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

SASDRT6 – Wild type frameshifting pseudoknot from SARS CoV2 virus

Frameshifting pseudoknot from SARS CoV2, wild type
MWexperimental 32 kDa
MWexpected 23 kDa
VPorod 40 nm3
log I(s) 1.56×102 1.56×101 1.56×100 1.56×10-1
Frameshifting pseudoknot from SARS CoV2, wild type small angle scattering data  s, nm-1
ln I(s)
Frameshifting pseudoknot from SARS CoV2, wild type Guinier plot ln 1.57×102 Rg: 2.7 nm 0 (2.7 nm)-2 s2
(sRg)2I(s)/I(0)
Frameshifting pseudoknot from SARS CoV2, wild type Kratky plot 1.104 0 √3 sRg
Dmax: 10.5 nm

Data validation

There are no models related to this curve.

Synchrotron SAXS data from solutions of wild type frameshifting pseudoknot RNA from SARS CoV2 virus 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 3.80 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.

Frameshifting pseudoknot from SARS CoV2, wild type
Mol. type   RNA
Olig. state   Monomer
Mon. MW   22.9 kDa
Sequence   FASTA