Dissecting the Conformational Heterogeneity of Stem-Loop Substructures of the Fifth Element in the 5'-Untranslated Region of SARS-CoV-2.

Mertinkus KR, Oxenfarth A, Richter C, Wacker A, Mata CP, Carazo JM, Schlundt A, Schwalbe H, J Am Chem Soc 146(44):30139-30154 (2024) Europe PMC

SASDVC3 – Sub-element stem-loop 5b within the SARS-CoV-2 5'ge element stem-loop 5 (5_SL5)

sub-element stem-loop 5b from SARS-CoV-2 5'genomic end
MWexperimental 8 kDa
MWexpected 8 kDa
log I(s) 7.23×101 7.23×100 7.23×10-1 7.23×10-2
sub-element stem-loop 5b from SARS-CoV-2 5'genomic end small angle scattering data  s, nm-1
ln I(s)
sub-element stem-loop 5b from SARS-CoV-2 5'genomic end Guinier plot ln 7.24×101 Rg: 1.4 nm 0 (1.4 nm)-2 s2
(sRg)2I(s)/I(0)
sub-element stem-loop 5b from SARS-CoV-2 5'genomic end Kratky plot 1.104 0 √3 sRg
p(r)
sub-element stem-loop 5b from SARS-CoV-2 5'genomic end pair distance distribution function Rg: 1.4 nm 0 Dmax: 4.3 nm

Data validation

Fits and models

log I(s)
 s, nm-1
sub-element stem-loop 5b from SARS-CoV-2 5'genomic end PYMOL model
Synchrotron SAXS data from solutions of Sub-element stem-loop 5b 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 BM29 beam line at the ESRF storage ring (Grenoble, France) using a Pilatus3 2M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.09919 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 2.50 mg/ml was measured at 20°C. 10 successive 1 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 5b from SARS-CoV-2 5'genomic end (5_SL5b)
Mol. type   RNA
Organism   Severe acute respiratory syndrome coronavirus 2
Olig. state   Monomer
Mon. MW   8.2 kDa
Sequence   FASTA