The dual PDZ domain from Postsynaptic density protein 95 forms a scaffold with peptide ligand

Rodzli N, Lockhart-Cairns M, Levy C, Chipperfield J, Bird L, Baldock C, Prince S, Biophysical Journal (2020) DOI

SASDGJ5 – The PDZ1-2 domain of postsynaptic density protein 95 (PSD-95) + glutathione (GSH) (diluted)

PDZ1-2 fragment of PSD-95/Disks large homolog 4
MWexperimental 21 kDa
MWexpected 21 kDa
VPorod 41 nm3
log I(s) 7.10×10-2 7.10×10-3 7.10×10-4 7.10×10-5
PDZ1-2 fragment of PSD-95/Disks large homolog 4 small angle scattering data  s, nm-1
ln I(s)
PDZ1-2 fragment of PSD-95/Disks large homolog 4 Guinier plot ln 7.10×10-2 Rg: 3.1 nm 0 (3.1 nm)-2 s2
(sRg)2I(s)/I(0)
PDZ1-2 fragment of PSD-95/Disks large homolog 4 Kratky plot 1.104 0 √3 sRg
p(r)
PDZ1-2 fragment of PSD-95/Disks large homolog 4 pair distance distribution function Rg: 2.6 nm 0 Dmax: 7.0 nm

Data validation

Fits and models

log I(s)
 s, nm-1
PDZ1-2 fragment of PSD-95/Disks large homolog 4 OTHER model
PDZ1-2 fragment of PSD-95/Disks large homolog 4 OTHER model
PDZ1-2 fragment of PSD-95/Disks large homolog 4 OTHER model
PDZ1-2 fragment of PSD-95/Disks large homolog 4 OTHER model
PDZ1-2 fragment of PSD-95/Disks large homolog 4 OTHER model
PDZ1-2 fragment of PSD-95/Disks large homolog 4 OTHER model
PDZ1-2 fragment of PSD-95/Disks large homolog 4 OTHER model
Synchrotron SAXS data from solutions of the PDZ1-2 domain of postsynaptic density protein 95 (PSD-95) + glutathione (GSH) (diluted) in 20 mM TRIS/HCl, 150 mM NaCl + 16 mM GSH, pH 8.5 were collected on the B21 beam line at the Diamond Light Source storage ring (Didcot, UK) using a Pilatus 2M detector at a sample-detector distance of 3.9 m and at a wavelength of λ = 0.1 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 3.00 mg/ml was measured. 17 successive 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.

Scattering data are fitted using the ATSAS OLIGOMER program using a suite of models. The ATSAS program FFMAKER was used to generate form factors for each model in the suite. Each model is assigned a volume fraction to fit the observed scattering profile. 3 monomer models are included, the first is a compact conformation of PDZ1-2 similar to PDB entries 6spv/6spz; the other two are domain models obtained from a representative run of the ATSAS EOM program with data projected to infinite dilution. Multimeric models are drawn from a "clustering Spacegroup", unit cell 14.8nm symmetry I2(1)3, and consist of identical copies of an extended conformation of PDZ1-2 (similar to PDB entry 3zrt) assembled by symmetry operations. In the order of deposition: Model number; Stoichiometry; MW (kDa); source; Volume fraction. 1; 1; 21; Crystal Structure; 0.069. 2; 1; 21; EOM; 0.085. 3; 1; 21; EOM; 0.537. 4; 2; 42; clustering Spacegroup; 0.199. 5; 4; 84; clustering Spacegroup; 0.034. 6; 8; 168; clustering Spacegroup; 0.077. 7; 12, 252; clustering Spacegroup; 0.000.

PDZ1-2 fragment of PSD-95/Disks large homolog 4 (PDZ1-2)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   20.8 kDa
 
UniProt   P78352 (55-249)
Sequence   FASTA