Acta Crystallographica. Section D, Structural Biology最新文献

{"title":"Radiation-dose effects in correlative X-ray/cryo-electron microscopy of frozen-hydrated biological samples.","authors":"Thorsten B Blum, Vincent Olieric, Ana Diaz, Takashi Ishikawa, Volodymyr M Korkhov","doi":"10.1107/S2059798326001427","DOIUrl":"10.1107/S2059798326001427","url":null,"abstract":"<p><p>In cryo-electron microscopy (cryo-EM), imaging of biological specimens is restricted by the limited field of view and by sample thickness. Hard X-ray imaging, with its ability to penetrate samples several tens of micrometres thick, offers a complementary approach for high-resolution visualization. A major concern is whether cryo-preserved samples can withstand the handling conditions at synchrotron facilities without excessive icing, and whether the radiation exposure during X-ray imaging compromises specimen integrity, thereby hindering subsequent attempts to achieve high-resolution 3D reconstructions via cryo-EM. To evaluate this, we deposited apoferritin samples on a cryo-EM grid, exposed them to varied X-ray doses typical for X-ray tomography experiments at a synchrotron facility, and subsequently analysed the exposed particles by cryo-EM. Despite the apparent damage sustained throughout the experiment, the samples remained amenable to cryo-EM analysis, with structural details at a resolution of ∼4 Å at the highest absorbed X-ray dose of 100 MGy. By comparison, a similar cryo-EM dataset of apoferritin particles that were not exposed to X-rays but were mounted on the same cryo-EM grid resulted in a 3D reconstruction at 3.17 Å resolution. Thus, while radiation damage may limit the high-resolution information in specimens processed by cryo-X-ray tomography, the cryo-preserved biological material exposed to these high X-ray doses can still be used for subsequent cryo-EM workflows aiming to obtain structural biology insights at intermediate to high resolution. These findings lay the groundwork for an integrated imaging workflow that combines X-ray and cryo-EM techniques to enable multiscale analysis of thick vitrified biological specimens.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"207-215"},"PeriodicalIF":3.8,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12954863/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147289115","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":"Deep-learning methods for contrast enhancement and artifact reduction in cryo-electron tomography: a systematic analysis of the state of the art and proposed improvements.","authors":"Henry N Jones, Aneesh Deshmukh, Kanupriya Pande","doi":"10.1107/S2059798326001166","DOIUrl":"10.1107/S2059798326001166","url":null,"abstract":"<p><p>Cryo-electron tomography (cryo-ET) has emerged as the preferred technique for visualizing the organization of macromolecular complexes in situ and resolving their structures at subnanometre resolution [Tegunov et al. (2021), Nat. Methods, 18, 186-193]. Despite improvements in data quality as a result of advances in detector technology, microscope stability and stage precision, the analysis and interpretation of tomograms remains challenging due to a low signal-to-noise ratio and reconstruction artifacts stemming from experimental constraints in specimen tilt during data collection resulting in a missing wedge in the Fourier space. Recently, self-supervised deep-learning methods have been proposed for contrast enhancement and reduction of resolution anisotropy in reconstructed tomograms. Here, we evaluate several state-of-the-art deep-learning methods which aim to improve the interpretability of cryo-ET reconstructions, with a focus on their performance on downstream tasks of template matching, subtomogram averaging and segmentation. We propose new training architectures and a loss function based on Fourier shell correlation that show improved performance over the standard U-Net with L₁/L₂ losses. We demonstrate our analysis on four diverse experimental datasets: purified 80S ribosomes, in situ Chlamydomonas reinhardtii, immature HIV-1 virus-like particles and INS-1E cells.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"168-186"},"PeriodicalIF":3.8,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12954857/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146225220","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":"CryoJAX: a cryo-electron microscopy image-simulation library in JAX.","authors":"Michael J O'Brien, David Silva-Sánchez, Geoffrey Woollard, Kwanghwi Je, Sonya M Hanson, Daniel J Needleman, Pilar Cossio, Erik Henning Thiede, Miro A Astore","doi":"10.1107/S2059798326000550","DOIUrl":"10.1107/S2059798326000550","url":null,"abstract":"<p><p>While cryo-electron microscopy (cryo-EM) has come to prominence in the last decade due to its ability to resolve biomolecular complexes at atomic resolution, advancements in experimental and computational methods have made cryo-EM promising for investigating intracellular organization and heterogeneous molecular states. A primary challenge for these alternative applications is the development of techniques for cryo-EM data analysis, which are very computationally demanding. To this end, it is advantageous to leverage advanced scientific computing frameworks for statistical analysis. One such framework is JAX, an emerging array-oriented Python numerical computing package for automatic differentiation and vectorization with a growing ecosystem for statistical inference and machine learning. We have developed cryoJAX, a cryo-EM image-simulation library for building computational data-analysis applications in JAX. CryoJAX is a flexible modeling language for cryo-EM image formation and therefore can support a wide range of data analysis downstream. By integrating with the JAX ecosystem, cryoJAX enables the development and deployment of algorithms for the growing breadth of scientific applications for cryo-EM.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"155-167"},"PeriodicalIF":3.8,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12954862/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146111863","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":"Updating direct methods V. Phasing when triplet invariants are estimated via the Patterson map.","authors":"Maria Cristina Burla, Gianluca Cascarano, Carmelo Giacovazzo, Giampiero Polidori","doi":"10.1107/S2059798326000732","DOIUrl":"10.1107/S2059798326000732","url":null,"abstract":"<p><p>In previous articles in this series, a novel probabilistic method was described which is capable of estimating triplet invariants using the Patterson map as prior information. The first experimental tests demonstrated the superiority of the new method compared with the traditional Cochran estimate. The advantages were so significant that the ab initio solution of macromolecular structures was considered to be feasible even when the data resolution is worse than 2 Å. However, several questions remained unanswered. For example: (i) which and how many Patterson peaks should be used to optimize a direct-methods phasing procedure applied to experimental data up to 2.2 Å resolution?, (ii) is the presence of heavy atoms a necessary ingredient for the validity of the method?, (iii) which and how many reflections must be used in the triplet search?, (iv) is the information contained in the Patterson map able to identify negative cosine triplets? and (v) may a computer program be made that routinary solves macromolecular structures with data resolution up to 2.2 Å? This article recalls these five unresolved questions and answers them. In particular, criteria have been defined to determine both the number of Patterson peaks to be actively used for triplet estimation and the number of reflections to be used in the triplet search. It has also been shown that the presence of heavy atoms is a necessary ingredient for success of the theory. In particular, the theory is unable to accurately identify triplet invariants with a negative cosine, but rather can identify enantiomorph-sensitive triplets. A paradox of the theory is discussed and resolved. Finally, a computer program is presented that is capable of automatically, with a few directives, solving some of the test structures at non-atomic resolution (proteins and nucleic acids) with data resolution up to 2.2 Å, but not in a straightforward way. The limitations of the computer program and its prospects are discussed.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"237-245"},"PeriodicalIF":3.8,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146140625","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":"Associating protein residues in the literature with structural data.","authors":"Melanie Vollmar, Simon Westrip, Sreenath Nair, Balakumaran Balasubramaniyan, Sameer Velankar, Louise Jones, Peter Strickland","doi":"10.1107/S2059798326000021","DOIUrl":"10.1107/S2059798326000021","url":null,"abstract":"<p><p>Protein structures are crucial in understanding the function, mechanism and disease-causing variants of proteins within any living cell. A number of experimental techniques are employed by researchers to determine such structures. Through structure inspection in molecular viewers, combined with supporting biochemical and biophysical experiments, scientists are able to identify the function of a protein, its reaction mechanism and effects caused by sequence variation. These detailed findings, supported by experimental results, are documented by being described in the scientific literature and by making the accompanying data open source. However, it has become increasingly difficult for a reader, in particular a non-expert, to access the correct additional information and assess the validity of the conclusions drawn based on experimental results. A reader is often required to resort to a number of different software packages to access the different data types. Here, we present a first-of-its-kind implementation of an artificial intelligence- and text-mining-supported software tool that allows the association of mentions in the text of one or more specific protein residues with their corresponding counterparts in the respective protein structure or structures. Our application allows a researcher to explore a residue of interest in the context of a publication and its respective protein structure, supported by its experimental evidence, in a single view. We describe model implementation, annotation extraction, downstream processing, dissemination and visualization at the IUCr and PDBe. The application presented is primarily aimed at readers of IUCr publications and users visiting the PDBe entry pages. However, we believe that in the future our application will be a valuable tool for reviewers of new submissions to IUCr journals and may even be useful as a curation tool involving the authors of a publication as annotation validators.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"113-125"},"PeriodicalIF":3.8,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12865887/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146049926","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":"Quantifying distributions of cryo-EM projections.","authors":"Alexandre G Urzhumtsev","doi":"10.1107/S2059798325011611","DOIUrl":"10.1107/S2059798325011611","url":null,"abstract":"<p><p>In cryo-electron microscopy, a set of two-dimensional projections collected from different viewing directions may complicate image processing and subsequent model building if the distribution of these views is non-uniform. View distributions are traditionally represented as color-coded two-dimensional diagrams. However, such diagrams can introduce distortions and are cumbersome to manipulate, store and compare across data sets; they do not provide a commonly accepted quantitative measure of uniformity. In this work, we propose a method to characterize these angular distributions quantitatively and to represent them as simple one-dimensional curves rather than two-dimensional colored diagrams. The suggested measures could be incorporated into databases such as EMDB to provide a compact, standardized description of the angular distribution of particle views.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"100-112"},"PeriodicalIF":3.8,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145996951","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":"How to mitigate the caveat emptor burden of human and machine users of the Protein Data Bank.","authors":"Alexander Wlodawer, Pawel Rubach, Zbigniew Dauter, Wojciech Dec, Dariusz Brzezinski, Wladek Minor, Mariusz Jaskolski","doi":"10.1107/S2059798325011477","DOIUrl":"10.1107/S2059798325011477","url":null,"abstract":"<p><p>It is postulated that the PDB should use the CAVEAT record more prominently to warn scientists using its archives of potential risks and errors.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"62-64"},"PeriodicalIF":3.8,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145916306","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":"Probing the statistics of sequence-dependent DNA conformations in solution using SAXS.","authors":"Heidar J Koning, Anuradha Pullakhandam, Andrew E Whitten, Charles S Bond, Michel Peyrard","doi":"10.1107/S2059798325011556","DOIUrl":"10.1107/S2059798325011556","url":null,"abstract":"<p><p>SAXS studies of four 60-base-pair DNA duplexes with sequences closely related to part of the GAGE6 (G-antigen 6) promoter have been performed to study the role of DNA conformations in solution and their potential relationship to DNA-protein binding. We show that the SAXS data can be analysed using a simple polymer model, which nevertheless quantitatively describes the average persistence length and torsional rigidity of the DNA double helix, to determine the statistical distribution of local conformations of the DNA in solution to high accuracy. Although the SAXS data are averaged over time and all spatial orientations of the molecules, for sequences which have some asymmetry in the data we show that the conformations can be oriented with respect to the sequence. This allows specific features detected by the analysis to be precisely related to the DNA sequence, opening up new opportunities for SAXS to investigate the properties of DNA in solution. The biological implications of these results are discussed.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"79-99"},"PeriodicalIF":3.8,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145996940","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":"Strategies for mitigating radiation damage and improving data completeness in 3D electron diffraction of protein crystals.","authors":"Alaa Shaikhqasem, Farzad Hamdi, Lisa Machner, Christoph Parthier, Constanze Breithaupt, Fotis L Kyrilis, Stephan M Feller, Panagiotis L Kastritis, Milton T Stubbs","doi":"10.1107/S2059798325011258","DOIUrl":"10.1107/S2059798325011258","url":null,"abstract":"<p><p>While 3D electron diffraction (3D-ED or microcrystal electron diffraction; MicroED) has emerged as a promising method for protein structure determination, its applicability is hindered by a high susceptibility to radiation damage, leading to a decreasing signal-to-noise ratio in consecutive diffraction patterns that limits the quality (resolution and redundancy) of the data. In addition, data completeness may be restricted due to the geometrical limitations of current sample holders and stages. Although specialized equipment can overcome these challenges, many laboratories do not have access to such instrumentation. In this work, we introduce an approach that addresses these issues using a commonly available 200 keV cryo-electron microscope. The multi-position acquisition technique that we present here combines (i) multiple data acquisitions from a single crystal over several tilt ranges and (ii) merging data from a small number of crystals each tilted about a different axis. The robustness of this approach is demonstrated by the de novo elucidation of a protein-peptide complex structure from only two orthorhombic microcrystals.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"11-22"},"PeriodicalIF":3.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12809435/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145773185","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":"The crystal structure of EpHTT, a hydroxycinnamoyl transferase from Echinacea purpurea.","authors":"Hui Bao, Di Jiang, Chengbing Tang, Zhijie Yin, Xiaofang Huang, Rao Fu, Yang Zhang, Zhonghan Li, Shiqian Qi, Haoyang Cai, Dan Tang","doi":"10.1107/S205979832501023X","DOIUrl":"10.1107/S205979832501023X","url":null,"abstract":"<p><p>Echinacea purpurea hydroxycinnamoyl-CoA:tartaric acid hydroxycinnamoyl transferase (EpHTT) is a cytosolic BAHD acyltransferase that catalyzes the transfer of caffeoyl groups to tartaric acid, a key step in chicoric acid biosynthesis. Understanding the structure of EpHTT is essential to elucidate the molecular basis of substrate recognition and catalytic specificity. Here, we report the crystal structure of apo-form EpHTT at 2.38 Å resolution, revealing a compact, globular architecture typical of the BAHD superfamily. The enzyme adopts a two-domain fold with conserved HXXXD and DFGWG motifs, forming a V-shaped catalytic cleft characteristic of BAHD acyltransferases. Structural comparison with homologous hydroxycinnamoyl transferase enzymes shows high conservation of the overall fold, while EpHTT exhibits unique adaptations that confer specificity for tartaric acid. These results provide a molecular framework for understanding the function and substrate specificity of HTT, offering insights for the metabolic engineering of chicoric acid production.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"43-52"},"PeriodicalIF":3.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145653141","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}