The use of cryo-EM and three-dimensional image reconstruction is becoming increasingly common. Our vision for this technique is to provide a straightforward manner in which users can proceed from raw data to a reliable 3D reconstruction through a pipeline that both facilitates management of the processing steps and makes the results at each step more transparent. Tightly integrated with a relational SQL database, Appion is a modular and transparent pipeline that extends existing software applications and procedures. The user manages and controls the software modules via web-based forms, and all results are similarly available using web-based viewers directly linked to the underlying database, enabling even naive users to quickly deduce the quality of their results. The Appion API was designed with the principle that applications should be compatible with a broad range of specimens and that libraries and routines are modular and extensible. Presented here is a description of the design and architecture of the working Appion pipeline prototype and some results of its use.

Solving the structure of macromolecular complexes using transmission electron microscopy can be an arduous task. Many of the steps in this process rely strongly on the aid of pre-existing structural knowledge, and are greatly complicated when this information is unavailable. Here we present two software tools meant to facilitate particle picking, an early stage in the single-particle processing of unknown macromolecules. The first tool, DoG Picker, is an efficient and reasonably general, particle picker based on the Difference of Gaussians (DoG) image transform. It can function alone, as a reference-free particle picker with the unique ability to sort particles based on size, or it can also be used as a way to bootstrap the creation of templates or training datasets for other particle pickers. The second tool is TiltPicker, an interactive graphical interface application designed to streamline the selection of particle pairs from tilted-pair datasets. In many respects, TiltPicker is a reimplementation of the SPIDER WEB tilted-particle picker, but built on modern computer frameworks making it easier to deploy and maintain. The TiltPicker program also includes several useful new features beyond those of its predecessor.

Highlights d The structure of the cardiac sodium channel reveals key functional features d The antiarrhythmic drug flecainide blocks the pore below the selectivity filter d The ion selectivity filter and inactivation gate are revealed in atomic detail d An arrhythmia mutation creates a pathogenic gating pore 2 Å in diameter

Coronavirus particles are enveloped and pleomorphic and are thus refractory to crystallization and symmetry-assisted reconstruction. A novel methodology of single-particle image analysis was applied to selected virus features to obtain a detailed model of the oligomeric state and spatial relationships among viral structural proteins. Two-dimensional images of the S, M, and N structural proteins of severe acute respiratory syndrome coronavirus and two other coronaviruses were refined to a resolution of ϳ4 nm. Proteins near the viral membrane were arranged in overlapping lattices surrounding a disordered core. Trimeric glycoprotein spikes were in register with four underlying ribonucleoprotein densities. However, the spikes were dispensable for ribonucleoprotein lattice formation. The ribonucleoprotein particles displayed coiled shapes when released from the viral membrane. Our results contribute to the understanding of the assembly pathway used by coronaviruses and other pleomorphic viruses and provide the first detailed view of coronavirus ultrastructure.

Acid sensing ion channels (ASICs) are trimeric1, proton-gated2,3 and sodiumselective4,5 members of the epithelial sodium channel/degenerin (ENaC/DEG) superfamily of ion channels6,7 and are expressed throughout vertebrate central and peripheral nervous systems. ASIC gating occurs on a millisecond time scale8 and can be largely described by a simple mechanism composed of three states: high pH resting, low pH open and low pH desensitized9. While previously solved x-ray structures of ASIC1a elucidated the conformations of the open10 and desensitized1,11 states, the structure of the high pH, resting state as well as detailed mechanisms for activation and desensitization have remained elusive. Here we present resting state structures of homotrimeric chicken ASIC1a at high pH determined by x-ray crystallography and single particle cryo-electron microscopy, informing a comprehensive molecular mechanism for proton-dependent gating in ASICs. In the resting state, the thumb domain has moved outward relative to its position in the open and desensitized states, expanding the ‘acidic pocket’. Activation thus involves ‘closure’ of the thumb into the acidic pocket, expansion of the lower palm domain and an iris-like opening of the channel gate. Furthermore, we demonstrate how the β11-β12 linkers demarcating upper and lower palm domains serve as a molecular ‘clutch’, undergoing a simple rearrangement to permit rapid desensitization.

P2X receptors are trimeric, non-selective cation channels activated by extracellular ATP. The P2X 7 receptor subtype is a pharmacological target because of involvement in apoptotic, inflammatory, and tumor progression pathways. It is the most structurally and functionally distinct P2X subtype, containing a unique cytoplasmic domain critical for the receptor to initiate apoptosis and not undergo desensitization. However, lack of structural information about the cytoplasmic domain has hindered understanding of the molecular mechanisms underlying these processes. We report cryoelectron microscopy structures of full-length rat P2X 7 receptor in apo and ATP-bound states. These structures reveal how one cytoplasmic element, the C-cys anchor, prevents desensitization by anchoring the pore-lining helix to the membrane with palmitoyl groups. They show a second cytoplasmic element with a unique fold, the cytoplasmic ballast, which unexpectedly contains a zinc ion complex and a guanosine nucleotide binding site. Our structures provide first insights into the architecture and function of a P2X receptor cytoplasmic domain.

SUMMARY The serotonin transporter (SERT) regulates neurotransmitter homeostasis through the sodium-and chloride-dependent recycling of serotonin into presynaptic neurons1–3. Major depression and anxiety disorders are treated using selective serotonin reuptake inhibitors (SSRIs), small molecules that competitively block substrate binding, prolonging neurotransmitter action2,4. The dopamine and norepinephrine transporters, together with SERT, are members of the neurotransmitter sodium symporter (NSS) family. Cocaine and amphetamines inhibit or modulate the transport activities of NSSs2,3 and genetic variants are associated with multiple neuropsychiatric disorders including attention deficit hyperactivity disorder, autism, and bipolar disorder2,5. Studies of bacterial NSS homologs, including LeuT, have shown how transmembrane helices (TMs) undergo conformational changes during the transport cycle, exposing a central binding site to either side of the membrane1,6–12. However, the conformational changes associated with transport in eukaryotic NSSs remain obscure. To elucidate structure-based mechanisms for transport in SERT, we turned to complexes with ibogaine, a centuries old hallucinogenic natural product with psychoactive and anti-addictive properties13,14 (Fig. 1a). Interestingly, ibogaine displays non-competitive inhibition of transport, yet it exhibits competitive binding toward SSRIs15,16. Here we report cryo-EM structures of SERT-ibogaine complexes captured in outward-open, occluded, and inward-open conformations. Ibogaine binds to the central binding site and closure of the extracellular gate largely involves movements of TMs 1b and 6a. Opening of the intracellular gate involves a hinge-like movement of TM1a and partial unwinding of TM5, which together create a permeation pathway enabling substrate and ion diffusion to the cytoplasm. These structures define the structural rearrangements that occur from outward-open to the inward-open conformations, providing insight into the mechanism of neurotransmitter transport and ibogaine inhibition.

Hematologic spread of carcinoma results in incurable metastasis; yet, the basic characteristics and travel mechanisms of cancer cells in the bloodstream are unknown. We have established a fluid phase biopsy approach that identifies circulating tumor cells (CTCs) without using surface protein-based enrichment and presents them in sufficiently high definition (HD) to satisfy diagnostic pathology image quality requirements. This “HD-CTC” assay finds >5 HD-CTCs/mL of blood in 80% of patients with metastatic prostate cancer (n=20), in 70% of patients with metastatic breast cancer (n=30), in 50% of patients with metastatic pancreatic cancer (n=18), and in 0% of normal controls (n=15). Additionally, it finds HD-CTC clusters ranging from 2 HDCTCs to greater than 30 HD-CTCs in the majority of these cancer patients. This initial validation of an enrichment-free assay demonstrates our ability to identify significant numbers of HD-CTCs in a majority of patients with prostate, breast and pancreatic cancers.