Long nonā€coding subgenomic flavivirus RNAs have extended 3D structures and are flexible in solution

Zhang Y, Zhang Y, Liu Z, Cheng M, Ma J, Wang Y, Qin C, Fang X, EMBO reports (2019) DOI

SASDGF3 – Xrn1 resistance RNA1 from Zika virus

Xrn1 resistance RNA2 from Zika virus
MWexperimental 22 kDa
MWexpected 22 kDa
VPorod 34 nm3
log I(s) 8.67×10-2 8.67×10-3 8.67×10-4 8.67×10-5
Xrn1 resistance RNA2 from Zika virus small angle scattering data  s, nm-1
ln I(s)
Xrn1 resistance RNA2 from Zika virus Guinier plot ln 8.67×10-2 Rg: 2.4 nm 0 (2.4 nm)-2 s2
(sRg)2I(s)/I(0)
Xrn1 resistance RNA2 from Zika virus Kratky plot 1.104 0 3 sRg
p(r)
Xrn1 resistance RNA2 from Zika virus pair distance distribution function Rg: 2.5 nm 0 Dmax: 8.5 nm

Data validation


Fits and models


log I(s)
 s, nm-1
Xrn1 resistance RNA2 from Zika virus OTHER model

log I(s)
 s, nm-1
Xrn1 resistance RNA2 from Zika virus DAMFILT model

Synchrotron SAXS data from solutions of Xrn1 resistance RNA1 from Zika 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 0.3 and 3 mg/ml were measured at 25°C. 30 successive 0.500 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).

Xrn1 resistance RNA2 from Zika virus (ZIKV-xrRNA2)
Mol. type   RNA
Organism   Zika virus
Olig. state   Monomer
Mon. MW   22.1 kDa
Sequence   FASTA
 
PDB code   5TPY