Long non-coding subgenomic flavivirus RNAs have extended 3D structures and are flexible in solution.

Zhang Y, Zhang Y, Liu ZY, Cheng ML, Ma J, Wang Y, Qin CF, Fang X, EMBO Rep 20(11):e47016 (2019) Europe PMC

SASDGS3 – DB12 from Dengue virus 2

DB12 from Dengue virus 2
MWexperimental 51 kDa
MWexpected 56 kDa
VPorod 96 nm3
log I(s) 1.07×10-1 1.07×10-2 1.07×10-3 1.07×10-4
DB12 from Dengue virus 2 small angle scattering data  s, nm-1
ln I(s)
DB12 from Dengue virus 2 Guinier plot ln 1.07×10-1 Rg: 4.7 nm 0 (4.7 nm)-2 s2
(sRg)2I(s)/I(0)
DB12 from Dengue virus 2 Kratky plot 1.104 0 3 sRg
p(r)
DB12 from Dengue virus 2 pair distance distribution function Rg: 4.9 nm 0 Dmax: 16.2 nm

Data validation


Fits and models


log I(s)
 s, nm-1
DB12 from Dengue virus 2 DAMFILT model

Synchrotron SAXS data from solutions of DB12 from Dengue virus 2 in 20mM Tris-HCl, 100mM NaCl, 5mM MgCl2, pH 7.5 were collected on the 12ID-B SAXS/WAXS beam line at the Advanced Photon Source (APS), Argonne National Laboratory storage ring (Lemont, IL, USA) using a Pilatus 2M detector at a sample-detector distance of 2 m and at a wavelength of λ = 0.08857 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.8 and 3 mg/ml were measured at 25°C. 29 successive 1 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted. The low angle data collected at lower concentrations were extrapolated to infinite dilution and merged with the higher concentration data to yield the final composite scattering curve.

The subtracted SAXS data series used to generate the final extrapolated to zero-concentration profile displayed in this entry are provided in the full entry zip archive. The ab initio dummy atom model represents the averaged spatial disposition of the RNA in solution (DAMFILT model), derived from several aligned individual models (corresponding fit).

DB12 from Dengue virus 2 (DENV DB12)
Mol. type   RNA
Organism   Dengue virus 2
Olig. state   Monomer
Mon. MW   55.9 kDa
Sequence   FASTA