The 5'-terminal stem-loop RNA element of SARS-CoV-2 features highly dynamic structural elements that are sensitive to differences in cellular pH.

Toews S, Wacker A, Faison EM, Duchardt-Ferner E, Richter C, Mathieu D, Bottaro S, Zhang Q, Schwalbe H, Nucleic Acids Res (2024) Europe PMC

SASDSP7 – 5’-terminal stem-loop 1 RNA element of SARS-CoV-2 (5_SL1)

5_SL1
MWI(0) 11 kDa
MWexpected 9 kDa
VPorod 16 nm3
log I(s) 6.50×10-2 6.50×10-3 6.50×10-4 6.50×10-5
5_SL1 small angle scattering data  s, nm-1
ln I(s)
5_SL1 Guinier plot ln 6.51×10-2 Rg: 1.7 nm 0 (1.7 nm)-2 s2
(sRg)2I(s)/I(0)
5_SL1 Kratky plot 1.104 0 √3 sRg
p(r)
5_SL1 pair distance distribution function Rg: 1.7 nm 0 Dmax: 5.5 nm

Data validation

Fits and models

log I(s)
 s, nm-1
5_SL1 DAMMIN model
Synchrotron SAXS data from solutions of the 5’-terminal stem-loop 1 RNA element of SARS-CoV-2 in 50 mM BisTris, 25 mM NaCl, pH 6.2 were collected on the EMBL P12 beam line at PETRA III (DESY; Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3.1 m and at a wavelength of λ = 0.124 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 1.50 mg/ml was measured at 298°C. 33 successive 0.950 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.

5_SL1 (SL1)
Mol. type   RNA
Organism   Severe acute respiratory syndrome coronavirus 2
Olig. state   Monomer
Mon. MW   9.5 kDa
Sequence   FASTA