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

SASDGQ3 – SL3 from West Nile virus

SL3 from West Nile virus
MWexperimental 25 kDa
MWexpected 23 kDa
VPorod 29 nm3
log I(s) 8.57×101 8.57×100 8.57×10-1 8.57×10-2
SL3 from West Nile virus small angle scattering data  s, nm-1
ln I(s)
SL3 from West Nile virus Guinier plot ln 8.58×101 Rg: 2.8 nm 0 (2.8 nm)-2 s2
SL3 from West Nile virus Kratky plot 1.104 0 3 sRg
SL3 from West Nile virus pair distance distribution function Rg: 2.9 nm 0 Dmax: 9.5 nm

Data validation

Fits and models

log I(s)
 s, nm-1
SL3 from West Nile virus DAMFILT model

Synchrotron SAXS data from solutions of SL3 from West Nile virus in 20mM Tris-HCl, 100mM NaCl, 5mM MgCl2, pH 7.5 were collected on the BL19U2 beam line at the Shanghai Synchrotron Radiation Facility (SSRF) storage ring (Shanghai, China) using a Pilatus 1M detector at a sample-detector distance of 2.3 m and at a wavelength of λ = 0.1033 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 2 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).

SL3 from West Nile virus (WNV SL3)
Mol. type   RNA
Organism   West Nile virus
Olig. state   Monomer
Mon. MW   23.2 kDa
Sequence   FASTA