Probing the conformational changes of in vivo overexpressed cell cycle regulator 6S ncRNA

Makraki E, Miliara S, Pagkalos M, Kokkinidis M, Mylonas E, Fadouloglou V, Frontiers in Molecular Biosciences 10 (2023) DOI

SASDQS4 – Escherichia coli 6S:pRNA complex

6S RNA (SsrS gene)
product RNA from E. coli 6S
MWexperimental 74 kDa
MWexpected 65 kDa
VPorod 260 nm3
log I(s) 3.37×10-2 3.37×10-3 3.37×10-4 3.37×10-5
6S RNA (SsrS gene) product RNA from E. coli 6S small angle scattering data  s, nm-1
ln I(s)
6S RNA (SsrS gene) product RNA from E. coli 6S Guinier plot ln 3.37×10-2 Rg: 4.9 nm 0 (4.9 nm)-2 s2
(sRg)2I(s)/I(0)
6S RNA (SsrS gene) product RNA from E. coli 6S Kratky plot 1.104 0 √3 sRg
p(r)
6S RNA (SsrS gene) product RNA from E. coli 6S pair distance distribution function Rg: 5.2 nm 0 Dmax: 20 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Escherichia coli 6S:pRNA complex Rg histogram Rg, nm
6S RNA (SsrS gene) product RNA from E. coli 6S EOM/RANCH model
Synchrotron SAXS data from solutions of Escherichia coli 6S:pRNA complex in 20 mM Tris-HCl, 200 mM KCl, 5 mM MgCl2, pH 8 were collected on the SWING beam line at SOLEIL (Saint-Aubin, France) using a AVIEX PCCD170170 detector at a sample-detector distance of 3.1 m and at a wavelength of λ = 0.1033 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 sample at 4 mg/ml was injected onto a column at 15°C. 252 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.

X-ray Exposure time = UNKNOWN. SEC column = UNKNOWN. Sample injection volume = UNKNOWN. Flow rate = UNKNOWN

6S RNA (SsrS gene)
Mol. type   RNA
Organism   Escherichia coli
Olig. state   Monomer
Mon. MW   58.9 kDa
Sequence   FASTA
 
product RNA from E. coli 6S (pRNA)
Mol. type   RNA
Organism   Escherichia coli
Olig. state   Monomer
Mon. MW   6.5 kDa
Sequence   FASTA