BMRB Entry 17188

Name: Solution structure of P2a-J2a/b-P2b of human telomerase RNA
Published: 2010-10-26

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PDB ID: 2l3e
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17188
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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 P2a-J2a/b-P2b of human telomerase RNA PubMed: 20966348

Deposition date: 2010-09-13 Original release date: 2010-10-26

Authors: Zhang, Qi; Kim, Nak-Kyoon; Peterson, Robert; Wang, Zhonghua; Feigon, Juli

Citation: Zhang, Qi; Kim, Nak-Kyoon; Peterson, Robert; Wang, Zhonghua; Feigon, Juli. "Inaugural Article: Structurally conserved five nucleotide bulge determines the overall topology of the core domain of human telomerase RNA." Proc. Natl. Acad. Sci. U.S.A. 107, 18761-18768 (2010).

Assembly members:
RNA_35-MER, polymer, 35 residues, 11164.710 Da.

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

Experimental source: Production method: reverse transcriptase

Entity Sequences (FASTA):
RNA_35-MER: GGCUUUUGCUCCCCGUGCUU CGGCACGGAAAAGCC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	235
15N chemical shifts	61
1H chemical shifts	309

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (35-MER)	1

Entities:

Entity 1, RNA (35-MER) 35 residues - 11164.710 Da.

1

G

C

U

G

C

U

2

C

G

U

G

C

U

3

C

G

C

A

C

G

A

4

A

G

C

Samples:

1_Un_H2O: RNA_35-MER 1.0 mM; H2O 90%; D2O 10%

2_F_H2O: P2ab RNA (35-MER), [U-98% 13C; U-98% 15N], 1.0 mM; H2O 90%; D2O 10%

3_A_D2O: P2ab RNA (35-MER), [U-13C; U-15N]-Ade, 1.0 mM; D2O 100%

4_C_D2O: P2ab RNA (35-MER), [U-13C; U-15N]-Cyt, 1.0 mM; D2O 100%

5_G_D2O: P2ab RNA (35-MER), [U-13C; U-15N]-Gua, 1.0 mM; D2O 100%

6_U_D2O: P2ab RNA (35-MER), [U-13C; U-15N]-Ura, 1.0 mM; D2O 100%

7_Un_D2O: P2ab RNA (35-MER) 1.0 mM; D2O 100%

8_F_D2O: P2ab RNA (35-MER), [U-98% 13C; U-98% 15N], 1.0 mM; D2O 100%

10C: ionic strength: 100 mM; pH: 6.4; pressure: 1 atm; temperature: 283.15 K

20C: ionic strength: 100 mM; pH: 6.4; pressure: 1 atm; temperature: 293.15 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 11echo NOESY	1_Un_H2O	isotropic	10C
2D Watergate NOESY	1_Un_H2O	isotropic	10C
2D 1H-1H NOESY	7_Un_D2O	isotropic	20C
2D 1H-1H TOCSY	7_Un_D2O	isotropic	20C
2D 1H-15N HSQC	2_F_H2O	isotropic	10C
2D 1H-15N HSQC	2_F_H2O	isotropic	20C
2D 1H-13C HSQC	2_F_H2O	isotropic	20C
2D 13C Filtered/Edited NOESY	3_A_D2O	isotropic	20C
2D 13C Filtered/Edited NOESY	4_C_D2O	isotropic	20C
2D 13C Filtered/Edited NOESY	5_G_D2O	isotropic	20C
2D 13C Filtered/Edited NOESY	6_U_D2O	isotropic	20C
2D HCCH-COSY	3_A_D2O	isotropic	20C
2D HCCH-COSY	4_C_D2O	isotropic	20C
2D HCCH-COSY	5_G_D2O	isotropic	20C
2D HCCH-COSY	6_U_D2O	isotropic	20C
3D HCCH-TOCSY	3_A_D2O	isotropic	20C
3D HCCH-TOCSY	4_C_D2O	isotropic	20C
3D HCCH-TOCSY	5_G_D2O	isotropic	20C
3D HCCH-TOCSY	6_U_D2O	isotropic	20C
2D 1H-13C HSQC	3_A_D2O	isotropic	20C
2D 1H-13C HSQC	4_C_D2O	isotropic	20C
2D 1H-13C HSQC	5_G_D2O	isotropic	20C
2D 1H-13C HSQC	6_U_D2O	isotropic	20C
2D 31P Spin echo difference CT-HSQC	3_A_D2O	isotropic	20C
2D 31P Spin echo difference CT-HSQC	4_C_D2O	isotropic	20C
2D 31P Spin echo difference CT-HSQC	5_G_D2O	isotropic	20C
2D 31P Spin echo difference CT-HSQC	6_U_D2O	isotropic	20C
2D 31P Spin echo difference CT-HCCH correlation	3_A_D2O	isotropic	20C
2D 31P Spin echo difference CT-HCCH correlation	4_C_D2O	isotropic	20C
2D 31P Spin echo difference CT-HCCH correlation	5_G_D2O	isotropic	20C
2D 31P Spin echo difference CT-HCCH correlation	6_U_D2O	isotropic	20C
2D 1H-13C HSQC	8_F_D2O	isotropic	20C
2D 1H-15N HSQC	2_F_H2O	anisotropic	20C
2D 1H-13C S3CT-HSQC	2_F_H2O	anisotropic	20C
2D 1H-13C S3CT-HSQC	2_F_H2O	isotropic	20C
2D HNNOESY	2_F_H2O	isotropic	10C
3D HCNCH	3_A_D2O	isotropic	20C
3D HCNCH	4_C_D2O	isotropic	20C
3D HCNCH	5_G_D2O	isotropic	20C
3D HCNCH	6_U_D2O	isotropic	20C

Software:

X-PLOR NIH v2.9.8, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis

SPARKY v3.110., Goddard - chemical shift assignment, data analysis, processing

xwinnmr, Bruker Biospin - collection, processing

NMR spectrometers:

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