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DOE OSTI · 3675662

Nickel Binding to the c-Src SH3 Domain Facilitates Crystallization

Calicdan, Xander (ORCID:0009000954405955)·Fisher, Oriana (ORCID:0000000332150831)·Ha, Byung (ORCID:0000000165940835)·Boggon, Titus (ORCID:0000000328621637)·Stiegler, Amy (ORCID:0000000304536104)
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Abstract

Introduction: Numerous X-ray crystal structures of the c-Src SH3 domain have provideda large sampling of atomic-level information for this important signaling domain. Multiple crystalforms have been reported, with variable crystal lattice contacts and chemical crystallizationconditions. Materials and Methods: We crystallized the c-Src SH3 domain in a crystallization buffercontaining NiCl2. Results: A unique crystal structure of the Src SH3 domain in the trigonal space group H32 isdetermined to 1.45 Å resolution. Crystal packing and anomalous scattering reveal that this crystalform is mediated by two ordered nickel ions provided by the crystallization buffer. Nickelcoordination occurs in a 2:2 stoichiometry, which dimerizes two SH3 domain monomers across apseudo-twofold rotation axis and involves the native N-terminal c-Src SH3 amino acid sequence, asurface-exposed histidine residue, and ordered water molecules. Discussion: This study provides an example of metal-mediated crystallization and metal binding byN-terminal protein residues, contrasting with the Amino-Terminal Copper and Nickel Binding(ATCUN) motif. Conclusion: Alternative avenues help widen the potential for future crystallography-based studiesof the c-Src SH3 domain.

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Calicdan, Xander (ORCID:0009000954405955), Fisher, Oriana (ORCID:0000000332150831), Ha, Byung (ORCID:0000000165940835), Boggon, Titus (ORCID:0000000328621637), Stiegler, Amy (ORCID:0000000304536104). 2025-09-01. Nickel Binding to the c-Src SH3 Domain Facilitates Crystallization. https://doi.org/10.2174/0109298665417324250929120040

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