Integrated structural model of the palladin-actin complex using XL-MS, docking, and SAXS

Rachel Sargent.

SASDVD6 – The Ig-like C2-type 4 domain (Ig4WT) of Palladin

Palladin
MWexperimental 10 kDa
MWexpected 12 kDa
VPorod 18 nm3
log I(s) 3.82×10-3 3.82×10-4 3.82×10-5 3.82×10-6
Palladin small angle scattering data  s, nm-1
ln I(s)
Palladin Guinier plot ln 3.82×10-3 Rg: 1.7 nm 0 (1.7 nm)-2 s2
(sRg)2I(s)/I(0)
Palladin Kratky plot 1.104 0 √3 sRg
p(r)
Palladin pair distance distribution function Rg: 1.8 nm 0 Dmax: 6.8 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Palladin SASREF model
log I(s)
 s, nm-1
Palladin SASREF model
Synchrotron SAXS data from solutions of the Ig-like C2-type 4 domain (Ig4WT) of palladin in 20 mM HEPES pH 7.4, 1 mM DTT, 100 mM NaCl were collected on the BL4-2 beam line at the Stanford Synchrotron Radiation Lightsource (SSRL; Menlo Park, CA, USA) using a Rayonix MX225-HE detector at a sample-detector distance of 1.2 m and at a wavelength of λ = 0.113 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.5 and 10 mg/ml were measured at 20°C. 12 successive 1 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 concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.

NOTE: Amino acid sequence discrepancies are noted between on aligning the model and the submitted amino acid sequence.

Palladin (Ig4WT)
Mol. type   Protein
Organism   Mus musculus
Olig. state   Monomer
Mon. MW   11.8 kDa
 
UniProt   Q9ET54 (1154-1257)
Sequence   FASTA