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Abstract

Introduction

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.

Materials and Methods

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

Results

A unique crystal structure of the Src SH3 domain in the trigonal space group 3 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.

Discussion

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.

Conclusion

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

© 2025 The Author(s). Published by Bentham Science Publishers.
This is an open access article published under CC BY 4.0 https://creativecommons.org/licenses/by/4.0/legalcode
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Nickel Binding to the c-Src SH3 Domain Facilitates Crystallization
Bentham Science Publishers ; https://doi.org/10.2174/0109298665417324250929120040
/content/journals/ppl/10.2174/0109298665417324250929120040
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1. Supplementary Tables, Figures, and Figure Legends file (Calicdan_Stiegler_PPL_submission-supplemen-tary.docx). 2. PDB submission validation report file (Calicdan-Stiegler-PDB-9OFX-Validation-Report.pdf). 3. Expression plasmid map file (Calicdan-Stiegler-hSrc-SH3NH_85-143_pET28a_Map.tiff). 4. Expression plasmid full sequence file (Calicdan-Stiegler-hSrc-SH3NH_85-143_pET28a.txt). Supplementary material is available on the publisher’s website along with the published article.

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  • Article Type:     Research Article
Keywords: c-Src tyrosine kinase ; crystal structure ; dimerization ; SH3 domain ; nickel coordination ; anomalous signal

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