BMRB Entry 18503

Name: NMR solution structure of the kappa-zeta region of S.cerevisiae group II intron ai5(gamma)
Published: 2013-02-14

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PDB ID: 2lu0
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR18503
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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 kappa-zeta region of S.cerevisiae group II intron ai5(gamma)

Deposition date:

2012-06-05

Original release date:

2013-02-14

Authors:

Donghi, Daniela; Pechlaner, Maria; Finazzo, Cinzia; Knobloch, Bernd; Sigel, Roland

Citation:

Citation: Donghi, Daniela; Pechlaner, Maria; Finazzo, Cinzia; Knobloch, Bernd; Sigel, Roland. "The structural stabilization of the three-way junction by Mg(II) represents the first step in the folding of a group II intron." Nucleic Acids Res. 41, 2489-2504 (2013).
PubMed: 23275550

Assembly members:

Assembly members:
RNA_(49-MER), polymer, 49 residues, 15800.554 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: cell free synthesis (using T7 polymerase)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA_(49-MER): GGAAUAUGCUCAACGAAAGU GAAUCAGCUUCGGCUGAGAG CUAAGUUCC

Data sets:

assigned_chemical_shifts
- chem_shifts_withoutMg
- chem_shifts_withMg

Data type	Count
13C chemical shifts	312
15N chemical shifts	95
1H chemical shifts	550

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (49-MER)	1

Entities:

Entity 1, RNA (49-MER) 49 residues - 15800.554 Da.

This construct represents residues 195-218 and 374-386 of group II intron ai5(gamma); residues 1,2,48 and 49 as well as residues 27-34 are additions that are not present in the intron.

1

G

A

U

A

U

G

C

U

2

C

A

C

G

A

G

U

3

G

A

U

C

A

G

C

U

4

C

G

C

U

G

A

G

A

G

5

C

U

A

G

U

C

Samples:

D1kz_wt_d2o: RNA (49-MER) 0.3-1.0 mM; potassium chloride 60 mM; EDTA 10 uM; magnesium chloride 0-12 mM

D1kz_deut_d2o: RNA (49-MER), [3',4',5',5 ,5-D5], 0.3-1.0 mM; potassium chloride 60 mM; EDTA 10 uM; magnesium chloride 0-12 mM

D1kz_lab_d2o: RNA (49-MER), [100% 13C; 100% 15N], 0.3-1 mM; potassium chloride 60 mM; EDTA 10 uM; magnesium chloride 0-12 mM

D1kz_wt_h2o: RNA (49-MER) 0.3-1.0 mM; potassium chloride 60 mM; EDTA 10 uM; magnesium chloride 0-12 mM

D1kz_lab_h2o: RNA (49-MER), [U-100% 13C; U-100% 15N], 0.3-1.0 mM; potassium chloride 60 mM; EDTA 10 uM; magnesium chloride 0-12 mM

300K_d2o: ionic strength: 60 mM; pD: 6.7; pressure: 1 atm; temperature: 300 K

275-285K_h2o: ionic strength: 60 mM; pH: 6.7; pressure: 1 atm; temperature: 280 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H TOCSY	D1kz_wt_d2o	isotropic	300K_d2o
2D 1H-1H NOESY	D1kz_wt_d2o	isotropic	300K_d2o
2D 1H-1H NOESY	D1kz_deut_d2o	isotropic	300K_d2o
2D 1H-1H NOESY	D1kz_wt_h2o	isotropic	275-285K_h2o
2D 1H-15N HSQC	D1kz_lab_h2o	isotropic	275-285K_h2o
2D 1H-13C HSQC	D1kz_lab_d2o	isotropic	300K_d2o
3D 1H-13C NOESY aliphatic	D1kz_wt_d2o	isotropic	300K_d2o
2D JNN HNN COSY	D1kz_lab_h2o	isotropic	275-285K_h2o
2D 1H-15N HSQC	D1kz_lab_d2o	isotropic	300K_d2o

Software:

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

SPARKY, Goddard - chemical shift assignment, data analysis, peak integration

X-PLOR NIH v2.30, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

Molmol, Koradi, Billeter and Wuthrich - data analysis

TOPSPIN, Bruker Biospin - collection, processing

NMR spectrometers:

Bruker Avance 700 MHz
Bruker Avance 600 MHz
Bruker Avance 900 MHz