Pub Date : 2025-12-11DOI: 10.1016/j.str.2025.11.011
Maxwell J. Bachochin, Kelly L. McGuire, Brian D. Cook, Qiaozhen Ye, Steven Silletti, Kevin D. Corbett, Elizabeth A. Komives, Mark A. Herzik
{"title":"An allosteric network governs Tom70 conformational dynamics to coordinate mitochondrial import","authors":"Maxwell J. Bachochin, Kelly L. McGuire, Brian D. Cook, Qiaozhen Ye, Steven Silletti, Kevin D. Corbett, Elizabeth A. Komives, Mark A. Herzik","doi":"10.1016/j.str.2025.11.011","DOIUrl":"https://doi.org/10.1016/j.str.2025.11.011","url":null,"abstract":"","PeriodicalId":22168,"journal":{"name":"Structure","volume":"11 2 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145731086","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 : 2025-12-10DOI: 10.1016/j.str.2025.11.012
Pu Hou, Jie Zhu, Rong-Cheng Yu, Feng Yang, Kang Du, Jing Li, Wen-Wen Kong, Jie Wang, Yuxing Chen, Cong-Zhao Zhou, Yong-Liang Jiang
Cyanophages, which are bacteriophages that specifically infect host cyanobacteria, also utilize the tail to initiate host recognition and adsorption. Owing to the limited structural information on cyanophages, our understanding of the mechanism by which cyanophages specifically recognize their hosts remains largely unknown. Here, we determined the intact cryoelectron microscopy structure of a freshwater cyanopodophage Pan3, which consists of an icosahedral shell and a short tail comprising four modular components: the dodecameric adaptor, hexameric nozzle, trimeric needle, and six heterohexameric tailspikes. Notably, each tailspike features an SGNH esterase domain fused to a lectin domain, forming a continuous groove complementary to the host lipopolysaccharide. These findings provide insights into the receptor engagement in Podoviridae, and establish a structural framework for cyanophage and host interactions that may guide future antibacterial interventions against harmful blooms.
{"title":"Cryo-EM structure of cyanopodophage Pan3 reveals a modular tail architecture for host recognition","authors":"Pu Hou, Jie Zhu, Rong-Cheng Yu, Feng Yang, Kang Du, Jing Li, Wen-Wen Kong, Jie Wang, Yuxing Chen, Cong-Zhao Zhou, Yong-Liang Jiang","doi":"10.1016/j.str.2025.11.012","DOIUrl":"https://doi.org/10.1016/j.str.2025.11.012","url":null,"abstract":"Cyanophages, which are bacteriophages that specifically infect host cyanobacteria, also utilize the tail to initiate host recognition and adsorption. Owing to the limited structural information on cyanophages, our understanding of the mechanism by which cyanophages specifically recognize their hosts remains largely unknown. Here, we determined the intact cryoelectron microscopy structure of a freshwater cyanopodophage Pan3, which consists of an icosahedral shell and a short tail comprising four modular components: the dodecameric adaptor, hexameric nozzle, trimeric needle, and six heterohexameric tailspikes. Notably, each tailspike features an SGNH esterase domain fused to a lectin domain, forming a continuous groove complementary to the host lipopolysaccharide. These findings provide insights into the receptor engagement in <em>Podoviridae</em>, and establish a structural framework for cyanophage and host interactions that may guide future antibacterial interventions against harmful blooms.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"8 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145718345","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 : 2025-12-05DOI: 10.1016/j.str.2025.11.009
The microtubule-associated protein tau is implicated in neurodegenerative diseases characterized by amyloid formation. Mutations associated with front…
微管相关蛋白tau与以淀粉样蛋白形成为特征的神经退行性疾病有关。与前…相关的突变
{"title":"Amyloid-motif-dependent tau self-assembly is modulated by isoform sequence context","authors":"","doi":"10.1016/j.str.2025.11.009","DOIUrl":"https://doi.org/10.1016/j.str.2025.11.009","url":null,"abstract":"The microtubule-associated protein tau is implicated in neurodegenerative diseases characterized by amyloid formation. Mutations associated with front…","PeriodicalId":22168,"journal":{"name":"Structure","volume":"372 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145689082","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 : 2025-12-04DOI: 10.1016/j.str.2025.11.008
Jakob R Riccabona,Johannes R Loeffler,Clara T Schoeder,Jens Meiler,Andrew B Ward,Monica Fernandez-Quintero
Deep-learning models have transformed structural biology by enabling reliable prediction of protein 3D structure models and providing confidence metrics such as predicted local distance difference test (pLDDT) to estimate local uncertainties. However, whether pLDDT reflects intrinsic protein flexibility remains unclear. Defining and quantifying flexibility and protein dynamics through experiments and computation is essential for advancing our ability to model and interpret conformational changes across different timescales.
{"title":"Rethinking what pLDDT really tells us about protein flexibility.","authors":"Jakob R Riccabona,Johannes R Loeffler,Clara T Schoeder,Jens Meiler,Andrew B Ward,Monica Fernandez-Quintero","doi":"10.1016/j.str.2025.11.008","DOIUrl":"https://doi.org/10.1016/j.str.2025.11.008","url":null,"abstract":"Deep-learning models have transformed structural biology by enabling reliable prediction of protein 3D structure models and providing confidence metrics such as predicted local distance difference test (pLDDT) to estimate local uncertainties. However, whether pLDDT reflects intrinsic protein flexibility remains unclear. Defining and quantifying flexibility and protein dynamics through experiments and computation is essential for advancing our ability to model and interpret conformational changes across different timescales.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"1 1","pages":"2010-2012"},"PeriodicalIF":5.7,"publicationDate":"2025-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145680631","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 : 2025-12-04DOI: 10.1016/j.str.2025.11.001
Iktae Kim, Jeong-Yong Suh
In this issue of Structure, Henriques et al.1 present structural snapshots that capture distinct conformational states of the type I-F Cas1-Cas2/3 integrase complex, illustrating that foreign DNA binding triggers a large-scale domain rearrangement that enables prespacer delivery to the CRISPR array.
{"title":"Capture first, then deliver!","authors":"Iktae Kim, Jeong-Yong Suh","doi":"10.1016/j.str.2025.11.001","DOIUrl":"https://doi.org/10.1016/j.str.2025.11.001","url":null,"abstract":"<p><p>In this issue of Structure, Henriques et al.<sup>1</sup> present structural snapshots that capture distinct conformational states of the type I-F Cas1-Cas2/3 integrase complex, illustrating that foreign DNA binding triggers a large-scale domain rearrangement that enables prespacer delivery to the CRISPR array.</p>","PeriodicalId":22168,"journal":{"name":"Structure","volume":"33 12","pages":"2008-2009"},"PeriodicalIF":4.3,"publicationDate":"2025-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145688277","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 : 2025-12-04DOI: 10.1016/j.str.2025.11.007
Kate L White, Jin Young Kang, Renhong Yan, Katherine M Davis, Qianglin Fang, Lorena Saelices Gomez, Anthony W P Fitzpatrick, Mohammad T Mazhab-Jafari, Tatiana Galochkina
As 2025 comes to an end, we want to highlight some of the rising young faculty members who have published their exciting work from different areas of structural biology in Structure this year. We have asked them to tell us more about their interests, careers, and research programs.
{"title":"Our authors in 2025.","authors":"Kate L White, Jin Young Kang, Renhong Yan, Katherine M Davis, Qianglin Fang, Lorena Saelices Gomez, Anthony W P Fitzpatrick, Mohammad T Mazhab-Jafari, Tatiana Galochkina","doi":"10.1016/j.str.2025.11.007","DOIUrl":"https://doi.org/10.1016/j.str.2025.11.007","url":null,"abstract":"<p><p>As 2025 comes to an end, we want to highlight some of the rising young faculty members who have published their exciting work from different areas of structural biology in Structure this year. We have asked them to tell us more about their interests, careers, and research programs.</p>","PeriodicalId":22168,"journal":{"name":"Structure","volume":"33 12","pages":"1999-2007"},"PeriodicalIF":4.3,"publicationDate":"2025-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145688254","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 : 2025-11-28DOI: 10.1016/j.str.2025.11.006
Binning Sun, Jing Zheng, Yuan Fu, Fengyuan Tian, Hao Xiao, Su Li, Lingpeng Cheng, Ping Chen, Hongrong Liu
Podophage tails are too short to traverse the cell envelope and require internal core proteins to assemble into a transmembrane channel for genome delivery during infection. However, high-resolution structures of near-complete cores remain scarce. Here, we present the near-atomic-resolution cryo-electron microscopy (cryo-EM) structure of the drug-resistant E. coli phage E1004, which features a T7-like core-portal-tail structure with six P22-like tailspikes. We found that the cylindrical core comprises four proteins: gp17, gp27, gp28, and gp29. Gp29 forms a tetramer, while gp28 and gp27 assemble into octamers. Notably, there are sixteen copies of gp17 in two conformations, distinct from the small core protein gp6.7 in T7. The gp17-gp27 complex reveals the mechanism for mediating the symmetry adjustment at the core-portal interface. Moreover, comparative analysis with other podophage cores highlights diversity in core protein composition and organization, particularly among the small core proteins. We propose that these variations represent evolutionary adaptations to diverse host envelopes.
{"title":"Cryo-EM structure of drug-resistant Escherichia coli phage E1004 reveals a conserved cylindrical core among podophages","authors":"Binning Sun, Jing Zheng, Yuan Fu, Fengyuan Tian, Hao Xiao, Su Li, Lingpeng Cheng, Ping Chen, Hongrong Liu","doi":"10.1016/j.str.2025.11.006","DOIUrl":"https://doi.org/10.1016/j.str.2025.11.006","url":null,"abstract":"Podophage tails are too short to traverse the cell envelope and require internal core proteins to assemble into a transmembrane channel for genome delivery during infection. However, high-resolution structures of near-complete cores remain scarce. Here, we present the near-atomic-resolution cryo-electron microscopy (cryo-EM) structure of the drug-resistant <em>E. coli</em> phage E1004, which features a T7-like core-portal-tail structure with six P22-like tailspikes. We found that the cylindrical core comprises four proteins: gp17, gp27, gp28, and gp29. Gp29 forms a tetramer, while gp28 and gp27 assemble into octamers. Notably, there are sixteen copies of gp17 in two conformations, distinct from the small core protein gp6.7 in T7. The gp17-gp27 complex reveals the mechanism for mediating the symmetry adjustment at the core-portal interface. Moreover, comparative analysis with other podophage cores highlights diversity in core protein composition and organization, particularly among the small core proteins. We propose that these variations represent evolutionary adaptations to diverse host envelopes.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"25 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145611929","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.2025.11.002
Ryan Ferrao, Jinjin Zhang, Chih-Chien Chou, Anthony Nieto, Derek Langeslay, Moon Chatterjee, Debi Jin, Magdeleine Hung, Ian Scott, Mark Nagel, Weimei Xing, Simon Letarte, Jenny Wang, Alexandre Ambrogelly, Eric B. Lansdon
Sacituzumab govitecan (SG) is a therapeutic antibody-drug conjugate globally approved for the treatment of breast cancer. SG targets the trophoblast cell-surface antigen-2 (Trop2) at the surface of cancer cells to deliver the cytotoxic topoisomerase I inhibitor SN-38 to the tumor microenvironment. SN-38 is covalently linked to the humanized monoclonal antibody (mAb) sacituzumab via a hydrolyzable linker. Here, we describe the 1.56-Å X-ray crystal structure and stoichiometry of the human Trop2 ectodomain in complex with a sacituzumab (hRS7) antigen-binding Fab fragment. The complex reveals a 2:2 stoichiometry where two sacituzumab Fabs bind across the two Trop2 dimer subunits, inducing a conformational change compared to the apo-structure. Cryo-electron microscopy (cryoEM) and size-exclusion chromatography in combination with multi-angle light scattering (SEC-MALS) analysis of the intact sacituzumab mAb bound to the Trop2 ECD reveals a complex whereby sacituzumab engages two Trop2 dimers in a 2:4 stoichiometry.
{"title":"The therapeutic antibody sacituzumab induces trophoblast cell-surface antigen-2 conformational rearrangement","authors":"Ryan Ferrao, Jinjin Zhang, Chih-Chien Chou, Anthony Nieto, Derek Langeslay, Moon Chatterjee, Debi Jin, Magdeleine Hung, Ian Scott, Mark Nagel, Weimei Xing, Simon Letarte, Jenny Wang, Alexandre Ambrogelly, Eric B. Lansdon","doi":"10.1016/j.str.2025.11.002","DOIUrl":"https://doi.org/10.1016/j.str.2025.11.002","url":null,"abstract":"Sacituzumab govitecan (SG) is a therapeutic antibody-drug conjugate globally approved for the treatment of breast cancer. SG targets the trophoblast cell-surface antigen-2 (Trop2) at the surface of cancer cells to deliver the cytotoxic topoisomerase I inhibitor SN-38 to the tumor microenvironment. SN-38 is covalently linked to the humanized monoclonal antibody (mAb) sacituzumab via a hydrolyzable linker. Here, we describe the 1.56-Å X-ray crystal structure and stoichiometry of the human Trop2 ectodomain in complex with a sacituzumab (hRS7) antigen-binding Fab fragment. The complex reveals a 2:2 stoichiometry where two sacituzumab Fabs bind across the two Trop2 dimer subunits, inducing a conformational change compared to the apo-structure. Cryo-electron microscopy (cryoEM) and size-exclusion chromatography in combination with multi-angle light scattering (SEC-MALS) analysis of the intact sacituzumab mAb bound to the Trop2 ECD reveals a complex whereby sacituzumab engages two Trop2 dimers in a 2:4 stoichiometry.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"195 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145609740","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.2025.11.004
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}
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