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Accurate helical parameter estimation based on cylindrical unrolling 基于圆柱展开的螺旋参数精确估计
IF 5.7 2区 生物学
Structure Pub Date : 2025-07-17 DOI: 10.1016/j.str.2025.06.008
Mingtao Huang, Jinying Ma, Xiaoyu Fu, Hongwei Wang, Yuan Shen, Xueming Li
{"title":"Accurate helical parameter estimation based on cylindrical unrolling","authors":"Mingtao Huang, Jinying Ma, Xiaoyu Fu, Hongwei Wang, Yuan Shen, Xueming Li","doi":"10.1016/j.str.2025.06.008","DOIUrl":"https://doi.org/10.1016/j.str.2025.06.008","url":null,"abstract":"Helical structure is fundamental for filamentous and tubular macromolecular assemblies that play crucial roles in structural scaffolding and signaling processes. Structure determination of these assemblies relies on the precise estimation of their helical parameters. Although layer-line-based methods are widely used, their application is often challenging due to structural flexibility and heterogeneity. Herein, we report a method for helical parameter estimation based on cylindrical unrolling, called helix is simple (HELIS), which is implemented in a software package with the same name. HELIS treats helical structures as rolled two-dimensional (2D) crystals. Estimation of the helical parameters of structures visualized by cryo-electron tomography (cryo-ET) is derived from simplified 2D reciprocal-lattice measurements. HELIS also incorporates auxiliary algorithms to trace and unbend curved filaments, determine relative polarity, and perform <em>in situ</em> helical reconstruction. HELIS is a comprehensive helical structure determination tool with high accuracy for helical parameter estimation that is applicable to various helical assemblies.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"12 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144645284","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}
引用次数: 0
Geometry-aware template matching for cryo-electron tomograms in Dynamo 基于几何感知的低温电子层析图模板匹配
IF 5.7 2区 生物学
Structure Pub Date : 2025-07-17 DOI: 10.1016/j.str.2025.06.009
Raffaele Coray, Daniel Castaño-Díez
{"title":"Geometry-aware template matching for cryo-electron tomograms in Dynamo","authors":"Raffaele Coray, Daniel Castaño-Díez","doi":"10.1016/j.str.2025.06.009","DOIUrl":"https://doi.org/10.1016/j.str.2025.06.009","url":null,"abstract":"Template matching has a long history of serving as a tool for the automated analysis of volumes in cryo-electron tomography (cryo-ET). Recent theoretical and computational studies of the technique have pinpointed the importance of using fine angular samplings and high resolution scans to attain meaningful results, thus highlighting the necessity of approaches that alleviate the computational burden inherent to this technique. We present the new module for model-aware template matching in <em>Dynamo</em>, an open-source tool that allows the integration of possibly available <em>a priori</em> information in the set-up of a template matching computation, leading—in favorable cases—to large computational gains, as the scanning effort can be more efficiently restricted to relevant spatial positions and dynamically defined angular orientations. This approach has been successfully tested on a representative range of sample geometries typically arising in tomography, modeling particles distributed over tubular, membranous, or vesicular structures.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"2 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144645458","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}
引用次数: 0
CryoEM-enabled visual proteomics reveals de novo structures of oligomeric protein complexes 冷冻电镜下的视觉蛋白质组学揭示了寡聚蛋白复合物的新结构
IF 5.7 2区 生物学
Structure Pub Date : 2025-07-14 DOI: 10.1016/j.str.2025.06.007
Yuanbo Shen, Ailiena O. Maggiolo, Tianzheng Zhang, Rebeccah A. Warmack
{"title":"CryoEM-enabled visual proteomics reveals de novo structures of oligomeric protein complexes","authors":"Yuanbo Shen, Ailiena O. Maggiolo, Tianzheng Zhang, Rebeccah A. Warmack","doi":"10.1016/j.str.2025.06.007","DOIUrl":"https://doi.org/10.1016/j.str.2025.06.007","url":null,"abstract":"Single particle cryoelectron microscopy (cryoEM) and cryoelectron tomography (cryoET) are powerful methods for unveiling unique and functionally relevant structural states. Aided by mass spectrometry and machine learning, they promise to facilitate the visual exploration of proteomes. Leveraging visual proteomics, we interrogate structures isolated from a complex cellular milieu by cryoEM to identify and classify molecular structures and complexes <em>de novo</em>. By comparing three automated model building programs, CryoID, DeepTracer, and ModelAngelo, we determine the identity of six distinct oligomeric protein complexes from partially purified extracts of the nitrogen-fixing bacterium <em>Azotobacter vinelandii</em> using both anaerobic and aerobic cryoEM, including two original oligomeric structures. Overall, by allowing the study of near-native oligomeric protein states, cryoEM-enabled visual proteomics reveals unique structures that correspond to relevant species observed <em>in situ</em>.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"677 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144622462","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}
引用次数: 0
Structural basis for no retinal binding in flotillin-associated rhodopsins 游离蛋白相关视紫红质无视网膜结合的结构基础
IF 5.7 2区 生物学
Structure Pub Date : 2025-07-11 DOI: 10.1016/j.str.2025.06.006
Kirill Kovalev, Artem Stetsenko, Florian Trunk, Egor Marin, Jose M. Haro-Moreno, Gerrit H.U. Lamm, Alexey Alekseev, Francisco Rodriguez-Valera, Thomas R. Schneider, Josef Wachtveitl, Albert Guskov
{"title":"Structural basis for no retinal binding in flotillin-associated rhodopsins","authors":"Kirill Kovalev, Artem Stetsenko, Florian Trunk, Egor Marin, Jose M. Haro-Moreno, Gerrit H.U. Lamm, Alexey Alekseev, Francisco Rodriguez-Valera, Thomas R. Schneider, Josef Wachtveitl, Albert Guskov","doi":"10.1016/j.str.2025.06.006","DOIUrl":"https://doi.org/10.1016/j.str.2025.06.006","url":null,"abstract":"Rhodopsins are light-sensitive membrane proteins capturing solar energy via a retinal cofactor covalently attached to a lysine residue. Several groups of rhodopsins lack the conserved lysine and showed no retinal binding. Recently, flotillin-associated rhodopsins (FArhodopsins or FARs) were identified and suggested to lack the retinal-binding pocket despite preserving the lysine residue in many members of the group. Here, we present cryoelectron microscopic (cryo-EM) structures of paralog FArhodopsin and proteorhodopsin from marine bacterium <em>Pseudothioglobus</em>, both forming pentamers similar to those of other microbial rhodopsins. We demonstrate no binding of retinal to the FArhodopsin despite preservation of the lysine residue and overall similarity of the protein fold and internal organization to those of the retinal-binding paralog. Mutational analysis confirmed that two amino acids, H84 and E120, prevent retinal binding within the FArhodopsin. Our work provides insights into the natural retinal loss in microbial rhodopsins and might contribute to the further understanding of FArhodopsins.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"35 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144602982","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}
引用次数: 0
Structures of USP7 in active and inactive states bound to DNMT1 revealed by cryo-EM 低温电镜显示USP7与DNMT1结合的活性和非活性结构
IF 5.7 2区 生物学
Structure Pub Date : 2025-07-10 DOI: 10.1016/j.str.2025.06.005
Nao Nakamura, Sae Yoshimi, Amika Kikuchi, Hiroki Onoda, Satomi Kori, Makoto Nakanishi, Atsuya Nishiyama, Kyohei Arita
{"title":"Structures of USP7 in active and inactive states bound to DNMT1 revealed by cryo-EM","authors":"Nao Nakamura, Sae Yoshimi, Amika Kikuchi, Hiroki Onoda, Satomi Kori, Makoto Nakanishi, Atsuya Nishiyama, Kyohei Arita","doi":"10.1016/j.str.2025.06.005","DOIUrl":"https://doi.org/10.1016/j.str.2025.06.005","url":null,"abstract":"The ubiquitin signal generated by UHRF1 is essential for DNA methylation maintenance by recruiting DNA methyltransferase 1 (DNMT1) to hemimethylated DNA through strong binding of its replication foci targeting sequence (RFTS) domain to ubiquitinated histone H3. The ubiquitin-specific protease 7 (USP7) forms a complex with DNMT1 and removes ubiquitin from H3. However, it remains unknown how USP7 deubiquitinates ubiquitinated H3 upon strong binding of the DNMT1 RFTS domain. Here, we show the activation mechanism of USP7 by combining biochemical and structural studies. USP7 is inactive toward ubiquitinated H3 in complex with the RFTS domain. However, when complexed with DNMT1, USP7 efficiently deubiquitinates ubiquitinated H3. Cryogenic electron microscopy (cryo-EM) single particle analysis revealed that USP7 bound to DNMT1 undergoes an open (inactive) and closed (active) conformational transition. Our findings provide mechanistic insights into the activation of USP7 upon binding to DNMT1 and contribute to a better understanding of the deubiquitination process in DNA methylation maintenance.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"11 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144594756","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}
引用次数: 0
Structure of a type II SMC Wadjet complex from Neobacillus vireti 病毒新杆菌II型SMC Wadjet复合物的结构
IF 5.7 2区 生物学
Structure Pub Date : 2025-07-07 DOI: 10.1016/j.str.2025.06.004
Florian Roisné-Hamelin, Hon Wing Liu, Stephan Gruber
{"title":"Structure of a type II SMC Wadjet complex from Neobacillus vireti","authors":"Florian Roisné-Hamelin, Hon Wing Liu, Stephan Gruber","doi":"10.1016/j.str.2025.06.004","DOIUrl":"https://doi.org/10.1016/j.str.2025.06.004","url":null,"abstract":"Structural maintenance of chromosome complexes are essential DNA-folding motors that facilitate critical cellular functions, including chromosome segregation and DNA repair. Wadjet systems are prokaryotic SMC complexes specialized in cellular immunity against plasmids. Type I Wadjet systems restrict plasmids via a DNA extrusion-cleavage reaction. Two other Wadjet types (II and III) have also been identified, however, their molecular characteristics are unclear. Here, we reconstituted a representative type II Wadjet system from <em>Neobacillus vireti</em>. We show that this system shares substrate selection and cleavage properties with type I but exhibits distinctive structural features, including a long elbow-distal coiled coil, a channel-less hinge, and a tandem KITE subunit. These features help identify the common and distinguishing architectural elements in the family of Wadjet systems and raise intriguing questions about the evolution of prokaryotic SMC complexes.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"42 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144568945","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}
引用次数: 0
Elucidating PTEN conformational dynamics and phosphatase regulation via integrative modeling and mutation prediction 通过综合建模和突变预测阐明PTEN构象动力学和磷酸酶调控
IF 5.7 2区 生物学
Structure Pub Date : 2025-07-03 DOI: 10.1016/j.str.2025.06.002
Jennifer Erin Dawson, Iris Nira Smith, Ann Marie Tushar, Charis Eng
{"title":"Elucidating PTEN conformational dynamics and phosphatase regulation via integrative modeling and mutation prediction","authors":"Jennifer Erin Dawson, Iris Nira Smith, Ann Marie Tushar, Charis Eng","doi":"10.1016/j.str.2025.06.002","DOIUrl":"https://doi.org/10.1016/j.str.2025.06.002","url":null,"abstract":"<em>PTEN</em> (Phosphatase and TENsin homolog deleted on chromosome ten) is a major tumor suppressor gene that is frequently mutated or lost under cancerous conditions. PTEN is a dual-specificity phosphatase that negatively regulates the PI3K/AKT/mTOR signaling pathway at the plasma membrane (PM). Its functional regulation and cellular localization are known to be conformationally driven. Access to the PM is phosphoregulated by open and closed PTEN forms. However, clarifying the underlying structural mechanisms is still an open avenue of research. Here, we apply an integrative structural modeling approach, combining coarse-grained and all-atom molecular dynamics with experimental crosslinking mass spectrometry. Conformational exchange between an “eased” form and a “strained” form brings the protein’s phosphatase and C2 domains closer together, blocking the catalytic site, and affecting the loops involved in PM binding. Our full-length PTEN models, AlphaMissense, and RaSP were used to better predict the consequences of PTEN mutations.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"51 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144547564","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}
引用次数: 0
AI-guided cryo-EM analysis untangles uromodulin lattices that safeguard kidneys 人工智能引导的低温电镜分析解开了保护肾脏的尿调蛋白晶格
IF 5.7 2区 生物学
Structure Pub Date : 2025-07-03 DOI: 10.1016/j.str.2025.06.003
Kelvin Han Chung Chong, Bin Wu
{"title":"AI-guided cryo-EM analysis untangles uromodulin lattices that safeguard kidneys","authors":"Kelvin Han Chung Chong, Bin Wu","doi":"10.1016/j.str.2025.06.003","DOIUrl":"https://doi.org/10.1016/j.str.2025.06.003","url":null,"abstract":"In this issue of <em>Structure</em>, Chang et al.<span><span><sup>1</sup></span></span> combined deep-learning cryoelectron microscopy (cryo-EM) particle picking and heterogeneous refinement to obtain structures of human uromodulin filament lattices that were isolated from urine samples. This work is an excellent example of AI-facilitated data processing of bulky semi-purified biological samples that likely will be commonly used in the future.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"26 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144547430","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}
引用次数: 0
Decoding the molecular choreography of colibactin: Structural insights into a genotoxic assembly line 解码大肠杆菌蛋白的分子编排：基因毒性装配线的结构洞察
IF 5.7 2区 生物学
Structure Pub Date : 2025-07-03 DOI: 10.1016/j.str.2025.06.001
Dandan Li, Zhijun Wang
{"title":"Decoding the molecular choreography of colibactin: Structural insights into a genotoxic assembly line","authors":"Dandan Li, Zhijun Wang","doi":"10.1016/j.str.2025.06.001","DOIUrl":"https://doi.org/10.1016/j.str.2025.06.001","url":null,"abstract":"The evolutionary fusion of modular polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) pathways unlocks chemical space that is inaccessible to either system alone. In this issue of <em>Structure</em>, Kim et al.<span><span><sup>1</sup></span></span> present cryoelectron microscopy (cryo-EM) structures of the colibactin biosynthetic enzymes ClbC and ClbI that reveal unprecedented insights into PKS-NRPS mechanisms.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"46 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144547546","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}
引用次数: 0
Modeling phase separation of biomolecular condensates with data-driven mass-conserving reaction-diffusion systems 用数据驱动的质量守恒反应-扩散系统模拟生物分子凝聚物的相分离
IF 5.7 2区 生物学
Structure Pub Date : 2025-06-25 DOI: 10.1016/j.str.2025.05.018
Cheng Li, Man-Ting Guo, Xiaoqing He, Quan-Xing Liu, Zhi Qi
{"title":"Modeling phase separation of biomolecular condensates with data-driven mass-conserving reaction-diffusion systems","authors":"Cheng Li, Man-Ting Guo, Xiaoqing He, Quan-Xing Liu, Zhi Qi","doi":"10.1016/j.str.2025.05.018","DOIUrl":"https://doi.org/10.1016/j.str.2025.05.018","url":null,"abstract":"Phase separation, as one important type of pattern formation, plays a critical role in regulating cellular processes and sustaining ecological resilience. Mass-conserving reaction-diffusion (MCRD) models have been proposed to capture the underlying principles of phase separation. However, previous studies have largely established only phenomenological analogies between MCRD dynamics and phase separation. Here, we identify an experimental model system based on the double-stranded DNA-human protein p53 interactive co-condensate (DPIC). Importantly, all parameters required for the MCRD model can be independently and directly measured in this system, without reliance on parameter estimation or unverified assumptions. We demonstrate that (1) the DPICs serve as an ideal experimental system for establishing a direct and quantitative bridge between experimental DPICs and the MCRD framework and (2) the MCRD model captures more than just a phenomenological resemblance to phase separation, and quantitatively reproduces the underlying dynamics.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"53 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144479504","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}
引用次数: 0
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