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

SASDGC5 – The PDZ1-2 domain of postsynaptic density protein 95 (PSD-95) bound to RRESEI peptide (diluted)

PDZ1-2 fragment of PSD-95/Disks large homolog 4
MWexperimental 21 kDa
MWexpected 21 kDa
VPorod 32 nm3
log I(s) 5.29×104 5.29×103 5.29×102 5.29×101
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 5.29×104 Rg: 2.6 nm 0 (2.6 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: 2.9 nm 0 Dmax: 12.4 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
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) bound to RRESEI peptide (diluted) in 20 mM TRIS/HCl, 150 mM NaCl + 5 mM RRESEI, pH 8.5 were collected on the EMBL P12 beam line at the PETRA III storage ring (Hamburg, Germany) using a Pilatus 2M 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 7.50 mg/ml was measured at 15°C. 16 successive 0.050 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.

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; 0.315. 2; 1; 21; EOM; 0.185. 3; 1; 21; EOM; 0.455. 4; 2; 42; clustering Spacegroup; 0.000. 5; 4; 84; clustering Spacegroup; 0.019. 6; 8; 168; clustering Spacegroup; 0.020. 7; 12, 252; clustering Spacegroup; 0.000. 8; 16, 336, clustering Spacegroup; 0.000. 9; 20, 420, clustering Spacegroup; 0.000. 10; 24, 504, clustering Spacegroup; 0.005.

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