BMRB Entry 31009
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31009
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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
- assigned_chemical_shifts
Data type | Count |
1H chemical shifts | 206 |
Additional metadata:
Assembly:
Entity Assembly ID | Entity Name | Entity ID |
---|---|---|
1 | unit_1 | 1 |
Entities:
Entity 1, unit_1 40 residues - 12929.753 Da.
1 | G | G | A | C | G | U | G | G | A | C | |
2 | C | G | A | C | U | U | C | G | G | U | |
3 | C | G | G | A | A | G | G | A | A | A | |
4 | C | U | U | A | A | C | G | U | C | C |
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:
Name | Sample | Sample state | Sample conditions |
---|---|---|---|
2D 1H-1H NOESY | sample_2 | isotropic | sample_conditions_1 |
2D 1H-1H TOCSY | sample_2 | isotropic | sample_conditions_1 |
2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
2D 1H-1H NOESY | sample_3 | isotropic | sample_conditions_1 |
2D 1H-1H TOCSY | sample_2 | isotropic | sample_conditions_1 |
2D 1H-1H NOESY | sample_2 | isotropic | sample_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