Pub Date : 2025-11-27DOI: 10.1016/j.str.2025.11.004
Ji Chen, Tao Li, Jiahua He, Sheng-You Huang
Accurate model building in intermediate-resolution cryo-EM maps normally requires flexible fitting of reliable initial structures. However, while deep learning-based methods such as AlphaFold2 can predict highly accurate structures, the predicted structures often differ from experimental EM maps on both global and local scales, which poses a great challenge to accurate model building in intermediate-resolution EM maps with such initial structures. Addressing the challenge, we propose CryoEvoBuild, an automated method for improved protein model building from intermediate-resolution EM maps through the effective integration of evolutionary and experimental information. CryoEvoBuild implements a novel domain-wise fitting, refinement, assembly, and rebuilding pipeline with a recycling framework guided by AlphaFold2. Extensive benchmarking on a diverse test set of 117 maps at 4.0–10.0 Å resolutions demonstrates that CryoEvoBuild significantly improves the accuracy of AF2-predicted structures and outperforms state-of-the-art approaches, including EMBuild and phenix.dock_and_rebuild.
{"title":"Protein model building for intermediate-resolution cryo-EM maps by integrating evolutionary and experimental information","authors":"Ji Chen, Tao Li, Jiahua He, Sheng-You Huang","doi":"10.1016/j.str.2025.11.004","DOIUrl":"https://doi.org/10.1016/j.str.2025.11.004","url":null,"abstract":"Accurate model building in intermediate-resolution cryo-EM maps normally requires flexible fitting of reliable initial structures. However, while deep learning-based methods such as AlphaFold2 can predict highly accurate structures, the predicted structures often differ from experimental EM maps on both global and local scales, which poses a great challenge to accurate model building in intermediate-resolution EM maps with such initial structures. Addressing the challenge, we propose CryoEvoBuild, an automated method for improved protein model building from intermediate-resolution EM maps through the effective integration of evolutionary and experimental information. CryoEvoBuild implements a novel domain-wise fitting, refinement, assembly, and rebuilding pipeline with a recycling framework guided by AlphaFold2. Extensive benchmarking on a diverse test set of 117 maps at 4.0–10.0 Å resolutions demonstrates that CryoEvoBuild significantly improves the accuracy of AF2-predicted structures and outperforms state-of-the-art approaches, including EMBuild and phenix.dock_and_rebuild.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"9 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145609741","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-27DOI: 10.1016/j.str.2025.11.003
Dieter Waschbüsch, Prosenjit Pal, Raja S. Nirujogi, Melanie Cavin, Jaijeet Singh, Dario R. Alessi, Amir R. Khan
Inherited mutations in VPS35 and LRRK2 kinase lead to hyperphosphorylation of Rab GTPases. RH2 domain-containing proteins from the RILP homology family, such as RILPL1, are Rab effectors that recognize the LRRK2-phosphorylated switch 2 threonine of phospho-Rab8A and phospho-Rab10. Phospho-Rabs are also seen on lysosomal membranes in complex with RILPL1 and TMEM55B, a 284-residue lysosomal membrane protein lacking homology to known proteins. Here, we report crystal structures of the cytosolic region 80–166 of TMEM55B alone and in complex with a C-terminal RILPL1 peptide, which we define as the TMEM55B-binding motif (TBM). The RILPL1 TBM sits in a shallow groove across two tandem RING-like domains of TMEM55B, each forming a Zn2+-stabilized 40-residue β-sandwich. Co-immunoprecipitation and mass spectrometry studies indicate that TMEM55B forms complexes independently of phospho-Rabs with conserved TBMs found in JIP3, JIP4, OCRL, WDR81, and TBC1D9B. These studies suggest that TMEM55B acts as a central hub for adaptor recruitment on lysosomes.
{"title":"Structural basis for binding of RILPL1 to TMEM55B reveals a lysosomal platform for adaptor assembly through a conserved peptide motif","authors":"Dieter Waschbüsch, Prosenjit Pal, Raja S. Nirujogi, Melanie Cavin, Jaijeet Singh, Dario R. Alessi, Amir R. Khan","doi":"10.1016/j.str.2025.11.003","DOIUrl":"https://doi.org/10.1016/j.str.2025.11.003","url":null,"abstract":"Inherited mutations in VPS35 and LRRK2 kinase lead to hyperphosphorylation of Rab GTPases. RH2 domain-containing proteins from the RILP homology family, such as RILPL1, are Rab effectors that recognize the LRRK2-phosphorylated switch 2 threonine of phospho-Rab8A and phospho-Rab10. Phospho-Rabs are also seen on lysosomal membranes in complex with RILPL1 and TMEM55B, a 284-residue lysosomal membrane protein lacking homology to known proteins. Here, we report crystal structures of the cytosolic region 80–166 of TMEM55B alone and in complex with a C-terminal RILPL1 peptide, which we define as the TMEM55B-binding motif (TBM). The RILPL1 TBM sits in a shallow groove across two tandem RING-like domains of TMEM55B, each forming a Zn<sup>2+</sup>-stabilized 40-residue β-sandwich. Co-immunoprecipitation and mass spectrometry studies indicate that TMEM55B forms complexes independently of phospho-Rabs with conserved TBMs found in JIP3, JIP4, OCRL, WDR81, and TBC1D9B. These studies suggest that TMEM55B acts as a central hub for adaptor recruitment on lysosomes.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"21 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145609742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-27DOI: 10.1016/j.str.2025.11.005
Emily N. Bianchini, Carolina Pérez-Segura, Haitao Liu, Laura Luckenbaugh, John Flanagan, Yuanheng Cai, John Shanklin, Adam Zlotnick, Jodi A. Hadden-Perilla, Jianming Hu, Joseph C.-Y. Wang
HBV causes chronic infections that can lead to severe liver disease, yet current treatments rarely achieve a cure. The HBV capsid is a critical therapeutic target, but structural insights have largely relied on E. coli-derived particles lacking native modifications. Here, we present near-atomic resolution cryo-electron microscopy (EM) structures of HBV capsids purified from human embryonic kidney (HEK-293T) cells, capturing authentic architecture and post-translational modifications. A hydrophobic pocket at the intradimer interface harbors lipid-like densities corresponding to stearic and palmitic acids, confirmed by gas chromatography-mass spectrometry. Molecular dynamics simulations revealed that pocket accessibility is regulated by rotamer states of Lys96, Phe97, and Gln99, supporting an induced fit model of fatty acid binding. Reduced phosphorylation and increased RNA content further modulate capsid conformation and pocket openness. These findings highlight the dynamic regulation of HBV capsid structure and provide a framework for understanding how capsid conformational dynamics contribute to viral assembly and envelopment.
{"title":"Cryo-EM structures of HBV capsids from human cells at near-atomic resolution","authors":"Emily N. Bianchini, Carolina Pérez-Segura, Haitao Liu, Laura Luckenbaugh, John Flanagan, Yuanheng Cai, John Shanklin, Adam Zlotnick, Jodi A. Hadden-Perilla, Jianming Hu, Joseph C.-Y. Wang","doi":"10.1016/j.str.2025.11.005","DOIUrl":"https://doi.org/10.1016/j.str.2025.11.005","url":null,"abstract":"HBV causes chronic infections that can lead to severe liver disease, yet current treatments rarely achieve a cure. The HBV capsid is a critical therapeutic target, but structural insights have largely relied on <em>E. coli</em>-derived particles lacking native modifications. Here, we present near-atomic resolution cryo-electron microscopy (EM) structures of HBV capsids purified from human embryonic kidney (HEK-293T) cells, capturing authentic architecture and post-translational modifications. A hydrophobic pocket at the intradimer interface harbors lipid-like densities corresponding to stearic and palmitic acids, confirmed by gas chromatography-mass spectrometry. Molecular dynamics simulations revealed that pocket accessibility is regulated by rotamer states of Lys96, Phe97, and Gln99, supporting an induced fit model of fatty acid binding. Reduced phosphorylation and increased RNA content further modulate capsid conformation and pocket openness. These findings highlight the dynamic regulation of HBV capsid structure and provide a framework for understanding how capsid conformational dynamics contribute to viral assembly and envelopment.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"71 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145609743","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-24DOI: 10.1016/j.str.2025.10.001
Kazuki Obashi, Marie-Paule Strub, Justin W. Taraska
Ca2+-triggered exocytosis from neurons and endocrine cells is regulated by neuronal soluble N-ethylmaleimide-sensitive factor attachment receptor (SNARE) proteins. Conformational changes in syntaxin-1—the plasma membrane t-SNARE—are essential for vesicle docking and exocytosis. The nature of these conformational changes on the plasma membrane in living cells, however, remains largely unknown. Here, we develop a fluorescence system to map short-range conformational changes in syntaxin-1a in native plasma membranes of unroofed cells. We use a fluorescence resonance energy transfer (FRET) technique that employs site-specific protein labeling with unnatural fluorescent amino acids as donor fluorophores and colored transition metal ion acceptors bound to engineered di-histidine sites to map angstrom-scale distances. We find that phosphatidylinositol 4,5-bisphosphate (PIP2) regulates a conformational change in syntaxin-1a by modulating the structure of syntaxin-1a and its interaction with Munc18-1. Our results uncover new regulatory mechanisms of syntaxin-1a by PIP2 in the steps leading to Ca2+-triggered exocytosis.
{"title":"A PIP2-stabilized syntaxin-1a structure mapped with transition metal ion FRET and unnatural fluorescent amino acids at the plasma membrane","authors":"Kazuki Obashi, Marie-Paule Strub, Justin W. Taraska","doi":"10.1016/j.str.2025.10.001","DOIUrl":"https://doi.org/10.1016/j.str.2025.10.001","url":null,"abstract":"Ca<sup>2+</sup>-triggered exocytosis from neurons and endocrine cells is regulated by neuronal soluble N-ethylmaleimide-sensitive factor attachment receptor (SNARE) proteins. Conformational changes in syntaxin-1—the plasma membrane t-SNARE—are essential for vesicle docking and exocytosis. The nature of these conformational changes on the plasma membrane in living cells, however, remains largely unknown. Here, we develop a fluorescence system to map short-range conformational changes in syntaxin-1a in native plasma membranes of unroofed cells. We use a fluorescence resonance energy transfer (FRET) technique that employs site-specific protein labeling with unnatural fluorescent amino acids as donor fluorophores and colored transition metal ion acceptors bound to engineered di-histidine sites to map angstrom-scale distances. We find that phosphatidylinositol 4,5-bisphosphate (PIP2) regulates a conformational change in syntaxin-1a by modulating the structure of syntaxin-1a and its interaction with Munc18-1. Our results uncover new regulatory mechanisms of syntaxin-1a by PIP2 in the steps leading to Ca<sup>2+</sup>-triggered exocytosis.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"167 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145583887","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Muscle-specific receptor tyrosine kinase (MuSK) is a single-pass transmembrane protein expressed on skeletal muscle. MuSK is activated by binding of nerve-derived agrin with the help of muscle coreceptor LRP4, leading to the clustering of acetylcholine receptors (AChR), which is required for the formation and maintenance of functional neuromuscular junctions. The structural mechanism of MuSK activation by physiological and artificial agonistic agents has remained elusive. In this study, we isolated a 27-residue linear peptide (L1) that binds human MuSK with high affinity. Genetic fusion of L1 to either the N or C termini of the human IgG Fc resulted in two different versions of MuSK dimerizers, denoted as L1-Fc and Fc-L1. Only Fc-L1 activated MuSK on myotubes and induced AChR clustering. Crystallographic analysis of MuSK-L1 interactions revealed that MuSK activation requires a particular dimeric conformation, pointing toward the importance of the lateral size of the receptor complex at the muscle cell surface.
{"title":"Muscle-specific tyrosine kinase activation by a peptide-based dimerizer is orientation dependent","authors":"Fumiya Mizutani, Kyoko Matoba, Hayden Peacock, Mitsuhiro Yamada, Emiko Mihara, Osamu Higuchi, Hiroaki Suga, Takao Arimori, Junichi Takagi","doi":"10.1016/j.str.2025.10.018","DOIUrl":"https://doi.org/10.1016/j.str.2025.10.018","url":null,"abstract":"Muscle-specific receptor tyrosine kinase (MuSK) is a single-pass transmembrane protein expressed on skeletal muscle. MuSK is activated by binding of nerve-derived agrin with the help of muscle coreceptor LRP4, leading to the clustering of acetylcholine receptors (AChR), which is required for the formation and maintenance of functional neuromuscular junctions. The structural mechanism of MuSK activation by physiological and artificial agonistic agents has remained elusive. In this study, we isolated a 27-residue linear peptide (L1) that binds human MuSK with high affinity. Genetic fusion of L1 to either the N or C termini of the human IgG Fc resulted in two different versions of MuSK dimerizers, denoted as L1-Fc and Fc-L1. Only Fc-L1 activated MuSK on myotubes and induced AChR clustering. Crystallographic analysis of MuSK-L1 interactions revealed that MuSK activation requires a particular dimeric conformation, pointing toward the importance of the lateral size of the receptor complex at the muscle cell surface.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"223 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145583815","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-21DOI: 10.1016/j.str.2025.10.017
Xing-Yu Yue, Guang-Lei Wang, Mei-Juan Zou, Fei Ma, Zheng-Yu Wang-Otomo, Michael T. Madigan, Long-Jiang Yu
Aerobic anoxygenic phototrophic bacteria (AAPB) are widely distributed in nature and they are important members of the marine phototrophic community. However, a structural and functional understanding of the AAPB photosynthetic apparatus is still lacking. Here, we present cryo-EM structures of the LH1-RC (core) and LH2 (peripheral) photocomplexes from the model aerobic phototroph Erythrobacter (Ery.) sanguineus. The LH1 αβ-heterodimers bind the carotenoids bacteriorubixanthinal and caloxanthin—pigments that are absent from anaerobic anoxygenic phototrophs—to form a closed ring structure. Ery. sanguineus LH1-RC contains a lipid-anchored polypeptide unrelated to any of the auxiliary proteins identified in the core complexes of purple bacteria so far. The Ery. sanguineus LH2 complex shows unique absorption characteristics, with its Qy transition being blue-shifted to 814 nm. This work provides structural insights into the unusual photosynthetic properties of AAPB and points to new avenues to further explore their biology.
{"title":"Cryo-EM structures of photocomplexes from the free-living aerobic anoxygenic phototrophic bacterium Erythrobacter sanguineus","authors":"Xing-Yu Yue, Guang-Lei Wang, Mei-Juan Zou, Fei Ma, Zheng-Yu Wang-Otomo, Michael T. Madigan, Long-Jiang Yu","doi":"10.1016/j.str.2025.10.017","DOIUrl":"https://doi.org/10.1016/j.str.2025.10.017","url":null,"abstract":"Aerobic anoxygenic phototrophic bacteria (AAPB) are widely distributed in nature and they are important members of the marine phototrophic community. However, a structural and functional understanding of the AAPB photosynthetic apparatus is still lacking. Here, we present cryo-EM structures of the LH1-RC (core) and LH2 (peripheral) photocomplexes from the model aerobic phototroph <em>Erythrobacter (Ery.) sanguineus</em>. The LH1 αβ-heterodimers bind the carotenoids bacteriorubixanthinal and caloxanthin—pigments that are absent from anaerobic anoxygenic phototrophs—to form a closed ring structure. <em>Ery. sanguineus</em> LH1-RC contains a lipid-anchored polypeptide unrelated to any of the auxiliary proteins identified in the core complexes of purple bacteria so far. The <em>Ery. sanguineus</em> LH2 complex shows unique absorption characteristics, with its Q<sub>y</sub> transition being blue-shifted to 814 nm. This work provides structural insights into the unusual photosynthetic properties of AAPB and points to new avenues to further explore their biology.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"165 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145567382","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-19DOI: 10.1016/j.str.2025.10.016
Daniel Wohlwend, Thilo Seifermann, Emmanuel Gnandt, Marta Vranas, Stefan Gerhardt, Thorsten Friedrich
Energy-converting NADH:ubiquinone oxidoreductase, respiratory complex I, is central to energy metabolism by coupling NADH oxidation and quinone reduction with proton translocation across the membrane. Electrons are transferred from the primary acceptor flavin mononucleotide via a chain of iron-sulfur clusters to quinone. The enigmatic cluster N1a is conserved, but not part of this electron transfer chain. We reported on variants of the complex in which N1a is not detectable by EPR spectroscopy. This was tentatively attributed to the lower redox potential of the variant N1a. However, it remained an open question, whether the variants contain this cluster at all. Here, we determined the structures of these variants by X-ray crystallography and cryogenic-electron microscopy. Cluster N1a is present in all variants and the shift of its redox potential is explained by nearby structural changes. A role of the cluster for the mechanism of the complex is discussed.
{"title":"Structural changes shifting the redox potential of the outlying cluster N1a in respiratory complex I","authors":"Daniel Wohlwend, Thilo Seifermann, Emmanuel Gnandt, Marta Vranas, Stefan Gerhardt, Thorsten Friedrich","doi":"10.1016/j.str.2025.10.016","DOIUrl":"https://doi.org/10.1016/j.str.2025.10.016","url":null,"abstract":"Energy-converting NADH:ubiquinone oxidoreductase, respiratory complex I, is central to energy metabolism by coupling NADH oxidation and quinone reduction with proton translocation across the membrane. Electrons are transferred from the primary acceptor flavin mononucleotide <em>via</em> a chain of iron-sulfur clusters to quinone. The enigmatic cluster N1a is conserved, but not part of this electron transfer chain. We reported on variants of the complex in which N1a is not detectable by EPR spectroscopy. This was tentatively attributed to the lower redox potential of the variant N1a. However, it remained an open question, whether the variants contain this cluster at all. Here, we determined the structures of these variants by X-ray crystallography and cryogenic-electron microscopy. Cluster N1a is present in all variants and the shift of its redox potential is explained by nearby structural changes. A role of the cluster for the mechanism of the complex is discussed.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"98 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145545801","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-14DOI: 10.1016/j.str.2025.10.014
Charlie Lovatt, Thomas O’Sullivan, Clara Ortega-de San Luis, Tomás J. Ryan, René A.W. Frank
Memory is incorporated into the brain as physicochemical changes to engram cells. These neuronal populations form complex neuroanatomical circuits, are modified by experiences to store information, and allow memory recall. At the molecular level, learning modifies synaptic communication to rewire engram circuits. How macromolecules are organized within engram synapses is unknown. Here, we establish engram labeling technology combined with cryogenic correlated light and electron microscopy (cryoCLEM)-guided cryogenic electron tomography (cryoET) to visualize the in-tissue 3D macromolecular architecture of engram synapses of a contextual fear memory within the mouse hippocampus. Engram synapses exhibited structural diversity of macromolecular constituents and organelles in both pre- and postsynaptic compartments and within the synaptic cleft, including in membrane proteins, synaptic vesicle occupancy, and F-actin copy number. This “engram to tomogram” approach, harnessing in vivo functional neuroscience and structural biology, provides a methodological framework for testing fundamental molecular plasticity mechanisms within engram circuits.
记忆通过印记细胞的物理化学变化被纳入大脑。这些神经元群形成了复杂的神经解剖回路，通过经历来存储信息，并允许记忆回忆。在分子水平上，学习改变突触通讯，重新连接印痕电路。大分子如何在印痕突触内组织尚不清楚。在这里，我们建立了结合低温相关光和电子显微镜（cryoCLEM）引导的低温电子断层扫描（cryogenic electron tomography, cryoET）的印迹标记技术，以可视化小鼠海马内情境恐惧记忆的印迹突触的组织内3D大分子结构。印迹突触在突触前和突触后室以及突触间隙内均表现出大分子成分和细胞器的结构多样性，包括膜蛋白、突触囊泡占用和f -肌动蛋白拷贝数。这种“印痕到断层成像”的方法，利用体内功能神经科学和结构生物学，为测试印痕电路中的基本分子可塑性机制提供了一种方法框架。
{"title":"Memory engram synapse 3D macromolecular architecture visualized by cryoCLEM-guided cryoET","authors":"Charlie Lovatt, Thomas O’Sullivan, Clara Ortega-de San Luis, Tomás J. Ryan, René A.W. Frank","doi":"10.1016/j.str.2025.10.014","DOIUrl":"https://doi.org/10.1016/j.str.2025.10.014","url":null,"abstract":"Memory is incorporated into the brain as physicochemical changes to engram cells. These neuronal populations form complex neuroanatomical circuits, are modified by experiences to store information, and allow memory recall. At the molecular level, learning modifies synaptic communication to rewire engram circuits. How macromolecules are organized within engram synapses is unknown. Here, we establish engram labeling technology combined with cryogenic correlated light and electron microscopy (cryoCLEM)-guided cryogenic electron tomography (cryoET) to visualize the in-tissue 3D macromolecular architecture of engram synapses of a contextual fear memory within the mouse hippocampus. Engram synapses exhibited structural diversity of macromolecular constituents and organelles in both pre- and postsynaptic compartments and within the synaptic cleft, including in membrane proteins, synaptic vesicle occupancy, and F-actin copy number. This “engram to tomogram” approach, harnessing <em>in vivo</em> functional neuroscience and structural biology, provides a methodological framework for testing fundamental molecular plasticity mechanisms within engram circuits.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"119 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145509014","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-06DOI: 10.1016/j.str.2025.10.007
Natalia Fuchs, Venera Weinhardt
In this issue of Structure, Deshmukh et al.1 reveal that β cells actively remodel insulin secretory granules in response to specific physiological cues, altering granule density, proinsulin processing, and spatial distribution. This stimulus-specific structural maturation highlights how β cells sculpt their secretory machinery, offering new insights into insulin release regulation.
{"title":"Soft X-ray tomography illuminates drug-induced changes in insulin granules","authors":"Natalia Fuchs, Venera Weinhardt","doi":"10.1016/j.str.2025.10.007","DOIUrl":"https://doi.org/10.1016/j.str.2025.10.007","url":null,"abstract":"In this issue of <em>Structure</em>, Deshmukh et al.<span><span><sup>1</sup></span></span> reveal that β cells actively remodel insulin secretory granules in response to specific physiological cues, altering granule density, proinsulin processing, and spatial distribution. This stimulus-specific structural maturation highlights how β cells sculpt their secretory machinery, offering new insights into insulin release regulation.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"105 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145447662","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Vibrio cholerae cytolysin (VCC) is a β-barrel pore-forming toxin (β-PFT). The membrane insertion of its pore-forming “pre-stem” motif is the most crucial step in the pore-formation mechanism. In the soluble monomeric form, pre-stem remains clamped against the central cytolysin domain by the so-called cradle loop. In the course of oligomeric pore-formation in the target membranes, the cradle loop gets detached from the pre-stem and reorients, thus allowing the pre-stem to extend and insert into the membrane. Here, we show that the specific cradle loop residue(s) play crucial roles in governing the pore-formation mechanism of VCC by establishing decisive interactions with the neighboring structural domains/modules. The alteration of the cradle loop residue, Y194 in particular, compromises the membrane-insertion of the pre-stem, and tends to arrest the membrane-bound toxin in the pre-pore-like oligomeric states. Our study suggests that the native cradle loop architecture, with its intact contacts with the surrounding interaction partners, is essential for VCC pore-formation.
{"title":"Cradle loop regulates β-barrel pore-formation mechanism of Vibrio cholerae cytolysin","authors":"Mahendra Singh, Arnab Chatterjee, Ananya Nayak, Prasenjit Naskar, Gurvinder Kaur, Jagannath Mondal, Somnath Dutta, Kausik Chattopadhyay","doi":"10.1016/j.str.2025.10.013","DOIUrl":"https://doi.org/10.1016/j.str.2025.10.013","url":null,"abstract":"<em>Vibrio cholerae</em> cytolysin (VCC) is a β-barrel pore-forming toxin (β-PFT). The membrane insertion of its pore-forming “pre-stem” motif is the most crucial step in the pore-formation mechanism. In the soluble monomeric form, pre-stem remains clamped against the central cytolysin domain by the so-called cradle loop. In the course of oligomeric pore-formation in the target membranes, the cradle loop gets detached from the pre-stem and reorients, thus allowing the pre-stem to extend and insert into the membrane. Here, we show that the specific cradle loop residue(s) play crucial roles in governing the pore-formation mechanism of VCC by establishing decisive interactions with the neighboring structural domains/modules. The alteration of the cradle loop residue, Y194 in particular, compromises the membrane-insertion of the pre-stem, and tends to arrest the membrane-bound toxin in the pre-pore-like oligomeric states. Our study suggests that the native cradle loop architecture, with its intact contacts with the surrounding interaction partners, is essential for VCC pore-formation.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"43 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145447659","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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