The pseudoknot structure of a viral RNA reveals a conserved mechanism for programmed exoribonuclease resistance

Sophie Korn.

SASDVV4 – ST9a RNA, WT (54 nucleotides in 10 mM MgCl2; monomer)

ST9 WT (54 nt RNA)
MWexperimental 14 kDa
MWexpected 17 kDa
VPorod 21 nm3
log I(s) 2.90×100 2.90×10-1 2.90×10-2 2.90×10-3
ST9 WT (54 nt RNA) small angle scattering data  s, nm-1
ln I(s)
ST9 WT (54 nt RNA) Guinier plot ln 2.90×100 Rg: 1.9 nm 0 (1.9 nm)-2 s2
(sRg)2I(s)/I(0)
ST9 WT (54 nt RNA) Kratky plot 1.104 0 √3 sRg
p(r)
ST9 WT (54 nt RNA) pair distance distribution function Rg: 1.8 nm 0 Dmax: 5.8 nm

Data validation

Fits and models

log I(s)
 s, nm-1
ST9 WT (54 nt RNA) PYMOL model
Synchrotron SAXS data from solutions of ST9 RNA WT, (54 nucleotides) in 50 mM Tris pH 7.5, 100 mM NaCl, 1 mM DTT, 10 mM MgCl2, 0.0002% w/v NaN3 were collected on the 16-ID (LiX) beam line at the National Synchrotron Light Source II (NSLS-II; Upton, NY, USA) using a Pilatus3 S 1M detector at a sample-detector distance of 4.1 m and at a wavelength of λ = 0.082 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 95.00 μl sample at 3 mg/ml was injected at a 0.75 ml/min flow rate onto a GE Superdex 200 Increase 10/300 column at 20°C. 1500 successive 2 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.

ST9 WT (54 nt RNA)
Mol. type   RNA
Olig. state   Monomer
Mon. MW   17.5 kDa
Sequence   FASTA