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Production, Crystallization, and Structure Determination of the IKK-binding Domain of NEMO

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Nickel Binding to the c-Src SH3 Domain Facilitates Crystallization.

Xander Calicdan¹, Oriana S Fisher², Byung Hak Ha³

¹Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.

Protein and Peptide Letters

|October 15, 2025

Summary

Nickel ions mediate a unique crystal structure of the c-Src SH3 domain, revealing novel metal-binding interactions at the N-terminus. This metal-mediated crystallization offers new avenues for structural studies.

Keywords:

SH3 domain anomalous signal c-Src tyrosine kinase crystal structure dimerization.nickel coordination

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Area of Science:

Structural Biology
Protein Crystallography
Biochemistry

Background:

The c-Src SH3 domain is crucial for cell signaling, with numerous X-ray crystal structures available.
Existing structures show variability in crystal contacts and crystallization conditions.

Purpose of the Study:

To explore novel crystallization methods for the c-Src SH3 domain.
To investigate metal-mediated crystal formation and binding interactions.

Main Methods:

Crystallization of the c-Src SH3 domain using a buffer containing nickel chloride (NiCl2).
Determination of the crystal structure using X-ray diffraction to 1.45 Å resolution.
Analysis of crystal packing and anomalous scattering to identify nickel ion coordination.

Main Results:

A unique trigonal crystal form (space group H32) of the c-Src SH3 domain was obtained.
Two ordered nickel ions mediated crystal packing, forming a 2:2 stoichiometry.
Nickel coordination involved the N-terminal sequence, a surface histidine, and water molecules, dimerizing SH3 monomers.

Conclusions:

This study demonstrates metal-mediated crystallization and N-terminal metal binding in proteins.
The findings contrast with known Amino-Terminal Copper and Nickel Binding (ATCUN) motifs.
This approach expands possibilities for future crystallography studies of the c-Src SH3 domain.