BMRB Entry 11014

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PDB ID: 2rn1
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR11014
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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:

Liquid crystal solution structure of the kissing complex formed by the apical loop of the HIV TAR RNA and a high affinity RNA aptamer optimized by SELEX.

Deposition date:

2007-12-05

Original release date:

2008-07-15

Authors:

Van Melckebeke, Helene; Devany, Matthew; Di Primo, Carmelo; Beaurain, Francois; Toulme, Jean-Jacques; Bryce, David; Boisbouvier, Jerome

Citation:

Citation: Van Melckebeke, Helene; Devany, Matthew; Di Primo, Carmelo; Beaurain, Francois; Toulme, Jean-Jacques; Bryce, David; Boisbouvier, Jerome. "Liquid-crystal NMR structure of HIV TAR RNA bound to its SELEX RNA aptamer reveals the origins of the high stability of the complex" Proc. Natl. Acad. Sci. U. S. A. 105, 9210-9215 (2008).
PubMed: 18607001

Assembly members:

Assembly members:
TAR, polymer, 16 residues, 5168.169 Da.
TAR*GA, polymer, 16 residues, 5112.145 Da.

Natural source:

Natural source: Common Name: HIV-1 Taxonomy ID: 11676 Superkingdom: Viruses Kingdom: not available Genus/species: Lentivirus Human immunodeficiency virus 1

Experimental source:

Experimental source: Production method: obtained from a vendor

Entity Sequences (FASTA):

Entity Sequences (FASTA):
TAR: GAGCCCUGGGAGGCUC
TAR*GA: GCUGGUCCCAGACAGC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	176
15N chemical shifts	9
1H chemical shifts	235

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	TAR	1
2	TAR*GA	2

Entities:

Entity 1, TAR 16 residues - 5168.169 Da.

This sequence is the apical loop of the HIV TAR RNA, stabilized by a GC base-pair.

1

G

A

G

C

U

G

2

A

G

C

U

C

Entity 2, TAR*GA 16 residues - 5112.145 Da.

The numbering begins at 17 (G17 C18 U19 G20 G21 U22 C23 C24 C25 A26 G27 A28 C29 A30 G31 C32).

1

G

C

U

G

U

C

A

2

G

A

C

A

G

C

Samples:

sample_1: TAR 1.3 mM; TAR*GA 1.3 mM; sodium phosphate 10 mM; sodium chloride 50 mM; EDTA 10 uM; sodium azide 0.4 g/L

sample_2: TAR 1.1 mM; TAR*GA 1.1 mM; sodium phosphate 10 mM; sodium chloride 50 mM; EDTA 10 uM; sodium azide 0.4 g/L

sample_3: TAR, [U-98% 13C; U-98% 15N], 0.37 mM; TAR*GA 0.74 mM; sodium phosphate 10 mM; sodium chloride 50 mM; EDTA 10 uM; sodium azide 0.4 g/L

sample_4: TAR 0.74 mM; TAR*GA, [U-98% 13C; U-98% 15N], 0.37 mM; sodium phosphate 10 mM; sodium chloride 50 mM; EDTA 10 uM; sodium azide 0.4 g/L

sample_5: TAR 1.6 mM; TAR*GA, [U-98% 13C; U-98% 15N], 0.8 mM; sodium phosphate 10 mM; sodium chloride 50 mM; EDTA 10 uM; sodium azide 0.4 g/L

sample_6: TAR, [U-98% 13C; U-98% 15N], 0.5 mM; TAR*GA 1.0 mM; sodium phosphate 10 mM; sodium chloride 50 mM; EDTA 10 uM; sodium azide 0.4 g/L

sample_7: TAR 1.8 mM; TAR*GA, [U-98% 13C; U-98% 15N], 0.9 mM; sodium phosphate 10 mM; sodium chloride 50 mM; EDTA 10 uM; sodium azide 0.4 g/L

sample_8: TAR, [U-98% 13C; U-98% 15N], 0.9 mM; TAR*GA 1.8 mM; sodium phosphate 10 mM; sodium chloride 50 mM; EDTA 10 uM; sodium azide 0.4 g/L

sample_conditions_1: ionic strength: 60 mM; pH: 6.6; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 60 mM; pH: 6.6; pressure: 1 atm; temperature: 283 K

sample_conditions_3: ionic strength: 60 mM; pH: 6.6; pressure: 1 atm; temperature: 278 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C TROSY NOESY	sample_7	isotropic	sample_conditions_1
2D JNN-COSY	sample_3	isotropic	sample_conditions_3
3D HCCH-COSY	sample_7	isotropic	sample_conditions_1
3D HCCH-COSY	sample_8	isotropic	sample_conditions_1
3D HCN	sample_7	isotropic	sample_conditions_1
3D HCN	sample_8	isotropic	sample_conditions_1
2D intra base TOCSY	sample_7	isotropic	sample_conditions_1
3D 1H-13C TROSY NOESY	sample_8	isotropic	sample_conditions_1
2D intra base TOCSY	sample_8	isotropic	sample_conditions_1
13C-1H spin state selective experiments	sample_8	isotropic	sample_conditions_1
13C-1H spin state selective experiments	sample_7	isotropic	sample_conditions_1
2D JNN-COSY	sample_4	isotropic	sample_conditions_3
13C-1H spin state selective experiments	sample_5	anisotropic	sample_conditions_1
13C-1H spin state selective experiments	sample_6	anisotropic	sample_conditions_1

Software:

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

FELIX v2000, Accelrys Software Inc. - chemical shift assignment, processing

InsightII, Accelrys Software Inc. - data analysis

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

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - chemical shift assignment, peak picking

CURVES v5.3, Lavery and sklenar, 1989 - data analysis

NMR spectrometers:

Varian INOVA 800 MHz
Varian INOVA 600 MHz