The low-resolution structural models of hepatitis C virus RNA subdomain 5BSL3.2 and its distal complex with domain 3'X point to conserved regulatory mechanisms within the Flaviviridae family.

Castillo-Martínez J, Fan L, Szewczyk MP, Wang YX, Gallego J, Nucleic Acids Res (2022) Europe PMC

SASDMQ4 – Hepatitis C virus RNA Domain 3'X mutant

Domain 3'X mutant
MWexperimental 31 kDa
MWexpected 32 kDa
VPorod 50 nm3
log I(s) 8.10×10-2 8.10×10-3 8.10×10-4 8.10×10-5
Domain 3'X mutant small angle scattering data  s, nm-1
ln I(s)
Domain 3'X mutant Guinier plot ln 8.11×10-2 Rg: 3.3 nm 0 (3.3 nm)-2 s2
(sRg)2I(s)/I(0)
Domain 3'X mutant Kratky plot 1.104 0 √3 sRg
p(r)
Domain 3'X mutant pair distance distribution function Rg: 3.5 nm 0 Dmax: 14.2 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Domain 3'X mutant DAMFILT model
Domain 3'X mutant DAMMIN model
Synchrotron SAXS data from solutions of the hepatitis C virus RNA Domain 3'X mutant in 10 mM Tris-HCl, 6 mM MgCl2, pH 7 were collected on the 12ID-B SAXS/WAXS beam line at the Advanced Photon Source (APS), Argonne National Laboratory (Lemont, IL, USA) using a Pilatus 2M detector at a sample-detector distance of 2 m and at a wavelength of λ = 0.0886 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.5 and 2 mg/ml were measured at 27°C. Eight 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 bead models presented in this entry include: 1) Top - The spatially aligned and volume/bead occupancy-corrected averaged representation calculated from the spatial alignment of a cohort of individual model reconstructions. 2) Bottom - An individual model reconstruction and associated individual model fit to the data.

Domain 3'X mutant (3'Xm)
Mol. type   RNA
Organism   Hepatitis C virus JFH-1
Olig. state   Monomer
Mon. MW   31.6 kDa
Sequence   FASTA