BMRB Entry 17671

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

Click here to enlarge.

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
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

Solution NMR Structure of the HIV-1 Exon Splicing Silencer 3

Deposition date:

2011-05-27

Original release date:

2012-03-07

Authors:

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

Citation:

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).
PubMed: 22154809

Assembly members:

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

Natural source:

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

Experimental source:

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

Entity Sequences (FASTA):

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
Hide all

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