Nickel Binding to the c-Src SH3 Domain Facilitates Crystallization

TL;DR

This paper shows how nickel ions help crystallize the c-Src SH3 domain, revealing a new structural arrangement and binding mechanism.

Contribution

The study demonstrates nickel-mediated crystallization and a novel metal-binding mechanism involving N-terminal residues.

Findings

Nickel ions in the crystallization buffer facilitated the formation of a unique trigonal crystal structure.

Nickel coordination in a 2:2 stoichiometry dimerizes SH3 domain monomers via a pseudo-twofold rotation axis.

The nickel binding involves the N-terminal sequence, a histidine residue, and water molecules.

Abstract

Numerous X-ray crystal structures of the c-Src SH3 domain have provided a large sampling of atomic-level information for this important signaling domain. Multiple crystal forms have been reported, with variable crystal lattice contacts and chemical crystallization conditions.

We crystallized the c-Src SH3 domain in a crystallization buffer containing NiCl2.

A unique crystal structure of the Src SH3 domain in the trigonal space group H32 is determined to 1.45 Å resolution. Crystal packing and anomalous scattering reveal that this crystal form is mediated by two ordered nickel ions provided by the crystallization buffer. Nickel coordination occurs in a 2:2 stoichiometry, which dimerizes two SH3 domain monomers across a pseudo-twofold rotation axis and involves the native N-terminal c-Src SH3 amino acid sequence, a surface-exposed histidine residue, and ordered water molecules.

This study provides an example of metal-mediated crystallization and metal binding by N-terminal protein residues, contrasting with the Amino-Terminal Copper and Nickel Binding (ATCUN) motif.

Alternative avenues help widen the potential for future crystallography-based studies of the c-Src SH3 domain.

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