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

Sophie Korn.

SASDV25 – ST9a RNA, PKmutant (59 nucleotides in 0 mM MgCl2; monomer)

ST9 PKmutant (59 nt RNA)
MWexperimental 23 kDa
MWexpected 19 kDa
VPorod 29 nm3
log I(s) 4.98×100 4.98×10-1 4.98×10-2 4.98×10-3
ST9 PKmutant (59 nt RNA) small angle scattering data  s, nm-1
ln I(s)
ST9 PKmutant (59 nt RNA) Guinier plot ln 4.99×100 Rg: 2.5 nm 0 (2.5 nm)-2 s2
(sRg)2I(s)/I(0)
ST9 PKmutant (59 nt RNA) Kratky plot 1.104 0 √3 sRg
p(r)
ST9 PKmutant (59 nt RNA) pair distance distribution function Rg: 2.6 nm 0 Dmax: 8.8 nm

Data validation

Fits and models

log I(s)
 s, nm-1
ST9 PKmutant (59 nt RNA) PYMOL model
log I(s)
 s, nm-1
ST9 PKmutant (59 nt RNA) RNAMASONRY model
Synchrotron SAXS data from solutions of ST9 RNA, PKmutant (59 nucleotides) in 50 mM Tris pH 7.5, 100 mM NaCl, 1 mM DTT, 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 3.6 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. 1200 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 PKmutant (59 nt RNA)
Mol. type   RNA
Olig. state   Monomer
Mon. MW   19.1 kDa
Sequence   FASTA