Modulation of the substrate specificity of the kinase PDK1 by distinct conformations of the full-length protein

Sacerdoti M, Gross L, Riley A, Zehnder K, Ghode A, Klinke S, Anand G, Paris K, Winkel A, Herbrand A, Godage H, Cozier G, Süß E, Schulze J, Pastor-Flores D, Bollini M, Cappellari M, Svergun D, Gräwert M, Aramendia P, Leroux A, Potter B, Camacho C, Biondi R, Science Signaling 16(789) (2023) DOI

SASDNL5 – Double mutant catalytic domain of 3-phosphoinositide-dependent protein kinase 1 (PDK1 50–359; Y188G Q292A)

3-phosphoinositide-dependent protein kinase 1 (Y188G Q292A)
MWexperimental 32 kDa
MWexpected 35 kDa
VPorod 57 nm3
log I(s) 1.76×103 1.76×102 1.76×101 1.76×100
3-phosphoinositide-dependent protein kinase 1 (Y188G Q292A) small angle scattering data  s, nm-1
ln I(s)
3-phosphoinositide-dependent protein kinase 1 (Y188G Q292A) Guinier plot ln 1.77×103 Rg: 2.4 nm 0 (2.4 nm)-2 s2
(sRg)2I(s)/I(0)
3-phosphoinositide-dependent protein kinase 1 (Y188G Q292A) Kratky plot 1.104 0 3 sRg
p(r)
3-phosphoinositide-dependent protein kinase 1 (Y188G Q292A) pair distance distribution function Rg: 2.3 nm 0 Dmax: 7 nm

Data validation


Fits and models


log I(s)
 s, nm-1
3-phosphoinositide-dependent protein kinase 1 (Y188G Q292A) SREFLEX model

log I(s)
 s, nm-1
3-phosphoinositide-dependent protein kinase 1 (Y188G Q292A) DAMMIF model

log I(s)
 s, nm-1
3-phosphoinositide-dependent protein kinase 1 (Y188G Q292A) DAMMIF model

Synchrotron SAXS data from solutions of the double mutant catalytic domain of PDK1 in 20 mM Tris-HCl pH 7.4, 250 mM NaCl, 1 mM DTT, were collected on the EMBL P12 beam line at PETRA III (DESY; Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 2.00 mg/ml was measured at 20°C. Five successive 0.100 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.

3-phosphoinositide-dependent protein kinase 1 (Y188G Q292A) (PDK1-CD dm)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   35.3 kDa
 
UniProt   O15530 (50-359)
Sequence   FASTA