Cryogenic electron microscopy and single-particle analysis.

About 20 years ago, the first three-dimensional (3D) reconstructions at subnanometer (<10-Å) resolution of an icosahedral virus assembly were obtained by cryogenic electron microscopy (cryo-EM) and single-particle analysis. Since then, thousands of structures have been determined to resolutions ranging from 30 Å to near atomic (<4 Å). Almost overnight, the recent development of direct electron detectors and the attendant improvement in analysis software have advanced the technology considerably. Near-atomic-resolution reconstructions can now be obtained, not only for megadalton macromolecular complexes or highly symmetrical assemblies but also for proteins of only a few hundred kilodaltons. We discuss the developments that led to this breakthrough in high-resolution structure determination by cryo-EM and point to challenges that lie ahead.

Dislocation-tuned ferroelectricity and ferromagnetism of the BiFeO3/SrRuO3 interface.

Misfit dislocations at a heteroepitaxial interface produce huge strain and, thus, have a significant impact on the properties of the interface. Here, we use scanning transmission electron microscopy to demonstrate a quantitative unit-cell-by-unit-cell mapping of the lattice parameters and octahedral rotations around misfit dislocations at the BiFeO3/SrRuO3 interface. We find that huge strain field is achieved near dislocations, i.e., above 5% within the first three unit cells of the core, which is typically larger than that achieved from the regular epitaxy thin-film approach, thus significantly altering the magnitude and direction of the local ferroelectric dipole in BiFeO3 and magnetic moments in SrRuO3 near the interface. The strain field and, thus, the structural distortion can be further tuned by the dislocation type. Our atomic-scale study helps us to understand the effects of dislocations in this ferroelectricity/ferromagnetism heterostructure. Such defect engineering allows us to tune the local ferroelectric and ferromagnetic order parameters and the interface electromagnetic coupling, providing new opportunities to design nanosized electronic and spintronic devices.

Seeing Atoms by Single-Particle Cryo-EM.

Nakane et al. and Yip et al., for the first time, demonstrate that, with recent technological advances, atomic-resolution structure determination can be achieved by single-particle cryo-electron microscopy (cryo-EM). This breakthrough opens the door for researchers to apply single-particle cryo-EM to obtain atomic structural information for a wide range of protein complexes.

Thermally Induced Irreversible Disorder in Interlayer Stacking of γ-GeSe.

The interlayer stacking shift in van der Waals (vdW) crystals represents an important degree of freedom to control various material properties, including magnetism, ferroelectricity, and electrical properties. On the other hand, the structural phase transitions driven by interlayer sliding in vdW crystals often exhibit thickness-dependent, sample-specific behaviors with significant hysteresis, complicating a clear understanding of their intrinsic nature. Here, the stacking configuration of the recently identified vdW crystal, γ-GeSe, is investigated, and the disordering manipulation of stacking sequence is demonstrated. It is observed that the well-ordered AB' stacking configuration in as-synthesized samples undergoes irreversible disordering upon Joule heating via electrical biasing or thermal treatment, as confirmed by atomic resolution scanning transmission electron microscopy (STEM). Statistical analysis of STEM data reveal the emergence of stacking disorder, with samples subjected to high electrical bias reaching the maximum levels of disorder. The energies of various stacking configurations and energy barriers for interlayer sliding are examined using first-principles calculation and a parameterized model to elucidate the key structural parameters related to stacking shift. The susceptibility of interlayer stacking to disorder through electrical or thermal treatments should be carefully considered to fully comprehend the structural and electrical properties of vdW crystals.

Crystal structure of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) frameshifting pseudoknot.

SARS-CoV-2 produces two long viral protein precursors from one open reading frame using a highly conserved RNA pseudoknot that enhances programmed -1 ribosomal frameshifting. The 1.3 Å-resolution X-ray structure of the pseudoknot reveals three coaxially stacked helices buttressed by idiosyncratic base triples from loop residues. This structure represents a frameshift-stimulating state that must be deformed by the ribosome and exhibits base-triple-adjacent pockets that could be targeted by future small-molecule therapeutics.

Atomic resolution imaging using a novel, compact and stiff scanning tunnelling microscope in cryogen-free superconducting magnet.

We present the design and performance of a novel scanning tunnelling microscope (STM) operating in a cryogen-free superconducting magnet. Our home-built STM head is compact (51.5 mm long and 20 mm in diameter) and has a single arm that provides complete openness in the scanning area between the tip and sample. The STM head consists of two piezoelectric tubes (PTs), a piezoelectric scanning tube (PST) mounted on a well-polished zirconia shaft, and a large PT housed in a sapphire tube called the motor tube. The main body of the STM head is made of tantalum. In this design, we fixed the sapphire tube to the frame with screws so that the tube's position can be changed quickly. To analyse the stiffness of the STM head unit, we identified the lowest eigenfrequencies with 3 and 4 kHz in the bending modes, 8 kHz in a torsional mode, and 9 kHz in a longitudinal mode by finite element analysis, and also measured the low drift rates in the X-Y plane and in the Z direction. The high performance of the home-built STM was demonstrated by images of the hexagonal graphite lattice at 300 K and in a sweeping magnetic field from 0 T to 9 T. Our results confirm the high stability, vibration resistance, insensitivity to high magnetic fields and the application potential of our newly developed STM for the investigation of low-frequency systems with high static support stiffness in physics, chemistry, material and biological sciences.

Atomic Resolution Imaging of Highly Air-Sensitive Monolayer and Twisted-Bilayer WTe2.

Bulk Td-WTe2 is a semimetal, while its monolayer counterpart is a two-dimensional (2D) topological insulator. Recently, electronic transport resembling a Luttinger liquid state was found in twisted-bilayer WTe2 (tWTe2) with a twist angle of ∼5°. Despite the strong interest in 2D WTe2 systems, little experimental information is available about their intrinsic microstructure, leaving obstacles in modeling their physical properties. The monolayer, and consequently tWTe2, are highly air-sensitive, and therefore, probing their atomic structures is difficult. In this study, we develop a robust method for atomic-resolution visualization of monolayers and tWTe2 obtained through mechanical exfoliation and fabrication. We confirm the high crystalline quality of mechanically exfoliated WTe2 samples and observe that tWTe2 with twist angles of ∼5 and ∼2° retains its pristine moiré structure without substantial deformations or reconstructions. The results provide a structural foundation for future electronic modeling of monolayer and tWTe2 moiré lattices.

Atomic Visualization of the 3D Charge Density Wave Stacking in 1T-TaS2 by Cryogenic Transmission Electron Microscopy.

Charge density waves (CDWs) in 1T-TaS2 maintain 2D ordering by forming periodic in-plane star-of-David (SOD) patterns, while they also intertwined with orbital order in the c axis. Recent theoretical calculations and surface measurements have explored 3D CDW configurations, but interlayer intertwining of a 2D CDW order remains elusive. Here, we investigate the in- and out-of-plane ordering of the commensurate CDW superstructure in a 1T-TaS2 thin flake in real space, using aberration-corrected cryogenic transmission electronic microscopy (cryo-TEM) in low-dose mode, far below the threshold dose for an electron-induced CDW phase transition. By scrutinizing the phase intensity variation of modulated Ta atoms, we visualize the penetrative 3D CDW stacking structure, revealing an intertwining multidomain structure with three types of vertical CDW stacking configurations. Our results provide microstructural evidence for the coexistence of local Mott insulation and metal phases and offer a paradigm for studying the CDW structure and correlation order in condensed-matter physics using cryo-TEM.

Structural Anisotropy-Driven Atomic Mechanisms of Phase Transformations in the Pt-Sn System.

Using in situ atomic-resolution scanning transmission electron microscopy, atomic movements and rearrangements associated with diffusive solid to solid phase transformations in the Pt-Sn system are captured to reveal details of the underlying atomistic mechanisms that drive these transformations. In the PtSn4 to PtSn2 phase transformation, a periodic superlattice substructure and a unique intermediate structure precede the nucleation and growth of the PtSn2 phase. At the atomic level, all stages of the transformation are templated by the anisotropic crystal structure of the parent PtSn4 phase. In the case of the PtSn2 to Pt2Sn3 transformation, the anisotropy in the structure of product Pt2Sn3 dictates the path of transformation. Analysis of atomic configurations at the transformation front elucidates the diffusion pathways and lattice distortions required for these phase transformations. Comparison of multiple Pt-Sn phase transformations reveals the structural parameters governing solid to solid phase transformations in this technologically interesting intermetallic system.

A review of the approaches used to solve sub-100 kDa membrane proteins by cryo-electron microscopy.

Membrane proteins (MPs) are essential components of all biological membranes, contributing to key cellular functions that include signalling, molecular transport and energy metabolism. Consequently, MPs are important biomedical targets for therapeutics discovery. Despite hardware and software developments in cryo-electron microscopy, as well as MP sample preparation, MPs smaller than 100 kDa remain difficult to study structurally. Significant investment is required to overcome low levels of naturally abundant protein, MP hydrophobicity as well as conformational and compositional instability. Here we have reviewed the sample preparation approaches that have been taken to successfully express, purify and prepare small MPs for analysis by cryo-EM (those with a total solved molecular weight of under 100 kDa), as well as examining the differing approaches towards data processing and ultimately obtaining a structural solution. We highlight common challenges at each stage in the process as well as strategies that have been developed to overcome these issues. Finally, we discuss future directions and opportunities for the study of sub-100 kDa membrane proteins by cryo-EM.

Advances in computational approaches to structure determination of alphaviruses and flaviviruses using cryo-electron microscopy.

Advancements in the field of cryo-electron microscopy (cryo-EM) have greatly contributed to our current understanding of virus structures and life cycles. In this review, we discuss the application of single particle cryo-electron microscopy (EM) for the structure elucidation of small enveloped icosahedral viruses, namely, alpha- and flaviviruses. We focus on technical advances in cryo-EM data collection, image processing, three-dimensional reconstruction, and refinement strategies for obtaining high-resolution structures of these viruses. Each of these developments enabled new insights into the alpha- and flavivirus architecture, leading to a better understanding of their biology, pathogenesis, immune response, immunogen design, and therapeutic development.

Atomic Origins of Enhanced Ferroelectricity in Nanocolumnar PbTiO3 /PbO Composite Thin Films.

Nanocomposite films hold great promise for multifunctional devices by integrating different functionalities within a single film. The microstructure of the precipitate/secondary phase is an essential element in designing composites' properties. The interphase strain between the matrix and secondary phase is responsible for strain-mediated functionalities, such as magnetoelectric coupling and ferroelectricity. However, a quantitative microstructure-dependent interphase strain characterization has been scarcely studied. Here, it is demonstrated that the PbTiO3 (PTO)/PbO composite system can be prepared in nano-spherical and nanocolumnar configurations by tuning the misfit strain, confirmed by a three-dimensional reconstructive microscopy technique. With the atomic resolution quantitative microscopy with a depth resolution of a few nanometers, it is discovered that the strained region in PTO is much larger and more uniform in nanocolumnar compared to nano-spherical composites, resulting in much enhanced ferroelectric properties. The interphase strain between PbO and PTO in the nanocolumnar structure leads to a giant c/a ratio of 1.20 (bulk value of 1.06), accompanied by a Ti polarization displacement of 0.48 Å and an effective ferroelectric polarization of 241.7 µC cm-2 , three times compared to the bulk value. The quantitative atomic-scale strain and polarization analysis on the interphase strain provides an important guideline for designing ferroelectric nanocomposites.

Structural Complexity in the Apparently Simple Crystal Structure of Be2 Ru.

The structural features of the hexagonal layered crystal structure of Be2 Ru (a=5.7508(3) Å, c=3.0044(2) Å, space group P 6 ‾ ${\bar{6}}$ 2m) were investigated by single crystal X-ray diffraction and transmission electron microscopy (TEM). The residual electron density and high-resolution TEM images show that the real structure can be described as an intergrowth of the main hexagonal matrix of the Fe2 P type with minor orthorhombic inclusions of its stacking variants. Such atomic arrangement is stabilized by the charge transfer from Be to Ru and by a system of polar three- and four-atomic bonds involving both components. The calculated electronic density of states (DOS) of Be2 Ru revealed, contrarily to typical intermetallic compounds, a pseudo gap (dip) in the vicinity of the Fermi level. The temperature dependence of the electrical resistivity of Be2 Ru shows metal behaviour in agreement with the non-zero DOS at the Fermi level.

A symmetry-derived mechanism for atomic resolution imaging.

We introduce an image-contrast mechanism for scanning transmission electron microscopy (STEM) that derives from the local symmetry within the specimen. For a given position of the electron probe on the specimen, the image intensity is determined by the degree of similarity between the exit electron-intensity distribution and a chosen symmetry operation applied to that distribution. The contrast mechanism detects both light and heavy atomic columns and is robust with respect to specimen thickness, electron-probe energy, and defocus. Atomic columns appear as sharp peaks that can be significantly narrower than for STEM images using conventional disk and annular detectors. This fundamentally different contrast mechanism complements conventional imaging modes and can be acquired simultaneously with them, expanding the power of STEM for materials characterization.

Atomic-scale observations of electrical and mechanical manipulation of topological polar flux closure.

The ability to controllably manipulate complex topological polar configurations such as polar flux-closures via external stimuli may allow the construction of new electromechanical and nanoelectronic devices. Here, using atomically resolved in situ scanning transmission electron microscopy, we find that the polar flux-closures in PbTiO3/SrTiO3 superlattice films are mobile and can be reversibly switched to ordinary single ferroelectric c or a domains under an applied electric field or stress. Specifically, the electric field initially drives movement of a flux-closure via domain wall motion and then breaks it to form intermediate a/c striped domains, whereas mechanical stress first squeezes the core of a flux-closure toward the interface and then form a/c domains with disappearance of the core. After removal of the external stimulus, the flux-closure structure spontaneously recovers. These observations can be precisely reproduced by phase field simulations, which also reveal the evolutions of the competing energies during phase transitions. Such reversible switching between flux-closures and ordinary ferroelectric states provides a foundation for potential electromechanical and nanoelectronic applications.

Improving Spatial and Elemental Associations in Analytical Field Ion Microscopy.

Chemically resolved atomic resolution imaging can give fundamental information about material properties. However, even today, a technique capable of such achievement is still only an ambition. Here, we take further steps in developing the analytical field ion microscopy (aFIM), which combines the atomic spatial resolution of field ion microscopy (FIM) with the time-of-flight spectrometry of atom probe tomography (APT). To improve the performance of aFIM that are limited in part by a high level of background, we implement bespoke flight path time-of-flight corrections normalized by the ion flight distances traversed in electrostatic simulations modeled explicitly for an atom probe chamber. We demonstrate effective filtering in the field evaporation events upon spatially and temporally correlated multiples, increasing the mass spectrum's signal-to-background. In an analysis of pure tungsten, mass peaks pertaining to individual W isotopes can be distinguished and identified, with the signal-to-background improving by three orders of magnitude over the raw data. We also use these algorithms for the analysis of a CoTaB amorphous film to demonstrate application of aFIM beyond pure metals and binary alloys. These approaches facilitate elemental identification of the FIM-imaged surface atoms, making analytical FIM more precise and reliable.

Atomic-Resolution Imaging of Small Organic Molecules on Graphene.

Here, we demonstrate atomic-resolution scanning transmission electron microscopy (STEM) imaging of light elements in small organic molecules on graphene. We use low-dose, room-temperature, aberration-corrected STEM to image 2D monolayer and bilayer molecular crystals, followed by advanced image processing methods to create high-quality composite images from ∼102-104 individual molecules. In metalated porphyrin and phthalocyanine derivatives, these images contain an elementally sensitive contrast with up to 1.3 Å resolution─sufficient to distinguish individual carbon and nitrogen atoms. Importantly, our methods can be applied to molecules with low masses (∼0.6 kDa) and nanocrystalline domains containing just a few hundred molecules, making it possible to study systems for which large crystals cannot easily be grown. Our approach is enabled by low-background graphene substrates, which we show increase the molecules' critical dose by 2-7×. These results indicate a new route for low-dose, atomic-resolution electron microscopy imaging to solve the structures of small organic molecules.

Ligand-Mediated Revival of Degraded α-CsPbI3 to Stable Highly Luminescent Perovskite.

Although α-CsPbI3 is regarded as an attractive optical luminophore, it is readily degraded to the optically inactive δ-phase under ambient conditions. Here, we present a simple approach to revive degraded ("optically sick") α-CsPbI3 through "medication" with thiol-containing ligands. The effect of different types of thiols is systematically studied through optical spectroscopy. The structural reconstruction of degraded α-CsPbI3 nanocrystals to cubic crystals in the presence of thiol-containing ligands is visualized through high-resolution transmission electron microscopy and supported by X-ray diffraction analysis. We found that 1-dodecanethiol (DSH) effectively revives degraded CsPbI3 and results in high immunity towards moisture and oxygen, hitherto unreported. DSH facilitates the passivation of surface defects and etching of degraded Cs4 PbI6 phase, thus reverting them back to the cubic CsPbI3 phase, leading to enhanced PL and environmental stability.

High-resolution structure of phosphoketolase from Bifidobacterium longum determined by cryo-EM single-particle analysis.

In bifidobacteria, phosphoketolase (PKT) plays a key role in the central hexose fermentation pathway called "bifid shunt." The three-dimensional structure of PKT from Bifidobacterium longum with co-enzyme thiamine diphosphate (ThDpp) was determined at 2.1 Å resolution by cryo-EM single-particle analysis using 196,147 particles to build up the structural model of a PKT octamer related by D4 symmetry. Although the cryo-EM structure of PKT was almost identical to the X-ray crystal structure previously determined at 2.2 Å resolution, several interesting structural features were observed in the cryo-EM structure. Because this structure was solved at relatively high resolution, it was observed that several amino acid residues adopt multiple conformations. Among them, Q546-D547-H548-N549 (the QN-loop) demonstrate the largest structural change, which seems to be related to the enzymatic function of PKT. The QN-loop is at the entrance to the substrate binding pocket. The minor conformer of the QN-loop is similar to the conformation of the QN-loop in the crystal structure. The major conformer is located further from ThDpp than the minor conformer. Interestingly, the major conformer in the cryo-EM structure of PKT resembles the corresponding loop structure of substrate-bound Escherichia coli transketolase. That is, the minor and major conformers may correspond to "closed" and "open" states for substrate access, respectively. Moreover, because of the high-resolution analysis, many water molecules were observed in the cryo-EM structure of PKT. Structural features of the water molecules in the cryo-EM structure are discussed and compared with water molecules observed in the crystal structure.

Perspective: Emerging strategies for determining atomic-resolution structures of macromolecular complexes within cells.

In principle, electron cryo-tomography (cryo-ET) of thin portions of cells provides high-resolution images of the three-dimensional spatial arrangement of all members of the proteome. In practice, however, radiation damage creates a tension between recording images at many different tilt angles, but at correspondingly reduced exposure levels, versus limiting the number of tilt angles in order to improve the signal-to-noise ratio (SNR). Either way, it is challenging to read the available information out at the level of atomic structure. Here, we first review work that explores the optimal strategy for data collection, which currently seems to favor the use of a limited angular range for tilting the sample or even the use of a single image to record the high-resolution information. Looking then to the future, we point to the alternative of so-called "deconvolution microscopy", which may be applied to tilt-series or optically-sectioned, focal series data. Recording data as a focal series has the advantage that little or no translational alignment of frames might be needed, and a three-dimensional reconstruction might require only 2/3 the number of images as does standard tomography. We also point to the unexploited potential of phase plates to increase the contrast, and thus to reduce the electron exposure levels while retaining the ability align and merge the data. In turn, using much lower exposures per image could have the advantage that high-resolution information is retained throughout the full data-set, whether recorded as a tilt series or a focal series of images.