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

SASDGW3 – DB12 from West Nile virus

DB12 from West Nile virus
MWexperimental 53 kDa
MWexpected 59 kDa
VPorod 160 nm3
log I(s) 5.45×10-2 5.45×10-3 5.45×10-4 5.45×10-5
DB12 from West Nile virus small angle scattering data  s, nm-1
ln I(s)
DB12 from West Nile virus Guinier plot ln 5.45×10-2 Rg: 3.9 nm 0 (3.9 nm)-2 s2
DB12 from West Nile virus Kratky plot 1.104 0 3 sRg
DB12 from West Nile virus pair distance distribution function Rg: 3.9 nm 0 Dmax: 13.4 nm

Data validation

Fits and models

log I(s)
 s, nm-1
DB12 from West Nile virus DAMFILT model

Synchrotron SAXS data from solutions of DB12 from West Nile virus 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. 30 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 West Nile virus (WNV DB12)
Mol. type   RNA
Organism   West Nile virus
Olig. state   Monomer
Mon. MW   59.2 kDa
Sequence   FASTA