Cryo-EM reveals the molecular mechanism of IP3 receptor channel opening

By Emily Overway

Research led by co-first authors Emily Schmitz, a graduate student in the Chemical and Physical Biology program, and Hirohide Takahashi, a research instructor in molecular physiology and biophysics, identified the structure of the human type-3 inositol 1,4,5-triphosphate, or IP₃, receptor in several conformations using cryo-electron microscopy. Schmitz and Takahasi, who work in the lab of Erkan Karakas, professor of molecular physiology and biophysics, published their research in March in Nature Communications.

We sat down with Karakas to learn more about the work.

What issue/problem does your research address?

IP₃ receptors receive a diverse array of signals from hormones, growth factors, and neurotransmitters. They also detect changes in metabolic states. IP₃ receptors respond to these signals and modulate downstream activity in all cell types by opening channel gates and allowing calcium to travel from the endoplasmic reticulum lumen to the cytoplasm; IP₃ and Ca²⁺ are necessary for IP₃ receptor activation, which is further potentiated by ATP binding.

There are three types of IP₃ receptors (types 1-3) that are involved in distinct signaling pathways that regulate learning, fertilization, gene expression, and apoptosis. Disruption of IP₃ receptor signaling is associated with several diseases, including cancer, diabetes, and neurological disorders. Recent structural studies revealed IP₃ receptor architecture, but fundamental questions regarding the mechanisms of ligand interactions and channel gating remain mostly unanswered.

What was unique about your approach to the research?

We used extensive screening and data analysis to obtain the structure of the receptor in active conformation, which is a challenging task for IP₃ receptors due to technical difficulties. In this study, we reported cryo-EM structures of the human type-3 IP₃ receptor in multiple gating conformations: IP₃-ATP-bound pre-active state with closed channels, IP₃-ATP-Ca²⁺-bound active state with an open channel, and IP₃-ATP-Ca²⁺-bound inactive state with a closed channel.

What were your findings?

IP₃ receptors are ion channels that open pores through the membrane upon binding of chemical ligands. In this study, we determined the structure of the receptor in multiple functional positions, including one where the channel is open. The structures reveal, at atomic resolution, how IP₃-induced conformational changes prime the receptor for activation by Ca²⁺, how Ca²⁺ binding leads to channel opening, and how ATP modulates the activity, providing insights into longstanding questions regarding the molecular mechanism underpinning receptor activation and gating.

What do you hope will be achieved with the research results in the short and long terms?

This study is fundamental for understanding IP₃ receptor biology. It will serve as a foundation for future experiments addressing biophysical and functional questions related to IP₃ receptors. It may also guide the design of pharmacological tools for targeting this class of proteins.

What are the benefits of this research?

Pathological dysregulation of IP₃ receptors and calcium signaling is implicated in autoimmune, cancer, metabolic, and neurodegenerative diseases, making IP₃ receptors promising targets for treatment of these diseases.

Where is this research taking you next? What will you personally be doing, or how will other researchers build on this work?

IP₃ receptors are protein complexes involved in many physiological processes. Our lab will continue to expand our knowledge of these receptors using structural biology as the primary tool.

Funding

This work was funded by the National Institutes of Health, Vanderbilt University, the Vanderbilt Diabetes and Research Training Center, and the Molecular Biophysics Training Program.

The authors would like to extend special thanks to Dr. Kunpeng Li at Case Western Reserve University; Theo Humphreys at the Pacific Northwest Center for Cryo-EM; and Elad Binshtein, Melissa Chambers, and Scott Collier at Vanderbilt University, all of whom assisted in the work.