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 31009

Title: DENV1 SLA three-way junction RNA (DenvSLAsh)   PubMed: 35750488

Deposition date: 2022-04-06 Original release date: 2022-06-30

Authors: Sun, Y.; Varani, G.; Seattle Structural Genomics Center for Infectious Disease (SSGCID), .

Citation: Sun, Y.; Varani, G.. "Structure of the Dengue Virus RNA Promoter"  RNA 28, 1210-1223 (2022).

Assembly members:
entity_1, polymer, 40 residues, 12929.753 Da.

Natural source:   Common Name: Dengue virus 1   Taxonomy ID: 11053   Superkingdom: Viruses   Kingdom: not available   Genus/species: Flavivirus Dengue virus 1

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
entity_1: GGACGUGGACCGACUUCGGU CGGAAGGAAACUUAACGUCC

Data sets:
Data typeCount
1H chemical shifts206

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11

Entities:

Entity 1, unit_1 40 residues - 12929.753 Da.

1   GGACGUGGAC
2   CGACUUCGGU
3   CGGAAGGAAA
4   CUUAACGUCC

Samples:

sample_1: RNA (40-MER) 1 mM; potassium phosphate 10 mM

sample_2: RNA (40-MER) 1 mM; potassium phosphate 10 mM

sample_3: RNA (40-MER), [U-2H], 1 mM; potassium phosphate 10 mM

sample_conditions_1: ionic strength: 50 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
2D 1H-1H TOCSYsample_2isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_3isotropicsample_conditions_1
2D 1H-1H TOCSYsample_2isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1

Software:

TopSpin, Bruker Biospin - collection, processing

NMRFAM-SPARKY, Lee W, Tonelli M, Markley JL - peak picking

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation

NMR spectrometers:

  • Bruker AVANCE III 600 MHz
  • Bruker AVANCE III 700 MHz
  • Bruker AVANCE III 800 MHz