), [U-100% 13C; U-100% 15N], 0.7 mM; potassium chloride 10 mM; EDTA 10 uM; D2O 10%; H2O 90%

labelled_h2o_phage: RNA (29-MER), [U-100% 13C; U-100% 15N], 0.7 mM; potassium chloride 10 mM; EDTA 10 uM; Pf1 phage 25.6 mg/mL; D2O 10%; H2O 90%

labelled_d2o: RNA (29-MER), [U-100% 13C; U-100% 15N], 0.7 mM; potassium chloride 10 mM; EDTA 10 uM; D2O 100%

deuterated_d2o: RNA (29-MER), [3',4',5',5'',5, 100% 2H], 0.6 mM; potassium chloride 10 mM; EDTA 10 uM; D2O 100%

h2o_293K: ionic strength: 10 mM; pH: 6.8; pressure: 1 atm; temperature: 293 K

d2o_293K: ionic strength: 10 mM; pD: 6.8; pressure: 1 atm; temperature: 293 K

h2o_278K: ionic strength: 10 mM; pH: 6.8; pressure: 1 atm; temperature: 278 K

h2o_298K: ionic strength: 10 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K

d2o_298K: ionic strength: 10 mM; pD: 6.8; pressure: 1 atm; temperature: 298 K

d2o_283K: ionic strength: 10 mM; pD: 6.8; pressure: 1 atm; temperature: 283 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	unlabelled_d2o	isotropic	d2o_293K
2D 1H-1H TOCSY	unlabelled_d2o	isotropic	d2o_293K
2D 1H-1H NOESY	unlabelled_d2o	isotropic	d2o_293K
2D 1H-1H NOESY	unlabelled_h2o	isotropic	h2o_278K
2D 1H-1H NOESY	unlabelled_h2o	isotropic	h2o_278K
2D 1H-13C HSQC aliphatic	labelled_h2o	isotropic	h2o_298K
2D 1H-13C HSQC aromatic	labelled_h2o	isotropic	h2o_298K
2D 1H-15N HSQC	labelled_h2o	isotropic	h2o_278K
2D 1H-13C HSQC aliphatic	labelled_h2o_phage	anisotropic	h2o_298K
2D 1H-13C HSQC aromatic	labelled_h2o_phage	anisotropic	h2o_298K
2D JNN HNN COSY	labelled_h2o	isotropic	h2o_278K
2D 1H-1H NOESY	unlabelled_d2o	isotropic	d2o_283K
2D 1H-1H NOESY	unlabelled_d2o	isotropic	d2o_298K
1D 31P	unlabelled_d2o	isotropic	d2o_293K
2D 1H-1H NOESY	deuterated_d2o	isotropic	d2o_293K

Software:

TOPSPIN v1.3, 2.0, 2.1, Bruker Biospin - collection, processing

SPARKY v3.1, Goddard - chemical shift assignment, data analysis, peak picking

DYANA v1.5, Guntert, Braun and Wuthrich - data analysis

CNSSOLVE v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - refinement, structure solution

X-PLOR NIH v2.24, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

NMR spectrometers:

Bruker Avance 700 MHz
Bruker Avance 600 MHz
Bruker Avance 500 MHz