Crystal structure of the Varkud satellite ribozyme.

Suslov NB, DasGupta S, Huang H, Fuller JR, Lilley DM, Rice PA, Piccirilli JA, Nat Chem Biol 11(11):840-6 (2015) Europe PMC

SASDAC9 – Varkud Satellite (VS) ribozyme in Tris

Varkud Satellite (VS) ribozyme
MWI(0) 125 kDa
MWexpected 120 kDa
VPorod 240 nm3
log I(s) 4.29×103 4.29×102 4.29×101 4.29×100
Varkud Satellite (VS) ribozyme small angle scattering data  s, nm-1
ln I(s)
Varkud Satellite (VS) ribozyme Guinier plot ln 4.30×103 Rg: 3.9 nm 0 (3.9 nm)-2 s2
Varkud Satellite (VS) ribozyme Kratky plot 1.104 0 3 sRg
Varkud Satellite (VS) ribozyme pair distance distribution function Rg: 4.1 nm 0 Dmax: 16.4 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Varkud Satellite (VS) ribozyme DAMMIN model

log I(s)
 s, nm-1
Varkud Satellite (VS) ribozyme NONE model

Synchrotron SAXS data from solutions of Varkud Satellite (VS) ribozyme in Tris in 10 mM Tris 25 mM KCl 5 mM MgCl2, pH 7.5 were collected on the 12.3.1 (SIBYLS) beam line at the Advanced Light Source (ALS) storage ring (Berkeley, CA, USA) using a Pilatus3 X 2M detector at a wavelength of λ = 0.103 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 1.5 and 4.5 mg/ml were measured . 24 successive 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. The low angle data collected at lower concentrations were extrapolated to infinite dilution and merged with the higher concentration data to yield the final composite scattering curve.

SAXS data from a catalytically inactive construct support the overall conformation and dimeric state of the VS ribozyme in its x-ray crystal structure.

Varkud Satellite (VS) ribozyme (G638A)
Mol. type   RNA
Organism   Neurospora
Olig. state   Dimer
Mon. MW   60.2 kDa
Sequence   FASTA