As a discipline, structural biology has been transformed by the three-dimensional electron microscopy (3DEM) “Resolution Revolution” made possible by convergence of robust cryo-preservation of vitrified biological materials, sample handling systems, and measurement stages operating a liquid nitrogen temperature, improvements in electron optics that preserve phase information at the atomic level, direct electron detectors (DEDs), high-speed computing with graphics processing units, and rapid advances in data acquisition and processing software. 3DEM structure information (atomic coordinates and related metadata) are archived in the open-access Protein Data Bank (PDB), which currently holds more than 11,000 3DEM structures of proteins and nucleic acids, and their complexes with one another and small-molecule ligands (~ 6% of the archive). Underlying experimental data (3DEM density maps and related metadata) are stored in the Electron Microscopy Data Bank (EMDB), which currently holds more than 21,000 3DEM density maps. After describing the history of the PDB and the Worldwide Protein Data Bank (wwPDB) partnership, which jointly manages both the PDB and EMDB archives, this review examines the origins of the resolution revolution and analyzes its impact on structural biology viewed through the lens of PDB holdings. Six areas of focus exemplifying the impact of 3DEM across the biosciences are discussed in detail (icosahedral viruses, ribosomes, integral membrane proteins, SARS-CoV-2 spike proteins, cryogenic electron tomography, and integrative structure determination combining 3DEM with complementary biophysical measurement techniques), followed by a review of 3DEM structure validation by the wwPDB that underscores the importance of community engagement.
Transmission electron microscopy (TEM) is essential for determining atomic scale structures in structural biology and materials science. In structural biology, three-dimensional structures of proteins are routinely determined from thousands of identical particles using phase-contrast TEM. In materials science, three-dimensional atomic structures of complex nanomaterials have been determined using atomic electron tomography (AET). However, neither of these methods can determine the three-dimensional atomic structure of heterogeneous nanomaterials containing light elements. Here, we perform ptychographic electron tomography from 34.5 million diffraction patterns to reconstruct an atomic resolution tilt series of a double wall-carbon nanotube (DW-CNT) encapsulating a complex ZrTe sandwich structure. Class averaging the resulting tilt series images and subpixel localization of the atomic peaks reveals a Zr11Te50structure containing a previously unobserved ZrTe2phase in the core. The experimental realization of atomic resolution ptychographic electron tomography will allow for the structural determination of a wide range of beam-sensitive nanomaterials containing light elements.
more » « less- Award ID(s):
- 1848079
- NSF-PAR ID:
- 10477074
- Publisher / Repository:
- Nature Publishing Group
- Date Published:
- Journal Name:
- Nature Communications
- Volume:
- 14
- Issue:
- 1
- ISSN:
- 2041-1723
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract The Protein Data Bank (PDB) archive is a rich source of information in the form of atomic‐level three‐dimensional (3D) structures of biomolecules experimentally determined using macromolecular crystallography, nuclear magnetic resonance (NMR) spectroscopy, and electron microscopy (3DEM). Originally established in 1971 as a resource for protein crystallographers to freely exchange data, today PDB data drive research and education across scientific disciplines. In 2011, the online portal PDB‐101 was launched to support teachers, students, and the general public in PDB archive exploration (
pdb101.rcsb.org ). Maintained by the Research Collaboratory for Structural Bioinformatics PDB, PDB‐101 aims to help train the next generation of PDB users and to promote the overall importance of structural biology and protein science to nonexperts. Regularly published features include the highly popularMolecule of the Month series, 3D model activities, molecular animation videos, and educational curricula. Materials are organized into various categories (Health and Disease, Molecules of Life, Biotech and Nanotech, and Structures and Structure Determination) and searchable by keyword. A biennial health focus frames new resource creation and provides topics for annual video challenges for high school students. Web analytics document that PDB‐101 materials relating to fundamental topics (e.g., hemoglobin, catalase) are highly accessed year‐on‐year. In addition, PDB‐101 materials created in response to topical health matters (e.g., Zika, measles, coronavirus) are well received. PDB‐101 shows how learning about the diverse shapes and functions of PDB structures promotes understanding of all aspects of biology, from the central dogma of biology to health and disease to biological energy. -
null (Ed.)Although scanning transmission electron microscopy (STEM) images of individual heavy atoms were reported 50 years ago, the applications of atomic-resolution STEM imaging became wide spread only after the practical realization of aberration correctors on field-emission STEM/TEM instruments to form sub-Ångstrom electron probes. The innovative designs and advances of electron optical systems, the fundamental understanding of electron–specimen interaction processes, and the advances in detector technology all played a major role in achieving the goal of atomic-resolution STEM imaging of practical materials. It is clear that tremendous advances in computer technology and electronics, image acquisition and processing algorithms, image simulations, and precision machining synergistically made atomic-resolution STEM imaging routinely accessible. It is anticipated that further hardware/software development is needed to achieve three-dimensional atomic-resolution STEM imaging with single-atom chemical sensitivity, even for electron-beam-sensitive materials. Artificial intelligence, machine learning, and big-data science are expected to significantly enhance the impact of STEM and associated techniques on many research fields such as materials science and engineering, quantum and nanoscale science, physics and chemistry, and biology and medicine. This review focuses on advances of STEM imaging from the invention of the field-emission electron gun to the realization of aberration-corrected and monochromated atomic-resolution STEM and its broad applications.more » « less
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Abstract Understanding of phase‐stability and nanoscale structural modulation during lithiation of layer materials demand comprehensive analysis of the Li‐containing phases in the solid‐state reaction products. Conventional chemical analysis methods in the transmission electron microscope (TEM) are not ideal to detect Li in partially intercalated nanodomains because Li atoms do not remain stationary under the focused electron beam. An alternate approach combining density functional theory (DFT) modeling and multislice image simulation has been explored in the present study to analyze the intercalated structures and to detect and quantify Li from the recorded high‐resolution TEM (HRTEM) micrographs of partially intercalated phases. HRTEM micrographs from partially lithiated graphite and MoS2show variations in the interlayer spacings, but are not usually directly interpretable. Hypothetical intercalated microstructures of graphite and MoS2supercells have been generated using atomic‐scale simulations with systematically varying Li concentrations. The measured interplanar spacings are compared with those of experimentally recorded HRTEM micrographs from lithiated graphite and MoS2. The results confirm the coexistence of different lithiated phases at localized domains. This understanding of phase transformation and the lithium quantification provides a basis for understanding the structural accommodation of layered materials during intercalation.
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Metal-ion batteries (e.g., lithium and sodium ion batteries) are the promising power sources for portable electronics, electric vehicles, and smart grids. Recent metal-ion batteries with organic liquid electrolytes still suffer from safety issues regarding inflammability and insufficient lifetime.1 As the next generation energy storage devices, all-solid-state batteries (ASSBs) have promising potentials for the improved safety, higher energy density, and longer cycle life than conventional Li-ion batteries.2 The nonflammable solid electrolytes (SEs), where only Li ions are mobile, could prevent battery combustion and explosion since the side reactions that cause safety issues as well as degradation of the battery performance are largely suppressed. However, their practical application is hampered by the high resistance arising at the solid–solid electrode–electrolyte interface (including cathode-electrolyte interface and anode-electrolyte interface).3 Several methods have been introduced to optimize the contact capability as well as the electrochemical/chemical stability between the metal anodes (i.e.: Li and Na) and the SEs, which exhibited decent results in decreasing the charge transfer resistance and broadening the range of the stable energy window (i.e., lowing the chemical potential of metal anode below the highest occupied molecular orbital of the SEs).4 Nevertheless, mitigation for the cathode in ASSB is tardily developed because: (1) the porous structure of the cathode is hard to be infiltrated by SEs;5 (2) SEs would be oxidized and decomposed by the high valence state elements at the surface of the cathode at high state of charge.5 Herein, we demonstrate a universal cathode design strategy to achieve superior contact capability and high electrochemical/chemical stability with SEs. Stereolithography is adopted as a manufacturing technique to realize a hierarchical three-dimensional (HTD) electrode architecture with micro-size channels, which is expected to provide larger contact areas with SEs. Then, the manufactured cathode is sintered at 700 °C in a reducing atmosphere (e.g.: H2) to accomplish the carbonization of the resin, delivering sufficiently high electronic conductivity for the cathode. To avoid the direct exposure of the cathode active materials to the SEs, oxidative chemical vapor deposition technique (oCVD) is leveraged to build conformal and highly conducting poly(3,4-ethylenedioxythiophene) (PEDOT) on the surface of the HTD cathode.6 To demonstrate our design strategy, both NCM811 and Na3V2(PO4)3 is selected as active materials in the HTD cathode, then each cathode is paired with organic (polyacrylonitrile-based) and inorganic (sulfur-based) SEs assembled into two batteries (total four batteries). SEM and TEM reveal the micro-size HTD structure with built-in channels. Featured by the HTD architecture, the intrinsic kinetic and thermodynamic conditions will be enhanced by larger surface contact areas, more active sites, improved infusion and electrolyte ion accessibility, and larger volume expansion capability. Disclosed by X-ray computed tomography, the interface between cathode and SEs in the four modified samples demonstrates higher homogeneity at the interface between the cathode and SEs than that of all other pristine samples. Atomic force microscopy is employed to measure the potential image of the cross-sectional interface by the peak force tapping mode. The average potential of modified samples is lower than that of pristine samples, which confirms a weakened space charge layer by the enhanced contact capability. In addition, through Electron Energy Loss Spectroscopy coupled with Scanning Transmission Electron Microscopy, the preserved interface between HTD cathode and SE is identified; however, the decomposing of the pristine cathode is clearly observed. In addition, Finite element method simulations validate that the diffusion dynamics of lithium ions is favored by HTD structure. Such a demonstrated universal strategy provides a new guideline to engineer cathode electrolyte interface by reconstructing electrode structures that can be applicable to all solid-state batteries in a wide range of chemical conditions.more » « less
