Diatom pyrenoids are encased in a protein shell that enables efficient CO fixation.

Pyrenoids are subcompartments of algal chloroplasts that increase the efficiency of Rubisco-driven CO fixation. Diatoms fix up to 20% of global CO, but their pyrenoids remain poorly characterized. Here, we used in vivo photo-crosslinking to identify pyrenoid shell (PyShell) proteins, which we localized to the pyrenoid periphery of model pennate and centric diatoms, Phaeodactylum tricornutum and Thalassiosira pseudonana.

In situ architecture of the ciliary base reveals the stepwise assembly of intraflagellar transport trains.

The cilium is an antenna-like organelle that performs numerous cellular functions, including motility, sensing, and signaling. The base of the cilium contains a selective barrier that regulates the entry of large intraflagellar transport (IFT) trains, which carry cargo proteins required for ciliary assembly and maintenance. However, the native architecture of the ciliary base and the process of IFT train assembly remain unresolved.

Membrane-anchored HDCR nanowires drive hydrogen-powered CO fixation.

Filamentous enzymes have been found in all domains of life, but the advantage of filamentation is often elusive. Some anaerobic, autotrophic bacteria have an unusual filamentous enzyme for CO fixation-hydrogen-dependent CO reductase (HDCR)-which directly converts H and CO into formic acid. HDCR reduces CO with a higher activity than any other known biological or chemical catalyst, and it has therefore gained considerable interest in two areas of global relevance: hydrogen storage and combating climate change by capturing atmospheric CO.

MemBrain: A deep learning-aided pipeline for detection of membrane proteins in Cryo-electron tomograms.

Background And Objective: Cryo-electron tomography (cryo-ET) is an imaging technique that enables 3D visualization of the native cellular environment at sub-nanometer resolution, providing unpreceded insights into the molecular organization of cells. However, cryo-electron tomograms suffer from low signal-to-noise ratios and anisotropic resolution, which makes subsequent image analysis challenging. In particular, the efficient detection of membrane-embedded proteins is a problem still lacking satisfactory solutions.

Cryo-EM structure of native human thyroglobulin.

The thyroglobulin (TG) protein is essential to thyroid hormone synthesis, plays a vital role in the regulation of metabolism, development and growth and serves as intraglandular iodine storage. Its architecture is conserved among vertebrates. Synthesis of triiodothyronine (T) and thyroxine (T) hormones depends on the conformation, iodination and post-translational modification of TG.

Deep learning improves macromolecule identification in 3D cellular cryo-electron tomograms.

Cryogenic electron tomography (cryo-ET) visualizes the 3D spatial distribution of macromolecules at nanometer resolution inside native cells. However, automated identification of macromolecules inside cellular tomograms is challenged by noise and reconstruction artifacts, as well as the presence of many molecular species in the crowded volumes. Here, we present DeepFinder, a computational procedure that uses artificial neural networks to simultaneously localize multiple classes of macromolecules.

Identification of a Dps contamination in Mitomycin-C-induced expression of Colicin Ia.

Colicins are bacterial toxins targeting Gram-negative bacteria, including E. coli and related Enterobacteriaceae strains. Some colicins form ion-gated pores in the inner membrane of attacked bacteria that are lethal to their target.

Author Correction: High-resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica.

A Correction to this paper has been published: https://doi.org/10.1038/s41467-020-19845-z .

High-resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica.

Urease converts urea into ammonia and carbon dioxide and makes urea available as a nitrogen source for all forms of life except animals. In human bacterial pathogens, ureases also aid in the invasion of acidic environments such as the stomach by raising the surrounding pH. Here, we report the structure of urease from the pathogen Yersinia enterocolitica at 2 Å resolution from cryo-electron microscopy.

Structural basis of Focal Adhesion Kinase activation on lipid membranes.

Focal adhesion kinase (FAK) is a key component of the membrane proximal signaling layer in focal adhesion complexes, regulating important cellular processes, including cell migration, proliferation, and survival. In the cytosol, FAK adopts an autoinhibited state but is activated upon recruitment into focal adhesions, yet how this occurs or what induces structural changes is unknown. Here, we employ cryo-electron microscopy to reveal how FAK associates with lipid membranes and how membrane interactions unlock FAK autoinhibition to promote activation.

Retrieving high-resolution information from disordered 2D crystals by single-particle cryo-EM.

Electron crystallography can reveal the structure of membrane proteins within 2D crystals under close-to-native conditions. High-resolution structural information can only be reached if crystals are perfectly flat and highly ordered. In practice, such crystals are difficult to obtain.

Image processing techniques for high-resolution structure determination from badly ordered 2D crystals.

2D electron crystallography can be used to study small membrane proteins in their native environment. Obtaining highly ordered 2D crystals is difficult and time-consuming. However, 2D crystals diffracting to only 10-12 Å can be prepared relatively conveniently in most cases.

Focus: The interface between data collection and data processing in cryo-EM.

We present a new software package called Focus that interfaces cryo-transmission electron microscopy (cryo-EM) data collection with computer image processing. Focus creates a user-friendly environment to import and manage data recorded by direct electron detectors and perform elemental image processing tasks in a high-throughput manner while new data is being acquired at the microscope. It provides the functionality required to remotely monitor the progress of data collection and data processing, which is essential now that automation in cryo-EM allows a steady flow of images of single particles, two-dimensional crystals, or electron tomography data to be recorded in overnight sessions.

Assessment of a nanocrystal 3-D morphology by the analysis of single HAADF-HRSTEM images.

This work presents the morphological characterization of CeO2 nanocrystals by the analysis of single unfiltered high-angle annular dark-field (HAADF)-high-resolution scanning transmission electron microscopy (HRSTEM) images. The thickness of each individual atomic column is estimated by the classification of its HAADF integrated intensity using a Gaussian mixture model. The resulting thickness maps obtained from two example nanocrystals with distinct morphology were analyzed with aid of the symmetry from the CeO2 crystallographic structure, providing an approximation for their 3-D morphology with high spatial resolution.

MEGACELL: a nanocrystal model construction software for HRTEM multislice simulation.

Image simulation has an invaluable importance for the accurate analysis of High Resolution Transmission Electron Microscope (HRTEM) results, especially due to its non-linear image formation mechanism. Because the as-obtained images cannot be interpreted in a straightforward fashion, the retrieval of both qualitative and quantitative information from HRTEM micrographs requires an iterative process including the simulation of a nanocrystal model and its comparison with experimental images. However most of the available image simulation software requires atom-by-atom coordinates as input for the calculations, which can be prohibitive for large finite crystals and/or low-symmetry systems and zone axis orientations.