Research Spotlight

2.0 Å cryo-EM structure of the 55 kDa nucleoplasmin domain of AtFKBP53

Journal of Structural Biology| 20 April 2025:108203| https://doi.org/10.1016/j.jsb.2025.108203

Nikhil Bharambe^*, Ketul Saharan^*, Dileep Vasudevan^#, Sandip Basak^#
(^*Co-first authors; ^#Co-corresponding authors)

ABSTRACT

The knowledge of three-dimensional structures of biological macromolecules is crucial for understanding the molecular mechanisms underlying disease pathology and for devising drugs targeting specific molecules. Single particle cryo-electron microscopy (Cryo-EM) has become indispensable for this purpose, particularly for large macromolecules and their complexes. However, its effectiveness has been limited in achieving near-atomic resolution for smaller macromolecules. This study presents the Cryo-EM structure of a 55 kDa pentameric AtFKBP53 nucleoplasmin domain at 2.0 Å nominal resolution. Our approach involves selecting the optimal grid for data collection and precise alignment of small particles to enhance the resolution of the final 3D reconstructed map. In this study, we systematically processed cryo-EM dataset of a small molecule to improve alignment, and this data processing strategy can be used as a guidance to process the cryo-EM data of other small molecules.