Structure of Dimeric and Tetrameric Complexes of the BAR Domain Protein PICK1 Determined by Small-Angle X-Ray Scattering.

Karlsen ML, Thorsen TS, Johner N, Ammendrup-Johnsen I, Erlendsson S, Tian X, Simonsen JB, Høiberg-Nielsen R, Christensen NM, Khelashvili G, Streicher W, Teilum K, Vestergaard B, Weinstein H, Gether U, Arleth L, Madsen KL, Structure 23(7):1258-1270 (2015) Europe PMC

SASDAB8 – Protein Interacting with C-kinase 1 (PICK1) LKV, dimer contribution (data decomposition).

PRKCA-binding protein
MWI(0) 92 kDa
MWexpected 93 kDa
VPorod 205 nm3
log I(s) 1.07×100 1.07×10-1 1.07×10-2 1.07×10-3
PRKCA-binding protein small angle scattering data  s, nm-1
ln I(s)
PRKCA-binding protein Guinier plot ln 1.07×100 Rg: 6.0 nm 0 (6.0 nm)-2 s2
(sRg)2I(s)/I(0)
PRKCA-binding protein Kratky plot 1.104 0 3 sRg
p(r)
PRKCA-binding protein pair distance distribution function Rg: 6.0 nm 0 Dmax: 20 nm

Data validation


Fits and models


log I(s)
 s, nm-1
Protein Interacting with C-kinase 1 (PICK1) LKV, dimer contribution (data decomposition). Rg histogram Rg, nm
PRKCA-binding protein EOM/RANCH model
PRKCA-binding protein EOM/RANCH model
PRKCA-binding protein EOM/RANCH model

Synchrotron SAXS data from solutions of Protein Interacting with C-kinase 1 (PICK1) LKV, dimer contribution (data decomposition). in 50 mM Tris 125 mM NaCl 0.01 vol% reduced TX-100, pH 7.4 were collected on the EMBL X33 beam line at the DORIS III, DESY storage ring (Hamburg, Germany) using a MAR 345 Image Plate detector (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 4.2 and 8.8 mg/ml were measured at 4°C. Four successive 40 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.

Structure and flexibility of PICK1 LKV mutant dimer was characterized by SAXS using data obtained by decomposing scattering from two polydisperse samples into dimer (and tetramer) contributions. To obtain the dimer scattering, two samples were measured at 4.4 and 8,8 mg/ml, and decomposed as described in the reference. Models were fitted to data using a combination of rigid body modelling and EOM, based on structural components defined by NMR and MD simulations. PDB files represent structures found in the optimal ensemble. All data, in addition to that displayed for this entry, are available in the .zip archive.

Tags: X33
PRKCA-binding protein
Mol. type   Protein
Organism   Rattus norvegicus
Olig. state   Dimer
Mon. MW   46.5 kDa
 
UniProt   Q9EP80 (2-416)
Sequence   FASTA