Translation dynamics in human cells visualized at high resolution reveal cancer drug action

Cryo-EM of Mitochondrial Complex I and ATP Synthase

Cryo-electron microscopy (cryo-EM) is the method of choice for investigating the structures of membrane protein complexes at high resolution under near-native conditions. This review focuses on recent cryo-EM work on mitochondrial complex I and ATP synthase. Single-particle cryo-EM structures of complex I from mammals, plants, and fungi extending to a resolution of 2 Å show different functional states, indicating consistent conformational changes of loops near the Q binding site, clusters of internal water molecules in the membrane arm, and an α-π transition in a membrane-spanning helix that opens and closes the proton transfer path. Cryo-EM structures of ATP synthase dimers from mammalian, yeast, and Polytomella mitochondria show several rotary states at a resolution of 2.7 to 3.5 Å. The new structures of complex I and ATP synthase are important steps along the way toward understanding the detailed molecular mechanisms of both complexes. Cryo-electron tomography and subtomogram averaging have the potential to resolve their high-resolution structures in situ.

Capturing eukaryotic ribosome dynamics in situ at high resolution

Many protein complexes are highly dynamic in cells; thus, characterizing their conformational changes in cells is crucial for unraveling their functions. Here, using cryo-electron microscopy, 451,700 ribosome particles from Saccharomyces cerevisiae cell lamellae were obtained to solve the 60S region to 2.9-Å resolution by in situ single-particle analysis. Over 20 distinct conformations were identified by three-dimensional classification with resolutions typically higher than 4 Å. These conformations were used to reconstruct a complete elongation cycle of eukaryotic translation with elongation factors (eEFs). We found that compact eEF2 anchors to the partially rotated ribosome after subunit rolling and hypothesize that it stabilizes the local conformation for peptidyl transfer. Moreover, open-eEF3 binding to a fully rotated ribosome was observed, whose conformational change was coupled with head swiveling and body back-rotation of the 40S subunit.

Structurally heterogeneous ribosomes cooperate in protein synthesis in bacterial cells

Ribosome heterogeneity is a paradigm in biology, pertaining to the existence of structurally distinct populations of ribosomes within a single organism or cell. This concept suggests that structurally distinct pools of ribosomes have different functional properties and may be used to translate specific mRNAs. However, it is unknown to what extent structural heterogeneity reflects genuine functional specialization rather than stochastic variations in ribosome assembly. Here, we address this question by combining cryo-electron microscopy and tomography to observe individual structurally heterogeneous ribosomes in bacterial cells. We show that 70% of ribosomes in Psychrobacter urativorans contain a second copy of the ribosomal protein bS20 at a previously unknown binding site on the large ribosomal subunit. We then determine that this second bS20 copy appears to be functionally neutral. This demonstrates that ribosome heterogeneity does not necessarily lead to functional specialization, even when it involves significant variations such as the presence or absence of a ribosomal protein. Instead, we show that heterogeneous ribosomes can cooperate in general protein synthesis rather than specialize in translating discrete populations of mRNA.

Xenon plasma focused ion beam lamella fabrication on high-pressure frozen specimens for structural cell biology

Cryo focused ion beam lamella preparation is a potent tool for in situ structural biology, enabling the study of macromolecules in their native cellular environments. However, throughput is currently limited, especially for thicker, more biologically complex samples. We describe how xenon plasma focused ion beam milling can be used for routine bulk milling of thicker, high-pressure frozen samples. We demonstrate lamellae preparation with a high success rate on these samples and determine a 4.0 Å structure of the Escherichia coli ribosome on these lamellae using sub volume averaging. We determine the effects on sample integrity of increased ion currents up to 60 nA during bulk milling of thicker planar samples, showing no measurable damage to macromolecules beyond an amorphous layer on the backside of the lamellae. The use of xenon results in substantial structural damage to particles up to approximately 30 nm in depth from the milled surfaces, and the effects of damage become negligibly small by 45 nm. Our results outline how the use of high currents using xenon plasma focused ion beam milling may be integrated into FIB milling regimes for preparing thin lamellae for high-resolution in situ structural biology.

A subcellular map of translational machinery composition and regulation at the single-molecule level

Millions of ribosomes are packed within mammalian cells, yet we lack tools to visualize them in toto and characterize their subcellular composition. In this study, we present ribosome expansion microscopy (RiboExM) to visualize individual ribosomes and an optogenetic proximity-labeling technique (ALIBi) to probe their composition. We generated a super-resolution ribosomal map, revealing subcellular translational hotspots and enrichment of 60S subunits near polysomes at the endoplasmic reticulum (ER). We found that Lsg1 tethers 60S to the ER and regulates translation of select proteins. Additionally, we discovered ribosome heterogeneity at mitochondria guiding translation of metabolism-related transcripts. Lastly, we visualized ribosomes in neurons, revealing a dynamic switch between monosomes and polysomes in neuronal translation. Together, these approaches enable exploration of ribosomal localization and composition at unprecedented resolution.

Nuclear pore permeability and fluid flow are modulated by its dilation state

Changing environmental conditions necessitate rapid adaptation of cytoplasmic and nuclear volumes. We use the slime mold Dictyostelium discoideum, known for its ability to tolerate extreme changes in osmolarity, to assess which role nuclear pore complexes (NPCs) play in achieving nuclear volume adaptation and relieving mechanical stress. We capitalize on the unique properties of D. discoideum to quantify fluid flow across NPCs. D. discoideum has an elaborate NPC structure in situ. Its dilation state affects NPC permeability for nucleocytosolic flow. Based on mathematical concepts adapted from hydrodynamics, we conceptualize this phenomenon as porous flow across NPCs, which is distinct from canonically characterized modes of nucleocytoplasmic transport because of its dependence on pressure. Viral NPC blockage decreased nucleocytosolic flow. Our results may be relevant for any biological conditions that entail rapid nuclear size adaptation, including metastasizing cancer cells, migrating cells, or differentiating tissues.

Rapid structural analysis of bacterial ribosomes in situ

Rapid structural analysis of purified proteins and their complexes has become increasingly common thanks to key methodological advances in cryo-electron microscopy (cryo-EM) and associated data processing software packages. In contrast, analogous structural analysis in cells via cryo-electron tomography (cryo-ET) remains challenging due to critical technical bottlenecks, including low-throughput sample preparation and imaging, and laborious data processing methods. Here, we describe a rapid in situ cryo-ET sample preparation and data analysis workflow that results in the routine determination of sub-nm resolution ribosomal structures. We apply this workflow to E. coli, producing a 5.8 Å structure of the 70S ribosome from cells in less than 10 days and facilitating the discovery of a minor population of 100S-like disomes. We envision our approach to be widely applicable to related bacterial samples.

Practical Guide for Implementing Cryogenic Electron Microscopy Structure Determination in Dermatology Research

Cryogenic electron microscopy (cryo-EM) and cryogenic electron tomography allow determination of structures of biological macromolecules in their native state in solution at atomic or near-atomic resolution. Recent advances in cryo-EM, that is, the "resolution revolution," and the establishment of national centers for cryo-EM data collection have remarkably expanded its applicability to practically all areas of health-related research. In this methods review, we highlighted the basics of single-particle cryo-EM and its application in the research of macromolecules and macromolecular complexes related to dermatology. We further illustrated a few examples of how this approach can be incorporated into drug development and study.

Methods to Study Poxvirus Structures by Cryo-EM Imaging Modalities

Poxviruses are double-stranded DNA viruses that represent the largest known highly pathogenic viruses infecting humans. They undergo dramatic morphological changes during their maturation process, resulting in structural differences between each virion, and their surface is decorated with more than a dozen randomly distributed surface proteins that facilitate viral entry. These are the main reasons poxviruses have eluded high-resolution structure determination. Over the last three decades, cryo-EM has developed into a mature technology that can increasingly overcome such problems of structural heterogeneity through advances in microscope technology and image processing algorithms. Here, we discuss the essential current modalities in cryo-EM, which promise to solve the structure of poxviruses in parts and as entire virions at near-atomic resolution. With a focus on cryo modalities, we provide an overview of methods, including volume microscopy by plasma ion beam milling, focused ion beam lamella preparation, subtomogram averaging, and single particle averaging. Protocols for poxvirus propagation, purification, and imaging by cryo-EM are presented. This chapter is aimed at experts and nonexpert researchers to help facilitate entry into the structural biology of this critical field in virology.

In situ analysis reveals the TRiC duty cycle and PDCD5 as an open-state cofactor

The ring-shaped chaperonin T-complex protein ring complex (TRiC; also known as chaperonin containing TCP-1, CCT) is an ATP-driven protein-folding machine that is essential for maintenance of cellular homeostasis1,2. Its dysfunction is related to cancer and neurodegenerative disease3,4. Despite its importance, how TRiC works in the cell remains unclear. Here we structurally analysed the architecture, conformational dynamics and spatial organization of the chaperonin TRiC in human cells using cryo-electron tomography. We resolved distinctive open, closed, substrate-bound and prefoldin-associated states of TRiC, and reconstructed its duty cycle in situ. The substrate-bound open and symmetrically closed TRiC states were equally abundant. Closed TRiC containing substrate forms distinctive clusters, indicative of spatial organization. Translation inhibition did not fundamentally change the distribution of duty cycle intermediates, but reduced substrate binding for all states as well as cluster formation. From our in-cell structures, we identified the programmed cell death protein 5 (PDCD5) as an interactor that specifically binds to almost all open but not closed TRiC, in a position that is compatible with both substrate and prefoldin binding. Our data support a model in which TRiC functions at near full occupancy to fold newly synthesized proteins inside cells. Defining the TRiC cycle and function inside cells lays the foundation to understand its dysfunction during cancer and neurodegeneration.

Structural dynamics of human ribosomes in situ reconstructed by exhaustive high-resolution template matching

Protein synthesis is central to life and requires the ribosome, which catalyzes the stepwise addition of amino acids to a polypeptide chain by undergoing a sequence of structural transformations. Here, we employed high-resolution template matching (HRTM) on cryoelectron microscopy (cryo-EM) images of directly cryofixed living cells to obtain a set of ribosomal configurations covering the entire elongation cycle, with each configuration occurring at its native abundance. HRTM's position and orientation precision and ability to detect small targets (∼300 kDa) made it possible to order these configurations along the reaction coordinate and to reconstruct molecular features of any configuration along the elongation cycle. Visualizing the cycle's structural dynamics by combining a sequence of >40 reconstructions into a 3D movie readily revealed component and ligand movements, some of them surprising, such as spring-like intramolecular motion, providing clues about the molecular mechanisms involved in some still mysterious steps during chain elongation.

Ubiquitin's Conformational Heterogeneity as Discerned by Nuclear Magnetic Resonance Spectroscopy

Visualizing a protein's molecular motions has been a long standing topic of research in the biophysics community. Largely this has been done by exploiting nuclear magnetic resonance spectroscopy (NMR), and arguably no protein's molecular motions have been better characterized by NMR than that of ubiquitin (Ub), a 76 amino acid polypeptide essential in ubiquitination-a key regulatory system within cells. Herein, we discuss ubiquitin's conformational plasticity as visualized, at atomic resolution, by more than 35 years of NMR work. In our discussions we point out the differences between data acquired in vitro, ex vivo, as well as in vivo and stress the need to investigate Ub's conformational plasticity in more biologically representative backgrounds.

The big chill: Growth of in situ structural biology with cryo-electron tomography

In situ structural biology with cryo-electron tomography (cryo-ET) and subtomogram averaging (StA) is evolving as a major method to understand the structure, function, and interactions of biological molecules in cells in a single experiment. Since its inception, the method has matured with some stellar highlights and with further opportunities to broaden its applications. In this short review, I want to provide a personal perspective on the developments in cryo-ET as I have seen it for the last ~20 years and outline the major steps that led to its success. This perspective highlights cryo-ET with my eyes as a junior researcher and my view on the present and past developments in hardware and software for in situ structural biology with cryo-ET.

Death by ribosome

Next to their essential role as protein production factories, ribosomes serve as molecular sensors of cell stress. Stalled and collided ribosomes trigger specific stress signaling, including the ribotoxic stress response (RSR). The RSR is initiated by the mitogen-activated protein (MAP)-3 kinase ZAKα in response to a plethora of translational aberrations, leading to activation of the stress-activated MAP kinases p38 and jun N-terminal kinase (JNK). Recent insights have highlighted an important role for the RSR pathway in triggering programmed cell death processes, including apoptosis and pyroptosis, in a broad range of physiologically relevant conditions. In this review, we summarize recent work on known links between programmed and accidental ribosome toxicity, RSR signaling, and cell death.

Conformational penalties: New insights into nucleic acid recognition

The energy cost accompanying changes in the structures of nucleic acids when they bind partner molecules is a significant but underappreciated thermodynamic contribution to binding affinity and specificity. This review highlights recent advances in measuring conformational penalties and determining their contribution to the recognition, folding, and regulatory activities of nucleic acids. Notable progress includes methods for measuring and structurally characterizing lowly populated conformational states, obtaining ensemble information in high throughput, for large macromolecular assemblies, and in complex cellular environments. Additionally, quantitative and predictive thermodynamic models have been developed that relate conformational penalties to nucleic acid-protein association and cellular activity. These studies underscore the crucial role of conformational penalties in nucleic acid recognition.

Decoding the molecular script of 2'-O-ribomethylation: Implications across CNS disorders

Emerging evidence underscores the critical role of impaired mRNA translation in various neurobiological conditions. Ribosomal RNA (rRNA), essential for protein synthesis, undergoes crucial post-transcriptional modifications such as 2'-O-ribose methylation, pseudouridylation, and base modifications. These modifications, particularly 2'-O-ribose methylation is vital for stabilizing rRNA structures and optimizing translation efficiency by regulating RNA integrity and its interactions with proteins. Concentrated in key regions like decoding sites and the peptidyl transferase center, dysregulation of these modifications can disrupt ribosomal function, contributing to the pathogenesis of diverse neurological conditions, including mental health disorders, developmental abnormalities, and neurodegenerative diseases. Mechanistically, 2'-O-ribose methylation involves interactions between small nucleolar RNAs (snoRNAs), snoRNPs, and fibrillarin, forming a complex regulatory network crucial for maintaining ribosomal integrity and function. Recent research highlights the association of defective ribosome biogenesis with a spectrum of CNS disorders, emphasizing the importance of understanding rRNA mechanisms in disease pathology. This review focuses on the pivotal role of 2'-O-ribose methylation in shaping ribosomal function and its potential implications for unraveling the pathophysiology of CNS disorders. Insights gained from studying these RNA modifications could pave the way for new therapeutic strategies targeting ribosomal dysfunction and associated neuropathological conditions, advancing precision medicine and therapeutic interventions.

The ribosome comes to life

The ribosome, together with its tRNA substrates, links genotype to phenotype by translating the genetic information carried by mRNA into protein. During the past half-century, the structure and mechanisms of action of the ribosome have emerged from mystery and confusion. It is now evident that the ribosome is an ancient RNA-based molecular machine of staggering structural complexity and that it is fundamentally similar in all living organisms. The three central functions of protein synthesis-decoding, catalysis of peptide bond formation, and translocation of mRNA and tRNA-are based on elegant mechanisms that evolved from the properties of RNA, the founding macromolecule of life. Moreover, all three of these functions (and even life itself) seem to proceed in defiance of entropy. Protein synthesis thus appears to exploit both the energy of GTP hydrolysis and peptide bond formation to constrain the directionality and accuracy of events taking place on the ribosome.

An image processing pipeline for electron cryo-tomography in RELION-5

Electron tomography of frozen, hydrated samples allows structure determination of macromolecular complexes that are embedded in complex environments. Provided that the target complexes may be localised in noisy, three-dimensional tomographic reconstructions, averaging images of multiple instances of these molecules can lead to structures with sufficient resolution for de novo atomic modelling. Although many research groups have contributed image processing tools for these tasks, a lack of standardisation and interoperability represents a barrier for newcomers to the field. Here, we present an image processing pipeline for electron tomography data in RELION-5, with functionality ranging from the import of unprocessed movies to the automated building of atomic models in the final maps. Our explicit definition of metadata items that describe the steps of our pipeline has been designed for interoperability with other software tools and provides a framework for further standardisation.

Kinetic mechanism and determinants of EF-P recruitment to translating ribosomes

EF-P is a translation factor that facilitates the formation of peptide bonds between consecutive prolines. Using FRET between EF-P and ribosomal protein bL33, we studied dynamics and specificity of EF-P binding to the ribosome. Our findings reveal that EF-P rapidly scans for a free E site and can bind to any ribosome containing a P-site tRNA, regardless of the ribosome's functional state. The interaction with uL1 is essential for EF-P binding, while the β-Lys modification of EF-P doubles the association rate. Specific interactions with the D-loop of tRNAPro or tRNAfMet and via the β-Lys group with the tRNA in the peptidyl transferase center reduce the rate of EF-P dissociation from the ribosome, providing the specificity for complexes that need help in catalyzing peptide bond formation. The nature of the E-site codon has little effect on EF-P binding kinetics. Although EF-P dissociation is reduced upon recognizing its correct tRNA substrate, it remains sufficiently rapid compared to tRNA translocation and does not affect the translocation rate. These results highlight the importance of EF-P's scanning-engagement mechanism for dynamic substrate recognition during rapid translation.

A machine learning approach uncovers principles and determinants of eukaryotic ribosome pausing

Nonuniform local translation speed dictates diverse protein biogenesis outcomes. To unify known and uncover unknown principles governing eukaryotic elongation rate, we developed a machine learning pipeline to analyze RiboSeq datasets. We find that the chemical nature of the incoming amino acid determines how codon optimality influences elongation rate, with hydrophobic residues more dependent on transfer RNA (tRNA) levels than charged residues. Unexpectedly, we find that wobble interactions exert a widespread effect on elongation pausing, with wobble-mediated decoding being slower than Watson-Crick decoding, irrespective of tRNA levels. Applying our ribosome pausing principles to ribosome collisions reveals that disomes arise upon apposition of fast-decoding and slow-decoding signatures. We conclude that codon choice and tRNA pools are evolutionarily constrained to harmonize elongation rate with cotranslational folding while minimizing wobble pairing and deleterious stalling.

The future of integrated structural biology

Instruct-ERIC, "the European Research Infrastructure Consortium for Structural biology research," is a pan-European distributed research infrastructure making high-end technologies and methods in structural biology available to users. Here, we describe the current state-of-the-art of integrated structural biology and discuss potential future scientific developments as an impulse for the scientific community, many of which are located in Europe and are associated with Instruct. We reflect on where to focus scientific and technological initiatives within the distributed Instruct research infrastructure. This review does not intend to make recommendations on funding requirements or initiatives directly, neither at the national nor the European level. However, it addresses future challenges and opportunities for the field, and foresees the need for a stronger coordination within the European and international research field of integrated structural biology to be able to respond timely to thematic topics that are often prioritized by calls for funding addressing societal needs.

Expanding insights from in situ cryo-EM

The combination of cryo-electron tomography and subtomogram analysis affords 3D high-resolution views of biological macromolecules in their native cellular environment, or in situ. Streamlined methods for acquiring and processing these data are advancing attainable resolutions into the realm of drug discovery. Yet regardless of resolution, structure prediction driven by artificial intelligence (AI) combined with subtomogram analysis is becoming powerful in understanding macromolecular assemblies. Automated and AI-assisted data mining is increasingly necessary to cope with the growing wealth of tomography data and to maximize the information obtained from them. Leveraging developments from AI and single-particle analysis could be essential in fulfilling the potential of in situ cryo-EM. Here, we highlight new developments for in situ cryo-EM and the emerging potential for AI in this process.

On the response of elongating ribosomes to forces opposing translocation

The elongation phase of protein synthesis is a cyclic, steady-state process. It follows that its directionality is determined by the thermodynamics of the accompanying chemical reactions, which strongly favor elongation. Its irreversibility is guaranteed by its coupling to those reactions, rather being a consequence of any of the conformational changes that occur as it unfolds. It also follows that, in general, the rate of elongation is not proportional to the forward rate constants of any of its steps, including its final, mechano-chemical step, translocation. Instead, the reciprocal of the rate of elongation should be linearly related to the reciprocal of those rate constants. When the results of experiments done a decade ago to measure the effect that forces opposing translocation have on the rate of elongation are reinterpreted in light of these findings, it becomes clear that translocation was rate limiting under conditions in which those experiments were done, and that it is likely to be a Brownian ratchet process, as was concluded earlier.

DomainFit: Identification of protein domains in cryo-EM maps at intermediate resolution using AlphaFold2-predicted models

Cryoelectron microscopy (cryo-EM) has revolutionized the structural determination of macromolecular complexes. With the paradigm shift to structure determination of highly complex endogenous macromolecular complexes ex vivo and in situ structural biology, there are an increasing number of structures of native complexes. These complexes often contain unidentified proteins, related to different cellular states or processes. Identifying proteins at resolutions lower than 4 Å remains challenging because side chains cannot be visualized reliably. Here, we present DomainFit, a program for semi-automated domain-level protein identification from cryo-EM maps, particularly at resolutions lower than 4 Å. By fitting domains from AlphaFold2-predicted models into cryo-EM maps, the program performs statistical analyses and attempts to identify the domains and protein candidates forming the density. Using DomainFit, we identified two microtubule inner proteins, one of which contains a CCDC81 domain and is exclusively localized in the proximal region of the doublet microtubule in Tetrahymena thermophila.

Structural biology in cellulo: Minding the gap between conceptualization and realization

Recent technological advances have deepened our perception of cellular structure. However, most structural data doesn't originate from intact cells, limiting our understanding of cellular processes. Here, we discuss current and future developments that will bring us towards a structural picture of the cell. Electron cryotomography is the standard bearer, with its ability to provide in cellulo snapshots. Single-particle electron microscopy (of purified biomolecules and of complex mixtures) and covalent crosslinking combined with mass spectrometry also have significant roles to play, as do artificial intelligence algorithms in their many guises. To integrate these multiple approaches, data curation and standardisation will be critical - as is the need to expand efforts beyond our current protein-centric view to the other (macro)molecules that sustain life.

CryoDRGN-ET: deep reconstructing generative networks for visualizing dynamic biomolecules inside cells

Advances in cryo-electron tomography (cryo-ET) have produced new opportunities to visualize the structures of dynamic macromolecules in native cellular environments. While cryo-ET can reveal structures at molecular resolution, image processing algorithms remain a bottleneck in resolving the heterogeneity of biomolecular structures in situ. Here, we introduce cryoDRGN-ET for heterogeneous reconstruction of cryo-ET subtomograms. CryoDRGN-ET learns a deep generative model of three-dimensional density maps directly from subtomogram tilt-series images and can capture states diverse in both composition and conformation. We validate this approach by recovering the known translational states in Mycoplasma pneumoniae ribosomes in situ. We then perform cryo-ET on cryogenic focused ion beam-milled Saccharomyces cerevisiae cells. CryoDRGN-ET reveals the structural landscape of S. cerevisiae ribosomes during translation and captures continuous motions of fatty acid synthase complexes inside cells. This method is openly available in the cryoDRGN software.

Cryo-focused ion beam for in situ structural biology: State of the art, challenges, and perspectives

Cryogenic-focused ion beam (cryo-FIB) instruments became essential for high-resolution imaging in cryo-preserved cells and tissues. Cryo-FIBs use accelerated ions to thin samples that would otherwise be too thick for cryo-electron microscopy (cryo-EM). This allows visualizing cellular ultrastructures in near-native frozen hydrated states. This review describes the current state-of-the-art capabilities of cryo-FIB technology and its applications in structural cell and tissue biology. We discuss recent advances in instrumentation, imaging modalities, automation, sample preparation protocols, and targeting techniques. We outline remaining challenges and future directions to make cryo-FIB more precise, enable higher throughput, and be widely accessible. Further improvements in targeting, efficiency, robust sample preparation, emerging ion sources, automation, and downstream electron tomography have the potential to reveal intricate molecular architectures across length scales inside cells and tissues. Cryo-FIB is poised to become an indispensable tool for preparing native biological systems in situ for high-resolution 3D structural analysis.

Visualizing the translation landscape in human cells at high resolution

Obtaining comprehensive structural descriptions of macromolecules within their natural cellular context holds immense potential for understanding fundamental biology and improving health. Here, we present the landscape of protein synthesis inside human cells in unprecedented detail obtained using an approach which combines automated cryo-focused ion beam (FIB) milling and in situ single-particle cryo-electron microscopy (cryo-EM). With this in situ cryo-EM approach we resolved a 2.19 Å consensus structure of the human 80S ribosome and unveiled its 21 distinct functional states, nearly all higher than 3 Å resolution. In contrast to in vitro studies, we identified protein factors, including SERBP1, EDF1 and NAC/3, not enriched on purified ribosomes. Most strikingly, we observed that SERBP1 binds to the ribosome in almost all translating and non-translating states to bridge the 60S and 40S ribosomal subunits. These newly observed binding sites suggest that SERBP1 may serve an important regulatory role in translation. We also uncovered a detailed interface between adjacent translating ribosomes which can form the helical polysome structure. Finally, we resolved high-resolution structures from cells treated with homoharringtonine and cycloheximide, and identified numerous polyamines bound to the ribosome, including a spermidine that interacts with cycloheximide bound at the E site of the ribosome, underscoring the importance of high-resolution in situ studies in the complex native environment. Collectively, our work represents a significant advancement in detailed structural studies within cellular contexts.

Repurposing homoharringtonine for thyroid cancer treatment through TIMP1/FAK/PI3K/AKT signaling pathway

Homoharringtonine (HHT), an alkaloid isolated from Cephalotaxus, is an effective anti-leukemia agent and exhibits inhibitory effects in various solid tumors. However, the impacts of HHT treatment on thyroid cancer (TC) remain unclear. Our findings demonstrated that HHT exhibited remarkable anti-TC activity that involved inhibiting cell proliferation, invasion, and migration, as well as inducing apoptosis. Proteomics analysis revealed that the expression of the tissue inhibitor of metalloproteinase 1 (TIMP1) was downregulated in TC cells after HHT treatment. TIMP1 overexpression promoted TC progression and partially reversed the anti-TC effects of HHT, while TIMP1 downregulation inhibited TC progression and enhanced the anti-TC effects of HHT. Furthermore, TIMP1 re-expression attenuated the enhancement of anti-TC effects of HHT induced by TIMP1 knockdown. Mechanistically, HHT exerted anti-TC effects by downregulating TIMP1 expression and then inactivating the FAK/PI3K/AKT signaling pathway. Taken together, our study demonstrated that HHT could inhibit TC progression by inhibiting the TIMP1/FAK/PI3K/AKT signaling pathway.

FilamentID reveals the composition and function of metabolic enzyme polymers during gametogenesis

Gamete formation and subsequent offspring development often involve extended phases of suspended cellular development or even dormancy. How cells adapt to recover and resume growth remains poorly understood. Here, we visualized budding yeast cells undergoing meiosis by cryo-electron tomography (cryoET) and discovered elaborate filamentous assemblies decorating the nucleus, cytoplasm, and mitochondria. To determine filament composition, we developed a "filament identification" (FilamentID) workflow that combines multiscale cryoET/cryo-electron microscopy (cryoEM) analyses of partially lysed cells or organelles. FilamentID identified the mitochondrial filaments as being composed of the conserved aldehyde dehydrogenase Ald4ALDH2 and the nucleoplasmic/cytoplasmic filaments as consisting of acetyl-coenzyme A (CoA) synthetase Acs1ACSS2. Structural characterization further revealed the mechanism underlying polymerization and enabled us to genetically perturb filament formation. Acs1 polymerization facilitates the recovery of chronologically aged spores and, more generally, the cell cycle re-entry of starved cells. FilamentID is broadly applicable to characterize filaments of unknown identity in diverse cellular contexts.

Bactericidal effect of tetracycline in E. coli strain ED1a may be associated with ribosome dysfunction

Ribosomes translate the genetic code into proteins. Recent technical advances have facilitated in situ structural analyses of ribosome functional states inside eukaryotic cells and the minimal bacterium Mycoplasma. However, such analyses of Gram-negative bacteria are lacking, despite their ribosomes being major antimicrobial drug targets. Here we compare two E. coli strains, a lab E. coli K-12 and human gut isolate E. coli ED1a, for which tetracycline exhibits bacteriostatic and bactericidal action, respectively. Using our approach for close-to-native E. coli sample preparation, we assess the two strains by cryo-ET and visualize their ribosomes at high resolution in situ. Upon tetracycline treatment, these exhibit virtually identical drug binding sites, yet the conformation distribution of ribosomal complexes differs. While K-12 retains ribosomes in a translation-competent state, tRNAs are lost in the vast majority of ED1a ribosomes. These structural findings together with the proteome-wide abundance and thermal stability assessments indicate that antibiotic responses are complex in cells and can differ between different strains of a single species, thus arguing that all relevant bacterial strains should be analyzed in situ when addressing antibiotic mode of action.

High-confidence 3D template matching for cryo-electron tomography

Visual proteomics attempts to build atlases of the molecular content of cells but the automated annotation of cryo electron tomograms remains challenging. Template matching (TM) and methods based on machine learning detect structural signatures of macromolecules. However, their applicability remains limited in terms of both the abundance and size of the molecular targets. Here we show that the performance of TM is greatly improved by using template-specific search parameter optimization and by including higher-resolution information. We establish a TM pipeline with systematically tuned parameters for the automated, objective and comprehensive identification of structures with confidence 10 to 100-fold above the noise level. We demonstrate high-fidelity and high-confidence localizations of nuclear pore complexes, vaults, ribosomes, proteasomes, fatty acid synthases, lipid membranes and microtubules, and individual subunits inside crowded eukaryotic cells. We provide software tools for the generic implementation of our method that is broadly applicable towards realizing visual proteomics.

FAM86A methylation of eEF2 links mRNA translation elongation to tumorigenesis

eEF2 post-translational modifications (PTMs) can profoundly affect mRNA translation dynamics. However, the physiologic function of eEF2K525 trimethylation (eEF2K525me3), a PTM catalyzed by the enzyme FAM86A, is unknown. Here, we find that FAM86A methylation of eEF2 regulates nascent elongation to promote protein synthesis and lung adenocarcinoma (LUAD) pathogenesis. The principal physiologic substrate of FAM86A is eEF2, with K525me3 modeled to facilitate productive eEF2-ribosome engagement during translocation. FAM86A depletion in LUAD cells causes 80S monosome accumulation and mRNA translation inhibition. FAM86A is overexpressed in LUAD and eEF2K525me3 levels increase through advancing LUAD disease stages. FAM86A knockdown attenuates LUAD cell proliferation and suppression of the FAM86A-eEF2K525me3 axis inhibits cancer cell and patient-derived LUAD xenograft growth in vivo. Finally, FAM86A ablation strongly attenuates tumor growth and extends survival in KRASG12C-driven LUAD mouse models. Thus, our work uncovers an eEF2 methylation-mediated mRNA translation elongation regulatory node and nominates FAM86A as an etiologic agent in LUAD.

STOPGAP: an open-source package for template matching, subtomogram alignment and classification

Cryo-electron tomography (cryo-ET) enables molecular-resolution 3D imaging of complex biological specimens such as viral particles, cellular sections and, in some cases, whole cells. This enables the structural characterization of molecules in their near-native environments, without the need for purification or separation, thereby preserving biological information such as conformational states and spatial relationships between different molecular species. Subtomogram averaging is an image-processing workflow that allows users to leverage cryo-ET data to identify and localize target molecules, determine high-resolution structures of repeating molecular species and classify different conformational states. Here, STOPGAP, an open-source package for subtomogram averaging that is designed to provide users with fine control over each of these steps, is described. In providing detailed descriptions of the image-processing algorithms that STOPGAP uses, this manuscript is also intended to serve as a technical resource to users as well as for further community-driven software development.

Thinner is not always better: Optimizing cryo-lamellae for subtomogram averaging

Cryo-electron tomography (cryo-ET) is a powerful method to elucidate subcellular architecture and to structurally analyze biomolecules in situ by subtomogram averaging, yet data quality critically depends on specimen thickness. Cells that are too thick for transmission imaging can be thinned into lamellae by cryo-focused ion beam (cryo-FIB) milling. Despite being a crucial parameter directly affecting attainable resolution, optimal lamella thickness has not been systematically investigated nor the extent of structural damage caused by gallium ions used for FIB milling. We thus systematically determined how resolution is affected by these parameters. We find that ion-induced damage does not affect regions more than 30 nanometers from either lamella surface and that up to ~180-nanometer lamella thickness does not negatively affect resolution. This shows that there is no need to generate very thin lamellae and lamella thickness can be chosen such that it captures cellular features of interest, thereby opening cryo-ET also for studies of large complexes.

Ultrastructural insights into cellular organization, energy storage and ribosomal dynamics of an ammonia-oxidizing archaeon from oligotrophic oceans

Introduction

Nitrososphaeria, formerly known as Thaumarchaeota, constitute a diverse and widespread group of ammonia-oxidizing archaea (AOA) inhabiting ubiquitously in marine and terrestrial environments, playing a pivotal role in global nitrogen cycling. Despite their importance in Earth's ecosystems, the cellular organization of AOA remains largely unexplored, leading to a significant unanswered question of how the machinery of these organisms underpins metabolic functions.

Methods

In this study, we combined spherical-chromatic-aberration-corrected cryo-electron tomography (cryo-ET), scanning transmission electron microscopy (STEM), and energy dispersive X-ray spectroscopy (EDS) to unveil the cellular organization and elemental composition of Nitrosopumilus maritimus SCM1, a representative member of marine Nitrososphaeria.

Results and Discussion

Our tomograms show the native ultrastructural morphology of SCM1 and one to several dense storage granules in the cytoplasm. STEM-EDS analysis identifies two types of storage granules: one type is possibly composed of polyphosphate and the other polyhydroxyalkanoate. With precise measurements using cryo-ET, we observed low quantity and density of ribosomes in SCM1 cells, which are in alignment with the documented slow growth of AOA in laboratory cultures. Collectively, these findings provide visual evidence supporting the resilience of AOA in the vast oligotrophic marine environment.

Structural highlights of macromolecular complexes and assemblies

The structures of macromolecular assemblies have given us deep insights into cellular processes and have profoundly impacted biological research and drug discovery. We highlight the structures of macromolecular assemblies that have been modeled using integrative and computational methods and describe how open access to these structures from structural archives has empowered the research community. The arsenal of experimental and computational methods for structure determination ensures a future where whole organelles and cells can be modeled.

Rapid structural analysis of bacterial ribosomes in situ

Rapid structural analysis of purified proteins and their complexes has become increasingly common thanks to key methodological advances in cryo-electron microscopy (cryo-EM) and associated data processing software packages. In contrast, analogous structural analysis in cells via cryo-electron tomography (cryo-ET) remains challenging due to critical technical bottlenecks, including low-throughput sample preparation and imaging, and laborious data processing methods. Here, we describe the development of a rapid in situ cryo-ET sample preparation and data analysis workflow that results in the routine determination of sub-nm resolution ribosomal structures. We apply this workflow to E. coli, producing a 5.8 Å structure of the 70S ribosome from cells in less than 10 days, and we expect this workflow will be widely applicable to related bacterial samples.

Visualization of translation reorganization upon persistent ribosome collision stress in mammalian cells

Aberrantly slow ribosomes incur collisions, a sentinel of stress that triggers quality control, signaling, and translation attenuation. Although each collision response has been studied in isolation, the net consequences of their collective actions in reshaping translation in cells is poorly understood. Here, we apply cryoelectron tomography to visualize the translation machinery in mammalian cells during persistent collision stress. We find that polysomes are compressed, with up to 30% of ribosomes in helical polysomes or collided disomes, some of which are bound to the stress effector GCN1. The native collision interface extends beyond the in vitro-characterized 40S and includes the L1 stalk and eEF2, possibly contributing to translocation inhibition. The accumulation of unresolved tRNA-bound 80S and 60S and aberrant 40S configurations identifies potentially limiting steps in collision responses. Our work provides a global view of the translation machinery in response to persistent collisions and a framework for quantitative analysis of translation dynamics in situ.

DeepSLICEM: Clustering CryoEM particles using deep image and similarity graph representations

Finding the 3D structure of proteins and their complexes has several applications, such as developing vaccines that target viral proteins effectively. Methods such as cryogenic electron microscopy (cryo-EM) have improved in their ability to capture high-resolution images, and when applied to a purified sample containing copies of a macromolecule, they can be used to produce a high-quality snapshot of different 2D orientations of the macromolecule, which can be combined to reconstruct its 3D structure. Instead of purifying a sample so that it contains only one macromolecule, a process that can be difficult, time-consuming, and expensive, a cell sample containing multiple particles can be photographed directly and separated into its constituent particles using computational methods. Previous work, SLICEM, has separated 2D projection images of different particles into their respective groups using 2 methods, clustering a graph with edges weighted by pairwise similarities of common lines of the 2D projections. In this work, we develop DeepSLICEM, a pipeline that clusters rich representations of 2D projections, obtained by combining graphical features from a similarity graph based on common lines, with additional image features extracted from a convolutional neural network. DeepSLICEM explores 6 pretrained convolutional neural networks and one supervised Siamese CNN for image representation, 10 pretrained deep graph neural networks for similarity graph node representations, and 4 methods for clustering, along with 8 methods for directly clustering the similarity graph. On 6 synthetic and experimental datasets, the DeepSLICEM pipeline finds 92 method combinations achieving better clustering accuracy than previous methods from SLICEM. Thus, in this paper, we demonstrate that deep neural networks have great potential for accurately separating mixtures of 2D projections of different macromolecules computationally.

Integrating cellular electron microscopy with multimodal data to explore biology across space and time

Biology spans a continuum of length and time scales. Individual experimental methods only glimpse discrete pieces of this spectrum but can be combined to construct a more holistic view. In this Review, we detail the latest advancements in volume electron microscopy (vEM) and cryo-electron tomography (cryo-ET), which together can visualize biological complexity across scales from the organization of cells in large tissues to the molecular details inside native cellular environments. In addition, we discuss emerging methodologies for integrating three-dimensional electron microscopy (3DEM) imaging with multimodal data, including fluorescence microscopy, mass spectrometry, single-particle analysis, and AI-based structure prediction. This multifaceted approach fills gaps in the biological continuum, providing functional context, spatial organization, molecular identity, and native interactions. We conclude with a perspective on incorporating diverse data into computational simulations that further bridge and extend length scales while integrating the dimension of time.

Protein dynamics underlying allosteric regulation

Allostery is the mechanism by which information and control are propagated in biomolecules. It regulates ligand binding, chemical reactions, and conformational changes. An increasing level of experimental resolution and control over allosteric mechanisms promises a deeper understanding of the molecular basis for life and powerful new therapeutics. In this review, we survey the literature for an up-to-date biological and theoretical understanding of protein allostery. By delineating five ways in which the energy landscape or the kinetics of a system may change to give rise to allostery, we aim to help the reader grasp its physical origins. To illustrate this framework, we examine three systems that display these forms of allostery: allosteric inhibitors of beta-lactamases, thermosensation of TRP channels, and the role of kinetic allostery in the function of kinases. Finally, we summarize the growing power of computational tools available to investigate the different forms of allostery presented in this review.

Understanding the cell: Future views of structural biology

Determining the structure and mechanisms of all individual functional modules of cells at high molecular detail has often been seen as equal to understanding how cells work. Recent technical advances have led to a flush of high-resolution structures of various macromolecular machines, but despite this wealth of detailed information, our understanding of cellular function remains incomplete. Here, we discuss present-day limitations of structural biology and highlight novel technologies that may enable us to analyze molecular functions directly inside cells. We predict that the progression toward structural cell biology will involve a shift toward conceptualizing a 4D virtual reality of cells using digital twins. These will capture cellular segments in a highly enriched molecular detail, include dynamic changes, and facilitate simulations of molecular processes, leading to novel and experimentally testable predictions. Transferring biological questions into algorithms that learn from the existing wealth of data and explore novel solutions may ultimately unveil how cells work.

Cool-contacts: Cryo-Electron Microscopy of Membrane Contact Sites and Their Components

Electron microscopy has played a pivotal role in elucidating the ultrastructure of membrane contact sites between cellular organelles. The advent of cryo-electron microscopy has ushered in the ability to determine atomic models of constituent proteins or protein complexes within sites of membrane contact through single particle analysis. Furthermore, it enables the visualization of the three-dimensional architecture of membrane contact sites, encompassing numerous copies of proteins, whether in vitro reconstituted or directly observed in situ using cryo-electron tomography. Nevertheless, there exists a scarcity of cryo-electron microscopy studies focused on the site of membrane contact and their constitutive proteins. This review provides an overview of the contributions made by cryo-electron microscopy to our understanding of membrane contact sites, outlines the associated limitations, and explores prospects in this field.

STOPGAP, an open-source package for template matching, subtomogram alignment, and classification

Cryo-electron tomography (cryo-ET) enables molecular-resolution 3D imaging of complex biological specimens such as viral particles, cellular sections, and in some cases, whole cells. This enables the structural characterization of molecules in their near-native environments, without the need for purification or separation, thereby preserving biological information such as conformational states and spatial relationships between different molecular species. Subtomogram averaging is an image processing workflow that allows users to leverage cryo-ET data to identify and localize target molecules, determine high-resolution structures of repeating molecular species, and classifying different conformational states. Here we describe STOPGAP, an open-source package for subtomogram averaging designed to provide users with fine control over each of these steps. In providing detailed descriptions of the image processing algorithms that STOPGAP uses, we intend for this manuscript to also serve as a technical resource to users as well as further community-driven software development.

Correlative Light and Electron Cryo-Microscopy Workflow Combining Micropatterning, Ice Shield, and an In-Chamber Fluorescence Light Microscope

In situ cryo-electron tomography (cryo-ET) is the most current, state-of-the-art technique to study cell machinery in its hydrated near-native state. The method provides ultrastructural details at sub-nanometer resolution for many components within the cellular context. Making use of recent advances in sample preparation techniques and combining this method with correlative light and electron microscopy (CLEM) approaches have enabled targeted molecular visualization. Nevertheless, the implementation has also added to the complexity of the workflow and introduced new obstacles in the way of streamlining and achieving high throughput, sample yield, and sample quality. Here, we report a detailed protocol by combining multiple newly available technologies to establish an integrated, high-throughput, optimized, and streamlined cryo-CLEM workflow for improved sample yield. Key features • PRIMO micropatterning allows precise cell positioning and maximum number of cell targets amenable to thinning with cryo focused-ion-beam-scanning electron microscopy. • CERES ice shield ensures that the lamellae remain free of ice contamination during the batch milling process. • METEOR in-chamber fluorescence microscope facilitates the targeted cryo focused-ion-beam (cryo FIB) milling of these targets. • Combining the three technologies into one cryo-CLEM workflow maximizes sample yield, throughput, and efficiency. Graphical overview.

DomainFit: Identification of Protein Domains in cryo-EM maps at Intermediate Resolution using AlphaFold2-predicted Models

Cryo-electron microscopy (cryo-EM) has revolutionized our understanding of macromolecular complexes, enabling high-resolution structure determination. With the paradigm shift to in situ structural biology recently driven by the ground-breaking development of cryo-focused ion beam milling and cryo-electron tomography, there are an increasing number of structures at sub-nanometer resolution of complexes solved directly within their cellular environment. These cellular complexes often contain unidentified proteins, related to different cellular states or processes. Identifying proteins at resolutions lower than 4 Å remains challenging because the side chains cannot be visualized reliably. Here, we present DomainFit, a program for automated domain-level protein identification from cryo-EM maps at resolutions lower than 4 Å. By fitting domains from artificial intelligence-predicted models such as AlphaFold2-predicted models into cryo-EM maps, the program performs statistical analyses and attempts to identify the proteins forming the density. Using DomainFit, we identified two microtubule inner proteins, one of them, a CCDC81 domain-containing protein, is exclusively localized in the proximal region of the doublet microtubule from the ciliate Tetrahymena thermophila. The flexibility and capability of DomainFit makes it a valuable tool for analyzing in situ structures.

UCSF ChimeraX: Tools for structure building and analysis

Advances in computational tools for atomic model building are leading to accurate models of large molecular assemblies seen in electron microscopy, often at challenging resolutions of 3-4 Å. We describe new methods in the UCSF ChimeraX molecular modeling package that take advantage of machine-learning structure predictions, provide likelihood-based fitting in maps, and compute per-residue scores to identify modeling errors. Additional model-building tools assist analysis of mutations, post-translational modifications, and interactions with ligands. We present the latest ChimeraX model-building capabilities, including several community-developed extensions. ChimeraX is available free of charge for noncommercial use at https://www.rbvi.ucsf.edu/chimerax.