Cryogenic Electron Microscopy Research Articles

Structures of the P. aeruginosa FleQ-FleN master regulators reveal large-scale conformational switching in motility and biofilm control.

Pseudomonas aeruginosa can cause a wide array of chronic and acute infections associated with its ability to rapidly switch between planktonic, biofilm, and dispersed lifestyles, each with a specific arsenal for bacterial survival and virulence. At the cellular level, many of the physiological transitions are orchestrated by the intracellular second messenger c-di-GMP and its receptor-effector FleQ. A bacterial enhancer binding protein, FleQ acts as a master regulator of both flagellar motility and adherence factor secretion and uses remarkably different transcription activation mechanisms depending on its dinucleotide loading state, adenosine triphosphatase (ATPase) activity, interactions with polymerase sigma (σ) factors, and complexation with a second ATPase, FleN. How the FleQ-FleN tandem can exert diverse effects through recognition of a conserved FleQ binding consensus has remained enigmatic. Here, we provide cryogenic electron microscopy (cryo-EM) structures of both c-di-GMP-bound and c-di-GMP-free FleQ-FleN complexes which deepen our understanding of the proteins' (di)nucleotide-dependent conformational switching and fine-tuned roles in gene expression regulation.

Ultra-sensitive hexagonal wurtzite zinc oxide-based electrochemical sensor for specific recognition of environmental trace N-(1,3-dimethylbutyl)-N′-phenyl-p-phenylenediamine

Emerging contaminant N-(1,3-dimethylbutyl)-N′-phenyl-p-phenylenediamine has caused severe threats to ecosystems, necessitating the development of highly sensitive detection methods. Herein, a reliable and ultra-sensitive electrochemical sensor based on a carbon paste electrode modified by hexagonal wurtzite zinc oxide was developed for selective determination and degradation of N-(1,3-dimethylbutyl)-N′-phenyl-p-phenylenediamine. Experimental results demonstrated the successful application of the sensor for detecting N-(1,3-dimethylbutyl)-N′-phenyl-p-phenylenediamine in soil samples. The contaminant contents were found to be 1.46–24.68 nmol L−1 in Zhengzhou City and 1.99–11.3 nmol L−1 in Pingdingshan City, respectively, along with a satisfactory recovery rate. Density functional theory calculations revealed that the hexagonal wurtzite zinc oxide crystal significantly decreased the activation energy of catalytic conversion compared to cubic sphalerite, resulting in a notable improvement in sensor response. Cryogenic electron microscopy technique further confirmed that the electrocatalytic degradation product of N-(1,3-dimethylbutyl)-N′-phenyl-p-phenylenediamine was not toxic N-(1,3-dimethylbutyl)-N′-phenyl-p-phenylenediamine quinone. Under optimal analysis conditions, the sensor achieved widely low as well as high linear ranges (0.1–800 nmol L−1 and 0.9–20 μmol L−1) with a low detection limitation (33 pmol L−1), indicating that such a highly sensitive and cost-effective electrochemical sensor has the potential for environmental pollutants monitoring.

A brain‐seeded fibril amplification models the aggregation process of tau in Alzheimer’s disease for drug discovery

AbstractBackgroundThe microtubule‐associated protein tau is implicated in the development of a class of diverse neurodegenerative disorders, referred to as tauopathies, with symptoms of dementia and parkinsonism. Tauopathies comprise more than 20 clinicopathological entities, including Alzheimer’s disease, which accounts for 70% of dementia cases worldwide. In combination with clinical diagnosis and neuropathology, the reconstruction of different tau filaments by cryogenic electron microscopy (cryo‐EM) further points to the presence of distinct tau folds. The knowledge of these disease‐specific aggregate conformers provides a platform for the establishment of novel diagnostic methods and more tailored therapeutic approaches.MethodIn order to investigate this problem, this project aims to selectively amplify tau in vitro from human brain homogenates affected by Alzheimer’s disease (AD) and Pick’s diseases (PiD). Kinetic analysis for drug discovery for the specific process of tau aggregation that takes place in Alzheimer’s disease was performed.ResultStrain discrimination was achieved, with a significant acceleration relative to the off‐target control, suggesting formation of two different fibril structures. Cryo‐EM was performed to confirm whether the in vitro AD‐like tau aggregates resembled those extracted from brains.We identify specific tau aggregation inhibitors, through in silico docking to binding sites on the surface of the cryo‐EM structure of tau fibrils adopting an AD fold.ConclusionThe application of this line of research is illustrated by a study of the aggregation kinetics of AD‐like tau fibrils, and of its potential in drug discovery. In perspective, the approach that we present offer novel opportunities for the systematic in vitro study of the tau aggregation process as it may happen in the human brain.References(WHO), W. H. O. et al. (2019). Dementia fact sheet.Alzheimer’s disease facts and figures. Alzheimer’s and Dementia 18, 700‐789 (2022).Chia, S. et al. Structure‐Based Discovery of Small‐Molecule Inhibitors of the Autocatalytic Proliferation of alpha‐Synuclein Aggregates. Mol Pharm (2022).

Abstract A086: NST-628 is a novel molecular glue that inhibits signaling and pathway reactivation in oncogenic RAS-MAPK cancers

Abstract Alterations in the RAS-MAPK pathway are identified in nearly 30% of cancers and are associated with poor patient prognosis. Although available therapies target various nodes of the RAS-MAPK pathway, clinical anti-tumor activity is limited by paradoxical bypass mechanisms, feedback signaling and pathway reactivation, and genetic resistance mechanisms. NST-628 aims to overcome the limitations of traditional RAS-MAPK pathway inhibitors by stabilizing all RAF-MEK complexes in a conformation that blocks MEK phosphorylation, to sequester these nodes from dynamic signaling processes that promote RAF-mediated bypass signaling. In comparison with clinically approved RAS-MAPK pathway inhibitors, only NST-628 robustly and durably decreases pathway reactivation, as measured by MEK phosphorylation, in KRAS-G13D tumor models in vitro and in vivo. Immunoprecipitation of endogenous ternary complexes demonstrates that NST-628 promotes potent stabilization of CRAF-MEK, BRAF-MEK, and ARAF-MEK complexes with complete shutdown of MEK, ERK, and RSK phosphorylation. Moreover, NST-628 treatment completely prevents RAF paralog heterodimerization in RAS-driven cells. Dose-dependent panRAF-MEK complex stabilization was confirmed using recombinant pre-formed CRAF-MEK, BRAF-MEK, and ARAF-MEK complexes, and MEK and RAF paralog affinity increases in the presence of NST-628 were quantified via surface plasmon resonance (SPR). In this assay, NST-628 significantly increased the affinity of MEK with both inactive monomeric and active dimeric RAF complexes. In parallel, we structurally characterized NST-628 bound to CRAF-MEK, BRAF-MEK, ARAF-MEK complexes using x-ray crystallography and cryogenic electron microscopy (cryo-EM). NST-628 binds the interfacial allosteric pocket along the MEK activation loop, thereby preventing RAF-mediated activation of MEK. We also demonstrate RAF paralog-specific pocket features that NST-628 can engage, helping us rationalize the large increase in affinity observed for MEK and CRAF in the presence of NST-628. The increased stabilization of CRAF-MEK complex by NST-628 may contribute to the decreased pathway reactivation in specific biomarker-driven tumors. Through our robust biophysical and cellular characterization coupled with novel structural insights, we have defined the unique mechanism of action for NST-628 and provide insight into its best-in-class potential in RAS-MAPK activated cancers. Citation Format: Bradley Quade, Meagan Ryan, Brooke Swalm, Steven Cohen, Zhong Fang, Aysegul Ozen, Xin Huang, Arvin C Dar, Yongxin Han, Klaus P Hoeflich, Margit Hagel, Michael Hale. NST-628 is a novel molecular glue that inhibits signaling and pathway reactivation in oncogenic RAS-MAPK cancers [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr A086.

Deep learning structural insights into heterotrimeric alternatively spliced P2X7 receptors.

P2X7 receptors (P2X7Rs) are membrane-bound ATP-gated ion channels that are composed of three subunits. Different subunit structures may be expressed due to alternative splicing of the P2RX7 gene, altering the receptor's function when combined with the wild-type P2X7A subunits. In this study, the application of the deep-learning method, AlphaFold2-Multimer (AF2M), for the generation of trimeric P2X7Rs was validated by comparing an AF2M-generated rat wild-type P2X7A receptor with a structure determined by cryogenic electron microscopy (cryo-EM) (Protein Data Bank Identification: 6U9V). The results suggested AF2M could firstly, accurately predict the structures of P2X7Rs and secondly, accurately identify the highest quality model through the ranking system. Subsequently, AF2M was used to generate models of heterotrimeric alternatively spliced P2X7Rs consisting of one or two wild-type P2X7A subunits in combination with one or two P2X7B, P2X7E, P2X7J, and P2X7L splice variant subunits. The top-ranking models were deemed valid based on AF2M's confidence measures, stability in molecular dynamics simulations, and consistent flexibility of the conserved regions between the models. The structure of the heterotrimeric receptors, which were missing key residues in the ATP binding sites and carboxyl terminal domains (CTDs) compared to the wild-type receptor, help to explain their observed functions. Overall, the models produced in this study (available as supplementary material) unlock the possibility of structure-based studies into the heterotrimeric P2X7Rs.

Development of wet adhesion of honeybee arolium incorporated polygonal structure with three-phase composite interfaces

Inspired by the dynamic wet adhesive systems in nature, various artificial adhesive surfaces have been developed but still face different challenges. Crucially, the theoretical mechanics of wet adhesives has never been sufficiently revealed. Here, we develop a novel adhesive mechanism for governing wet adhesion and investigate the biological models of honeybee arolium for reproducing the natural wet adhesive systems. Micro-nano structures of honeybee arolium and arolium-prints were observed by Cryogenic scanning electron microscopy (Cryo-SEM), and the air pockets were found in the contact interface notably. Subsequently, the adhesive models with a three-phase composite interface (including air pockets, liquid secretion, and hexagonal frames of arolium), were formed to analyze the wet adhesion of honeybee arolium. The results of theoretical calculations and experiments indicated an enhanced adhesive mechanism of the honeybee by liquid self-sucking effects and air-embolism effects. Under these effects, normal and shear adhesion can be adjusted by controlling the proportion of liquid secretion and air pockets in the contact zone. Notably, the air-embolism effects contribute to the optimal coupling of smaller normal adhesion with greater shear adhesion, which is beneficial for the high stride frequency of honeybees. These works can provide a fresh perspective on the development of bio-inspired wet adhesive surfaces.

Disease-specific tau filaments assemble via polymorphic intermediates

Intermediate species in the assembly of amyloid filaments are believed to play a central role in neurodegenerative diseases and may constitute important targets for therapeutic intervention1,2. However, structural information about intermediate species has been scarce and the molecular mechanisms by which amyloids assemble remain largely unknown. Here we use time-resolved cryogenic electron microscopy to study the in vitro assembly of recombinant truncated tau (amino acid residues 297–391) into paired helical filaments of Alzheimer’s disease or into filaments of chronic traumatic encephalopathy3. We report the formation of a shared first intermediate amyloid filament, with an ordered core comprising residues 302–316. Nuclear magnetic resonance indicates that the same residues adopt rigid, β-strand-like conformations in monomeric tau. At later time points, the first intermediate amyloid disappears and we observe many different intermediate amyloid filaments, with structures that depend on the reaction conditions. At the end of both assembly reactions, most intermediate amyloids disappear and filaments with the same ordered cores as those from human brains remain. Our results provide structural insights into the processes of primary and secondary nucleation of amyloid assembly, with implications for the design of new therapies.

MRNA reading frame maintenance during eukaryotic ribosome translocation.

One of the most critical steps of protein synthesis is coupled translocation of messenger RNA (mRNA)and transfer RNAs (tRNAs)required to advance the mRNA reading frame by one codon. In eukaryotes, translocation is accelerated and its fidelity is maintained by elongation factor 2 (eEF2)1,2. At present, only a few snapshots of eukaryotic ribosome translocation have been reported3-5. Here we report ten high-resolution cryogenic-electron microscopy(cryo-EM) structures of the elongating eukaryotic ribosome bound to the full translocation module consisting of mRNA, peptidyl-tRNA and deacylated tRNA, seven of which also contained ribosome-bound, naturally modified eEF2. This study recapitulates mRNA-tRNA2-growing peptide module progression through the ribosome, from the earliest states of eEF2 translocase accommodation until the very late stages of the process, and shows an intricate network of interactions preventing the slippage of the translational reading frame. We demonstrate how the accuracy of eukaryotic translocation relies on eukaryote-specific elements of the 80S ribosome, eEF2 and tRNAs. Our findings shed light on the mechanism of translation arrest by the anti-fungal eEF2-binding inhibitor, sordarin. We also propose that the sterically constrained environment imposed by diphthamide, a conserved eukaryotic posttranslational modification in eEF2, not only stabilizes correct Watson-Crick codon-anticodon interactions but may also uncover erroneous peptidyl-tRNA, and therefore contribute to higher accuracy of protein synthesis in eukaryotes.

Pyrimidine Starvation Is a Targetable Cancer Vulnerability: Mechanisms of Nucleotide Homeostasis

Introduction: Acute myeloid leukemia (AML) is a heterogeneous disease, though all AML exhibit a characteristic block in differentiation. Hence, much effort has been made to develop small molecules that promote leukemic cell differentiation in the treatment of AML. In 2016 we identified the enzyme dihydroorotate dehydrogenase (DHODH) as a therapeutic target in AML. DHODH is a mitochondrial enzyme that converts dihydroorotate to orotate in the 4th step of de novo pyrimidine synthesis. Without DHODH enzymatic activity, a cell is forced to rely on autophagy or extracellular salvage to maintain its intracellular pyrimidine pool. DHODH inhibitor therapy has shown broad preclinical efficacy across multiple cancer types including, glioma, neuroblastoma, breast, small cell lung and pancreatic cancer suggesting that malignant cells are specifically impaired in their ability to maintain nucleotide homeostasis during periods of limited availability. Despite these very encouraging pre-clinical results, the translation into human clinical trials has been met with limited anti-cancer activity and therapeutic success. This discordance between pre-clinical and clinical benefit likely speaks to our limited understanding of how normal and malignant cells respond to pyrimidine starvation. Methods: Using in vitro and in vivo assays to compare normal hematopoietic progenitor and leukemic cells we interrogated key nodes in pyrimidine synthesis to identify the mechanisms behind this selective, anti-leukemic activity in the context of nucleotide starvation: [1] Nucleotide measurement by HPLC, [2] Flux experiments by isotopic tracing, [3] Polysome profiling to compare the transcriptome and translatome, [4] Quantification of ribosome recycling by examining the lysosomes following ultracentrifugation and [5] Direct visualization of lysosomes using new techniques in cryogenic electron microscopy. Results: Treatment of leukemia cells with brequinar blocked de novo synthesis and led to the rapid depletion of intracellular pyrimidines. In comparison, normal hematopoietic CD34 positive progenitor cells had less depletion, suggesting a selective vulnerability of leukemic cells over normal cells. We used isotopically labeled glutamine (15N) and uridine (13C) to quantify the contribution of de novo synthesis and extracellular salvage under control and starvation conditions. The leukemia cell line THP1 showed a higher reliance on de novo synthesis than normal CD34 positive hematopoietic progenitors ( Figure 1A, left graphs). Furthermore, following DHODH inhibition, THP1 cells were less capable of extracellular salvage compared to normal cells ( Figure 1A, right graphs). Polysome profiling analysis in THP1 cells showed a dramatic decrease in translating ribosomes as well as dramatic decrease in ribosomal RNA. We identified a short-list of 22 genes whose translation is prioritized during nucleotide deprivation. Following DHODH inhibition and nucleotide starvation, cells upregulate their number of lysosomes, as quantified by flow cytometry. In addition, the contents of the lysosome include ribosomal proteins, whose abundance increased during nucleotide starvation, suggesting an ongoing recycling of ribosomes to meet the nucleotide demand of leukemic cells during starvation. Finally, for the first time we have been able to directly visualize (by cryogenic electron microscopy) ribosomes within lysosomes during periods of nucleotide starvation, a finding that was completely absent in leukemia cells cultured under normal conditions ( Figure 1B). Conclusion: We hypothesized that the transformation from normal to malignant cell is accompanied by changes in nucleotide metabolism that render the transformed cells more reliant on de novo synthesis, establishing a metabolic vulnerability (and inherent therapeutic window) in the use of DHODH inhibitors. Our work confirms that leukemic blasts differ in their dependence on de novo nucleotide synthesis and its ability to garner nucleotides via salvage or autophagy pathways. This balance appears to be disturbed in the setting of malignancy such that leukemic cells are empirically more sensitive to treatment targeting pyrimidine synthesis. Understanding the differences in how leukemic and normal cells handle their nucleotide pools at baseline, and under starvation conditions, will guide the clinical utility of this class of inhibitors.

Cryo-EM Structure of Coagulation Factor VIII Bound to a Patient-Derived Anti-A2 Domain Antibody Inhibitor

Coagulation factor VIII (FVIII) promotes hemostasis by binding to activated factor IX on activated platelet surfaces to form the intrinsic tenase complex. The formation of inhibitory antibodies against FVIII occurs in approximately 30% of congenital hemophilia A patients receiving FVIII replacement therapy, significantly complicating treatments. By identifying the FVIII amino acids which bind to pathogenic inhibitory antibodies, FVIII replacement therapies can be engineered with reduced immunogenicity. Here, we aimed to structurally characterize FVIII bound to NB11B2, a patient-derived antibody inhibitor which binds to the A2 domain and disrupts tenase complex activity, using cryogenic electron microscopy (cryo-EM). The FVIII:NB11B2 structure was solved to a global resolution of 4.0 Å, representing the first structure of FVIII bound to an anti-A2 domain antibody inhibitor. Structural analysis revealed that NB11B2 binds to a discontinuous epitope encompassing FVIII residues S470-P472, R490-K493, and P502-E507. Furthermore, our structure identified a 20° swivel-like movement adopted by the C2 domain while the C1 domain remains immobile, consistent with a previous X-ray crystal structure of FVIII bound to an anti-C1 domain inhibitor. These results provide the structural basis for inhibition of FVIII by NB11B2 and elucidate a novel role for portions of the FVIII A2 domain in regulating tenase complex assembly and/or activity.

Elucidating the Structural Dynamics of Integrin α IIbβ 3 from Native Platelet Membranes By Cryo-EM Coupled with Build and Retrieve Data Processing Methodology

Background: Platelets play a critical role in physiological processes by sensing the extracellular environment through their membrane proteins. Changing the quantity or quality of these proteins can profoundly affect platelet physiology and impact health. The native membrane environment provides essential additional regulatory cues that impact the protein structure and mechanism of action. Single-particle cryogenic electron microscopy (cryo-EM) has transformed structural biology by allowing high-resolution structures of membrane proteins and large macromolecules to be solved from highly purified, homogeneous samples. Our recent breakthroughs in data processing make it feasible to obtain high-resolution protein structures from crude preparations in their native environments by integrating cryo-EM with the novel “Build and Retrieve” (BaR) data processing methodology. By performing in silico purification, image sorting, and model building from large heterogenous datasets, this iterative bottom-up methodology opens new avenues for an in-depth systems biology approach with structural biology that will uncover how the native environment, including lipid and metal binding, post-translational modifications, and co-factor associations regulate platelet function at the molecular level. Method: Whole blood was collected, and the platelet membrane proteins were solubilized by 1% n-Dodecyl-β-D-Maltoside (DDM) and incorporated into lipidic nanodisc MSP1E3D1 directly from the endogenous source. After being enriched by size exclusion chromatography, the mixture of proteins at ~200 kDa was directly applied on cryo-EM grids. Data were collected on Titan Krios G3i cryogenic transmission electron microscope equipped with a BioQuantum K3 camera. All data processing was done in cryoSPARC using the BaR protocol. The near-atomic-resolution cryo-EM maps were used for protein identification using the program phenix.sequence_from_map in the PHENIX suite. The final protein models were built by Coot and refined by PHENIX. Results: We have used using cryo-EM followed by the BaR method to solve the first unmodified integrin α IIbβ 3 structure directly from resting human platelet membranes in its inactivated and intermediate states at 2.76Å and 2.49Å, respectively. From these two structures, we observed the ion binding sites at the β1-domain and β-propeller domain in agreement with previous “classical” α IIbβ 3 structural studies using a purified sample. More importantly, we were able to assign endogenous N-linked glycan sites, which reflected how glycosylation naturally regulates α IIbβ 3 dynamic and function on resting human platelets. Finally, we also solved a novel third unique dimer conformation of α IIbβ 3 at 2.61Å formed by two intermediate-states of α IIbβ 3. This may indicate a previously unknown self-regulatory mechanism of α IIbβ 3 in its native environment. Conclusion: In conclusion, our data show the power of using cryo-EM with the BaR method to uncover novel structures directly from natural sources to identify unrecognized regulation mechanisms for proteins without artifacts due to purification processes. A distinct advantage of the BaR method is that it is an unbiased approach for solving multiple structures from raw samples, which highlights the potential of building a protein structural atlas from platelets. These data have the potential to enrich our understanding of platelet signaling circuitry and foster the development of higher-quality diagnoses and treatments for patients with platelet disorders.

Baited reconstruction with 2D template matching for high-resolution structure determination in vitro and in vivo without template bias.

Previously we showed that 2D template matching (2DTM) can be used to localize macromolecular complexes in images recorded by cryogenic electron microscopy (cryo-EM) with high precision, even in the presence of noise and cellular background (Lucas et al., 2021; Lucas et al., 2022). Here, we show that once localized, these particles may be averaged together to generate high-resolution 3D reconstructions. However, regions included in the template may suffer from template bias, leading to inflated resolution estimates and making the interpretation of high-resolution features unreliable. We evaluate conditions that minimize template bias while retaining the benefits of high-precision localization, and we show that molecular features not present in the template can be reconstructed at high resolution from targets found by 2DTM, extending prior work at low-resolution. Moreover, we present a quantitative metric for template bias to aid the interpretation of 3D reconstructions calculated with particles localized using high-resolution templates and fine angular sampling.

Baited reconstruction with 2D template matching for high-resolution structure determination in vitro and in vivo without template bias

Previously we showed that 2D template matching (2DTM) can be used to localize macromolecular complexes in images recorded by cryogenic electron microscopy (cryo-EM) with high precision, even in the presence of noise and cellular background (Lucas et al., 2021; Lucas et al., 2022). Here, we show that once localized, these particles may be averaged together to generate high-resolution 3D reconstructions. However, regions included in the template may suffer from template bias, leading to inflated resolution estimates and making the interpretation of high-resolution features unreliable. We evaluate conditions that minimize template bias while retaining the benefits of high-precision localization, and we show that molecular features not present in the template can be reconstructed at high resolution from targets found by 2DTM, extending prior work at low-resolution. Moreover, we present a quantitative metric for template bias to aid the interpretation of 3D reconstructions calculated with particles localized using high-resolution templates and fine angular sampling.

Structural architecture of the acidic region of the B domain of coagulation factor V

BackgroundCoagulation factor (F)V features an A1-A2-B-A3-C1-C2 domain organization and functions as the inactive precursor of FVa, a component of the prothrombinase complex required for rapid thrombin generation in the penultimate step of the coagulation cascade. An intramolecular interaction within the large B domain (residues 710-1545) involves the basic region (BR, residues 963-1008) and acidic region (AR, residues 1493-1537) and locks FV in its inactive state. However, structural information on this important regulatory interaction or on the separate architecture of the AR and BR remains elusive due to conformational disorder of the B domain. ObjectivesTo reveal the structure of the BR-AR interaction or of its separate components. MethodsThe structure of FV is solved by cryogenic electron microscopy. ResultsA new 3.05 Å resolution cryogenic electron microscopy structure of FV confirms the overall organization of the A and C domains but resolves the segment 1507 to 1545 within a largely disordered B domain. The segment contains most of the AR and is organized as recently reported in FV short, a spliced variant of FV with a significantly shorter and less disordered B domain. ConclusionThe similar architecture of the AR in FV and FV short provides structural context for physiologically important interactions of this region with the BR in FV and with the basic C-terminal end of tissue factor pathway inhibitor α in FV short.

Structural insights into intron catalysis and dynamics during splicing

The group II intron ribonucleoprotein is an archetypal splicing system with numerous mechanistic parallels to the spliceosome, including excision of lariat introns1,2. Despite the importance of branching in RNA metabolism, structural understanding of this process has remained elusive. Here we present a comprehensive analysis of three single-particle cryogenic electron microscopy structures captured along the splicing pathway. They reveal the network of molecular interactions that specifies the branchpoint adenosine and positions key functional groups to catalyse lariat formation and coordinate exon ligation. The structures also reveal conformational rearrangements of the branch helix and the mechanism of splice site exchange that facilitate the transition from branching to ligation. These findings shed light on the evolution of splicing and highlight the conservation of structural components, catalytic mechanism and dynamical strategies retained through time in premessenger RNA splicing machines.

Structure of the N-RNA/P interface indicates mode of L/P recruitment to the nucleocapsid of human metapneumovirus

Human metapneumovirus (HMPV) is a major cause of respiratory illness in young children. The HMPV polymerase (L) binds an obligate cofactor, the phosphoprotein (P). During replication and transcription, the L/P complex traverses the viral RNA genome, which is encapsidated within nucleoproteins (N). An essential interaction between N and a C-terminal region of P tethers the L/P polymerase to the template. This N-P interaction is also involved in the formation of cytoplasmic viral factories in infected cells, called inclusion bodies. To define how the polymerase component P recognizes N-encapsidated RNA (N-RNA) we employed cryogenic electron microscopy (cryo-EM) and molecular dynamics simulations, coupled to activity assays and imaging of inclusion bodies in cells. We report a 2.9 Å resolution structure of a triple-complex between multimeric N, bound to both RNA and the C-terminal region of P. Furthermore, we also present cryo-EM structures of assembled N in different oligomeric states, highlighting the plasticity of N. Combined with our functional assays, these structural data delineate in molecular detail how P attaches to N-RNA whilst retaining substantial conformational dynamics. Moreover, the N-RNA-P triple complex structure provides a molecular blueprint for the design of therapeutics to potentially disrupt the attachment of L/P to its template.

Electron counting with direct electron detectors in MicroED

The combination of high sensitivity and rapid readout makes it possible for electron-counting detectors to record cryogenic electron microscopy data faster and more accurately without increasing the number of electrons used for data collection. This is especially useful for MicroED of macromolecular crystals where the strength of the diffracted signal at high resolution is comparable to the surrounding background. The ability to decrease fluence also alleviates concerns about radiation damage which limits the information that can be recovered from a diffraction measurement. The major concern with electron-counting direct detectors lies at the low end of the resolution spectrum: their limited linear range makes strong low-resolution reflections susceptible to coincidence loss and careful data collection is required to avoid compromising data quality. Nevertheless, these cameras are increasingly deployed in cryo-EM facilities, and several have been successfully used for MicroED. Provided coincidence loss can be minimized, electron-counting detectors bring high potential rewards.

Molecular view of ER membrane remodeling by the Sec61/TRAP translocon.

Protein translocation across the endoplasmic reticulum (ER) membrane is an essential step during protein entry into the secretory pathway. The conserved Sec61 protein-conducting channel facilitates polypeptide translocation and coordinates cotranslational polypeptide-processing events. In cells, the majority of Sec61 is stably associated with a heterotetrameric membrane protein complex, the translocon-associated protein complex (TRAP), yet the mechanism by which TRAP assists in polypeptide translocation remains unknown. Here, we present the structure of the core Sec61/TRAP complex bound to a mammalian ribosome by cryogenic electron microscopy (cryo-EM). Ribosome interactions anchor the Sec61/TRAP complex in a conformation that renders the ER membrane locally thinner by significantly curving its lumenal leaflet. We propose that TRAP stabilizes the ribosome exit tunnel to assist nascent polypeptide insertion through Sec61 and provides a ratcheting mechanism into the ER lumen mediated by direct polypeptide interactions.

Improving resolution and resolvability of single-particle cryoEM structures using Gaussian mixture models.

Cryogenic electron microscopy is widely used in structural biology, but its resolution is often limited by the dynamics of the macromolecule. Here we developed a refinement protocol based on Gaussian mixture models that integrates particle orientation and conformation estimation and improves the alignment for flexible domains of protein structures. We demonstrated this protocol on multiple datasets, resulting in improved resolution and resolvability, locally and globally, by visual and quantitative measures.

Cryo-EM of Aβ fibrils from mouse models find tg-APPArcSwe fibrils resemble those found in patients with sporadic Alzheimer’s disease

The use of transgenic mice displaying amyloid-β (Aβ) brain pathology has been essential for the preclinical assessment of new treatment strategies for Alzheimer’s disease. However, the properties of Aβ in such mice have not been systematically compared to Aβ in the brains of patients with Alzheimer’s disease. Here, we determined the structures of nine ex vivo Aβ fibrils from six different mouse models by cryogenic-electron microscopy. We found novel Aβ fibril structures in the APP/PS1, ARTE10 and tg-SwDI models, whereas the human type II filament fold was found in the ARTE10, tg-APPSwe and APP23 models. The tg-APPArcSwe mice showed an Aβ fibril whose structure resembles the human type I filament found in patients with sporadic Alzheimer’s disease. A detailed assessment of the Aβ fibril structure is key to the selection of adequate mouse models for the preclinical development of novel plaque-targeting therapeutics and positron emission tomography imaging tracers in Alzheimer’s disease.