Atomistic structure of the SARS-CoV-2 pseudoknot in solution from SAXS-driven molecular dynamics.

He W, San Emeterio J, Woodside MT, Kirmizialtin S, Pollack L, Nucleic Acids Res (2023) Europe PMC

SASDRU6 – Non frameshifting variant of SARS CoV2 frameshifting pseudoknot

Variant: non frameshifting pseudoknot from SARS CoV2 genome
MWexperimental 30 kDa
MWexpected 23 kDa
VPorod 38 nm3
log I(s) 1.62×102 1.62×101 1.62×100 1.62×10-1
Variant: non frameshifting pseudoknot from SARS CoV2 genome small angle scattering data  s, nm-1
ln I(s)
Variant: non frameshifting pseudoknot from SARS CoV2 genome Guinier plot ln 1.62×102 Rg: 2.8 nm 0 (2.8 nm)-2 s2
(sRg)2I(s)/I(0)
Variant: non frameshifting pseudoknot from SARS CoV2 genome Kratky plot 1.104 0 √3 sRg
Dmax: 13.5 nm

Data validation

There are no models related to this curve.

Synchrotron SAXS data from solutions of non-frameshifting variant of SARS CoV2 frameshifting pseudoknot RNA in 50 mM MOPS, 130 mM KCl, pH 7.5 were collected on the 16-ID (LiX) beam line at the National Synchrotron Light Source II (NSLS-II; Upton, NY, USA) using a Pilatus / 1M SAXS detector detector at a sample-detector distance of 3.6 m and at a wavelength of λ = 0.082 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 4.30 mg/ml was measured at 20°C. Five 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.

Variant: non frameshifting pseudoknot from SARS CoV2 genome
Mol. type   RNA
Olig. state   Monomer
Mon. MW   22.9 kDa
Sequence   FASTA