Immunosuppressive Yersinia Effector YopM Binds DEAD Box Helicase DDX3 to Control Ribosomal S6 Kinase in the Nucleus of Host Cells.

Berneking L, Schnapp M, Rumm A, Trasak C, Ruckdeschel K, Alawi M, Grundhoff A, Kikhney AG, Koch-Nolte F, Buck F, Perbandt M, Betzel C, Svergun DI, Hentschke M, Aepfelbacher M, PLoS Pathog 12(6):e1005660 (2016) Europe PMC

SASDAW8 – 2:1 YopM:DDX3 complex

Yersinia outer protein M (34-481)
DEAD box RNA helicase DDX3 (51-418)
MWexperimental 123 kDa
MWexpected 142 kDa
VPorod 190 nm3
log I(s) 7.45×103 7.45×102 7.45×101 7.45×100
Yersinia outer protein M (34-481) DEAD box RNA helicase DDX3 (51-418) small angle scattering data  s, nm-1
ln I(s)
Yersinia outer protein M (34-481) DEAD box RNA helicase DDX3 (51-418) Guinier plot ln 7.46×103 Rg: 4.0 nm 0 (4.0 nm)-2 s2
(sRg)2I(s)/I(0)
Yersinia outer protein M (34-481) DEAD box RNA helicase DDX3 (51-418) Kratky plot 1.104 0 √3 sRg
p(r)
Yersinia outer protein M (34-481) DEAD box RNA helicase DDX3 (51-418) pair distance distribution function Rg: 4.0 nm 0 Dmax: 15 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Yersinia outer protein M (34-481) DEAD box RNA helicase DDX3 (51-418) SASREF model
log I(s)
 s, nm-1
Yersinia outer protein M (34-481) DEAD box RNA helicase DDX3 (51-418) DAMMIF model
Synchrotron SAXS data from solutions of 2:1 YopM:DDX3 complex in 50 mM HEPES 150 mM NaCl, pH 7.5 were collected on the EMBL P12 beam line at the PETRA III storage ring (DESY; Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3.1 m and at a wavelength of λ = 0.12 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.7 and 10.6 mg/ml were measured at 23°C. 20 successive 0.050 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 concentrations were extrapolated to infinite dilution and merged with the higher concentration data to yield the final composite scattering curve.

A complex composed of two YopM_34-481 molecules and one DDX3_51-418

Yersinia outer protein M (34-481) (YopM)
Mol. type   Protein
Organism   Yersinia enterocolitica
Olig. state   Dimer
Mon. MW   50.3 kDa
Sequence   FASTA
 
DEAD box RNA helicase DDX3 (51-418) (DDX3)
Mol. type   Protein
Organism   Yersinia enterocolitica
Olig. state   Monomer
Mon. MW   41.5 kDa