Journal of Structural Biology: X最新文献

DiameTR: A cryo-EM tool for diameter sorting of tubular samples DiameTR：用于管状样品直径分选的低温电镜工具

IF 5.1

Journal of Structural Biology: X Pub Date : 2025-09-02 DOI: 10.1016/j.yjsbx.2025.100136

Ruizhi Peng , Heidy Elkhaligy , Timothy Grant , Scott M. Stagg

{"title":"DiameTR: A cryo-EM tool for diameter sorting of tubular samples","authors":"Ruizhi Peng , Heidy Elkhaligy , Timothy Grant , Scott M. Stagg","doi":"10.1016/j.yjsbx.2025.100136","DOIUrl":"10.1016/j.yjsbx.2025.100136","url":null,"abstract":"<div><div>Tubular structures are ubiquitous in biological systems and have been a focal point of cryo-electron microscopy (cryo-EM) structural analysis since the technique’s inception. A critical step in processing tubular cryo-EM data is particle classification by diameter, as uniformity in diameter is a prerequisite for high-resolution three-dimensional reconstructions. Conventional methods rely on cross-correlation-based algorithms, which require prior knowledge to generate reference images, or iterative two-dimensional (2D) classification, that align and cluster particles into a predefined number of classes—a process that is both time-consuming and subjective. To address these limitations, we developed diameTR, a computational tool that rapidly determines tubular diameters in a prior knowledge-free and reference-free manner using GPU-accelerated processing on a per-particle basis. When applied to homogeneous datasets, diameTR yields narrow diameter distributions aligning closely with published values. For heterogeneous samples, it enables the separation of subsets with distinct diameters, validated by 2D averaging. Notably, diameTR identified an unreported smaller diameter subset of particles with new helical symmetry parameters in the previously published KpFtsZ-Monobody dataset. Collectively, diameTR represents a robust, efficient solution for diameter determination in tubular cryo-EM samples, eliminating the need for extensive human intervention while significantly accelerating processing.</div></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"12 ","pages":"Article 100136"},"PeriodicalIF":5.1,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145044704","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The J-shape of β2GPI reveals a cryptic discontinuous epitope across domains I and II β2GPI呈j形，在结构域I和II之间有一个隐隐约约的不连续表位

IF 5.1

Journal of Structural Biology: X Pub Date : 2025-08-20 DOI: 10.1016/j.yjsbx.2025.100135

C.J. Lalaurie , M. Kulke , N. Geist , M. Delcea , P.A. Dalby , T.C.R. McDonnell

{"title":"The J-shape of β2GPI reveals a cryptic discontinuous epitope across domains I and II","authors":"C.J. Lalaurie , M. Kulke , N. Geist , M. Delcea , P.A. Dalby , T.C.R. McDonnell","doi":"10.1016/j.yjsbx.2025.100135","DOIUrl":"10.1016/j.yjsbx.2025.100135","url":null,"abstract":"<div><div>Beta-2-Glycoprotein I is the main target for pathogenic antiphospholipid syndrome autoantibodies. It can adopt several conformations, including an O-shape and two more linear J- and S-shapes. The <em>in vivo</em> existence of the O-shape is debated, and doubt remains pertaining to the pathogenic impact of each shape. Studies have shown that APS antibodies react weakly with the O-shape and bind to the linear shapes due to the exposure of a cryptic epitope in the 1st domain. How the protein transitions from O-shape to the linear shapes remains unknown. While the main epitope is widely recognised as the R39-R43 peptide, there is evidence pointing to a discontinuous epitope across domains I and II (DI & DII). We used molecular dynamics simulations to examine the potential pathways of conformational shift from the O-shape to the open forms, and the impact of plasmin clipping on these pathways. Through these studies, starting in a theorised O-shape, we identified that peptides R39-R43, T50-N56 and R63-F67 become more exposed and have increased stability in the J- and S-shapes relative to the O-shape. These changes are likely due to a shift in DII of the T106-G109 loop, which twists to form contacts with the DI K33-Y36 loop. The R39-R43 peptide is brought closer to R63-F67 suggesting a more complex DI epitope than previously theorised. These effects were observed in the wild type and plasmin clipped model, with the effect being larger in the latter. These results are in good agreement with the increased antibody binding observed experimentally for the clipped protein. We therefore suggest that we have been able to identify the structural mechanism at the residue level which results in increased antibody binding in the J-Shape, and specifically in the clipped protein.</div></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"12 ","pages":"Article 100135"},"PeriodicalIF":5.1,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144885800","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Automated removal of corrupted tilts in cryo-electron tomography 冷冻电子断层扫描中损坏倾斜的自动去除

IF 3.5

Journal of Structural Biology: X Pub Date : 2025-07-17 DOI: 10.1016/j.yjsbx.2025.100130

Tomáš Majtner, Beata Turoňová

引用次数: 0

Crystal structure reveals the hydrophilic R1 group impairs NDM-1–ligand binding via water penetration at L3 晶体结构显示亲水性R1基团通过水渗透在L3破坏ndm -1配体的结合

IF 3.5

Journal of Structural Biology: X Pub Date : 2025-07-01 DOI: 10.1016/j.yjsbx.2025.100133

Xiangrui Shi , Huijuan Yang , Yujie Dai , Hui Zhao , Yuhang Li , Yanxi Li , Xin Zhou , Hailong Yan , Qinghua Zhang , Wei Liu

{"title":"Crystal structure reveals the hydrophilic R1 group impairs NDM-1–ligand binding via water penetration at L3","authors":"Xiangrui Shi , Huijuan Yang , Yujie Dai , Hui Zhao , Yuhang Li , Yanxi Li , Xin Zhou , Hailong Yan , Qinghua Zhang , Wei Liu","doi":"10.1016/j.yjsbx.2025.100133","DOIUrl":"10.1016/j.yjsbx.2025.100133","url":null,"abstract":"<div><div>The global spread of New Delhi metallo-β-lactamases (NDMs) has exacerbated the antimicrobial resistance crisis. This study resolved the crystal structure of NDM-1 hydrolyzing amoxicillin for the first time, revealed that the hydroxyl group in the R1 moiety of amoxicillin anchors a key water molecule (Wat1) via hydrogen bond, inducing a conformational shift in Met67 (average displacement of 3.8 Å compared to its position in complexes with ampicillin, penicillin G, and penicillin V) and impairing the hydrophobic interaction between the loop 3 and the substrate. Molecular dynamics simulations confirmed that the π-π stacking contact time between amoxicillin and the L3 critical residue Phe70 decreased to 4.3 % (ampicillin: 12.3 %), with a binding energy reduction of 10.5 kcal/mol. Steady-state kinetics showed that amoxicillin exhibited a 2.2-fold higher <em>K</em><sub>m</sub> and a 5.2-fold higher <em>k</em><sub>cat</sub> compared to ampicillin, demonstrating that hydrophilic R1 groups impair enzyme-substrate binding. This work demonstrates the essential role of hydrophobic interactions in L3-mediated substrate binding and provides a novel strategy for designing L3-targeted NDM-1 inhibitors: maximize hydrophobicity and minimize polar surface area in the L3 contact region to block water penetration, thereby stabilizing the inhibitor-L3 interaction.</div></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"12 ","pages":"Article 100133"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144523258","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Indel-driven evolution of the canavanine tRNA-editing deacetylase enzyme CtdA indel驱动的牛磺酸trna编辑去乙酰化酶CtdA的进化

IF 3.5

Journal of Structural Biology: X Pub Date : 2025-06-18 DOI: 10.1016/j.yjsbx.2025.100132

Nino Tabagari , Franziskus Hauth , Jennifer R. Fleming , Jörg S. Hartig , Olga Mayans

{"title":"Indel-driven evolution of the canavanine tRNA-editing deacetylase enzyme CtdA","authors":"Nino Tabagari , Franziskus Hauth , Jennifer R. Fleming , Jörg S. Hartig , Olga Mayans","doi":"10.1016/j.yjsbx.2025.100132","DOIUrl":"10.1016/j.yjsbx.2025.100132","url":null,"abstract":"<div><div>Proteins are heteropolymers composed of twenty standard amino acids, but over 500 non-proteogenic amino acids exist in nature that can be misincorporated into proteins. Canavanine is an antimetabolite of the chemically similar L-arginine. It can be utilized by bacteria such as <em>Pseudomonas canavaninivorans</em> in the legume rhizome as a sole source of carbon and nitrogen. However, canavanine misincorporates in proteins of this bacterium as its arginyl-tRNA synthetase loads tRNA<sup>Arg</sup> with both canavanine and arginine. Canavanyl-tRNA<sup>Arg</sup> deacetylase (CtdA) removes canavanine from misloaded tRNA<sup>Arg</sup>, preventing its protein toxicity, being the first enzyme known to edit tRNA mischarged with a non-proteinogenic amino acid. We have elucidated CtdA’s crystal structure and studied its active site using site-directed mutagenesis. We found that CtdA is a small monomeric enzyme with a central, deep cavity that predictably is the canavanine binding site and a positively charged surface area that likely coordinates the CCA-3′ tRNA attachment sequence. CtdA is distantly related to the B3/B4 <em>cis</em>-editing domains of the multi-subunit enzyme Phenylalanine-tRNA-Synthetase (PheRS). CdtA and B3/B4 domains from bacterial and archaeal/eukaryotic origin are three subclasses of a conserved 3D-fold that differ in type-specific indels, which shape the substrate binding site. We propose a class-unifying nomenclature of secondary structure for this fold. In CtdA, residues Y104, N105, E118 and E191 are relevant for catalysis, of which N105 is conserved in bacterial B3/B4 domains. Residue N105 is in proximity of the canavanyl-ribose junction and might coordinate the nucleophilic water molecule that attacks the substrate, possibly sharing a mechanistic role in CtdA and bacterial B3/B4 editing enzymes.</div></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"12 ","pages":"Article 100132"},"PeriodicalIF":3.5,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144490599","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Snake venom defensins: Defining the structural and functional characteristics of the toxin family 蛇毒防御素：定义毒素家族的结构和功能特征

IF 3.5

Journal of Structural Biology: X Pub Date : 2025-06-01 DOI: 10.1016/j.yjsbx.2025.100129

David Melendez-Martinez , Adriana Morales-Martinez , Iliana Vanessa Almanza-Campos , Francisco Sierra-Valdez , Miguel Borja , Alejandro Carbajal-Saucedo , Christopher L. Parkinson , Jorge Benavides

{"title":"Snake venom defensins: Defining the structural and functional characteristics of the toxin family","authors":"David Melendez-Martinez , Adriana Morales-Martinez , Iliana Vanessa Almanza-Campos , Francisco Sierra-Valdez , Miguel Borja , Alejandro Carbajal-Saucedo , Christopher L. Parkinson , Jorge Benavides","doi":"10.1016/j.yjsbx.2025.100129","DOIUrl":"10.1016/j.yjsbx.2025.100129","url":null,"abstract":"<div><div>Snake venom defensins are a toxin family found in rattlesnake venoms (<em>Crotalus</em>) which are comprised of crotamine-like peptides and myotoxins. Their tertiary structure resembles the β-defensin family structure. Toxins from this family, such as crotamine (<em>C. durissus terrificus</em>) and myotoxin a (<em>C. viridis viridis</em>), have been described to generate paralysis through K<sub>v</sub> 1.3 channel blockade, using three functional basic-hydrophobic dyads (Y-K, R-W, and R-W). However, the structural and functional properties of other snake venom defensins are scarcely described. For that reason, we evaluated the structural–functional characteristics of the rattlesnake venom defensins on the K<sub>v</sub> 1.3 channel through <em>in silico</em> analysis. 38 snake venom defensins were found to be peptides from 41 to 48 residues with a highly conserved sequence. The three-dimensional structures had great similitude (RMSD, <1.1 Å). Moreover, molecular dynamics simulations showed that the structures were stable (0.445 ± 0.23 nm). It was found that the snake venom defensins contain two or three basic-hydrophobic dyads, the first one is present in the N-terminal region of the defensin comprised by YK. The dyads two and three are contiguous, forming a motif in the γ-core, of which there are seven phenotypes: RWKW, RWRW, PWRR, PWKR, RWKR, RLGW, and GWRR. These dyads played a key role in the interaction of the defensins with the pore residues of the K<sub>v</sub>1.3 channel. These results demonstrated that snake venom defensins have common structural and functional properties, interacting with the K<sub>v</sub> 1.3 channel through the basic-hydrophobic dyads.</div></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"11 ","pages":"Article 100129"},"PeriodicalIF":3.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144190517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Tracing the aggregation pathway of the scaffold protein DISC1: Structural implications for chronic mental illnesses 追踪支架蛋白DISC1的聚集途径：慢性精神疾病的结构意义

IF 3.5

Journal of Structural Biology: X Pub Date : 2025-05-24 DOI: 10.1016/j.yjsbx.2025.100128

Abhishek Cukkemane , Nina Becker , Tatsiana Kupreichyk , Henrike Heise , Dieter Willbold , Oliver H. Weiergräber

{"title":"Tracing the aggregation pathway of the scaffold protein DISC1: Structural implications for chronic mental illnesses","authors":"Abhishek Cukkemane , Nina Becker , Tatsiana Kupreichyk , Henrike Heise , Dieter Willbold , Oliver H. Weiergräber","doi":"10.1016/j.yjsbx.2025.100128","DOIUrl":"10.1016/j.yjsbx.2025.100128","url":null,"abstract":"<div><div>Disrupted in schizophrenia 1 (DISC1) is a pleiotropic scaffold protein that is postulated to comprise large disordered regions and four distinct structured segments with a high proportion of helical or coiled-coil fold. DISC1 associates with over 300 proteins and is associated with several physiological roles ranging from mitosis to cellular differentiation. Yet, the structural features of the protein are poorly characterized. The C-terminal region (C-region, res. 691–836) forms a tetramer and can also aggregate into amyloid-like fibers, potentially linked to schizophrenia and other chronic mental illnesses. Using a combination of biophysical and structural biology applications, we investigate the structural heterogeneity of three mutants of the C-region, viz., the S713E, S704C and L807-frameshift mutants. We provide evidence for the plasticity of the C region; a thin border separates the conformational flexibility of DISC1 required for interaction with a myriad of partners from disruptive aggregation. Snapshots of aggregates and fibrils growing from a nucleus are presented, along with data supporting the role of the minimal fibrillizing element in the C-region, the β-core. This segment also houses a stretch of residues that is critical for the binding of NDEL1 proteins in the mitotic spindle complex and is absent in the non-binding splice variant DISC1Δ22aa. Physiologically, both the splice variant and the fibers represent loss-of-function states that disrupt cellular division. Our findings highlight the need to decipher the structural elements within the DISC1 C-region to comprehend its physiological role and aggregation-related anomalies, and to establish a rationale for drug development.</div></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"11 ","pages":"Article 100128"},"PeriodicalIF":3.5,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144137732","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Crystal structure of the CCA-adding enzyme from Arabidopsis thaliana 拟南芥cca添加酶的晶体结构

IF 3.5

Journal of Structural Biology: X Pub Date : 2025-05-23 DOI: 10.1016/j.yjsbx.2025.100127

Xiao Wang, Yuan-Yuan Li, Zi-Yan Dou, Jia Wang, Lin Liu

引用次数: 0

pytom-match-pick: A tophat-transform constraint for automated classification in template matching python -match-pick：模板匹配中自动分类的tophat-transform约束

IF 3.5

Journal of Structural Biology: X Pub Date : 2025-05-02 DOI: 10.1016/j.yjsbx.2025.100125

Marten L. Chaillet , Sander Roet , Remco C. Veltkamp , Friedrich Förster

{"title":"pytom-match-pick: A tophat-transform constraint for automated classification in template matching","authors":"Marten L. Chaillet , Sander Roet , Remco C. Veltkamp , Friedrich Förster","doi":"10.1016/j.yjsbx.2025.100125","DOIUrl":"10.1016/j.yjsbx.2025.100125","url":null,"abstract":"<div><div>Template matching (TM) in cryo-electron tomography (cryo-ET) enables <em>in situ</em> detection and localization of known macromolecules. However, TM faces challenges of weak signal of the macromolecules and interfering features with a high signal-to-noise ratio, which are often addressed by time-consuming, subjective manual curation of results. To improve the detection performance we introduce pytom-match-pick, a GPU-accelerated, open-source command line interface for enhanced TM in cryo-ET. Using pytom-match-pick, we first quantify the effects of point spread function (PSF) weighting and show that a tilt-weighted PSF outperforms a binary wedge with a single defocus estimate. We also assess previously introduced background normalization methods for classification performance. This indicates that phase randomization is more effective than spectrum whitening in reducing false positives. Furthermore, a novel application of the tophat transform on score maps, combined with a dual-constraint thresholding strategy, reduces false positives and improves precision. We benchmarked pytom-match-pick on public datasets, demonstrating improved classification and localization of macromolecules like ribosomal subunits and proteasomes that led to fewer artifacts in subtomogram averages. This tool promises to advance visual proteomics by improving the efficiency and accuracy of macromolecule detection in cellular contexts.</div></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"11 ","pages":"Article 100125"},"PeriodicalIF":3.5,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143922897","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Generation of shark single-domain antibodies as an aid for Cryo-EM structure determination of membrane proteins: Use hyaluronan synthase as an example 鲨鱼单域抗体的产生作为膜蛋白低温电镜结构测定的辅助：以透明质酸合成酶为例

IF 3.5

Journal of Structural Biology: X Pub Date : 2025-04-29 DOI: 10.1016/j.yjsbx.2025.100126

Penghui Deng , Xiaoyue Zhang , Jianqing Wen , Mingce Xu , Pengwei Li , Hao Wang , Yunchen Bi

{"title":"Generation of shark single-domain antibodies as an aid for Cryo-EM structure determination of membrane proteins: Use hyaluronan synthase as an example","authors":"Penghui Deng , Xiaoyue Zhang , Jianqing Wen , Mingce Xu , Pengwei Li , Hao Wang , Yunchen Bi","doi":"10.1016/j.yjsbx.2025.100126","DOIUrl":"10.1016/j.yjsbx.2025.100126","url":null,"abstract":"<div><div>In cartilaginous fish, the immunoglobulin new antigen receptor (IgNAR) is naturally devoid of light chains. The variable regions of IgNAR (VNARs) are solely responsible for antigen recognition, similar to VHHs (variable domain of the heavy chain of heavy-chain antibodies) in camelids. Although VNARs have attracted growing interest, generating VNARs against membrane proteins remains challenging. Furthermore, the structure of a VNAR in complex with a membrane protein has not yet been reported. This study features a membrane protein, Chlorella virus hyaluronan synthase (CvHAS), and provides a comprehensive methodological approach to generate its specific shark VNARs, addressing several major concerns and important optimizations. We showed that shark physiological urea pressure was tolerable for CvHAS, and indirect immobilization was strongly preferred over passive adsorption for membrane proteins. Together with optimizations to improve mononuclear cell (MC) viability and VNAR expression efficiency, we successfully generated S2F6, a CvHAS-specific VNAR with nM-level high affinity. The structure of the CvHAS-S2F6 complex was then determined by cryogenic electron microscopy (cryo-EM), reporting the first membrane protein and VNAR complex structure. It shows that S2F6 binds to the cytoplasmic domain of CvHAS, with a different epitope than the reported CvHAS-specific VHHs. This study provides valuable insights into developing VNARs for membrane proteins and their applications in structural biology.</div></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":"11 ","pages":"Article 100126"},"PeriodicalIF":3.5,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143918313","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0