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

SASDVX2 – Full-length SARS-CoV-2 5'ge element stem-loop 5 (5_SL5)

full stem-loop 5 of SARS-CoV-2 5'genomic end
MWexperimental 49 kDa
MWexpected 48 kDa
log I(s) 1.98×104 1.98×103 1.98×102 1.98×101
full stem-loop 5 of SARS-CoV-2 5'genomic end small angle scattering data  s, nm-1
ln I(s)
full stem-loop 5 of SARS-CoV-2 5'genomic end Guinier plot ln 1.99×104 Rg: 4.3 nm 0 (4.3 nm)-2 s2
(sRg)2I(s)/I(0)
full stem-loop 5 of SARS-CoV-2 5'genomic end Kratky plot 1.104 0 √3 sRg
p(r)
full stem-loop 5 of SARS-CoV-2 5'genomic end pair distance distribution function Rg: 4.4 nm 0 Dmax: 13.8 nm

Data validation

Fits and models

log I(s)
 s, nm-1
full stem-loop 5 of SARS-CoV-2 5'genomic end PYMOL model
log I(s)
 s, nm-1
full stem-loop 5 of SARS-CoV-2 5'genomic end DAMMIF model
Synchrotron SAXS data from solutions of Full-length 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 10°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.

full stem-loop 5 of SARS-CoV-2 5'genomic end (5_SL5)
Mol. type   RNA
Organism   Severe acute respiratory syndrome coronavirus 2
Olig. state   Monomer
Mon. MW   48.3 kDa
Sequence   FASTA