High-resolution structure of stem-loop 4 from the 5'-UTR of SARS-CoV-2 solved by solution state NMR.

Vögele J, Hymon D, Martins J, Ferner J, Jonker HRA, Hargrove AE, Weigand JE, Wacker A, Schwalbe H, Wöhnert J, Duchardt-Ferner E, Nucleic Acids Res (2023) Europe PMC

SASDRV7 – SARS-CoV-2 5' untranslated region stem-loop 4 RNA (5_SL4) in phosphate buffer

stem-loop 4 from SARS-CoV-2 5'-UTR
MWexperimental 15 kDa
MWexpected 14 kDa
VPorod 22 nm3
log I(s) 6.34×103 6.34×102 6.34×101 6.34×100
stem-loop 4 from SARS-CoV-2 5'-UTR small angle scattering data  s, nm-1
ln I(s)
stem-loop 4 from SARS-CoV-2 5'-UTR Guinier plot ln 6.34×103 Rg: 2.1 nm 0 (2.1 nm)-2 s2
(sRg)2I(s)/I(0)
stem-loop 4 from SARS-CoV-2 5'-UTR Kratky plot 1.104 0 3 sRg
p(r)
stem-loop 4 from SARS-CoV-2 5'-UTR pair distance distribution function Rg: 2.1 nm 0 Dmax: 7.0 nm

Data validation


There are no models related to this curve.

Synchrotron SAXS data from solutions of SARS-CoV-2 5' untranslated region stem-loop 4 RNA (5_SL4) in 25 mM potassium phosphate pH 6.5, 150 mM KCl, 2 mM TCEP, were collected on the EMBL P12 beam line at PETRA III (DESY, Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124028 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 4.50 mg/ml was measured at 20°C. 40 successive 0.095 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.

TCEP was added to minimize radiation damage.

stem-loop 4 from SARS-CoV-2 5'-UTR (5_SL4)
Mol. type   RNA
Organism   SARS coronavirus 2-Wuhan
Olig. state   Monomer
Mon. MW   14.1 kDa
Sequence   FASTA