Cryo-EM structure of human type-3 inositol triphosphate receptor reveals the presence of a self-binding peptide that acts as an antagonist

Abstract

Calcium-mediated signaling through inositol 1,4,5-triphosphate receptors (IP3Rs) is essential for the regulation of numerous physiological processes, including fertilization, muscle contraction, apoptosis, secretion, and synaptic plasticity. Deregulation of IP3Rs leads to pathological calcium signaling and is implicated in many common diseases, including cancer and neurodegenerative, autoimmune, and metabolic diseases. Revealing the mechanism of activation and inhibition of this ion channel will be critical to an improved understanding of the biological processes that are controlled by IP3Rs. Here, we report structural findings of the human type-3 IP3R (IP3R-3) obtained by cryo-EM (at an overall resolution of 3.8 Å), revealing an unanticipated regulatory mechanism where a loop distantly located in the primary sequence occupies the IP3-binding site and competitively inhibits IP3 binding. We propose that this inhibitory mechanism must differ qualitatively among IP3R subtypes because of their diverse loop sequences, potentially serving as a key molecular determinant of subtype-specific calcium signaling in IP3Rs. In summary, our structural characterization of human IP3R-3 provides critical insights into the mechanistic function of IP3Rs and into subtype-specific regulation of these important calcium-regulatory channels.

Cryo-EM structure of type 1 IP3R channel in a lipid bilayer

“…This domain-swapped arrangement is likely made possible by the relatively long lateral TM4-5 helix. Notably, the cryo-EM density maps of IP 3 R1 solved in this study are of higher quality than any of the IP 3 R structures reported to date [4][5][6][7] . The improved density features were observed throughout the entire channel protein, and most of the protein domains exhibit wellresolved side-chain densities (Supplementary Figs.…”

“…The improved density features were observed throughout the entire channel protein, and most of the protein domains exhibit wellresolved side-chain densities (Supplementary Figs. 3 and 4) to allow for unambiguous building of atomic models for~83% of the protein, including additional structural elements in the TM region that were not previously resolved (see "Methods" section; Supplementary Table 1) [4][5][6][7] . Both IP 3 R1-ND and IP 3 R1-LMNG structures showed the additional protein densities at the lumenal vestibule that were discerned as two antiparallel, membraneassociated (MA) helices, MA1 and MA2, that form a membraneembedded helix-loop-helix structure comprising residues P2307-G2349 (Fig.…”

“…To understand how IP 3 R channels convey their gating through the interplay of its two primary agonists, IP 3 and Ca 2+ , structures of IP 3 Rs in both the apo-and ligand-bound states have been determined at nearatomic resolutions by single-particle electron cryo-microscopy (cryo-EM). These structures were determined in a detergentbased aqueous environment, allowing for channel solubility [4][5][6][7] . However, ion channels reside in biological membranes, and lipids are proven to play important physiological roles in maintaining their structural-functional integrity.…”

Dominant mutations in ITPR3 cause Charcot‐Marie‐Tooth disease

“…2A). We assessed the affected residues using published IP 3 R structures 24‐26 . p.Val615 is located in the armadillo repeat domain (ARM1), just after the IP 3 ‐binding domain (running from aa 1 to ~ aa 600).…”

“…We assessed the affected residues using published IP 3 R structures. [24][25][26] p.Val615 is located in the armadillo repeat domain (ARM1), just after the IP 3 -binding domain (running from aa 1 to~aa 600). p.Arg2524 is located in the transmembrane domain (TMD) and lies in the channel pore (Fig.…”