Cryo-electron Microscopy Research Articles

Novel Amorphous Nitride‐Halide Solid Electrolytes with Enhanced Performance for All‐Solid‐State Batteries

Solid electrolytes (SEs) in all‐solid‐state batteries (ASSBs) are garnering considerable attention for their potential applications in next‐generation energy storage systems. Amorphous SEs with dual‐anion hold great promise for achieving favorable performance, such as high ionic conductivity and good compatibility with electrodes within ASSBs. Here, we discover a family of amorphous nitride‐halide SEs, Li3xMClyNx (M = Ta or La, 1 ≤ 3x ≤ 1.4, y = 5 or 3), which can achieve ionic conductivities up to 7.34 mS cm‒1 at 30 °C. The amorphous properties and local structures are investigated using powder X‐ray diffraction, cryogenic transmission electron microscopy, and atomic pair distribution function analysis. Impressively, ASSBs employing amorphous Li3xTaCl5Nx have demonstrated good performance at high rates and charging voltages, as well as at low temperature.

Novel Amorphous Nitride-Halide Solid Electrolytes with Enhanced Performance for All-Solid-State Batteries.

Solid electrolytes (SEs) in all-solid-state batteries (ASSBs) are garnering considerable attention for their potential applications in next-generation energy storage systems. Amorphous SEs with dual-anion hold great promise for achieving favorable performance, such as high ionic conductivity and good compatibility with electrodes within ASSBs. Here, we discover a family of amorphous nitride-halide SEs, Li3xMClyNx (M = Ta or La, 1 ≤ 3x ≤ 1.4, y = 5 or 3), which can achieve ionic conductivities up to 7.34 mS cm‒1 at 30 °C. The amorphous properties and local structures are investigated using powder X-ray diffraction, cryogenic transmission electron microscopy, and atomic pair distribution function analysis. Impressively, ASSBs employing amorphous Li3xTaCl5Nx have demonstrated good performance at high rates and charging voltages, as well as at low temperature.

Dephosphorylation and ion binding in prokaryotic calcium transport

Calcium (Ca 2+ ) signaling is fundamental to cellular processes in both eukaryotic and prokaryotic organisms. While the mechanisms underlying eukaryotic Ca 2+ transport are well documented, an understanding of prokaryotic transport remains nascent. LMCA1, a Ca 2+ adenosine triphosphatase (ATPase) from Listeria monocytogenes , has emerged as a prototype for elucidating structure and dynamics in prokaryotic Ca 2+ transport. Here, we used a multidisciplinary approach integrating kinetics, structure, and dynamics to unravel the intricacies of LMCA1 function. A cryo–electron microscopy (cryo-EM) structure of a Ca 2+ -bound E1 state showed ion coordination by Asp 720 , Asn 716 , and Glu 292 . Time-resolved x-ray solution scattering experiments identified phosphorylation as the rate-determining step. A cryo-EM E2P state structure exhibited remarkable similarities to a SERCA1a E2-P* state, which highlights the essential role of the unique P-A domain interface in enhancing dephosphorylation rates and reconciles earlier proposed mechanisms. Our study underscores the distinctiveness between eukaryotic and prokaryotic Ca 2+ ATPase transport systems and positions LMCA1 as a promising drug target for developing antimicrobial strategies.

Protein complex structure modeling by cross-modal alignment between cryo-EM maps and protein sequences

Cryo-electron microscopy (cryo-EM) technique is widely used for protein structure determination. Current automatic cryo-EM protein complex modeling methods mostly rely on prior chain separation. However, chain separation without sequence guidance often suffers from errors caused by cross-chain interaction or noise densities, which would accumulate and mislead the subsequent steps. Here, we present EModelX, a fully automated cryo-EM protein complex structure modeling method, which achieves sequence-guiding modeling through cross-modal alignments between cryo-EM maps and protein sequences. EModelX first employs multi-task deep learning to predict Cα atoms, backbone atoms, and amino acid types from cryo-EM maps, which is subsequently used to sample Cα traces with amino acid profiles. The profiles are then aligned with protein sequences to obtain initial structural models, which yielded an average RMSD of 1.17 Å in our test set, approaching atomic-level precision in recovering PDB-deposited structures. After filling unmodeled gaps through sequence-guiding Cα threading, the final models achieved an average TM-score of 0.808, outperforming the state-of-the-art method. The further combination with AlphaFold can improve the average TM-score to 0.911. Analyzes conducted by comparing some EModelX-built models and PDB structures highlight its potential to improve PDB structures. EModelX is accessible at https://bio-web1.nscc-gz.cn/app/EModelX.

An approach for coherent periodogram averaging of tilt-series data for improved CTF estimation.

Cryo-electron microscopy (cryo-EM) has become an indispensable technique for determining three-dimensional structures of biological macromolecules. A critical aspect of achieving high-resolution cryo-EM reconstructions is accurately determining and correcting for the microscope's contrast transfer function (CTF). The CTF introduces defocus-dependent distortions during imaging; if not properly accounted for, the CTF can distort features in and limit the resolution of 3D reconstructions. For tilt-series data used in cryo-electron tomography (cryo-ET), CTF estimation becomes even more challenging due to the tilt of the specimen, which introduces a defocus gradient across the field of view, as well as the low dose and signal in individual tilt images. Here, we describe a simple algorithm to improve the accuracy of CTF estimation of tilted images by leveraging the tilt-series alignment parameters determined for tomographic reconstruction to explicitly account for the tilted specimen geometry. In brief, each tilt image is divided into patches, each of which are then stretched according to their defocus shift. These are then summed to provide a coherent power spectra at the tilt axis, which can then be used in standard CTF estimation algorithms. This uses all the data in each image to enhance the visibility of Thon rings, thereby improving high-resolution CTF estimation and subsequent enhancements in the resolution of subtomogram averages.

Architectures of photosynthetic RC-LH1 supercomplexes from Rhodobacter blasticus.

The reaction center-light-harvesting complex 1 (RC-LH1) plays an essential role in the primary reactions of bacterial photosynthesis. Here, we present high-resolution structures of native monomeric and dimeric RC-LH1 supercomplexes from Rhodobacter (Rba.) blasticus using cryo-electron microscopy. The RC-LH1 monomer is composed of an RC encircled by an open LH1 ring comprising 15 αβ heterodimers and a PufX transmembrane polypeptide. In the RC-LH1 dimer, two crossing PufX polypeptides mediate dimerization. Unlike Rhodabacter sphaeroides counterpart, Rba. blasticus RC-LH1 dimer has a less bent conformation, lacks the PufY subunit near the LH1 opening, and includes two extra LH1 αβ subunits, forming a more enclosed S-shaped LH1 ring. Spectroscopic assays reveal that these unique structural features are accompanied by changes in the kinetics of quinone/quinol trafficking between RC-LH1 and cytochrome bc1. Our findings reveal the assembly principles and structural variability of photosynthetic RC-LH1 supercomplexes, highlighting diverse strategies used by phototrophic bacteria to optimize light-harvesting and electron transfer in competitive environments.

Structural basis of antimicrobial membrane coat assembly by human GBP1.

Guanylate-binding proteins (GBPs) are interferon-inducible guanosine triphosphate hydrolases (GTPases) mediating host defense against intracellular pathogens. Their antimicrobial activity hinges on their ability to self-associate and coat pathogen-associated compartments or cytosolic bacteria. Coat formation depends on GTPase activity but how nucleotide binding and hydrolysis prime coat formation remains unclear. Here, we report the cryo-electron microscopy structure of the full-length human GBP1 dimer in its guanine nucleotide-bound state and describe the molecular ultrastructure of the GBP1 coat on liposomes and bacterial lipopolysaccharide membranes. Conformational changes of the middle and GTPase effector domains expose the isoprenylated C terminus for membrane association. The α-helical middle domains form a parallel, crossover arrangement essential for coat formation and position the extended effector domain for intercalation into the lipopolysaccharide layer of gram-negative membranes. Nucleotide binding and hydrolysis create oligomeric scaffolds with contractile abilities that promote membrane extrusion and fragmentation. Our data offer a structural and mechanistic framework for understanding GBP1 effector functions in intracellular immunity.

Mechanism of nucleosomal H2A K13/15 monoubiquitination and adjacent dual monoubiquitination by RNF168.

The DNA damage repair regulatory protein RNF168, a monomeric RING-type E3 ligase, has a crucial role in regulating cell fate and DNA repair by specific and efficient ubiquitination of the adjacent K13 and K15 (K13/15) sites at the H2A N-terminal tail. However, understanding how RNF168 coordinates with its cognate E2 enzyme UbcH5c to site-specifically ubiquitinate H2A K13/15 has long been hampered by the lack of high-resolution structures of RNF168 and UbcH5c~Ub (ubiquitin) in complex with nucleosomes. Here we developed chemical strategies and determined the cryo-electron microscopy structures of the RNF168-UbcH5c~Ub-nucleosome complex captured in transient H2A K13/15 monoubiquitination and adjacent dual monoubiquitination reactions, providing a 'helix-anchoring' mode for monomeric E3 ligase RNF168 on nucleosome in contrast to the 'compass-binding' mode of dimeric E3 ligases. Our work not only provides structural snapshots of H2A K13/15 site-specific monoubiquitination and adjacent dual monoubiquitination but also offers a near-atomic-resolution structural framework for understanding pathogenic amino acid substitutions and physiological modifications of RNF168.

Structures of the Foamy virus fusion protein reveal an unexpected link with the F protein of paramyxo- and pneumoviruses.

Foamy viruses (FVs) constitute a subfamily of retroviruses. Their envelope (Env) glycoprotein drives the merger of viral and cellular membranes during entry into cells. The only available structures of retroviral Envs are those from human and simian immunodeficiency viruses from the subfamily of orthoretroviruses, which are only distantly related to the FVs. We report the cryo-electron microscopy structures of the FV Env ectodomain in the pre- and post-fusion states, which unexpectedly demonstrate structural similarity with the fusion protein (F) of paramyxo- and pneumoviruses, implying an evolutionary link between the viral fusogens. We describe the structural features that are unique to the FV Env and propose a mechanistic model for its conformational change, highlighting how the interplay of its structural elements could drive membrane fusion and viral entry. The structural knowledge on the FV Env now provides a framework for functional investigations, which can benefit the design of FV Env variants with improved features for use as gene therapy vectors.

Filament structures unveil the dynamic organization of human acetyl-CoA carboxylase.

Human acetyl-coenzyme A (CoA) carboxylases (ACCs) catalyze the carboxylation of acetyl-CoA, which is the rate-limiting step in fatty acid synthesis. The molecular mechanism underlying the dynamic organization of ACCs is largely unknown. Here, we determined the cryo-electron microscopy (EM) structure of human ACC1 in its inactive state, which forms a unique filament structure and is in complex with acetyl-CoA. We also determined the cryo-EM structure of human ACC1 activated by dephosphorylation and citrate treatment, at a resolution of 2.55 Å. Notably, the covalently linked biotin binds to a site that is distant from the acetyl-CoA binding site when acetyl-CoA is absent, suggesting a potential coordination between biotin binding and acetyl-CoA binding. These findings provide insights into the structural dynamics and regulatory mechanisms of human ACCs.

Structural insights into human zinc transporter ZnT1 mediated Zn2+ efflux

Zinc transporter 1 (ZnT1), the principal carrier of cytosolic zinc to the extracellular milieu, is important for cellular zinc homeostasis and resistance to zinc toxicity. Despite recent advancements in the structural characterization of various zinc transporters, the mechanism by which ZnTs-mediated Zn2+ translocation is coupled with H+ or Ca2+ remains unclear. To visualize the transport dynamics, we determined the cryo-electron microscopy (cryo-EM) structures of human ZnT1 at different functional states. ZnT1 dimerizes via extensive interactions between the cytosolic (CTD), the transmembrane (TMD), and the unique cysteine-rich extracellular (ECD) domains. At pH 7.5, both protomers adopt an outward-facing (OF) conformation, with Zn2+ ions coordinated at the TMD binding site by distinct compositions. At pH 6.0, ZnT1 complexed with Zn2+ exhibits various conformations [OF/OF, OF/IF (inward-facing), and IF/IF]. These conformational snapshots, together with biochemical investigation and molecular dynamic simulations, shed light on the mechanism underlying the proton-dependence of ZnT1 transport.

Structural insights into inhibitor mechanisms on immature HIV-1 Gag lattice revealed by high-resolution in situ single-particle cryo-EM.

HIV-1 inhibitors, such as Bevirimat (BVM) and Lenacapavir (LEN), block the production and maturation of infectious virions. However, their mechanisms remain unclear due to the absence of high-resolution structures for BVM complexes and LEN's structural data being limited to the mature capsid. Utilizing perforated virus-like particles (VLPs) produced from mammalian cells, we developed an approach to determine in situ cryo-electron microscopy (cryo-EM) structures of HIV-1 with inhibitors. This allowed for the first structural determination of the native immature HIV-1 particle with BVM and LEN bound inside the VLPs at high resolutions. Our findings offer a more accurate model of BVM engaging the Gag lattice and, importantly, demonstrate that LEN not only binds the mature capsid but also targets the immature lattice in a distinct manner. The binding of LEN induces a conformational change in the capsid protein (CA) region and alters the architecture of the Gag lattice, which may affect the maturation process. These insights expand our understanding of the inhibitory mechanisms of BVM and LEN on HIV-1 and provide valuable clues for the design of future inhibitors.

CryoSeek: A strategy for bioentity discovery using cryoelectron microscopy

Structural biology is experiencing a paradigm shift from targeted structural determination to structure-guided discovery of previously uncharacterized bioentities. We employed cryoelectron microscopy (cryo-EM) to analyze filtered water samples collected from the Tsinghua Lotus Pond. Here, we report the structural determination and characterization of two highly similar helical fibrils, named TLP-1a and TLP-1b, each approximately 8 nm in diameter with a 15-Å wide tunnel. These fibrils are assembled from a similar protein protomer, whose structure was conveniently automodeled in CryoNet. The protomer structure does not match any available experimental structures, but shares the same fold as many predicted structures of unknown functions. The amino-terminal β strand of protomer n + 4 inserts into a cleft in protomer n to complete an immunoglobulin (Ig)-like domain. This packing mechanism, known as donor-strand exchange (DSE), has been observed in several bacterial pilus assemblies, wherein the donor is protomer n + 1. Despite distinct shape and thickness, this reminiscence suggests that TLP-1a/b fibrils may represent uncharacterized bacterial pili. Our study demonstrates an emerging paradigm in structural biology, where high-resolution structural determination precedes and drives the identification and characterization of completely unknown objects.

Size-Dependent Core-Shell Fine Structures and Oxygen Evolution Activity of Electrochemical IrOx Nanoparticles Revealed by Cryogenic Electron Microscopy.

Electrochemically oxidized amorphous iridium oxides (IrOx) offer significantly improved electrocatalytic activities on the oxygen evolution reaction (OER) compared to crystalline IrO2, yet the origin of their decent activity and their size-dependent properties have not been fully understood. An important argument is the formation of deprotonated oxygen species not only at the topmost surface but also at the near surface, which creates an electrophilic character that activates the OER electrocatalysis. However, high spatial resolution identification of the electrophilic oxygen species remains unachieved. We address this hitherto-unresolved problem on size-selected electrochemical IrOx nanoparticles (NPs) by using cryogenic scanning transmission electron microscopy combined with electron energy loss spectroscopy, which enables simultaneous atomic detection of the near surface compositional and electronic structures with minimal damage that are further correlated with their size-dependent OER activities. Depending on the particle size, the electrochemical IrOx NPs showed distinctly different core-shell fine structures ranging from amorphous and hydrous IrOxHy NPs to a "metallic Ir core/sub-stoichiometric IrOx interlayer/amorphous IrOxHy shell" NP structure. Moreover, the formation of deprotonated, electrophilic oxygen is directly identified at the substoichiometric IrOx interface layer. These features account for a previously unestablished particle size effect of the electrochemical IrOx NPs, showing increasing water oxidation reactivity with an increasing nanoparticle size. Our results provide important insights into how subsurface oxygen chemistry controls the surface reactivity in the nanoscale Ir-based OER electrocatalysts.

Micro-electromechanical system-based cryogenic and heating in situ transmission electron microscopy for investigating phase transitions and domain evolution in single-crystal BaTiO3

Investigating phase transitions between ferroelectric states is crucial for understanding the nucleation, dynamics, and kinetics of domains, both before and after transformation. Here, we assess all phase transitions and domain evolutions in single-crystal BaTiO3 by implementing microelectromechanical systems (MEMS)-based in situ cryogenic (cryo-) and heating transmission electron microscopy (TEM) by continuously varying sample temperatures from -175 °C to 200 °C. Every possible phase-cubic, tetragonal, orthorhombic, and rhombohedral - was identified. An ultra-stable imaging condition was achieved with a mean drift speed of 1.52 nm/min, providing unique opportunities for atomic resolution in situ scanning TEM with a wide temperature range. Furthermore, domain nucleation and evolution across phase transitions were investigated using complementary dielectric measurements, optical microscopy, and a phenomenological model. This study underscores the effectiveness and utility of MEMS-based in situ cryo-/heating TEM in revealing phase transitions and domain structures in ferroelectric materials.

MreC-MreD structure reveals a multifaceted interface that controls MreC conformation.

The peptidoglycan (PG) cell wall is critical for bacterial growth and survival and is a primary antibiotic target. MreD is an essential accessory factor of the Rod complex, which carries out PG synthesis during elongation, yet little is known about how MreD facilitates this process. Here, we present the cryo-electron microscopy structure of Thermus thermophilus MreD in complex with another essential Rod complex component, MreC. The structure reveals that a periplasmic-facing pocket of MreD interacts with multiple membrane-proximal regions of MreC. We use single-molecule FRET to show that MreD controls the conformation of MreC through these contacts, inducing a state primed for Rod complex activation. Using E. coli as a model, we demonstrate that disrupting these interactions abolishes Rod complex activity in vivo . Our findings reveal the role of MreD in bacterial cell shape determination and highlight its potential as an antibiotic target.

Structural basis for Vipp1 membrane binding: from loose coats and carpets to ring and rod assemblies.

Vesicle-inducing protein in plastids 1 (Vipp1) is critical for thylakoid membrane biogenesis and maintenance. Although Vipp1 has recently been identified as a member of the endosomal sorting complexes required for transport III superfamily, it is still unknown how Vipp1 remodels membranes. Here, we present cryo-electron microscopy structures of Synechocystis Vipp1 interacting with membranes: seven structures of helical and stacked-ring assemblies at 5-7-Å resolution engulfing membranes and three carpet structures covering lipid vesicles at ~20-Å resolution using subtomogram averaging. By analyzing ten structures of N-terminally truncated Vipp1, we show that helix α0 is essential for membrane tubulation and forms the membrane-anchoring domain of Vipp1. Lastly, using a conformation-restrained Vipp1 mutant, we reduced the structural plasticity of Vipp1 and determined two structures of Vipp1 at 3.0-Å resolution, resolving the molecular details of membrane-anchoring and intersubunit contacts of helix α0. Our data reveal membrane curvature-dependent structural transitions from carpets to rings and rods, some of which are capable of inducing and/or stabilizing high local membrane curvature triggering membrane fusion.

Structural mechanism of HP1⍺-dependent transcriptional repression and chromatin compaction

Heterochromatin protein 1 (HP1) plays a central role in establishing and maintaining constitutive heterochromatin. However, the mechanisms underlying HP1-nucleosome interactions and their contributions to heterochromatin functions remain elusive. Here, we present the cryoelectron microscopy (cryo-EM) structure of an HP1α dimer bound to an H2A.Z-nucleosome, revealing two distinct HP1α-nucleosome interfaces. The primary HP1α binding site is located at the N terminus of histone H3, specifically at the trimethylated lysine 9(K9me3) region, while a secondary binding site is situated near histone H2B, close to nucleosome superhelical location 4 (SHL4). Our biochemical data further demonstrates that HP1α binding influences the dynamics of DNA on the nucleosome. It promotes DNA unwrapping near the nucleosome entry and exit sites while concurrently restricting DNA accessibility in the vicinity of SHL4. Our study offers a model for HP1α-mediated heterochromatin maintenance and gene silencing. It also sheds light on the H3K9me-independent role of HP1 in responding to DNA damage.

Ribosomes hibernate on mitochondria during cellular stress.

Cell survival under nutrient-deprived conditions relies on cells' ability to adapt their organelles and rewire their metabolic pathways. In yeast, glucose depletion induces a stress response mediated by mitochondrial fragmentation and sequestration of cytosolic ribosomes on mitochondria. This cellular adaptation promotes survival under harsh environmental conditions; however, the underlying mechanism of this response remains unknown. Here, we demonstrate that upon glucose depletion protein synthesis is halted. Cryo-electron microscopy structure of the ribosomes show that they are devoid of both tRNA and mRNA, and a subset of the particles depicted a conformational change in rRNA H69 that could prevent tRNA binding. Our in situ structural analyses reveal that the hibernating ribosomes tether to fragmented mitochondria and establish eukaryotic-specific, higher-order storage structures by assembling into oligomeric arrays on the mitochondrial surface. Notably, we show that hibernating ribosomes exclusively bind to the outer mitochondrial membrane via the small ribosomal subunit during cellular stress. We identify the ribosomal protein Cpc2/RACK1 as the molecule mediating ribosomal tethering to mitochondria. This study unveils the molecular mechanism connecting mitochondrial stress with the shutdown of protein synthesis and broadens our understanding of cellular responses to nutrient scarcity and cell quiescence.

From Ions to Crystals: A Comprehensive View of the Non-Classical Nucleation of Calcium Sulfate.

After years ofintensive research andnumerous important observations, our understanding of the early stages of crystallization is still limited due to the complexity of the underlying processes and their elusive character. In the present work, we provide a detailed view on the nucleation of calcium sulfate mineralization - an abundant mineral with broad use in construction industry - in aqueous systems at ambient conditions. As experimental basis, a co-titration procedure with potentiometric, turbidimetric and conductometric detection was developed, allowing solution speciation and the formation of crystallization precursors to be monitored quantitatively as the level of nominal (super)saturation gradually increases. The nature and spatiotemporal evolution of these precursors was further elucidated by time-resolved small-angle X-ray scattering (SAXS) and analytical ultracentrifugation (AUC) experiments, complemented by cryogenic transmission electron microscopy (cryo-TEM) as a direct imaging technique. The results reveal how ions associate into nanometric primary species, which subsequently aggregate and develop anisotropic order by intrinsic structural reorganization. Our observations challenge the common understanding of fundamental notions such as the nucleation barrier or the meaning of supersaturation, with broad implications for mineralization phenomena in general and the formation of calcium sulfate in geochemical settings and industrial applications in particular.