Structural heterogeneity and dynamics in the apical stem loop of s2m from SARS-CoV-2 Delta by an integrative NMR spectroscopy and MD simulation approach.

Wirtz Martin MA, Makowski JA, Matzel T, Kensinger AH, Herr A, Richter C, Jonker HRA, Wacker A, Evanseck JD, Schwalbe H, Nucleic Acids Res 53(12) (2025) Europe PMC

SASDXB3 – Apical stem loop of stem loop 2 motif in Delta variant of SARS-CoV-2 (s2m Delta_short)

apical stem loop of stem loop 2 motif (s2m) in Delta variant of SARS-CoV-2
MWexperimental 7 kDa
MWexpected 8 kDa
log I(s) 4.18×10-2 4.18×10-3 4.18×10-4 4.18×10-5
apical stem loop of stem loop 2 motif (s2m) in Delta variant of SARS-CoV-2 small angle scattering data  s, nm-1
ln I(s)
apical stem loop of stem loop 2 motif (s2m) in Delta variant of SARS-CoV-2 Guinier plot ln 4.19×10-2 Rg: 1.4 nm 0 (1.4 nm)-2 s2
(sRg)2I(s)/I(0)
apical stem loop of stem loop 2 motif (s2m) in Delta variant of SARS-CoV-2 Kratky plot 1.104 0 √3 sRg

Data validation

There are no models related to this curve.

Synchrotron SAXS data from solutions of Apical stem loop of stem loop 2 motif in Delta variant of SARS-CoV-2 (s2m Delta_short) in 50 mM Bis-Tris, 25 mM NaCl, pH 6.4 were collected on the EMBL P12 beam line at the PETRA III storage ring (DESY; Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.12398 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 25°C. 33 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.

apical stem loop of stem loop 2 motif (s2m) in Delta variant of SARS-CoV-2 (s2m Delta_short)
Mol. type   RNA
Organism   SARS-Coronavirus-2 Delta
Olig. state   Monomer
Mon. MW   8.1 kDa
Sequence   FASTA