BMRB Entry 17436

Name: Structure of the HIV-1 frameshift site RNA bound to a small molecule inhibitor of viral replication
Published: 2011-06-16

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PDB ID: 2l94
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17436
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Structure of the HIV-1 frameshift site RNA bound to a small molecule inhibitor of viral replication PubMed: 21648432

Deposition date: 2011-01-29 Original release date: 2011-06-16

Authors: Marcheschi, Ryan; Tonelli, Marco; Kumar, Arvind; Butcher, Samuel

Citation: Marcheschi, Ryan; Tonelli, Marco; Kumar, Arvind; Butcher, Samuel. "Structure of the HIV-1 frameshift site RNA bound to a small molecule inhibitor of viral replication." ACS Chem. Biol. 6, 857-864 (2011).

Assembly members:
RNA_(45-MER), polymer, 45 residues, 14519.805 Da.
L94, non-polymer, 336.519 Da.

Natural source: Common Name: Human immunodeficiency virus Taxonomy ID: 12721 Superkingdom: not available Kingdom: virus Genus/species: Lentivirus not available

Experimental source: Production method: in vitro transcription Host organism: E. coli - cell free

Entity Sequences (FASTA):
RNA_(45-MER): GGGAAGAUCUGGCCUUCCCA CAAGGGAAGGCCAGGGAAUC UUCCC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	76
1H chemical shifts	363

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (45-MER)	1
2	DB	2

Entities:

Entity 1, RNA (45-MER) 45 residues - 14519.805 Da.

1

G

A

G

A

U

C

U

2

G

C

U

C

A

3

C

A

G

A

G

4

C

A

G

A

U

C

5

U

C

Entity 2, DB - C18 H36 N6 - 336.519 Da.

1

L94

Samples:

750_uM_RNA:DB213_H2O: RNA (45-MER) 0.75 mM; DB213 0.75 mM; DSS 20 uM; potassium chloride 20 mM; TRIS, [U-2H], 10 mM; H2O 90%; D2O 10%

750_uM_RNA:DB213_D2O: RNA (45-MER) 0.75 mM; DB213 0.75 mM; DSS 20 uM; potassium chloride 20 mM; TRIS, [U-2H], 10 mM; D2O 100%

1.5_mM_RNA:DB213_D2O: RNA (45-MER) 1.5 mM; DB213 1.5 mM; DSS 40 uM; potassium chloride 40 mM; TRIS, [U-2H], 20 mM; D2O 100%

1.5_mM_RNA:DB213_Pf1_D2O: RNA (45-MER) 1.5 mM; DB213 1.5 mM; DSS 40 uM; potassium chloride 40 mM; TRIS, [U-2H], 20 mM; Pf1 phage 4.5 mg; D2O 100%

H2O_samples: ionic strength: 20 mM; pH: 7.0; pressure: 1 atm; temperature: 283 K

D2O_samples: ionic strength: 20 mM; pH: 7.0; pressure: 1 atm; temperature: 308 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	750_uM_RNA:DB213_H2O	isotropic	H2O_samples
2D 1H-1H NOESY	750_uM_RNA:DB213_D2O	isotropic	D2O_samples
2D 1H-1H TOCSY	750_uM_RNA:DB213_D2O	isotropic	D2O_samples
2D 1H-13C HSQC	1.5_mM_RNA:DB213_D2O	isotropic	D2O_samples
2D 1H-13C HSQC	1.5_mM_RNA:DB213_Pf1_D2O	anisotropic	D2O_samples

Software:

HADDOCK v2.0, Alexandre Bonvin, Utrecht University - docking, refinement, structure solution

AMBER v9.0, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement, structure solution

SPARKY, Goddard - chemical shift assignment, data analysis, peak picking

SYBYL v8.0, Tripos - data analysis, geometry optimization

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

xwinnmr v3.5, Bruker Biospin - collection, processing

VNMRJ, Varian - collection

PALES, Markus Zweckstetter, Ad Bax - data analysis

PyMol, DeLano Scientific - data analysis

NMR spectrometers:

Bruker DMX 750 MHz
Varian Avance 900 MHz