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Open data
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Basic information
Entry | Database: PDB / ID: 7lyf | ||||||
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Title | Dengue virus RNA promoter stem-loop A fused with tRNA-scaffold | ||||||
![]() | RNA promoter stem-loop A fused with tRNA | ||||||
![]() | RNA | ||||||
Function / homology | : / RNA / RNA (> 10) / RNA (> 100)![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Lee, E.H. / Choi, K.H. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structures of flavivirus RNA promoters suggest two binding modes with NS5 polymerase. Authors: Lee, E. / Bujalowski, P.J. / Teramoto, T. / Gottipati, K. / Scott, S.D. / Padmanabhan, R. / Choi, K.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.9 KB | Display | ![]() |
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PDB format | ![]() | 64.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 402.4 KB | Display | ![]() |
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Full document | ![]() | 413.1 KB | Display | |
Data in XML | ![]() | 7.4 KB | Display | |
Data in CIF | ![]() | 9.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7lygC ![]() 1tn1S ![]() 5ew4S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: RNA chain | Mass: 44869.621 Da / Num. of mol.: 1 Fragment: Residues 1-32 and 81-139 form the tRNA scaffold, whereas residues 33-80 match to residues 69-116 of the Dengue virus 2 complete genome GB:KP188569.1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.83 Å3/Da / Density % sol: 67.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 100 mM sodium cacodylate pH 6.9, 9% (w/v) polyethylene glycol 8000, 200 mM KCl, and 100 mM magnesium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jun 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 3.366→50 Å / Num. obs: 10308 / % possible obs: 97.2 % / Redundancy: 7.1 % / CC1/2: 0.991 / Net I/σ(I): 37 |
Reflection shell | Resolution: 3.37→3.46 Å / Num. unique obs: 10308 / CC1/2: 0.636 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1TN1,5EW4 Resolution: 3.4→33.688 Å / SU ML: 0.59 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.39 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 252.2 Å2 / Biso mean: 155.1158 Å2 / Biso min: 74.06 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.4→33.688 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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