Solution structures of DEAD-box helicase DDX3X reveal the N-terminal extension binds RNA to modulate catalysis and influence conformation

Sarah Atkinson.

SASDRA5 – 15 nucleotide RNA duplex (ATP-dependent RNA helicase DDX3X binding target)

15 nucleotide RNA duplex (ATP-dependent RNA helicase DDX3X binding target)
MWexperimental 7 kDa
MWexpected 10 kDa
VPorod 14 nm3
log I(s) 2.51×10-3 2.51×10-4 2.51×10-5 2.51×10-6
15 nucleotide RNA duplex (ATP-dependent RNA helicase DDX3X binding target) small angle scattering data  s, nm-1
ln I(s)
15 nucleotide RNA duplex (ATP-dependent RNA helicase DDX3X binding target) Guinier plot ln 2.51×10-3 Rg: 1.5 nm 0 (1.5 nm)-2 s2
(sRg)2I(s)/I(0)
15 nucleotide RNA duplex (ATP-dependent RNA helicase DDX3X binding target) Kratky plot 1.104 0 √3 sRg
p(r)
15 nucleotide RNA duplex (ATP-dependent RNA helicase DDX3X binding target) pair distance distribution function Rg: 1.5 nm 0 Dmax: 4.2 nm

Data validation

Fits and models

log I(s)
 s, nm-1
15 nucleotide RNA duplex (ATP-dependent RNA helicase DDX3X binding target) DAMMIF model
15 nucleotide RNA duplex (ATP-dependent RNA helicase DDX3X binding target) DAMMIF model
Synchrotron SAXS data from solutions of a 15 nucleotide RNA duplex (ATP-dependent RNA helicase DDX3X binding target) in 20 mM Tris, 150 mM NaCl, 10% (v/v) glycerol, 1 mM TCEP, pH 8 were collected on the SAXS/WAXS beam line at the Australian Synchrotron (Melbourne, Australia) using a Pilatus 1M detector at a sample-detector distance of 1.4 m and at a wavelength of λ = 0.103 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 50.00 μl sample at 10 mg/ml was injected at a 0.30 ml/min flow rate onto a GE Superdex 200 5/150 column at 16°C. 31 successive 1 second frames were collected through the sample SEC elution peak. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

15 nucleotide RNA duplex (ATP-dependent RNA helicase DDX3X binding target)
Mol. type   RNA
Olig. state   Dimer
Mon. MW   4.8 kDa
Sequence   FASTA