An integrative NMR-SAXS approach for structural determination of large RNAs defines the substrate-free state of a trans-cleaving Neurospora Varkud Satellite ribozyme

Pierre Dagenais.

SASDKX3 – Minimal trans Varkud Satellite (VS) ribozyme without MgCl2

Neurospora Varkud Satellite minimal trans ribozyme
MWexperimental 37 kDa
MWexpected 33 kDa
VPorod 55 nm3
log I(s) 1.03×101 1.03×100 1.03×10-1 1.03×10-2
Neurospora Varkud Satellite minimal trans ribozyme small angle scattering data  s, nm-1
ln I(s)
Neurospora Varkud Satellite minimal trans ribozyme Guinier plot ln 1.03×101 Rg: 3.6 nm 0 (3.6 nm)-2 s2
(sRg)2I(s)/I(0)
Neurospora Varkud Satellite minimal trans ribozyme Kratky plot 1.104 0 3 sRg
p(r)
Neurospora Varkud Satellite minimal trans ribozyme pair distance distribution function Rg: 3.7 nm 0 Dmax: 12.4 nm

Data validation


There are no models related to this curve.

SAXS data from solutions of the minimal trans VS ribozyme in 50 mM MES, 50 mM KCl, pH 6.5, were collected using a Xenocs BioXolver L with MetalJet equipped with a Pilatus3 R 300K detector (Université de Montréal, Montréal, Canada) at a sample-detector distance of 0.6 m and at a wavelength of λ = 0.134 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.5 and 0.5 mg/ml were measured at 20°C. 10 successive 30 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.

Neurospora Varkud Satellite minimal trans ribozyme (VS ribozyme TR4P)
Mol. type   RNA
Organism   Neurospora crassa
Olig. state   Monomer
Mon. MW   32.7 kDa
Sequence   FASTA