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 17671

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

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:
Data typeCount
13C chemical shifts143
15N chemical shifts16
1H chemical shifts185

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1RNA (27-MER)1

Entities:

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

1   5GPGAUCCAUUC
2   GAUUAGUGAA
3   CGGAUCC

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:

NameSampleSample stateSample conditions
2D 1H-15N HSQChiv_exon_splicing_silencer_3isotropicsample_conditions_1
2D HNN-COSYhiv_exon_splicing_silencer_3isotropicsample_conditions_1
2D 1H-1H NOESYhiv_exon_splicing_silencer_3isotropicsample_conditions_1
2D 1H-1H TOCSYhiv_exon_splicing_silencer_3isotropicsample_conditions_1
2D 1H-13C HMQChiv_exon_splicing_silencer_3isotropicsample_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

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