Crystallographic home-source X-ray data for theatomic-resolution experimental phasing of theShank3 SH3 domain structure frompseudomerohedrally twinned crystals

Abstract By far most macromolecular crystallographic data collection and experimental phasing is nowadays carried out using synchrotron radiation. Here, we present two crystallographic datasets collected on a home-source X-ray diffractometer, which can per se be use to experimentally solve the atomic-resolution crystal structure of the Src homology 3(SH3)-like domain from the postsynaptic protein Shank3. The refined structure was described in the article “Structure of an unconventional SH3 domain from the postsynaptic density protein Shank3 at ultrahigh resolution” (Ponna et al., 2017) [1]. Crystals of the Shank3 SH3 domain were derivatized through soaking in 1 M sodium iodide prior to diffraction data collection at a wavelength of 1.54 Å. High-resolution data are reported for a native crystal to 1.01 Å and an iodide-derivatized one to 1.60 Å. The crystals suffered from several anomalies affecting experimental phasing: a high fraction (34–40%) of pseudomerohedral twinning, significant pseudotranslational symmetry (> 15%) with the operator 0.5,0,0.5, and a low solvent content. Twinning with the operator h,-k,-l is made possible by the space group P21 coupled with a unit cell β angle of 90.0°. The data can be used to repeat and optimize derivatization and phasing procedures, to understand halide interactions with protein surfaces, to promote the use of home X-ray sources for protein structure determination, as well as for educational purposes and protocol development

Structural basis for PDZ domain interactions in the post-synaptic density scaffolding protein Shank3

The Shank proteins are crucial scaffolding elements of the post‐synaptic density (PSD). One of the best‐characterized domains in Shank is the PDZ domain, which binds to C‐terminal segments of several other PSD proteins. We carried out a detailed structural analysis of Shank3 PDZ domain‐peptide complexes, to understand determinants of binding affinity towards different ligand proteins. Ligand peptides from four different proteins were cocrystallized with the Shank3 PDZ domain, and binding affinities were determined calorimetrically. In addition to conserved class I interactions between the first and third C‐terminal peptide residue and Shank3, side chain interactions of other residues in the peptide with the PDZ domain are important factors in defining affinity. Structural conservation suggests that the binding specificities of the PDZ domains from different Shanks are similar. Two conserved buried water molecules in PDZ domains may affect correct local folding of ligand recognition determinants. The solution structure of a tandem Shank3 construct containing the SH3 and PDZ domains showed that the two domains are close to each other, which could be of relevance, when recognizing and binding full target proteins. The SH3 domain did not affect the affinity of the PDZ domain towards short target peptides, and the schizophrenia‐linked Shank3 mutation R536W in the linker between the domains had no effect on the structure or peptide interactions of the Shank3 SH3‐PDZ unit. Our data show the spatial arrangement of two adjacent Shank domains and pinpoint affinity determinants for short PDZ domain ligands with limited sequence homology