Journal of structural biology最新文献

{"title":"Scientific Laudatio for Professor Andreas Engel.","authors":"Dimitrios Fotiadis, Shirley A Müller, Daniel J Müller","doi":"10.1016/j.jsb.2026.108324","DOIUrl":"https://doi.org/10.1016/j.jsb.2026.108324","url":null,"abstract":"<p><p>With the passing of Andreas Engel on 1 April 2026, the structural biology and biophysics communities have lost one of their most visionary and influential scientists. Over a career spanning more than five decades, Andreas fundamentally shaped how we visualize and understand biological macromolecules at the nanoscale. His pioneering contributions to scanning transmission electron microscopy (STEM), atomic force microscopy (AFM) and electron crystallography opened entirely new avenues for studying the architecture and function of membrane proteins and supramolecular complexes.</p>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":" ","pages":"108324"},"PeriodicalIF":2.7,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147856609","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Announcement: Journal of Structural Biology: Paper of the year","authors":"Sergio Pantano","doi":"10.1016/j.jsb.2025.108275","DOIUrl":"10.1016/j.jsb.2025.108275","url":null,"abstract":"","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"218 1","pages":"Article 108275"},"PeriodicalIF":2.7,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145743145","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Disorder, dynamics, and regulation of proteins and nucleic acids","authors":"George P. Lisi","doi":"10.1016/j.jsb.2026.108285","DOIUrl":"10.1016/j.jsb.2026.108285","url":null,"abstract":"","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"218 1","pages":"Article 108285"},"PeriodicalIF":2.7,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145917846","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structure of the type VI secretion protein VgrS from Salmonella Typhimurium","authors":"Kartik Sachar ,&nbsp;Matthew Van Schepdael ,&nbsp;Karsen L. Winters,&nbsp;Gerd Prehna","doi":"10.1016/j.jsb.2026.108297","DOIUrl":"10.1016/j.jsb.2026.108297","url":null,"abstract":"<div><div>Enteric bacterial pathogens employ various strategies to colonize the intestine and cause diseases ranging from gastroenteritis to systemic infections. For example, <em>Salmonella enterica</em> utilizes a nanomachine known as the type VI secretion system (T6SS) to facilitate colonization of the host gut. However, the varied mechanistic details of how the T6SS is loaded with effector proteins remains to be elucidated. Here, we present an X-ray crystal structure of the <em>Salmonella</em> Typhimurium VgrG (VgrS) that serves as platform for T6SS effector loading. Compared to other known structures of VgrG proteins, the VgrS trimer adopts an alternative open conformation within the gp27 region base. The open conformation is due to an extended loop conformation in the gp27 region. This conformation creates a domain extension which docks into the neighboring monomer sequentially around the trimer. Additionally, a comparative structural analysis of VgrS with other VgrG proteins reveals molecular variations that may contribute to specific effector loading mechanisms. Our structural data and molecular analysis highlight the observation that the T6SS of each bacterial species or strain is unique.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"218 1","pages":"Article 108297"},"PeriodicalIF":2.7,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146194920","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"From selenium to sulfur: predictive modeling unveils conformational and bonding changes in selenoproteins","authors":"Shiqi Luo ,&nbsp;Xinnan Liu ,&nbsp;Xia Wang ,&nbsp;Haotian Liu ,&nbsp;Wei Ge","doi":"10.1016/j.jsb.2025.108278","DOIUrl":"10.1016/j.jsb.2025.108278","url":null,"abstract":"<div><div>Selenoproteins, defined by the incorporation of the 21st amino acid — selenocysteine (Sec) — orchestrate essential redox, endocrine, and metabolic pathways in humans, yet high‑resolution structures exist for only a minority of the 25 family members. Leveraging the AlphaFold 3 (AF3), we generated full‑length atomic models for all human selenoproteins together with in‑silico Sec-to-Cys variants. AF3 achieved high confidence for 22 proteins and sub‑Å agreement with the one experimentally solved glutathione peroxidase 4 (GPX4). Global comparison of native and mutant models revealed that Sec-to-Cys substitution preserves overall fold in nineteen proteins but locally disrupts or re‑wires intramolecular selenenyl‑sulfide linkages in six cases. Structure‑based clustering uncovered a conserved “Se‑thioredoxin‑like” core in fifteen selenoproteins. AF3 additionally predicted potential GPX4 homodimeric assemblies, consistent with the dimeric forms observed in native gels from brain tissue and cell lines. Together, these AF3 models constitute the comprehensive structural atlas of the human selenoproteome, elucidate the fold‑specific positioning of Sec. The dataset provides a foundation for mechanistic dissection, evolutionary analyses, and rational drug design targeting selenium‑dependent redox biology.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"218 1","pages":"Article 108278"},"PeriodicalIF":2.7,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145743108","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural basis for spectral red shift and UVA absorption in the microalgal water-soluble astaxanthin-binding protein AstaP-pink1","authors":"Tamaki Mitsui ,&nbsp;Yasuhito Shomura ,&nbsp;Maiko Furubayashi ,&nbsp;Ryuichi Kato ,&nbsp;Shinichi Takaichi ,&nbsp;Shinji Kawasaki","doi":"10.1016/j.jsb.2026.108288","DOIUrl":"10.1016/j.jsb.2026.108288","url":null,"abstract":"<div><div>AstaPs are water-soluble, photooxidative stress-inducible astaxanthin (AXT)-binding proteins found only in Scenedesmaceae microalgae, where they play a central role in survival under severe photooxidative stress. Here, we focused on the unique function of AstaP-pink1, which converts orange AXT into a pink form and generates a UVA absorption spectrum upon protein binding. AstaP-pink1 was expressed in genetically engineered <em>Escherichia coli</em> strains capable of synthesizing AXT. The host strain harboring pAC-Asta produced adonixanthin, AXT, and zeaxanthin in an approximate ratio of 5:3:2, whereas the strain carrying pMF573 predominantly produced AXT (∼90 % of total carotenoid). Co-expression of the gene encoding AstaP-pink1 in these strains resulted in moderate and selective AXT binding, accompanied by a spectral red shift and UVA absorption, thereby generating pink coloration. Crystal structure analysis of AXT-bound recombinant AstaP-pink1 (rAstaP-pink1) revealed both similarities and differences in AXT binding compared with rAstaP-orange1. Density functional theory (DFT) calculations based on the crystal structure suggested that the larger red shift than that of AstaP-orange1 and the distinct UVA absorption are derived from the conformation of AXT that is compelled by binding to AstaP-pink1. This study suggests that AXT binding by AstaP-pink1 not only facilitates the water solubilization of AXT but also generates the observed spectral properties.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"218 1","pages":"Article 108288"},"PeriodicalIF":2.7,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145917910","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Crystal structure of glyoxysomal citrate synthase 3 from Arabidopsis thaliana reveals a novel oligomeric state","authors":"Kazuya Nishio ,&nbsp;Kenji Takagi ,&nbsp;Tsunehiro Mizushima","doi":"10.1016/j.jsb.2026.108293","DOIUrl":"10.1016/j.jsb.2026.108293","url":null,"abstract":"<div><div>Citrate synthase (CS) is a pivotal enzyme in carbohydrate and energy metabolism, with distinct isoforms present in various eukaryotic compartments, including mitochondria and glyoxysomes in plants. While CSs exhibit diverse oligomeric states, detailed structural information on higher plant non-mitochondrial Type II CSs has been limited. We herein determined the crystal structures of CS 3 from <em>Arabidopsis thaliana</em> (<em>At</em>CSY3) in complex with oxaloacetate (OAA) and acetyl-coenzyme A (CoA)-OAA at resolutions of 2.0 and 1.7 Å, respectively. These structures revealed that <em>At</em>CSY3 can form a homo-tetrameric assembly that is distinct from the hexameric <em>Escherichia coli</em> CS and the octameric <em>Ananas comosus</em> CS. The tetrameric arrangement observed in the crystal structure is mediated by hydrogen-bonding and hydrophobic interactions between subunits. Gel filtration chromatography further suggests the presence of a tetrameric species in solution under the purification conditions. Ligand density was observed near the interface between the two dimers in the tetrameric structure; however, no experimental evidence is currently available to determine whether ligand binding affects the oligomeric state or enzymatic activity of <em>At</em>CSY3. These structures illustrate the structural diversity of CS oligomerization and provide a structural basis for studies of plant glyoxysomal CSs.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"218 1","pages":"Article 108293"},"PeriodicalIF":2.7,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146044139","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Corrigendum to “Crystal structure of glyoxysomal citrate synthase 3 from Arabidopsis thaliana reveals a Novel Oligomeric State”. [J. Struct. Biol. 218(1) (2026) 108293]","authors":"Kazuya Nishio ,&nbsp;Kenji Takagi ,&nbsp;Tsunehiro Mizushima","doi":"10.1016/j.jsb.2026.108296","DOIUrl":"10.1016/j.jsb.2026.108296","url":null,"abstract":"","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"218 1","pages":"Article 108296"},"PeriodicalIF":2.7,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146194908","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nanostructural evolution during carious and demineralisation process of human dentine using small angle X-ray scattering tensor tomography","authors":"Tayyaba Rabnawaz ,&nbsp;Nathanael Leung ,&nbsp;Leonard C. Nielsen ,&nbsp;Robert A. Harper ,&nbsp;Richard M. Shelton ,&nbsp;Gabriel Landini ,&nbsp;Tim Snow ,&nbsp;Andy Smith ,&nbsp;Nick Terrill ,&nbsp;Marianne Liebi ,&nbsp;Tan Sui","doi":"10.1016/j.jsb.2025.108284","DOIUrl":"10.1016/j.jsb.2025.108284","url":null,"abstract":"<div><div>Dental caries, one of the most prevalent non-communicable diseases worldwide, is characterised by the progressive deterioration of the structure and mechanical properties of dental hard tissues. In human teeth, dentine is the most abundant mineralised tissue, forming the primary support material. To assess changes in the mechanical properties of dentine caused by dental caries and acid erosion, it is crucial to understand the relationship between organic and inorganic dentine components and their organisation into a 3D anisotropic structure at the nanoscale. Over the past 20 years, alterations in dentine structure caused by caries and artificial demineralisation have been reported using conventional microscopy techniques. However, due to the limited spatial resolution of these techniques, the 3D structural organisation including orientation and degree of alignment of mineralised collagen fibrils at the nanoscale, has not been fully explored. This study investigated alterations in the 3D structure of normal, carious and artificially demineralised dentine using SAXS tensor tomography (SASTT). This technique enabled the observation of differences in the local orientation of organic and inorganic components, as well as variations in local scattering intensity, resulting from natural caries and artificial demineralisation. In comparison to normal dentine, caries caused minor orientational differences of both components but had a major impact on the local X-ray scattering intensity. After artificial demineralisation of the dentine, most of the mineral was lost in the outer layers, resulting in a greater reduction in scattering intensity than that caused by caries.</div></div><div><h3>Significance</h3><div>The remarkable mechanical properties of human dentine arise from its complex hierarchical 3D structure. In this article, we have investigated the 3D structural alterations in dentine, caused by caries and artificial demineralisation. For this detailed investigation, SAXS tensor tomography (SASTT) has been implemented on the I22 beamline at Diamond Light Source, UK. SASTT is a technique that can probe the nanostructure of dentine, yielding orientation and degree of alignment of the mineralised collagen fibrils, while also providing a 3D reciprocal space map to investigate the detailed non-uniform scattering intensity distribution in all directions. The initial SASTT data provide insights into dentine structural alterations caused by caries and artificial demineralisation, facilitating further exploration of structure–mechanical property relationships, which may lead to improve the development of novel biomimetic materials for dental applications.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"218 1","pages":"Article 108284"},"PeriodicalIF":2.7,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145880745","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Distribution and size of scallop patterns at the human dentin enamel junction revealed with micro tomography","authors":"Pierre-Yves Collart-Dutilleul ,&nbsp;T. Cloitre ,&nbsp;D. Carayon ,&nbsp;A. Slimani ,&nbsp;H. Salehi ,&nbsp;H. Tassery ,&nbsp;F. Cuisinier ,&nbsp;A. Desoutter","doi":"10.1016/j.jsb.2026.108289","DOIUrl":"10.1016/j.jsb.2026.108289","url":null,"abstract":"<div><div>The dentin–enamel junction (DEJ) plays a critical role in tooth biomechanics, acting as a tough, crack-deflecting interface between the brittle enamel and the more resilient dentin. Although previous studies have described the DEJ using histology and electron microscopy techniques, the three-dimensional (3D) distribution and structural heterogeneity of scallop patterns along the DEJ remain poorly understood. Here, we combined high-resolution X-ray microcomputed tomography (µCT) with multiphoton microscopy (MPM) to investigate scallop morphology, spatial distribution, and collagen fiber organization across human teeth.</div><div>Non-carious human teeth (n = 35) were scanned at 5 µm resolution, allowing 3D reconstruction of the DEJ surface. Scallop size, distribution, and root mean square (RMS) roughness were quantified across mesial, distal, buccal, and lingual faces of incisors, canines, premolars, and molars. MPM with second harmonic generation (SHG) provided complementary imaging of collagen fiber presence within scallop structures.</div><div>Scallop size depended primarily on location but also on tooth type: the largest scallops (&gt;150 µm) were concentrated on mesial and distal faces at interproximal contact areas, while molars lacked large scallops entirely. RMS roughness confirmed significant topographic heterogeneity between regions. SHG imaging showed high collagen density at scallop peaks.</div><div>These findings provide the first whole-tooth 3D mapping of scallop patterns, supporting the hypothesis that scalloped DEJ structures enhance crack resistance and mechanical resilience. Further studies using higher-resolution imaging and comparative models across species may clarify the developmental and functional origins of these unique microstructures.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"218 1","pages":"Article 108289"},"PeriodicalIF":2.7,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145939562","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}