Acta crystallographica. Section F, Structural biology communications最新文献

{"title":"PERC: a suite of software tools for the curation of cryoEM data with application to simulation, modeling and machine learning.","authors":"Beatriz Costa-Gomes, Joel Greer, Nikolai Juraschko, James Parkhurst, Jola Mirecka, Marjan Famili, Camila Rangel-Smith, Oliver Strickson, Alan Lowe, Mark Basham, Tom Burnley","doi":"10.1107/S2053230X25007575","DOIUrl":"10.1107/S2053230X25007575","url":null,"abstract":"<p><p>Ease of access to data, tools and models expedites scientific research. In structural biology there are now numerous open repositories of experimental and simulated data sets. Being able to easily access and utilize these is crucial to allow researchers to make optimal use of their research effort. The tools presented here are useful for collating existing public cryoEM data sets and/or creating new synthetic cryoEM data sets to aid the development of novel data processing and interpretation algorithms. In recent years, structural biology has seen the development of a multitude of machine-learning-based algorithms to aid numerous steps in the processing and reconstruction of experimental data sets and the use of these approaches has become widespread. Developing such techniques in structural biology requires access to large data sets, which can be cumbersome to curate and unwieldy to make use of. In this paper, we present a suite of Python software packages, which we collectively refer to as PERC (profet, EMPIARreader and CAKED). These are designed to reduce the burden which data curation places upon structural biology research. The protein structure fetcher (profet) package allows users to conveniently download and cleave sequences or structures from the Protein Data Bank or AlphaFold databases. EMPIARreader allows lazy loading of Electron Microscopy Public Image Archive data sets in a machine-learning-compatible structure. The Class Aggregator for Key Electron-microscopy Data (CAKED) package is designed to seamlessly facilitate the training of machine-learning models on electron microscopy data, including electron-cryo-microscopy-specific data augmentation and labeling. These packages may be utilized independently or as building blocks in workflows. All are available in open-source repositories and designed to be easily extensible to facilitate more advanced workflows if required.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":" ","pages":"441-450"},"PeriodicalIF":1.1,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12485494/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145022593","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Introduction to the SAMPREP special issue","authors":"Kushol Gupta","doi":"10.1107/S2053230X25007976","DOIUrl":"10.1107/S2053230X25007976","url":null,"abstract":"<p>The focused issue on the SAMPREP workshop is introduced. The virtual issue is available at https://journals.iucr.org/special_issues/2025/samprep23/.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 10","pages":"406-407"},"PeriodicalIF":1.1,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145063203","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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 d-aspartate oxidase from Cryptococcus humicola UJ1","authors":"Masaru Goto,&nbsp;Risako Nonaka,&nbsp;Taichi Mizobuchi,&nbsp;Daiki Imanishi,&nbsp;Shouji Takahashi","doi":"10.1107/S2053230X25008192","DOIUrl":"10.1107/S2053230X25008192","url":null,"abstract":"<p>The enzyme <span>d</span>-aspartate oxidase (DDO) oxidizes acidic <span>d</span>-amino acids using the coenzyme flavin adenine dinucleotide to generate the corresponding α-keto acids and ammonia. DDO differs from <span>d</span>-amino-acid oxidase (DAAO), which acts on neutral and basic <span>d</span>-amino acids. Although the enzymatic properties of DDO have been characterized in several species, the structure of DDO had remained unclear. The structure of DDO derived from <i>Cryptococcus humicola</i> strain UJ1 (chDDO) was determined by X-ray crystallography at 1.70 Å resolution. While the three-dimensional structures of DAAOs are known to be homodimers, chDDO forms a homotetramer. This difference was found to be caused by the deletion of one loop and the insertion of two loops.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 10","pages":"434-440"},"PeriodicalIF":1.1,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145084830","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tetrameric structure of Bacillus subtilis DegQ and its predicted interaction with the DegS–DegU two-component system","authors":"Zui Fujimoto,&nbsp;Naomi Kishine,&nbsp;Kengo Saitou,&nbsp;Keitarou Kimura","doi":"10.1107/S2053230X25007903","DOIUrl":"10.1107/S2053230X25007903","url":null,"abstract":"<p><i>Bacillus subtilis</i> DegQ is a 46-amino-acid regulatory protein involved in the DegS–DegU two-component system. DegQ promotes the phosphorylation of DegU by DegS, switching the function of DegU from competence to the induction of poly-γ-glutamate production. To elucidate its structural role, we determined the crystal structures of wild-type DegQ and its mutant DegQS25L. Each DegQ monomer folds into a single α-helix, and four monomers assemble into a tetramer characterized by a four-helix coiled-coil structure. Within the tetramer, two adjacent helices are oriented in the same direction, while the other two are oriented oppositely, forming a pseudo-twofold symmetric arrangement. The mutant form displays disrupted symmetry due to altered helix packing, which is caused by shifts in the coiled-coil heptad register induced by the mutation. Structural predictions using <i>AlphaFold</i>3 suggest that DegQ likely binds to the N-terminal helix bundle of DegS, either as a dimer or as individual monomers. These findings provide structural insight into DegQ oligomerization and its potential role in modulating DegS autophosphorylation and DegU binding.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 10","pages":"425-433"},"PeriodicalIF":1.1,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145038794","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biochemical characterization and preliminary X-ray crystallographic analysis of cyanobacterial α-glucan phosphorylases","authors":"Airi Ikuta,&nbsp;Eiji Suzuki,&nbsp;Ryuichiro Suzuki","doi":"10.1107/S2053230X25007770","DOIUrl":"10.1107/S2053230X25007770","url":null,"abstract":"<p>Several cyanobacterial species, including <i>Crocosphaera subtropica</i> ATCC 51142, accumulate cyanobacterial starch instead of glycogen, although nearly all cyanobacteria accumulate glycogen. The glycogen-producing <i>Synechococcus elongatus</i> PCC 7942 possesses one α-glucan phosphorylase (Pho) isozyme, whereas strain 51142 has three Pho isozymes. Based on their primary structures, these enzymes belong to glycosyl transferase (GT) family 35, with the cyanobacterial GT35-type Phos further subdivided into types I–III. In this study, to elucidate the significance of the coexistence of multiple GT35-type Pho isozymes, those from strain 51142 (type I, cce_1629; type II, cce_1603 and cce_5186) and strain 7942 (type I, Synpcc7942_0244) were overexpressed in <i>Escherichia coli</i> and biochemically characterized. All isozymes catalysed the phosphorolysis and reverse phosphorolysis reactions. The type I isozyme from a cyanobacterial starch-producing strain (cce_1629) differed in substrate specificity and specific activity compared with the others. The behaviour towards the effectors (AMP and ATP) of the type I and type II isozymes differed from each other. These findings enhance our understanding of the roles of cyanobacterial Pho isozymes in α-glucan metabolism. Furthermore, recombinant cce_1603 was crystallized using the hanging-drop vapour-diffusion method. Crystals were obtained at 293 K in the presence of 10 m<i>M</i> maltoheptaose, 45%(<i>w</i>/<i>v</i>) PEG 400, 0.1 <i>M</i> Tris–HCl pH 8.0, 0.2 <i>M</i> lithium sulfate. The crystals belonged to space group <i>R</i>32 (hexagonal setting) with unit-cell parameters <i>a</i> = <i>b</i> = 267.23, <i>c</i> = 204.43 Å, and diffracted to beyond 2.70 Å resolution. Matthews coefficient calculations indicated the presence of two molecules in the asymmetric unit. Structural determination is currently under way. The crystal structure of cce_1603 will aid in the understanding of the structural basis of cyanobacterial GT35-type Pho isozymes.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 10","pages":"417-424"},"PeriodicalIF":1.1,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145032362","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Improved structure of mouse gasdermin D: a new blueprint for structure-based drug design","authors":"Luigi De Colibus,&nbsp;Patryk Ludzia,&nbsp;Antonio Biasutto,&nbsp;Andrea Pica,&nbsp;Jonathan T. S. Hopper,&nbsp;Ali Jazayeri,&nbsp;Katharina L. Dürr","doi":"10.1107/S2053230X25007149","DOIUrl":"10.1107/S2053230X25007149","url":null,"abstract":"<p>Gasdermin D (GSDMD) is a protein that has gained significant attention in recent years due to its crucial role in inflammatory cell death, particularly pyroptosis. Pyroptosis is a highly inflammatory form of programmed cell death that is triggered by various microbial infections and sterile inflammatory stimuli. GSDMD acts as an executioner molecule in this process, leading to the release of pro-inflammatory cytokines and amplifying the immune response. Here, we present a higher resolution, significantly improved apo crystal structure of the deposited mouse structure model that will be beneficial for structure-based drug-design approaches towards this important pharmacological target.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 10","pages":"408-415"},"PeriodicalIF":1.1,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144991192","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 10","pages":"441-450"},"PeriodicalIF":1.1,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145196716","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 9","pages":"381-387"},"PeriodicalIF":1.1,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144923692","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 9","pages":"388-397"},"PeriodicalIF":1.1,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144923693","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 9","pages":"398-405"},"PeriodicalIF":1.1,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144923694","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}