BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 11014

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.   PubMed: 18607001

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

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).

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

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

Experimental source:   Production method: obtained from a vendor

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

Data sets:
Data typeCount
13C chemical shifts176
15N chemical shifts9
1H chemical shifts235

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1TAR1
2TAR*GA2

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   GAGCCCUGGG
2   AGGCUC

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   GCUGGUCCCA
2   GACAGC

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:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_2isotropicsample_conditions_2
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
3D 1H-13C TROSY NOESYsample_7isotropicsample_conditions_1
2D JNN-COSYsample_3isotropicsample_conditions_3
3D HCCH-COSYsample_7isotropicsample_conditions_1
3D HCCH-COSYsample_8isotropicsample_conditions_1
3D HCNsample_7isotropicsample_conditions_1
3D HCNsample_8isotropicsample_conditions_1
2D intra base TOCSYsample_7isotropicsample_conditions_1
3D 1H-13C TROSY NOESYsample_8isotropicsample_conditions_1
2D intra base TOCSYsample_8isotropicsample_conditions_1
13C-1H spin state selective experimentssample_8isotropicsample_conditions_1
13C-1H spin state selective experimentssample_7isotropicsample_conditions_1
2D JNN-COSYsample_4isotropicsample_conditions_3
13C-1H spin state selective experimentssample_5anisotropicsample_conditions_1
13C-1H spin state selective experimentssample_6anisotropicsample_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

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