Structure and target interaction of a G-quadruplex RNA-aptamer.

Szameit K, Berg K, Kruspe S, Valentini E, Magbanua E, Kwiatkowski M, Chauvot de Beauchêne I, Krichel B, Schamoni K, Uetrecht C, Svergun DI, Schlüter H, Zacharias M, Hahn U, RNA Biol 13(10):973-987 (2016) Europe PMC

SASDAZ7 – IL-6R AIR-3A 2:4 complex

AIR-3A
Interleukin-6 receptor subunit alpha
MWexperimental 150 kDa
MWexpected 107 kDa
VPorod 150 nm3
log I(s) 3.62×103 3.62×102 3.62×101 3.62×100
AIR-3A Interleukin-6 receptor subunit alpha small angle scattering data  s, nm-1
ln I(s)
AIR-3A Interleukin-6 receptor subunit alpha Guinier plot ln 3.63×103 Rg: 6.7 nm 0 (6.7 nm)-2 s2
(sRg)2I(s)/I(0)
AIR-3A Interleukin-6 receptor subunit alpha Kratky plot 1.104 0 √3 sRg
p(r)
AIR-3A Interleukin-6 receptor subunit alpha pair distance distribution function Rg: 6.6 nm 0 Dmax: 25 nm

Data validation

Fits and models

log I(s)
 s, nm-1
AIR-3A Interleukin-6 receptor subunit alpha DAMMIF model
log I(s)
 s, nm-1
AIR-3A Interleukin-6 receptor subunit alpha CORAL model
Synchrotron SAXS data from solutions of IL-6R AIR-3A 2:4 complex in water, pH 7.5 were collected on the B21 beam line at the Diamond Light Source storage ring (Didcot, UK) using a Pilatus 2M detector at a sample-detector distance of 3.9 m and (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 0.20 mg/ml was measured. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

The CORAL model fits the experimental curve with a Chi-squared-value of 1.43. The model appears slightly smaller probably because of the presence of free RNA dimers in solution.

AIR-3A
Mol. type   RNA
Olig. state   Monomers
Mon. MW   6.4 kDa
Sequence   FASTA
 
Interleukin-6 receptor subunit alpha (IL-6R)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Dimer
Mon. MW   41.0 kDa
 
UniProt   P08887
Sequence   FASTA
 
PDB ID   1N26