Molecular insights on CALX-CBD12 inter-domain dynamics from MD simulations, RDCs and SAXS.

de Souza Degenhardt MF, Vitale PAM, Abiko LA, Zacharias M, Sattler M, Oliveira CLP, Salinas RK, Biophys J (2021) Europe PMC

SASDL36 – CBD12 of CALX1.1 in the calcium-bound state

AT07459p
MWI(0) 33 kDa
MWexpected 30 kDa
VPorod 40 nm3
log I(s) 1.12×10-1 1.12×10-2 1.12×10-3 1.12×10-4
AT07459p small angle scattering data  s, nm-1
ln I(s)
AT07459p Guinier plot ln 1.12×10-1 Rg: 2.7 nm 0 (2.7 nm)-2 s2
(sRg)2I(s)/I(0)
AT07459p Kratky plot 1.104 0 √3 sRg
p(r)
AT07459p pair distance distribution function Rg: 2.9 nm 0 Dmax: 9.3 nm

Data validation

Fits and models

log I(s)
 s, nm-1
CBD12 of CALX1.1 in the calcium-bound state Rg histogram Rg, nm
AT07459p MOLECULAR DYNAMICS FRAME model
log I(s)
 s, nm-1
AT07459p DAMFILT model
log I(s)
 s, nm-1
AT07459p PDB (PROTEIN DATA BANK) model
SAXS data from solutions of CBD12 of CALX1.1 in the calcium-bound state in 20 mM Tris, 5 mM β-mercaptoethanol, 200 mM NaCl, 1% v/v glycerol, 0.8 mM CaCl2, pH 7.4 were collected using a Xenocs-Xeuss instrument (Institute of Physics, University of São Paulo, Brazil) equipped with a Pilatus detector at a sample-detector distance of 0.8 m and at a wavelength of λ = 0.15418 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 5.25 mg/ml was measured at 24°C. 24 successive 1800 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.

AT07459p (CBD12)
Mol. type   Protein
Organism   Drosophila melanogaster
Olig. state   Monomer
Mon. MW   29.9 kDa
 
UniProt   Q9VDG5 (442-697)
Sequence   FASTA
 
PDB ID   3RB5