BMRB Entry 17671

Name: Solution NMR Structure of the HIV-1 Exon Splicing Silencer 3
Published: 2012-03-07

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PDB ID: 2ldl
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17671
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Solution NMR Structure of the HIV-1 Exon Splicing Silencer 3 PubMed: 22154809

Deposition date: 2011-05-27 Original release date: 2012-03-07

Authors: Mishler, Clay; Levengood, Jeffrey; Johnson, Charles; Rajan, Prashant; Znosko, Brent

Citation: Levengood, Jeffrey; Rollins, Carrie; Mishler, Clay; Johnson, Charles; Miner, Grace; Rajan, Prashant; Znosko, Brent; Tolbert, Blanton. "Solution Structure of the HIV-1 Exon Splicing Silencer 3." J. Mol. Biol. 415, 680-698 (2012).

Assembly members:
RNA_(27-MER), polymer, 27 residues, 8650.235 Da.

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

Experimental source: Production method: cell free synthesis Host organism: in vitro transcription

Entity Sequences (FASTA):
RNA_(27-MER): XGAUCCAUUCGAUUAGUGAA CGGAUCC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	143
15N chemical shifts	16
1H chemical shifts	185

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (27-MER)	1

Entities:

Entity 1, RNA (27-MER) 27 residues - 8650.235 Da.

1

5GP

G

A

U

C

A

U

C

2

G

A

U

A

G

U

G

A

3

C

G

A

U

C

Samples:

hiv_exon_splicing_silencer_3: RNA (27-MER)1 – 2 mM; RNA (27-MER), [U-100% 15N], 0.5 – 1 mM; RNA (27-MER), [U-100% 13C], 0.5 – 1 mM; RNA (27-MER), [U-2H], 0.5 – 1 mM; potassium chloride 120 mM; potassium phosphate 20 mM; cacodylate 10 mM; EDTA 0.5 mM; D2O 100%

sample_conditions_1: ionic strength: 150 mM; pH: 5.5; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	hiv_exon_splicing_silencer_3	isotropic	sample_conditions_1
2D HNN-COSY	hiv_exon_splicing_silencer_3	isotropic	sample_conditions_1
2D 1H-1H NOESY	hiv_exon_splicing_silencer_3	isotropic	sample_conditions_1
2D 1H-1H TOCSY	hiv_exon_splicing_silencer_3	isotropic	sample_conditions_1
2D 1H-13C HMQC	hiv_exon_splicing_silencer_3	isotropic	sample_conditions_1

Software:

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

NMRView, Johnson, One Moon Scientific - chemical shift assignment

NMR spectrometers:

Bruker Avance 850 MHz
Bruker Avance 600 MHz
Bruker DMX 500 MHz