BMRB Entry 18893

Name: NMR solution structure of the d3&#039;-hairpin of the group II intron Sc.ai5gamma including EBS1 bound to IBS1
Published: 2013-12-16

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PDB ID: 2m23
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR18893
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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 of the group II intron Sc.ai5gamma including EBS1 bound to IBS1

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.
RNA_(7-MER), polymer, 7 residues, 2197.370 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
RNA_(7-MER): CAGUGUC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	78
15N chemical shifts	13
1H chemical shifts	306

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
2	RNA_(7-MER)	2

Entities:

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

part of intron domain one; postion 5-25 correspond to 315-335 on Sc.ai5gamma 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

Entity 2, RNA_(7-MER) 7 residues - 2197.370 Da.

sequence corresponds to the last 7 nt of the 5' exon (position 25336-25342 in gene)

1

C

A

G

U

G

U

C

Samples:

unlabelled_d2o: RNA (29-MER)0.5 – 0.9 mM; RNA_(7-MER)0.5 – 0.9 mM; potassium chloride 110 mM; EDTA 10 uM; D2O 100%

unlabelled_h2o: RNA (29-MER)0.5 – 0.9 mM; RNA_(7-MER)0.5 – 0.9 mM; potassium chloride 110 mM; EDTA 10 uM; D2O 10%; H2O 90%

labelled_d2o: RNA (29-MER), [U-100% 13C; U-100% 15N], 0.5 mM; RNA_(7-MER) 0.5 mM; potassium chloride 110 mM; EDTA 10 uM; D2O 100%

labelled_h2o: RNA (29-MER), [U-100% 13C; U-100% 15N], 0.5 mM; RNA_(7-MER) 0.5 mM; potassium chloride 110 mM; EDTA 10 uM; D2O 10%; H2O 90%

deuterated_d2o: RNA (29-MER), [3',4',5',5'',5-100% 2H], 0.6 mM; RNA_(7-MER) 0.6 mM; potassium chloride 110 mM; EDTA 10 uM; D2O 100%

labelled_h2o_phage: RNA (29-MER), [U-100% 13C; U-100% 15N], 0.5 mM; RNA_(7-MER) 0.5 mM; potassium chloride 110 mM; EDTA 10 uM; Pf1 phage 25.6 mg/mL; D2O 10%; H2O 90%

d2o_298K: ionic strength: 110 mM; pD: 6.8; pressure: 1 atm; temperature: 298 K

h2o_278K: ionic strength: 110 mM; pH: 6.8; pressure: 1 atm; temperature: 278 K

h2o_293K: ionic strength: 110 mM; pH: 6.8; pressure: 1 atm; temperature: 293 K

h2o_298K: ionic strength: 110 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	unlabelled_d2o	isotropic	d2o_298K
2D 1H-1H NOESY	unlabelled_d2o	isotropic	d2o_298K
2D 1H-1H TOCSY	unlabelled_d2o	isotropic	d2o_298K
2D 1H-1H NOESY	deuterated_d2o	isotropic	d2o_298K
2D 1H-13C HSQC aliphatic	labelled_h2o	isotropic	h2o_298K
2D 1H-13C HSQC aliphatic	labelled_h2o_phage	anisotropic	h2o_298K
2D 1H-15N HSQC	labelled_h2o	isotropic	h2o_278K
2D 1H-13C HSQC aromatic	labelled_h2o	isotropic	h2o_298K
2D 1H-13C HSQC aromatic	labelled_h2o_phage	anisotropic	h2o_298K
2D 1H-13C HSQC aliphatic	labelled_d2o	isotropic	d2o_298K
2D 1H-13C HSQC aromatic	labelled_d2o	isotropic	d2o_298K
2D 1H-1H NOESY	unlabelled_h2o	isotropic	h2o_278K
2D 1H-1H NOESY	unlabelled_h2o	isotropic	h2o_278K
2D 1H-1H NOESY	unlabelled_h2o	isotropic	h2o_293K
2D JNN HNN COSY	labelled_h2o	isotropic	h2o_278K
1D-31P	unlabelled_d2o	isotropic	d2o_298K
F1,2 X-filtered 1H-1H NOESY	labelled_h2o	isotropic	h2o_298K
F1,2 X-filtered 1H-1H TOCSY	labelled_h2o	isotropic	h2o_298K

Software:

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

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

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

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