BMRB Entry 19260

Name: A pyrimidine motif triple helix in the Kluyveromyces lactis telomerase RNA pseudoknot is essential for function in vivo
Published: 2013-06-17

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PDB ID: 2m8k
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR19260
MolProbity Validation Chart

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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:

A pyrimidine motif triple helix in the Kluyveromyces lactis telomerase RNA pseudoknot is essential for function in vivo

Deposition date:

2013-05-22

Original release date:

2013-06-17

Authors:

Cash, Darian; Cohen, Osnat; Kim, Nak-Kyoon; Shefer, Kinneret; Brown, Yogev; Ulyanov, Nikolai; Tzfati, Yehuda; Feigon, Juli

Citation:

Citation: Cash, Darian; Cohen, Osnat; Kim, Nak-Kyoon; Shefer, Kinneret; Brown, Yogev; Ulyanov, Nikolai; Tzfati, Yehuda; Feigon, Juli. "A pyrimidine motif triple helix in the Kluyveromyces lactis telomerase RNA pseudoknot is essential for function in vivo" Proc. Natl. Acad. Sci. U.S.A. ., .-..

Assembly members:

Assembly members:
RNA_(48-MER), polymer, 48 residues, 15152.975 Da.

Natural source:

Natural source: Common Name: ascomycetes Taxonomy ID: 28985 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Kluyveromyces Lactis

Experimental source:

Experimental source: Production method: chemical synthesis Host organism: in vitro Vector: not applicable

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA_(48-MER): GGUUUCUUUUUAGUGAUUUU UCCAAACCCCUUUGUGCAAA AAUCAUUA

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	247
15N chemical shifts	32
1H chemical shifts	339

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA_(48-MER)	1

Entities:

Entity 1, RNA_(48-MER) 48 residues - 15152.975 Da.

1

G

U

C

U

2

U

A

G

U

G

A

U

3

U

C

A

C

4

U

G

U

G

C

A

5

A

U

C

A

U

A

Samples:

sample_1: RNA_(48-MER) 1 mM; TRIS 10 mM; Magnesium Chloride 0.5 mM; H2O 90%; D2O 10%

sample_2: RNA_(48-MER) 1 mM; TRIS 10 mM; Magnesium Chloride 0.5 mM; D2O 100%

sample_3: RNA_(48-MER), [U-98% 13C; U-98% 15N]-Ade,Uri, 1 mM; TRIS 10 mM; Magnesium Chloride 0.5 mM; H2O 90%; D2O 10%

sample_4: RNA_(48-MER), [U-98% 13C; U-98% 15N]-Ade,Uri, 1 mM; TRIS 10 mM; Magnesium Chloride 0.5 mM; D2O 100%

sample_5: RNA_(48-MER), [U-98% 13C; U-98% 15N]-Cyt,Gua, 1 mM; TRIS 10 mM; Magnesium Chloride 0.5 mM; H2O 90%; D2O 10%

sample_6: RNA_(48-MER), [U-98% 13C; U-98% 15N]-Cyt,Gua, 1 mM; TRIS 10 mM; Magnesium Chloride 0.5 mM; D2O 100%

sample_7: RNA_(48-MER), [U-98% 13C; U-98% 15N]-Ade,Uri,Cyt,Gua, 1 mM; TRIS 10 mM; Magnesium Chloride 0.5 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 10 mM; pH: 6.3; pressure: 1 atm; temperature: 283 K

sample_conditions_2: ionic strength: 10 mM; pH: 6.3; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 11echo NOESY	sample_1	isotropic	sample_conditions_1
2D 13C Filtered/Edited NOESY	sample_4	isotropic	sample_conditions_2
2D 13C Filtered/Edited NOESY	sample_6	isotropic	sample_conditions_2
2D NOESY presat	sample_2	isotropic	sample_conditions_2
2D HCCH-COSY, 3D HCCH-TOCSY	sample_4	isotropic	sample_conditions_2
2D HCCH COSY, 3D HCCH-TOCSY	sample_6	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_4	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_6	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_7	isotropic	sample_conditions_2
2D HNNOESY	sample_3	isotropic	sample_conditions_1
2D HNNOESY	sample_5	isotropic	sample_conditions_1
HNN-COSY	sample_3	isotropic	sample_conditions_1
HNN-COSY	sample_5	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_5	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_2

Software:

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

Molmol, Koradi, Billeter and Wuthrich - data analysis, structure solution

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - chemical shift calculation, data analysis, peak picking

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

xwinnmr, Bruker Biospin - chemical shift assignment, data analysis, processing

TOPSPIN, Bruker Biospin - chemical shift assignment, data analysis, processing

NMR spectrometers:

Bruker Avance 800 MHz
Bruker DRX 600 MHz
Bruker DRX 500 MHz
Bruker DRX 500 MHz