SL5-derived RNA elements from the SARS-CoV-2 5'genomic end

Andreas Schlundt.

SASDVY2 – Sub-element stem-loop 5a within the SARS-CoV-2 5'ge element stem-loop 5 (5_SL5)

sub-element stem-loop 5a from SARS-CoV-2 5'genomic end
MWI(0) 11 kDa
MWexpected 11 kDa
log I(s) 4.99×103 4.99×102 4.99×101 4.99×100
sub-element stem-loop 5a from SARS-CoV-2 5'genomic end small angle scattering data  s, nm-1
ln I(s)
sub-element stem-loop 5a from SARS-CoV-2 5'genomic end Guinier plot ln 5.00×103 Rg: 1.9 nm 0 (1.9 nm)-2 s2
(sRg)2I(s)/I(0)
sub-element stem-loop 5a from SARS-CoV-2 5'genomic end Kratky plot 1.104 0 √3 sRg
p(r)
sub-element stem-loop 5a from SARS-CoV-2 5'genomic end pair distance distribution function Rg: 1.9 nm 0 Dmax: 6 nm

Data validation

Fits and models

log I(s)
 s, nm-1
sub-element stem-loop 5a from SARS-CoV-2 5'genomic end PYMOL model
Synchrotron SAXS data from solutions of Sub-element stem-loop 5a within the SARS-CoV-2 5'ge element stem-loop 5 (5_SL5) in 25 mM potassium phosphate, 50 mM KCl, pH 6.2 were collected on the EMBL P12 beam line at the PETRA III storage ring (DESY; Hamburg, Germany) using a Pilatus 2M 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 1.00 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.

sub-element stem-loop 5a from SARS-CoV-2 5'genomic end (5_SL5a)
Mol. type   RNA
Organism   Severe acute respiratory syndrome coronavirus 2
Olig. state   Monomer
Mon. MW   10.6 kDa
Sequence   FASTA