Spatial arrangement of functional domains in OxyS stress response sRNA

Stih V, Amenitsch H, Plavec J, Podbevsek P, RNA :rna.079618.123 (2023) DOI

SASDQP8 – OxyS sRNA in HEPES buffer pH 6.8, 50 mM NaCl

Stress response regulating small RNA OxyS
MWexperimental 39 kDa
MWexpected 36 kDa
VPorod 68 nm3
log I(s) 9.67×100 9.67×10-1 9.67×10-2 9.67×10-3
Stress response regulating small RNA OxyS small angle scattering data  s, nm-1
ln I(s)
Stress response regulating small RNA OxyS Guinier plot ln 9.67×100 Rg: 4.8 nm 0 (4.8 nm)-2 s2
(sRg)2I(s)/I(0)
Stress response regulating small RNA OxyS Kratky plot 1.104 0 3 sRg
p(r)
Stress response regulating small RNA OxyS pair distance distribution function Rg: 4.6 nm 0 Dmax: 15.5 nm

Data validation


Fits and models


log I(s)
 s, nm-1
Stress response regulating small RNA OxyS OTHER [STATIC IMAGE] model

log I(s)
 s, nm-1
Stress response regulating small RNA OxyS DAMMIF model

Synchrotron SAXS data from solutions of OxyS sRNA in 50 mM HEPES pH 6.8, 50 mM NaCl were collected on the Austrian SAXS 5.2L beam line at ELETTRA (Trieste, Italy) using a Pilatus3 1M detector at a sample-detector distance of 1.5 m and at a wavelength of λ = 0.154 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 1.1 and 4.5 mg/ml were measured at 25°C. 18 successive 10 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. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.

The individual models of the DNA ensemble (pdb format) are made available in the full entry zip archive. The dummy atom model (DAM) displayed in this entry is derived from the minimized spatial alignment of an individual model cohort, corrected for volume and bead occupancy. The resulting DAMFILT model does not reflect the corresponding fit to the data.

Stress response regulating small RNA OxyS (sRNA OxyS)
Mol. type   RNA
Organism   Escherichia coli
Olig. state   Monomer
Mon. MW   35.8 kDa
Sequence   FASTA