BMRB Entry 30132

Name: Solution structure of P2a-J2a/b-P2b of medaka telomerase RNA
Published: 2016-08-22

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PDB ID: 5kqe
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30132
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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:

Solution structure of P2a-J2a/b-P2b of medaka telomerase RNA

Deposition date:

2016-07-06

Original release date:

2016-08-22

Authors:

Wang, Y.; Feigon, J.

Citation:

Citation: Wang, Y.; Yesselman, J.; Zhang, Q.; Kang, M.; Feigon, J.. "Structural conservation in the template/pseudoknot domain of vertebrate telomerase RNA from teleost fish to human" Proc. Natl. Acad. Sci. U. S. A. 113, E5125-E5134 (2016).
PubMed: 27531956

Assembly members:

Assembly members:
entity_1, polymer, 36 residues, 11464.795 Da.

Natural source:

Natural source: Common Name: Japanese medaka Taxonomy ID: 8090 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Oryzias latipes

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GGGUGUACUUAACGUUUGCU UCGGCAAACUACAUCC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	206
15N chemical shifts	37
1H chemical shifts	272

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 36 residues - 11464.795 Da.

1

G

U

G

U

A

C

U

2

A

C

G

U

G

C

U

3

U

C

G

C

A

C

U

4

A

C

A

U

C

Samples:

sample_2: Telomerase RNA P2ab, [U-13C; U-15N], 1.0 mM; potassium chloride 100 mM; sodium phosphate 10 mM

sample_3: Telomerase RNA P2ab 1.0 mM; potassium chloride 100 mM; sodium phosphate 10 mM

sample_4: Telomerase RNA P2ab 1.0 mM; potassium chloride 100 mM; sodium phosphate 10 mM

sample_5: Telomerase RNA P2ab, [U-13C; U-15N], 1.0 mM; potassium chloride 100 mM; sodium phosphate 10 mM

sample_conditions_1: ionic strength: 100 mM; pH: 6.4; pressure: 1 atm; temperature: 283 K

sample_conditions_2: ionic strength: 100 mM; pH: 6.4; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_3	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_3	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_4	isotropic	sample_conditions_2
2D 1H-1H TOCSY	sample_4	isotropic	sample_conditions_2
2D 1H-15N HSQC	sample_5	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_5	isotropic	sample_conditions_2
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
2D filtered/edited NOESY	sample_2	isotropic	sample_conditions_2
2D DQF-COSY	sample_3	isotropic	sample_conditions_1
JNN-COSY	sample_3	isotropic	sample_conditions_1

Software:

SPARKY, Goddard - chemical shift assignment, peak picking

TOPSPIN, Bruker Biospin - collection, processing

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

X-PLOR NIH v2.42, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

NMR spectrometers:

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