The Primary Information of Ryanodine Receptor
1. Summary
The ryanodine receptors (RyRs) are cation-selective channels that release Ca2+ from an intracellular Ca2+ storing compartment, the endo/sarcoplasmic reticulum, during an action potential in a process known as excitation–contraction coupling [1]. In mammalian organisms, RyRs are found in a wide variety of cell types, including neurons, exocrine cells, epithelial cells, lymphocytes, and many more. They are known mostly for their involvement in excitation-contraction coupling, releasing Ca2+ from the SR and thus driving muscle contraction. Three different isoforms (RyR1,RyR2RyR3) have been found to date. RyR1 is widely expressed in skeletal muscle and was the first one to be cloned. RyR2 is found primarily in the heart, and RyR3 was originally identified in the brain[2], although each isoform is found in many different cell types. They share ∼65% sequence identity, and the largest degree of difference is found in three "divergent regions" throughout the sequence, known as D1 (residues 4254–4631 in RyR1), D2 (residues 1342–1403), and D3 (residues 1872–1923) [3].
Since their purification from muscle tissues, the structures of RyRs have been studied extensively. To date, crystal structures that describe the entire channel structure are not available, but several cryo-EM studies have reached resolutions near 10 Å. These studies agree very well on the overall structure of the receptor [4]. The basic architecture can be described as a mushroom, with a large cap representing ∼80% of the volume located in the cytoplasm and the stalk crossing the membrane into the SR/ER lumen. The transmembrane region measures 120 × 120 × 60 Å, whereas the cytoplasmic area measures ∼270 × 270 × 100 Å. These two major parts are connected via four thick columns. An interesting and important feature is that the RyR cytoplasmic head does not form a rigid block. Instead, there are many solvent-filled cavities and numerous globular masses that may correspond to individual or groups of folded domains. To aid with the structural description of RyRs, several portions have received names, including "clamps," "handles," and a "central rim" that surrounds a central cavity. There has been much debate about the number of transmembrane helices, but the overall consensus now is that there are either six or eight segments per subunit. Five or six of these can be detected in the cryo-EM maps. The inner helices create the pore-forming region, and sequence homology suggests an arrangement similar to various tetrameric ion channel structures [4].
2. Binding Sites
Inhibitor
The anthranilic diamide chlorantraniliprole (CHL) binds to a pocket in the pVSD domain, close to its interface with the CSol domain [5].
Activator
des Georges et al. reported putative binding sites for three major activating ligands, Ca2+, ATP, and caffeine, on a near-atomic resolution structure of RyR1 [6]. They proposed that the Ca2+-binding site is located in the core domain just above the transmembrane domain and consists of several negatively charged residues in the core solenoid (CSol) domain and carboxyl-terminal domain (CTD). Caffeine, a xanthine derivative, is a potent and common activator of all known RyR isoforms and greatly enhances Ca2+ sensitivity of the channel. The putative caffeine-binding site is located just below the Ca2+-binding site and consists of several hydrophobic residues from different domains [7].
3. Target List
| ICDB_Pro ID | Protein Name | Organism | Uniprot Accession Number | Gene Name |
|---|---|---|---|---|
| ICDB_Pro_0023 | Ryanodine receptor 3 | Mus musculus (Mouse) | A2AGL3 | Ryr3 |
| ICDB_Pro_0839 | Ryanodine receptor 3 | Homo sapiens (Human) | Q15413 | RYR3;HBRR |
| ICDB_Pro_1642 | Ryanodine receptor 3 | Oryctolagus cuniculus (Rabbit) | Q9TS33 | RYR3 |