Biophysical characterization of honey bee virus untranslated regions

Jenna M Letain, Trushar R Patel, University of Lethbridge Dept. of Chemistry and Biochemistry Thesis (2024) URL

SASDVX7 – Sacbrood virus 5' untranslated region RNA (SBV 5'UTR)

SBV 5'UTR
MWexperimental 79 kDa
MWexpected 61 kDa
VPorod 120 nm3
log I(s) 4.14×10-2 4.14×10-3 4.14×10-4 4.14×10-5
SBV 5'UTR small angle scattering data  s, nm-1
ln I(s)
SBV 5'UTR Guinier plot ln 4.15×10-2 Rg: 4.9 nm 0 (4.9 nm)-2 s2
(sRg)2I(s)/I(0)
SBV 5'UTR Kratky plot 1.104 0 √3 sRg
p(r)
SBV 5'UTR pair distance distribution function Rg: 4.9 nm 0 Dmax: 15.1 nm

Data validation

Fits and models

log I(s)
 s, nm-1
SBV 5'UTR DAMMIN model
log I(s)
 s, nm-1
SBV 5'UTR DAMMIN model
log I(s)
 s, nm-1
SBV 5'UTR DAMMIN model
Synchrotron SAXS data from solutions of sacbrood virus 5' untranslated region RNA (SBV 5'UTR) in 10 mM Bis-Tris, 100 mM NaCl, 5 mM MgCl2, 15 mM KCl, 5% glycerol, pH 6 were collected on the B21 beam line at the Diamond Light Source (Didcot, UK) using a Eiger 4M detector at a sample-detector distance of 3.7 m and at a wavelength of λ = 0.094 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 50.00 μl sample at 1 mg/ml was injected at a 0.16 ml/min flow rate onto a Shodex KW403-4F column at 20°C. 600 successive 3 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.

SBV 5'UTR
Mol. type   RNA
Organism   Sacbrood virus
Olig. state   Monomer
Mon. MW   61.5 kDa
Sequence   FASTA