BMRB Entry 6477

Name: Solution structure of the P2b-P3 pseudoknot from human telomerase RNA
Published: 2006-02-17

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PDB ID: 1ymo
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR6477
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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:

Solution structure of the P2b-P3 pseudoknot from human telomerase RNA

Deposition date:

2005-02-02

Original release date:

2006-02-17

Authors:

Theimer, C.; Blois, C.; Feigon, J.

Citation:

Citation: Theimer, C.; Blois, C.; Feigon, J.. "Structure of the human telomerase RNA pseudoknot reveals conserved tertiary interactions essential for function." Mol. Cell 17, 671-682 (2005).
PubMed: 15749017

Assembly members:

Assembly members:
Telomerase RNA P2b-P3 pseudoknot, polymer, 47 residues, Formula weight is not available

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: enzymatic semi-synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Telomerase RNA P2b-P3 pseudoknot: GGGCUGUUUUUCUCGCUGAC UUUCAGCCCCAAACAAAAAA GUCAGCA

Data sets:

assigned_chemical_shifts
- chemical_shift_set_1

Data type	Count
13C chemical shifts	273
15N chemical shifts	73
1H chemical shifts	336

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Telomerase RNA P2b-P3 pseudoknot	1

Entities:

Entity 1, Telomerase RNA P2b-P3 pseudoknot 47 residues - Formula weight is not available

1

G

C

U

G

U

2

U

C

U

C

G

C

U

G

A

C

3

U

C

A

G

C

4

A

C

A

5

G

U

C

A

G

C

A

Samples:

sample_1: Telomerase RNA P2b-P3 pseudoknot 0.8 mM; sodium phosphate buffer 10 mM; KCl 200 mM; EDTA 50 uM; sodium azide 0.2%; H2O 95%; D2O 5%

sample_2: Telomerase RNA P2b-P3 pseudoknot 0.8 mM; sodium phosphate buffer 10 mM; KCl 200 mM; EDTA 50 uM; sodium azide 0.2%; D2O 100%

sample_3: Telomerase RNA P2b-P3 pseudoknot, [U-13C; U-15N], 0.8 mM; sodium phosphate buffer 10 mM; KCl 200 mM; EDTA 50 uM; sodium azide 0.2%; H2O 95%; D2O 5%

sample_4: Telomerase RNA P2b-P3 pseudoknot, [U-13C; U-15N], 0.8 mM; sodium phosphate buffer 10 mM; KCl 200 mM; EDTA 50 uM; sodium azide 0.2%; D2O 100%

sample_5: Telomerase RNA P2b-P3 pseudoknot, [U-13C; U-15N]-A, 0.8 mM; sodium phosphate buffer 10 mM; KCl 200 mM; EDTA 50 uM; sodium azide 0.2%; H2O 95%; D2O 5%

sample_6: Telomerase RNA P2b-P3 pseudoknot, [U-13C; U-15N]-A, 0.8 mM; sodium phosphate buffer 10 mM; KCl 200 mM; EDTA 50 uM; sodium azide 0.2%; D2O 100%

sample_7: Telomerase RNA P2b-P3 pseudoknot, [U-13C; U-15N]-C, 0.8 mM; sodium phosphate buffer 10 mM; KCl 200 mM; EDTA 50 uM; sodium azide 0.2%; H2O 95%; D2O 5%

sample_8: Telomerase RNA P2b-P3 pseudoknot, [U-13C; U-15N]-C, 0.8 mM; sodium phosphate buffer 10 mM; KCl 200 mM; EDTA 50 uM; sodium azide 0.2%; D2O 100%

sample_9: Telomerase RNA P2b-P3 pseudoknot, [U-13C; U-15N]-G, 0.8 mM; sodium phosphate buffer 10 mM; KCl 200 mM; EDTA 50 uM; sodium azide 0.2%; H2O 95%; D2O 5%

sample_10: Telomerase RNA P2b-P3 pseudoknot, [U-13C; U-15N]-G, 0.8 mM; sodium phosphate buffer 10 mM; KCl 200 mM; EDTA 50 uM; sodium azide 0.2%; D2O 100%

sample_11: Telomerase RNA P2b-P3 pseudoknot, [U-13C; U-15N]-U, 0.8 mM; sodium phosphate buffer 10 mM; KCl 200 mM; EDTA 50 uM; sodium azide 0.2%; H2O 95%; D2O 5%

sample_12: Telomerase RNA P2b-P3 pseudoknot, [U-13C; U-15N]-U, 0.8 mM; sodium phosphate buffer 10 mM; KCl 200 mM; EDTA 50 uM; sodium azide 0.2%; D2O 100%

sample_cond_1: ionic strength: 200 mM; pH: 6.3; pressure: 1 atm; temperature: 283 K

sample_cond_2: ionic strength: 200 mM; pH: 6.3; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D NOESY (11echo and watergate)	not available	not available	not available
2D NOESY	not available	not available	not available
2D TOCSY (presat)	not available	not available	not available
2D 15N-HMQC	not available	not available	not available
2D 15N-CPMG-NOESY	not available	not available	not available
2D JNN-HNN-COSY	not available	not available	not available
2D 13C-HSQC	not available	not available	not available
2D HCCH COSY	not available	not available	not available
3D HCCH-TOCSY	not available	not available	not available
2D 13C filtered/edited NOESYs	not available	not available	not available

Software:

xwinnmr v2.6 - collection, processing

AURELIA v3.108 - data analysis

X-PLOR NIH v1.0.6 - refinement, structure solution

NMR spectrometers:

Bruker AVANCE 800 MHz