Most don't know about CryoEM. To bring more of an awareness of this technique I'm happy to share experimentally solved maps with their corresponding EMDB ID, paper abstract, and reference. Once this list is complete, I'll then move onto summarizing findings, explaining the impact of each entry, and finally composing the content to be prepared as paper-back. Work in progress! # Senses & Perception ## Low-Light Vision: EMD-13485 ![[emd_13485_rawmap.map_xmax.jpeg]] ![[emd_13485_rawmap.map_ymax.jpeg]] ![[emd_13485_rawmap.map_zmax.jpeg]] Many organisms sense light using rhodopsins, photoreceptive proteins containing a retinal chromophore. Here we report the discovery, structure and biophysical characterization of bestrhodopsins, a microbial rhodopsin subfamily from marine unicellular algae, in which one rhodopsin domain of eight transmembrane helices or, more often, two such domains in tandem, are C-terminally fused to a bestrophin channel. Cryo-EM analysis of a rhodopsin-rhodopsin-bestrophin fusion revealed that it forms a pentameric megacomplex (~700 kDa) with five rhodopsin pseudodimers surrounding the channel in the center. Bestrhodopsins are metastable and undergo photoconversion between red- and green-absorbing or green- and UVA-absorbing forms in the different variants. The retinal chromophore, in a unique binding pocket, photoisomerizes from all-trans to 11-cis form. Heterologously expressed bestrhodopsin behaves as a light-modulated anion channel. > **Rozenberg A, Kaczmarczyk I, Matzov D, Vierock J, Nagata T, Sugiura M, Katayama K, Kawasaki Y, Konno M, Nagasaka Y, Aoyama M. Rhodopsin-bestrophin fusion proteins from unicellular algae form gigantic pentameric ion channels. Nature structural & molecular biology. 2022 Jun;29(6):592-603.** ## Smell: EMD-7352 ![[emd_7352.map_xmax.jpeg]] ![[emd_7352.map_ymax.jpeg]] ![[emd_7352.map_zmax.jpeg]] The olfactory system must recognize and discriminate amongst an enormous variety of chemicals in the environment. To contend with such diversity, insects have evolved a family of odorant-gated ion channels comprised of a highly conserved co-receptor (Orco) and a divergent odorant receptor (OR) that confers chemical specificity. Here, we present the single-particle cryo-electron microscopy structure of an Orco homomer from the parasitic fig wasp Apocrypta bakeri at 3.5 Å resolution, providing structural insight into this receptor family. Orco possesses a novel channel architecture, with four subunits symmetrically arranged around a central pore that diverges into four lateral conduits that open to the cytosol. The Orco tetramer has few inter-subunit interactions within the membrane and is bound together by a small cytoplasmic anchor domain. The minimal sequence conservation among ORs maps largely to the pore and anchor domain, shedding light on how the architecture of this receptor family accommodates its remarkable sequence diversity and facilitates the evolution of odour tuning.The olfactory system must recognize and discriminate amongst an enormous variety of chemicals in the environment. To contend with such diversity, insects have evolved a family of odorant-gated ion channels comprised of a highly conserved co-receptor (Orco) and a divergent odorant receptor (OR) that confers chemical specificity. Here, we present the single-particle cryo-electron microscopy structure of an Orco homomer from the parasitic fig wasp Apocrypta bakeri at 3.5 Å resolution, providing structural insight into this receptor family. Orco possesses a novel channel architecture, with four subunits symmetrically arranged around a central pore that diverges into four lateral conduits that open to the cytosol. The Orco tetramer has few inter-subunit interactions within the membrane and is bound together by a small cytoplasmic anchor domain. The minimal sequence conservation among ORs maps largely to the pore and anchor domain, shedding light on how the architecture of this receptor family accommodates its remarkable sequence diversity and facilitates the evolution of odour tuning. > **Butterwick JA, Del Mármol J, Kim KH, Kahlson MA, Rogow JA, Walz T, Ruta V. Cryo-EM structure of the insect olfactory receptor Orco. Nature. 2018 Aug 23;560(7719):447-52.** ## Sweet: EMD-64484 ![[emd_64484_rawmap.map_xprojection.jpeg]] ![[emd_64484_rawmap.map_yprojection.jpeg]] ![[emd_64484_rawmap.map_zprojection.jpeg]] Sweet taste perception influences dietary choices and metabolic health. The human sweet taste receptor, a class C G-protein-coupled receptor (GPCR) heterodimer composed of TAS1R2 and TAS1R3 (refs. 1,2), senses a wide range of sweet compounds-including natural sugars, artificial sweeteners and sweet proteins-and affects metabolic regulation beyond taste. However, the lack of three-dimensional structures hinders our understanding of its precise working mechanism. Here we present cryo-electron microscopy structures of the full-length human sweet taste receptor in apo and sucralose-bound states. These structures reveal a distinct asymmetric heterodimer architecture, with sucralose binding exclusively to the Venus flytrap domain of TAS1R2. Combining mutagenesis and molecular dynamics simulations, this work delineates the sweetener-recognition modes in TAS1R2. Structural comparisons further uncover conformational changes upon ligand binding and a unique activation mechanism. These findings illuminate the signal transduction mechanisms of chemosensory receptors in the class C GPCR family and provide the molecular basis for the design of a new generation of sweeteners. > **Shi Z, Xu W, Wu L, Yue X, Liu S, Ding W, Zhang J, Meng B, Zhao L, Liu X, Liu J. Structural and functional characterization of human sweet taste receptor. Nature. 2025 Jun 24:1-3.** ## Bitter: EMD-33365 ![[emd_33365_rawmap.map_xprojection.jpeg]] ![[emd_33365_rawmap.map_yprojection.jpeg]] ![[emd_33365_rawmap.map_zprojection.jpeg]] Taste sensing is a sophisticated chemosensory process, and bitter taste perception is mediated by type 2 taste receptors (TAS2Rs), or class T G protein-coupled receptors. Understanding the detailed molecular mechanisms behind taste sensation is hindered by a lack of experimental receptor structures. Here, we report the cryo-electron microscopy structures of human TAS2R46 complexed with chimeric mini-G protein gustducin, in both strychnine-bound and apo forms. Several features of TAS2R46 are disclosed, including distinct receptor structures that compare with known GPCRs, a new "toggle switch," activation-related motifs, and precoupling with mini-G protein gustducin. Furthermore, the dynamic extracellular and more-static intracellular parts of TAS2R46 suggest possible diverse ligand-recognition and activation processes. This study provides a basis for further exploration of other bitter taste receptors and their therapeutic applications. > **Xu W, Wu L, Liu S, Liu X, Zhou C, Zhang J, Fu Y, Guo Y, Wu Y, Tan Q, Wang L. Structural basis for strychnine activation of human bitter taste receptor TAS2R46. Science. 2022 Sep 16;377(6612):1298-304.** ## Sour: EMD-9360 ![[emd_9360.map_xstd.jpeg]] ![[emd_9360.map_ystd.jpeg]] ![[emd_9360.map_zstd.jpeg]] Otopetrins (Otop1-Otop3) comprise one of two known eukaryotic proton-selective channel families. Otop1 is required for otoconia formation and a candidate mammalian sour taste receptor. Here we report cryo-EM structures of zebrafish Otop1 and chicken Otop3 in lipid nanodiscs. The structures reveal a dimeric architecture, with each subunit forming 12 transmembrane helices divided into structurally similar amino (N) and carboxy (C) domains. Cholesterol-like molecules occupy various sites in Otop1 and Otop3 and occlude a central tunnel. In molecular dynamics simulations, hydrophilic vestibules formed by the N and C domains and in the intrasubunit interface between N and C domains form conduits for water entry into the membrane core, suggesting three potential proton conduction pathways. By mutagenesis, we tested the roles of charged residues in each putative permeation pathway. Our results provide a structural basis for understanding selective proton permeation and gating of this conserved family of proton channels. > **Saotome K, Teng B, Tsui CC, Lee WH, Tu YH, Kaplan JP, Sansom MS, Liman ER, Ward AB. Structures of the otopetrin proton channels Otop1 and Otop3. Nature structural & molecular biology. 2019 Jun;26(6):518-25.** ## Taste Complexity: EMD-61204 ![[emd_61204_rawmap.map_xprojection.jpeg]] ![[emd_61204_rawmap.map_yprojection.jpeg]] ![[emd_61204_rawmap.map_zprojection.jpeg]] Taste is a key element for food palatability and is strongly influenced by the five basic tastes and other taste sensations, such as fatty orosensation, and koku perception, which indicates taste complexity, mouthfulness and lastingness. This study focuses on the taste modifier γ-glutamyl-valyl-glycine (γ-EVG), a potent kokumi substance that enhances taste and koku perception by modulating the calcium-sensing receptor (CaSR). We used cryo-electron microscopy to determine the structure of the CaSR/γ-EVG complex at a resolution of 3.55 Å. Structural analysis revealed important interactions between γ-EVG and the CaSR, involving key residues, such as Pro39, Phe42, Arg66, Ser147, and Glu297. Mutagenesis experiments demonstrated the importance of these residues in peptide binding. Each γ-EVG residue contributed to its binding to the orthosteric ligand binding site of the CaSR. These findings elucidate the molecular basis of kokumi peptide recognition by the CaSR and contribute to a better understanding of positive allosteric modulators of the CaSR. In addition, this research provides valuable insights into the functionality of class C G-protein-coupled receptors in taste perception, potentially informing the development of new taste modifiers and advancing the field of food science. > **Yamaguchi H, Kitajima S, Suzuki H, Suzuki S, Nishikawa K, Kamegawa A, Fujiyoshi Y, Takahashi K, Tagami U, Maruyama Y, Kuroda M. Cryo-EM structure of the calcium-sensing receptor complexed with the kokumi substance γ-glutamyl-valyl-glycine. Scientific Reports. 2025 Jan 31;15(1):3894.** ## Hunger: EMD-63421 ![[emd_63421_rawmap.map_xprojection.jpeg]] ![[emd_63421_rawmap.map_yprojection.jpeg]] ![[emd_63421_rawmap.map_zprojection.jpeg]] Mammalian cells regulate growth by integrating environmental cues through the mammalian target of rapamycin complex 1 (mTORC1) signaling pathway. The human GATOR2 complex, comprising WDR59, WDR24, Mios, Sec13, and Seh1l, is key to mTORC1 regulation. Under amino acid deprivation, GATOR2 is inhibited through interactions with cytosolic leucine sensor Sestrin2 and arginine sensor cytosolic arginine sensor for mTORC1 subunit 1 (CASTOR1). Amino acid abundance relieves this inhibition, allowing GATOR2 to antagonize the repressor GATOR1. Despite its importance, GATOR2's inhibition mechanisms were unclear. Here, we present cryo-electron microscopy (cryo-EM) structures of GATOR2 in three inhibitory states: CASTOR1 bound, Sestrin2 bound, and dual bound. CASTOR1 engages the Mios WD40 β-propellers, while Sestrin2 interacts with the WDR24-Seh1l subcomplex, inducing conformational movements. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) reveals dynamic motions in apo-GATOR2 and its complexes with amino acid sensors, as well as the effects of amino acid supplementation. These findings unravel the interactions between GATOR2 and amino acid sensors, providing a perspective on the regulation of the mTORC1 pathway by nutrient-sensing machinery. > **Su MY, Teng F, Wang S, Mai X, Zeng H, Li J, Song X, Wang X, Stjepanovic G. Cryo-EM structures of amino acid sensors bound to the human GATOR2 complex. Cell Reports. 2025 Aug 26;44(8).** ## Thirst: ## Nausea: EMD-7883 ![[emd_7883.map_xmax.jpeg]] ![[emd_7883.map_ymax.jpeg]] ![[emd_7883.map_zmax.jpeg]] The 5-HT3A serotonin receptor, a cationic pentameric ligand-gated ion channel (pLGIC), is the clinical target for management of nausea and vomiting associated with radiation and chemotherapies2. Upon binding, serotonin induces a global conformational change that encompasses the ligand-binding extracellular domain (ECD), the transmembrane domain (TMD) and the intracellular domain (ICD), the molecular details of which are unclear. Here we present two serotonin-bound structures of the full-length 5-HT3A receptor in distinct conformations at 3.32 Å and 3.89 Å resolution that reveal the mechanism underlying channel activation. In comparison to the apo 5-HT3A receptor, serotonin-bound states underwent a large twisting motion in the ECD and TMD, leading to the opening of a 165 Å permeation pathway. Notably, this motion results in the creation of lateral portals for ion permeation at the interface of the TMD and ICD. Combined with molecular dynamics simulations, these structures provide novel insights into conformational coupling across domains and functional modulation. > **Basak S, Gicheru Y, Rao S, Sansom MS, Chakrapani S. Cryo-EM reveals two distinct serotonin-bound conformations of full-length 5-HT3A receptor. Nature. 2018 Nov 8;563(7730):270-4.** ## Hearing & Balance: EMD-26741 ![[emd_26741.map_xprojection.jpeg]] ![[emd_26741.map_yprojection.jpeg]] ![[emd_26741.map_zprojection.jpeg]] The initial step in the sensory transduction pathway underpinning hearing and balance in mammals involves the conversion of force into the gating of a mechanosensory transduction channel1. Despite the profound socioeconomic impacts of hearing disorders and the fundamental biological significance of understanding mechanosensory transduction, the composition, structure and mechanism of the mechanosensory transduction complex have remained poorly characterized. Here we report the single-particle cryo-electron microscopy structure of the native transmembrane channel-like protein 1 (TMC-1) mechanosensory transduction complex isolated from Caenorhabditis elegans. The two-fold symmetric complex is composed of two copies each of the pore-forming TMC-1 subunit, the calcium-binding protein CALM-1 and the transmembrane inner ear protein TMIE. CALM-1 makes extensive contacts with the cytoplasmic face of the TMC-1 subunits, whereas the single-pass TMIE subunits reside on the periphery of the complex, poised like the handles of an accordion. A subset of complexes additionally includes a single arrestin-like protein, arrestin domain protein (ARRD-6), bound to a CALM-1 subunit. Single-particle reconstructions and molecular dynamics simulations show how the mechanosensory transduction complex deforms the membrane bilayer and suggest crucial roles for lipid-protein interactions in the mechanism by which mechanical force is transduced to ion channel gating. > **Jeong H, Clark S, Goehring A, Dehghani-Ghahnaviyeh S, Rasouli A, Tajkhorshid E, Gouaux E. Structures of the TMC-1 complex illuminate mechanosensory transduction. Nature. 2022 Oct 27;610(7933):796-803.** ## Itch: EMD-36233 ![[emd_36233_rawmap.map_xmax.jpeg]] ![[emd_36233_rawmap.map_ymax.jpeg]] ![[emd_36233_rawmap.map_zmax.jpeg]] MRGPRX1, a Mas-related GPCR (MRGPR), is a key receptor for itch perception and targeting MRGPRX1 may have potential to treat both chronic itch and pain. Here we report cryo-EM structures of the MRGPRX1-Gi1 and MRGPRX1-Gq trimers in complex with two peptide ligands, BAM8-22 and CNF-Tx2. These structures reveal a shallow orthosteric pocket and its conformational plasticity for sensing multiple different peptidic itch allergens. Distinct from MRGPRX2, MRGPRX1 contains a unique pocket feature at the extracellular ends of TM3 and TM4 to accommodate the peptide C-terminal "RF/RY" motif, which could serve as key mechanisms for peptidic allergen recognition. Below the ligand binding pocket, the G6.48XP6.50F6.51G6.52X(2)F/W6.55 motif is essential for the inward tilting of the upper end of TM6 to induce receptor activation. Moreover, structural features inside the ligand pocket and on the cytoplasmic side of MRGPRX1 are identified as key elements for both Gi and Gq signaling. Collectively, our studies provide structural insights into understanding itch sensation, MRGPRX1 activation, and downstream G protein signaling. > **Guo L, Zhang Y, Fang G, Tie L, Zhuang Y, Xue C, Liu Q, Zhang M, Zhu K, You C, Xu P. Ligand recognition and G protein coupling of the human itch receptor MRGPRX1. Nature communications. 2023 Aug 17;14(1):5004.** ## Touch, Pressure & Body Position: EMD-39205 ![[emd_39205.map_xprojection.jpeg]] ![[emd_39205.map_yprojection.jpeg]] ![[emd_39205.map_zprojection.jpeg]] PIEZO channels transmit mechanical force signals to cells, allowing them to make critical decisions during development and in pathophysiological conditions. Their fast/slow inactivation modes have been implicated in mechanopathologies but remain poorly understood. Here, we report several near-atomic resolution cryo-EM structures of fast-inactivating wild-type human PIEZO1 (hPIEZO1) and its slow-inactivating channelopathy mutants with or without its auxiliary subunit MDFIC. Our results suggest that hPIEZO1 has a more flattened and extended architecture than curved mouse PIEZO1 (mPIEZO1). The multi-lipidated MDFIC subunits insert laterally into the hPIEZO1 pore module like mPIEZO1, resulting in a more curved and extended state. Interestingly, the high-resolution structures suggest that the pore lipids, which directly seal the central hydrophobic pore, may be involved in the rapid inactivation of hPIEZO1. While the severe hereditary erythrocytosis mutant R2456H significantly slows down the inactivation of hPIEZO1, the hPIEZO1-R2456H-MDFIC complex shows a more curved and contracted structure with an inner helix twist due to the broken link between the pore lipid and R2456H. These results suggest that the pore lipids may be involved in the mechanopathological rapid inactivation mechanism of PIEZO channels. > **Shan Y, Guo X, Zhang M, Chen M, Li Y, Zhang M, Pei D. Structure of human PIEZO1 and its slow-inactivating channelopathy mutants. Elife. 2025 Jul 16;13:RP101923.** ## Heat, Capsaicin & Cut-Onion Eye Tearing: EMD-23479 ![[emd_23479.map_xprojection.jpeg]] ![[emd_23479.map_yprojection.jpeg]] ![[emd_23479.map_zprojection.jpeg]] Transient receptor potential vanilloid member 1 (TRPV1) is a Ca2+-permeable cation channel that serves as the primary heat and capsaicin sensor in humans. Using cryo-EM, we have determined the structures of apo and capsaicin-bound full-length rat TRPV1 reconstituted into lipid nanodiscs over a range of temperatures. This has allowed us to visualize the noxious heat-induced opening of TRPV1 in the presence of capsaicin. Notably, noxious heat-dependent TRPV1 opening comprises stepwise conformational transitions. Global conformational changes across multiple subdomains of TRPV1 are followed by the rearrangement of the outer pore, leading to gate opening. Solvent-accessible surface area analyses and functional studies suggest that a subset of residues form an interaction network that is directly involved in heat sensing. Our study provides a glimpse of the molecular principles underlying noxious physical and chemical stimuli sensing by TRPV1, which can be extended to other thermal sensing ion channels. > **Kwon DH, Zhang F, Suo Y, Bouvette J, Borgnia MJ, Lee SY. Heat-dependent opening of TRPV1 in the presence of capsaicin. Nature structural & molecular biology. 2021 Jul;28(7):554-63.** ## Cool & Menthol: EMD-20450 ![[emd_20450.map_xprojection.jpeg]] ![[emd_20450.map_yprojection.jpeg]] ![[emd_20450.map_zprojection.jpeg]] Transient receptor potential channel subfamily A member 1 (TRPA1) is a Ca 2+ -permeable cation channel that serves as one of the primary sensors of environmental irritants and noxious substances. Many TRPA1 agonists are electrophiles that are recognized by TRPA1 via covalent bond modifications of specific cysteine residues located in the cytoplasmic domains. However, a mechanistic understanding of electrophile sensing by TRPA1 has been limited due to a lack of high-resolution structural information. Here, we present the cryoelectron microscopy (cryo-EM) structures of nanodisc-reconstituted ligand-free TRPA1 and TRPA1 in complex with the covalent agonists JT010 and BITC at 2.8, 2.9, and 3.1 Å, respectively. Our structural and functional studies provide the molecular basis for electrophile recognition by the extraordinarily reactive C621 in TRPA1 and mechanistic insights into electrophile-dependent conformational changes in TRPA1. This work also provides a platform for future drug development targeting TRPA1. > **Suo Y, Wang Z, Zubcevic L, Hsu AL, He Q, Borgnia MJ, Ji RR, Lee SY. Structural insights into electrophile irritant sensing by the human TRPA1 channel. Neuron. 2020 Mar 4;105(5):882-94.** ## Pain: ## Fatigue: [No CryoEM Map] G-protein-coupled receptors (GPCRs) are essential components of the signalling network throughout the body. To understand the molecular mechanism of G-protein-mediated signalling, solved structures of receptors in inactive conformations and in the active conformation coupled to a G protein are necessary. Here we present the structure of the adenosine A(2A) receptor (A(2A)R) bound to an engineered G protein, mini-Gs, at 3.4 Å resolution. Mini-Gs binds to A(2A)R through an extensive interface (1,048 Å2) that is similar, but not identical, to the interface between Gs and the β2-adrenergic receptor. The transition of the receptor from an agonist-bound active-intermediate state to an active G-protein-bound state is characterized by a 14 Å shift of the cytoplasmic end of transmembrane helix 6 (H6) away from the receptor core, slight changes in the positions of the cytoplasmic ends of H5 and H7 and rotamer changes of the amino acid side chains Arg3.50, Tyr5.58 and Tyr7.53. There are no substantial differences in the extracellular half of the receptor around the ligand binding pocket. The A(2A)R-mini-Gs structure highlights both the diversity and similarity in G-protein coupling to GPCRs and hints at the potential complexity of the molecular basis for G-protein specificity. > **Carpenter B, Nehmé R, Warne T, Leslie AG, Tate CG. Structure of the adenosine A2A receptor bound to an engineered G protein. Nature. 2016 Aug 4;536(7614):104-7.** ## Breathing: ## Learning & Memory: EMD-21535 ![[emd_21535.map_xprojection.jpeg]] ![[emd_21535.map_yprojection.jpeg]] ![[emd_21535.map_zprojection.jpeg]] Calcium/calmodulin-dependent protein kinase II (CaMKII) plays a central role in Ca2+ signaling throughout the body. In the hippocampus, CaMKII is required for learning and memory. Vertebrate genomes encode four CaMKII homologs: CaMKIIα, CaMKIIβ, CaMKIIγ, and CaMKIIδ. All CaMKIIs consist of a kinase domain, a regulatory segment, a variable linker region, and a hub domain, which is responsible for oligomerization. The four proteins differ primarily in linker length and composition because of extensive alternative splicing. Here, we report the heterogeneity of CaMKII transcripts in three complex samples of human hippocampus using deep sequencing. We showed that hippocampal cells contain a diverse collection of over 70 CaMKII transcripts from all four CaMKII-encoding genes. We characterized the Ca2+/CaM sensitivity of hippocampal CaMKII variants spanning a broad range of linker lengths and compositions. The effect of the variable linker on Ca2+/CaM sensitivity depended on the kinase and hub domains. Moreover, we revealed a previously uncharacterized role for the hub domain as an allosteric regulator of kinase activity, which may provide a pharmacological target for modulating CaMKII activity. Using small-angle x-ray scattering and single-particle cryo-electron microscopy (cryo-EM), we present evidence for extensive interactions between the kinase and the hub domains, even in the presence of a 30-residue linker. Together, these data suggest that Ca2+/CaM sensitivity in CaMKII is homolog dependent and includes substantial contributions from the hub domain. Our sequencing approach, combined with biochemistry, provides insights into understanding the complex pool of endogenous CaMKII splice variants. > **Sloutsky R, Dziedzic N, Dunn MJ, Bates RM, Torres-Ocampo AP, Boopathy S, Page B, Weeks JG, Chao LH, Stratton MM. Heterogeneity in human hippocampal CaMKII transcripts reveals allosteric hub-dependent regulation. Science signaling. 2020 Jul 21;13(641):eaaz0240.** # Acute & Chronic Disease # General Species # De Novo