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Nature · Nov 19, 2025

Structural basis of regulated N-glycosylation at the secretory translocon

Most human secretory pathway proteins are N-glycosylated by oligosaccharyltransferase (OST) complexes as they enter the endoplasmic reticulum (ER)1,2,3. Recent work revealed a substrate-assisted mechanism by which N-glycosylation of the chaperone glucose-regulated protein 94 (GRP94) is regulated to control cell surface receptor signalling4. Here we report the structure of a natively isolated GRP94 folding intermediate tethered to a specialized CCDC134-bound translocon. Together with functional analysis, the data reveal how a conserved N-terminal extension in GRP94 inhibits OST-A and how structural rearrangements within the translocon shield the tethered nascent chain from inappropriate OST-B glycosylation. These interactions depend on a hydrophobic CCDC134 groove, which recognizes a non-native conformation of nascent GRP94. Our results define a mechanism of regulated N-glycosylation and illustrate how the nascent chain remodels the translocon to facilitate its own biogenesis.

Cryoelectron microscopy Endoplasmic reticulum Glycosylation Protein translocation biology
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Nature · Nov 19, 2025

ZAK activation at the collided ribosome

Ribosome collisions activate the ribotoxic stress response mediated by the MAP3K ZAK, which in turn regulates cell-fate consequences through downstream phosphorylation of the MAPKs p38 and JNK1. Despite the critical role of ZAK during cellular stress, a mechanistic and structural understanding of ZAK–ribosome interactions and how these lead to activation remain elusive. Here we combine biochemistry and cryo-electron microscopy to discover distinct ZAK–ribosome interactions required for constitutive recruitment and for activation. We find that upon induction of ribosome collisions, interactions between ZAK and the ribosomal protein RACK1 enable its activation by dimerization of its SAM domains at the collision interface. Furthermore, we discover how this process is negatively regulated by the ribosome-binding protein SERBP1 to prevent constitutive ZAK activation. Characterization of novel SAM variants as well as a known pathogenic variant of the SAM domain of ZAK supports a key role of the SAM domain in regulating kinase activity on and off the ribosome, with some mutants bypassing the ribosome requirement for ZAK activation. Collectively, our data provide a mechanistic blueprint of the kinase activity of ZAK at the collided ribosome interface.

Cryoelectron microscopy Ribosome biology
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Nature · Nov 12, 2025

Potent neutralization of Marburg virus by a vaccine-elicited antibody

Marburg virus (MARV) is a filovirus that causes a severe and often lethal hemorrhagic fever1,2. Despite the increasing frequency of MARV outbreaks, no vaccines or therapeutics are licensed for use in humans. Here, we designed mutations that improve the expression, thermostability, and immunogenicity of the prefusion MARV glycoprotein (GP) ectodomain trimer, which is the sole target of neutralizing antibodies and vaccines in development3–8. We discovered a fully human, pan-marburgvirus monoclonal antibody, MARV16, that broadly neutralizes all MARV isolates as well as Ravn virus and Dehong virus with 40 to 100-fold increased potency relative to previously described antibodies9. Moreover, MARV16 provides therapeutic protection in guinea pigs challenged with MARV. We determined a cryo-electron microscopy structure of MARV16-bound MARV GP showing that MARV16 recognizes a prefusion-specific epitope spanning GP1 and GP2, blocking receptor binding and preventing conformational changes required for viral entry. We further reveal the architecture of the MARV GP glycan cap, which shields the receptor binding site (RBS), underscoring architectural similarities with distantly related filovirus GPs. MARV16 and previously identified RBS-directed antibodies9–11can bind MARV GP simultaneously. These antibody cocktails require multiple mutations to escape neutralization by both antibodies, paving the way for MARV therapeutics resilient to viral evolution. MARV GP stabilization along with the discovery of MARV16 advance prevention and treatment options for MARV.

Cryoelectron microscopy Marburg virus Protein vaccines biology
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Nature · Nov 05, 2025

Structural snapshots capture nucleotide release at the μ-opioid receptor

As a member of the G protein-coupled receptor superfamily, the μ-opioid receptor (MOR) activates heterotrimeric G proteins by opening the Gα α-helical domain (AHD) to enable GDP–GTP exchange, with GDP release representing the rate-limiting step1,2. Here, using pharmacological assays, we show that agonist efficacy correlates with decreased GDP affinity, promoting GTP exchange, whereas antagonists increase GDP affinity, dampening activation. Further investigating this phenomenon, we provide 8 unique structural models and 16 cryogenic electron microscopy maps of MOR with naloxone or loperamide, capturing several intermediate conformations along the activation pathway. These include four GDP-bound states with previously undescribed receptor–G protein interfaces, AHD arrangements and transitions in the nucleotide-binding pocket required for GDP release. Naloxone stalls MOR in a ‘latent’ state, whereas loperamide promotes an ‘engaged’ state, which is structurally poised for opening of the AHD domain and subsequent GDP release. These findings, supported by molecular dynamics simulations, identify GDP-bound intermediates and AHD conformations as key determinants of nucleotide exchange rates, providing structural and mechanistic insights into G protein activation and ligand efficacy with broad implications for G protein-coupled receptor pharmacology.

Cryoelectron microscopy Receptor pharmacology biology
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Nature · Nov 05, 2025

Atomically accurate de novo design of antibodies with RFdiffusion

Despite the central role of antibodies in modern medicine, no method currently exists to design novel, epitope-specific antibodies entirely in silico. Instead, antibody discovery currently relies on immunization, random library screening or the isolation of antibodies directly from patients1. Here we demonstrate that combining computational protein design using a fine-tuned RFdiffusion2network with yeast display screening enables the de novo generation of antibody variable heavy chains (VHHs), single-chain variable fragments (scFvs) and full antibodies that bind to user-specified epitopes with atomic-level precision. We experimentally characterize VHH binders to four disease-relevant epitopes. Cryo-electron microscopy confirms the binding pose of designed VHHs targeting influenza haemagglutinin andClostridium difficiletoxin B (TcdB). A high-resolution structure of the influenza-targeting VHH confirms atomic accuracy of the designed complementarity-determining regions (CDRs). Although initial computational designs exhibit modest affinity (tens to hundreds of nanomolarKd), affinity maturation using OrthoRep3enables production of single-digit nanomolar binders that maintain the intended epitope selectivity. We further demonstrate the de novo design of scFvs to TcdB and a PHOX2B peptide–MHC complex by combining designed heavy-chain and light-chain CDRs. Cryo-electron microscopy confirms the binding pose for two distinct TcdB scFvs, with high-resolution data for one design verifying the atomically accurate design of the conformations of all six CDR loops. Our approach establishes a framework for the computational design, screening and characterization of fully de novo antibodies with atomic-level precision in both structure and epitope targeting.

Cryoelectron microscopy Protein design biology
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Nature · Nov 05, 2025

Synthetic α-synuclein fibrils replicate in mice causing MSA-like pathology

Multiple-system atrophy (MSA) is a rapidly progressive neurodegenerative disease of unknown cause, typically affecting individuals aged 50–60 years and leading to death within a decade1,2,3. It is characterized by glial cytoplasmic inclusions (GCIs) composed of fibrillar α-synuclein (aSyn)4,5,6,7,8, the formation of which shows parallels with prion propagation9,10. While fibrils extracted from brains of individuals with MSA have been structurally characterized11, their ability to replicate in a protein-only manner has been questioned12, and their ability to induce GCIs in vivo remains unexplored. By contrast, the synthetic fibril strain 1B13,14, assembled from recombinant human aSyn, self-replicates in vitro and induces GCIs in mice15—suggesting direct relevance to MSA—but lacks scrutiny at the atomic scale. Here we report high-resolution structural analyses of 1B fibrils and of fibrils extracted from diseased mice injected with 1B that developed GCIs (1BP). We show in vivo that conformational templating enables fibril strain replication, resulting in MSA-like inclusion pathology. Notably, the structures of 1B and 1BPare highly similar and mimic the fold of aSyn observed in one protofilament of fibrils isolated from patients with MSA11. Moreover, reinjection of crude mouse brain homogenates containing 1BPinto new mice reproduces the same MSA-like pathology induced by the parent synthetic seed 1B. Our findings identify 1B as a synthetic pathogen capable of self-replication in vivo and reveal structural features of 1B and 1BPthat may underlie MSA pathology, offering insights for therapeutic strategies.

Cryoelectron microscopy Diseases of the nervous system biology mouse experiments
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Nature · Oct 29, 2025

Mechanism of conductance control and neurosteroid binding in NMDA receptors

Ion-channel activity reflects a combination of open probability and unitary conductance1. Many channels display subconductance states that modulate signalling strength2,3, yet the structural mechanisms governing conductance levels remain incompletely understood. Here we report that conductance levels are controlled by the bending patterns of pore-forming transmembrane helices in the heterotetrameric neuronal channel GluN1a-2BN-methyl-D-aspartate receptor (NMDAR). Our single-particle electron cryomicroscopy (cryo-EM) analyses demonstrate that an endogenous neurosteroid and synthetic positive allosteric modulator (PAM), 24S-hydroxycholesterol (24S-HC), binds to a juxtamembrane pocket in the GluN2B subunit and stabilizes the fully open-gate conformation, where GluN1a M3 and GluN2B M3′ pore-forming helices are bent to dilate the channel pore. By contrast, EU1622-240 binds to the same GluN2B juxtamembrane pocket and a distinct juxtamembrane pocket in GluN1a to stabilize a sub-open state whereby only the GluN2B M3′ helix is bent. Consistent with the varying extents of gate opening, the single-channel recordings predominantly show full-conductance and subconductance states in the presence of 24S-HC and EU1622-240, respectively. Another class of neurosteroid, pregnenolone sulfate, engages a similar GluN2B pocket, but two molecules bind simultaneously, revealing a diverse neurosteroid recognition pattern. Our study identifies that the juxtamembrane pockets are critical structural hubs for modulating conductance levels in NMDAR.

Cryoelectron microscopy Ion channels in the nervous system biology
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Nature · Oct 29, 2025

Helicase-mediated mechanism of SSU processome maturation and disassembly

Eukaryotic ribosomal small subunit (SSU) assembly requires the SSU processome, a nucleolar precursor containing the RNA chaperone U3 small nucleolar RNA (snoRNA). The underlying molecular mechanisms of SSU processome maturation, remodelling, disassembly and RNA quality control, and the transitions between states remain unknown owing to a paucity of intermediates1,2,3. Here we report 16 native SSU processome structures alongside genetic data, revealing how two helicases, the Mtr4-exosome and Dhr1, are controlled for accurate and unidirectional ribosome biogenesis. Our data show how irreversible pre-ribosomal RNA degradation by the redundantly tethered RNA exosome couples the transformation of the SSU processome into a pre-40S particle, during which Utp14 can probe evolving surfaces, ultimately positioning and activating Dhr1 to unwind the U3 snoRNA and initiate nucleolar pre-40S release. This study highlights a paradigm for large dynamic RNA–protein complexes in which irreversible RNA degradation drives compositional changes and communicates these changes to govern enzyme activity while maintaining overall quality control.

Cryoelectron microscopy RNA folding biology
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Nature · Oct 01, 2025

A new paradigm for outer membrane protein biogenesis in the Bacteroidota

In Gram-negative bacteria, the outer membrane is the first line of defence against antimicrobial agents and immunological attacks1. A key part of outer membrane biogenesis is the insertion of outer membrane proteins by the β-barrel-assembly machinery (BAM)2–4. Here we report the cryo-electron microscopy structure of a BAM complex isolated from Flavobacterium johnsoniae, a member of the Bacteroidota, a phylum that includes key human commensals and major anaerobic pathogens. This BAM complex is extensively modified from the canonical Escherichia coli system and includes an extracellular canopy that overhangs the substrate folding site and a subunit that inserts into the BAM pore. The novel BamG and BamH subunits that are involved in forming the extracellular canopy are required for BAM function and are conserved across the Bacteroidota, suggesting that they form an essential extension to the canonical BAM core in this phylum. For BamH, isolation of a suppressor mutation enables the separation of its essential and non-essential functions. The need for a highly remodelled and enhanced BAM complex reflects the unusually complex membrane proteins found in the outer membrane of the Bacteroidota. Structural and biochemical studies of the β-barrel-assembly machinery from Flavobacterium johnsoniae reveal a subunit composition and assembly that are distinct from those of the canonical Escherichia coli complex.

Bacterial secretion Cryoelectron microscopy Microbiology Structural Biology Cryo-EM
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Nature · Sep 17, 2025

Structural basis for mTORC1 activation on the lysosomal membrane

The mechanistic target of rapamycin complex 1 (mTORC1) integrates growth factor (GF) and nutrient signals to stimulate anabolic processes connected to cell growth and inhibit catabolic processes such as autophagy1,2. GF signalling through the tuberous sclerosis complex regulates the lysosomally localized small GTPase RAS homologue enriched in brain (RHEB)3. Direct binding of RHEB–GTP to the mTOR kinase subunit of mTORC1 allosterically activates the kinase by inducing a large-scale conformational change4. Here we reconstituted mTORC1 activation on membranes by RHEB, RAGs and Ragulator. Cryo-electron microscopy showed that RAPTOR and mTOR interact directly with the membrane. Full engagement of the membrane anchors is required for optimal alignment of the catalytic residues in the mTOR kinase active site. Converging signals from GFs and nutrients drive mTORC1 recruitment to and activation on lysosomal membrane in a four-step process, consisting of (1) RAG–Ragulator-driven recruitment to within ~100 Å of the lysosomal membrane; (2) RHEB-driven recruitment to within ~40 Å; (3) RAPTOR–membrane engagement and intermediate enzyme activation; and (4) mTOR–membrane engagement and full enzyme activation. RHEB and membrane engagement combined leads to full catalytic activation and structurally explains GF and nutrient signal integration at the lysosome.

Cell signalling Cryoelectron microscopy Cell Biology Cryo-EM Structural Biology Metabolism
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Nature · Sep 16, 2025

Delta-type glutamate receptors are ligand-gated ion channels

Delta-type ionotropic glutamate receptors (iGluRs), or GluDs, are members of the iGluR ligand-gated ion channel family, yet their function remains enigmatic1. Although GluDs are widely expressed in the brain, play key roles in synaptic organization, and harbor disease-linked mutations, whether they retain iGluR-like channel function is debated as currents have not been directly observed2,3. Here, we define GluDs as ligand-gated ion channels that are tightly regulated in cellular contexts by purifying human GluD2 (hGluD2) and directly characterizing its structure and function using cryo-electron microscopy (cryoEM) and bilayer recordings. We show that hGluD2 is activated by D-serine and γ-aminobutyric acid (GABA), with augmented activation at physiological temperatures. We reveal that hGluD2 contains an ion channel directly coupled to clamshell-like ligand-binding domains (LBDs), which are coordinated by the amino terminal domain (ATD) above the ion channel. Ligand binding triggers channel opening via an asymmetric mechanism, and a cerebellar ataxia point mutation in the LBD rearranges the receptor architecture and induces leak currents. Our findings demonstrate that GluDs possess the intrinsic biophysical properties of ligand-gated ion channels, reconciling prior conflicting observations to establish a framework for understanding their cellular regulation and for developing therapies targeting GluD2.

Cryoelectron microscopy Ion channels in the nervous system Ligand-gated ion channels Neuroscience Cryo-EM Human Structural Biology
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Nature · Sep 03, 2025

A nanobody specific to prefusion glycoprotein B neutralizes HSV-1 and HSV-2

The nine human herpesviruses, including herpes simplex virus 1 and 2, human cytomegalovirus and Epstein–Barr virus, present a significant burden to global public health1. Their envelopes contain at least ten different glycoproteins, which are necessary for host cell tropism, attachment and entry2. The best conserved among them, glycoprotein B (gB), is essential as it performs membrane fusion by undergoing extensive rearrangements from a prefusion to postfusion conformation. At present, there are no antiviral drugs targeting gB or neutralizing antibodies directed against its prefusion form, because of the difficulty in structurally determining and using this metastable conformation. Here we show the isolation of prefusion-specific nanobodies, one of which exhibits strong neutralizing and cross-species activity. By mutational stabilization we solved the herpes simplex virus 1 gB full-length prefusion structure, which allowed the bound epitope to be determined. Our analyses show the membrane-embedded regions of gB and previously unresolved structural features3,4, including a new fusion loop arrangement, providing insights into the initial conformational changes required for membrane fusion. Binding an epitope spanning three domains, proximal only in the prefusion state, the nanobody keeps wild-type HSV-2 gB in this conformation and enabled its native prefusion structure to be determined. This also indicates the mode of neutralization and an attractive avenue for antiviral interventions.

Cryoelectron microscopy Herpes virus Membrane fusion Membrane proteins Viral infection Immunology Structural Biology Cryo-EM Human Drug Development
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Nature · Aug 20, 2025

SLC45A4is a pain gene encoding a neuronal polyamine transporter

Polyamines are regulatory metabolites with key roles in transcription, translation, cell signalling and autophagy1. They are implicated in multiple neurological disorders, including stroke, epilepsy and neurodegeneration, and can regulate neuronal excitability through interactions with ion channels2. Polyamines have been linked to pain, showing altered levels in human persistent pain states and modulation of pain behaviour in animal models3. However, the systems governing polyamine transport within the nervous system remain unclear. Here, undertaking a genome-wide association study (GWAS) of chronic pain intensity in the UK Biobank (UKB), we found a significant association between pain intensity and variants mapping to theSLC45A4gene locus. In the mouse nervous system,Slc45a4expression is enriched in all sensory neuron subtypes within the dorsal root ganglion, including nociceptors. Cell-based assays show that SLC45A4 is a selective plasma membrane polyamine transporter, and the cryo-electron microscopy (cryo-EM) structure reveals a regulatory domain and basis for polyamine recognition. Mice lacking SLC45A4 show normal mechanosensitivity but reduced sensitivity to noxious heat- and algogen-induced tonic pain that is associated with reduced excitability of C-polymodal nociceptors. Our findings therefore establish a role for neuronal polyamine transport in pain perception and identify a target for therapeutic intervention in pain treatment.

Chronic pain Cryoelectron microscopy Genome-wide association studies Transporters in the nervous system Neuroscience Cryo-EM Mouse Human Drug Development
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Nature · Aug 20, 2025

Molecular mechanism of ultrafast transport by plasma membrane Ca2+-ATPases

Tight control of intracellular Ca2+levels is fundamental as they are used to control numerous signal transduction pathways1. Plasma membrane Ca2+-ATPases (PMCAs) have a crucial role in this process by extruding Ca2+against a steep concentration gradient from the cytosol to the extracellular space2. Although new details of PMCA biology are constantly being uncovered, the structural basis of the most distinguishing features of these pumps, namely, transport rates in the kilohertz range and regulation of activity by the plasma membrane phospholipid PtdIns(4,5)P2, has so far remained elusive. Here we present the structures of mouse PMCA2 in the presence and absence of its accessory subunit neuroplastin in eight different stages of its transport cycle. Combined with whole-cell recordings that accurately track PMCA-mediated Ca2+extrusion in intact cells, these structures enable us to establish the first comprehensive transport model for a PMCA, reveal the role of disease-causing mutations and uncover the structural underpinnings of regulatory PMCA–phospholipid interaction. The transport cycle-dependent dynamics of PtdIns(4,5)P2are fundamental for its role as a ‘latch’ promoting the fast release of Ca2+and opening a passageway for counter-ions. These actions are required for maintaining the ultra-fast transport cycle. Moreover, we identify the PtdIns(4,5)P2-binding site as an unanticipated target for drug-mediated manipulation of intracellular Ca2+levels. Our work provides detailed structural insights into the uniquely fast operation of native PMCA-type Ca2+pumps and its control by membrane lipids and drugs.

Cryoelectron microscopy Membrane proteins Structural Biology Cryo-EM Mouse Cell Biology Drug Development
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Nature · Aug 20, 2025

Structural basis for the dynamic regulation of mTORC1 by amino acids

The mechanistic target of rapamycin complex 1 (mTORC1) anchors a conserved signalling pathway that regulates growth in response to nutrient availability1,2,3,4,5. Amino acids activate mTORC1 through the Rag GTPases, which are regulated by GATOR, a supercomplex consisting of GATOR1, KICSTOR and the nutrient-sensing hub GATOR2 (refs.6,7,8,9). GATOR2 forms an octagonal cage, with its distinct WD40 domain β-propellers interacting with GATOR1 and the leucine sensors Sestrin1 and Sestrin2 (SESN1 and SESN2) and the arginine sensor CASTOR1 (ref.10). The mechanisms through which these sensors regulate GATOR2 and how they detach from it upon binding their cognate amino acids remain unknown. Here, using cryo-electron microscopy, we determined the structures of a stabilized GATOR2 bound to either Sestrin2 or CASTOR1. The sensors occupy distinct and non-overlapping binding sites, disruption of which selectively impairs the ability of mTORC1 to sense individual amino acids. We also resolved the apo (leucine-free) structure of Sestrin2 and characterized the amino acid-induced structural rearrangements within Sestrin2 and CASTOR1 that trigger their dissociation from GATOR2. Binding of either sensor restricts the dynamic WDR24 β-propeller of GATOR2, a domain essential for nutrient-dependent mTORC1 activation. These findings reveal the allosteric mechanisms that convey amino acid sufficiency to GATOR2 and the ensuing structural changes that lead to mTORC1 activation.

Cryoelectron microscopy Nutrient signalling TOR signalling Structural Biology Cryo-EM Metabolism Cell Biology