BMRB Entry 17408

Name: Chemical probe bound to HIV TAR RNA
Published: 2012-08-14

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PDB ID: 2l8h
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17408
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Chemical probe bound to HIV TAR RNA PubMed: 21763501

Deposition date: 2011-01-12 Original release date: 2012-08-14

Authors: Davidson, Amy; Begley, Darren; Lau, Carmen; Varani, Gabriele

Citation: Davidson, Amy; Begley, Darren; Lau, Carmen; Varani, Gabriele. "A small-molecule probe induces a conformation in HIV TAR RNA capable of binding drug-like fragments" J. Mol. Biol. 410, 984-996 (2011).

Assembly members:
HIV_TAR_RNA, polymer, 29 residues, 132.116 Da.
ARG, non-polymer, 175.209 Da.
L8H, non-polymer, 173.211 Da.

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

Experimental source: Production method: enzymatic semisynthesis

Entity Sequences (FASTA):
HIV_TAR_RNA: GGCAGAUCUGAGCCUGGGAG CUCUCUGCC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	177

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	HIV TAR RNA	1
2	ARGININE	2
3	4-METHOXYNAPHTHALEN-2-AMINE	3

Entities:

Entity 1, HIV TAR RNA 29 residues - 132.116 Da.

1

G

C

A

G

A

U

C

U

G

2

A

G

C

U

G

A

G

3

C

U

C

U

C

U

G

C

Entity 2, ARGININE - C6 H15 N4 O2 - 175.209 Da.

1

ARG

Entity 3, 4-METHOXYNAPHTHALEN-2-AMINE - C11 H11 N O - 173.211 Da.

1

L8H

Samples:

sample_1: HIV TAR RNA 1 mM; ARGININE 4 mM; 4-METHOXYNAPHTHALEN-2-AMINE 4 mM; potassium phosphate 10 mM

sample_2: HIV TAR RNA 1 mM; ARGININE 4 mM; 4-METHOXYNAPHTHALEN-2-AMINE 4 mM; potassium phosphate 10 mM

sample_3: HIV TAR RNA, [U-100% 13C; U-100% 15N], 1 mM; ARGININE 4 mM; 4-METHOXYNAPHTHALEN-2-AMINE 4 mM; potassium phosphate 10 mM

sample_conditions_2: ionic strength: 10 mM; pH: 6.6; pressure: 1 atm; temperature: 277 K

sample_conditions_1: ionic strength: 10 mM; pH: 6.6; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
1H-1H NOESY	sample_1	isotropic	sample_conditions_1
1H-1H NOESY with WATERGATE	sample_2	isotropic	sample_conditions_2
1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
HCCH-COSY	sample_3	isotropic	sample_conditions_1
13C HSQC-NOESY	sample_3	isotropic	sample_conditions_1

Software:

X-PLOR, Brunger A. T. et.al. - refinement

NMR spectrometers:

Bruker DRX 500 MHz
Bruker DMX 600 MHz