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

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Published on: December 28, 2019

Nickel binding to 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.

Biorxiv : the Preprint Server for Biology

|June 4, 2025

Summary

Researchers discovered a new crystal structure for the Src SH3 domain using nickel ions. This unique metal-mediated dimerization offers an alternative method for Src SH3 domain crystallization.

Keywords:

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

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Published on: January 10, 2018

Area of Science:

Structural biology
Protein crystallography
Biochemistry

Background:

The Src SH3 domain is a crucial signaling module in cellular pathways.
Previous studies have characterized various crystal forms of the Src SH3 domain under different conditions.
Understanding the structural dynamics of SH3 domains is key to deciphering their function.

Purpose of the Study:

To report a novel crystal structure of the Src SH3 domain.
To elucidate the role of nickel ions in mediating crystal formation.
To explore alternative crystallization strategies for the Src SH3 domain.

Main Methods:

X-ray crystallography to determine atomic-level structure.
Analysis of crystal packing and anomalous scattering data.
Characterization of nickel ion coordination and stoichiometry.

Main Results:

A unique crystal structure of the Src SH3 domain was obtained in the trigonal space group H3₂ at 1.45 Å resolution.
Two ordered nickel ions mediated crystal packing through a 2:2 stoichiometry.
Nickel coordination involved the N-terminal sequence, a surface histidine, and water molecules, forming dimers across a pseudo-twofold axis.

Conclusions:

This study presents a novel metal-mediated dimerization mechanism for Src SH3 domain crystallization.
The findings offer an alternative approach to crystallizing the Src SH3 domain, distinct from the ATCUN motif.
This work expands the understanding of protein-metal interactions in crystal engineering.