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.

SASDKW3 – Stem-loop VI from the Neurospora Varkud Satellite (VS) ribozyme

Neurospora Varkud Satellite ribozyme stem-loop VI
MWexperimental 8 kDa
MWexpected 8 kDa
VPorod 8 nm3
log I(s) 6.31×100 6.31×10-1 6.31×10-2 6.31×10-3
Neurospora Varkud Satellite ribozyme stem-loop VI small angle scattering data  s, nm-1
ln I(s)
Neurospora Varkud Satellite ribozyme stem-loop VI Guinier plot ln 6.31×100 Rg: 1.6 nm 0 (1.6 nm)-2 s2
(sRg)2I(s)/I(0)
Neurospora Varkud Satellite ribozyme stem-loop VI Kratky plot 1.104 0 3 sRg
p(r)
Neurospora Varkud Satellite ribozyme stem-loop VI pair distance distribution function Rg: 1.7 nm 0 Dmax: 6.1 nm

Data validation


Fits and models


log I(s)
 s, nm-1
Neurospora Varkud Satellite ribozyme stem-loop VI PDB (PROTEIN DATA BANK) model

Synchrotron SAXS data from solutions of stem-loop VI from the VS ribozyme in 50 mM MES, 50 mM KCl, 5 mM MgCl2, pH 6.5 were collected on the G1 beam line at the Cornell High Energy Synchrotron Source (CHESS; Ithaca, NY, USA) using a Pilatus 100K detector at a sample-detector distance of 1.5 m and at a wavelength of λ = 0.1245 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 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.

Neurospora Varkud Satellite ribozyme stem-loop VI (VS ribozyme SLVI)
Mol. type   RNA
Organism   Neurospora crassa
Olig. state   Monomer
Mon. MW   8.5 kDa
Sequence   FASTA