Acta Crystallographica. Section D, Structural Biology最新文献

{"title":"QwenCryoMarker: a universal post-processing framework for contamination-aware particle cleaning.","authors":"Yunhai Sun, Jiahao Zhao, Nan Xu, Lei Wang, Wei Ding, Ming Li","doi":"10.1107/S2059798326007679","DOIUrl":"10.1107/S2059798326007679","url":null,"abstract":"<p><p>Cryo-electron microscopy (cryo-EM) micrographs are frequently contaminated by carbon edges, ice crystals, ethane bubbles and other high-contrast artifacts. These contaminants trigger abundant false positives in automated particle pickers, severely hampering downstream 3D reconstruction. Existing methods either avoid contamination implicitly (requiring dataset-specific tuning) or rely on rule-based filters that fail on complex contamination patterns. Here, we present QwenCryoMarker, a universal post-processing framework that converts the outputs of arbitrary particle pickers into clean, high-precision particle sets. Our pipeline consists of two core stages: (i) a visual large model (Qwen-Image-Edit-2511) fine-tuned via supervised learning to generate pixel-accurate binary contamination masks from raw micrographs and (ii) a lightweight contamination-aware filtering module that discards particles when the contamination proportion within their surrounding circular region exceeds a predefined threshold ratio. Contamination is defined as all micrograph regions unsuitable for reliable particle picking and subsequent 3D reconstruction, including carbon edges, ice crystals, ethane bubbles, miscellaneous debris and dense protein aggregates. The framework features plug-and-play deployment: it requires no per-dataset parameter tuning or extra retraining, and maintains compatibility with classical pickers (blob detection, template matching) as well as deep learning-based pickers (Topaz, crYOLO etc.). We validate QwenCryoMarker on five diverse CryoPPP benchmark datasets across four representative particle pickers. Quantitatively, our method consistently boosts precision with an average absolute gain of 0.009 and lifts the F₁-score, while recall only drops slightly by an average of 0.008. Segmentation benchmarking shows our model reaches a mean intersection over union (IoU) of 0.629, surpassing that of the state-of-the-art MicrographCleaner (0.551) by 14.2%. We further compare against multiple segmentation baselines: U-Net (0.448), DeepLabV3+ (0.488), SAM (0.475), ASOCEM (0.195) and IceBreaker (0.433). A downstream reconstruction case study on EMPIAR-10017 verifies that particles filtered by QwenCryoMarker yield cleaner 2D class averages and higher resolution 3D density maps (3.88 versus 3.97 Å). Qualitative visualization also confirms that QwenCryoMarker stably eliminates false particles located on carbon films and ice crystals, independent of the upstream particle-picking algorithm. By encapsulating contamination suppression as a universal, model-agnostic post-processing module, QwenCryoMarker offers a practical, robust, easy-to-deploy toolkit that greatly improves particle-set quality without modifying existing cryo-EM workflows. The framework is fully open-source and can be seamlessly integrated into mainstream cryo-EM processing pipelines.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"1093-1110"},"PeriodicalIF":4.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148786889","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":"KAT6A-inhibitor co-crystal structures: tackling a challenging crystallization target via two alternative approaches.","authors":"Vera Puetter, Léa Bouché, Katrin Nowak-Reppel, Steven J Ferrara, Stefan N Gradl, Daniel Korr, Craig A Strathdee, Antonius Ter Laak, Roman C Hillig","doi":"10.1107/S2059798326008545","DOIUrl":"10.1107/S2059798326008545","url":null,"abstract":"<p><p>The histone lysine acetyltransferase KAT6A belongs to the MYST family of lysine acetyltransferases which consists of five isoforms. KAT6A (and its paralog KAT6B) have emerged as a promising epigenetic drug targets in cancer, supported by recent clinical data. As support for our high-throughput screening approach aimed at discovering new inhibitors of KAT6A, we developed a crystallization platform system termed KAT6A^mutCys in which four surface cysteine residues of KAT6A were mutated to serine. This construct crystallizes readily when in complex with its cofactor AcCoA. The obtained co-crystals were successfully used in a back-soaking approach in which AcCoA was soaked out of the crystals and small-molecule inhibitors were soaked in. In parallel, we explored a previously published surrogate approach termed MYST^cryst in which active-site residues of the related, but easier to crystallize, enzyme KAT8 were mutated to those found in KAT6A. By comparing co-crystal structures of the same ligand bound to KAT6A from our Cys-to-Ser approach and to mutated KAT8 (MYST^cryst) we found that the KAT8 surrogate approach indeed successfully reproduced the binding mode observed in the KAT6A structure, while delivering structures with significantly higher resolution. The MYST^cryst approach was therefore employed to determine the binding modes of two further small-molecule inhibitors, both from our KAT6A inhibitor optimization program and from a competitor lead series. These structures reveal alternative inhibitor conformations at the binding-site entry and the importance of filling a hydrophobic subpocket in the interior of the binding pocket. These insights will aid future efforts towards the development of KAT6A inhibitors as anticancer drugs.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"1111-1124"},"PeriodicalIF":4.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13532696/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148823911","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":"Influence of heme and pH on the oligomeric states of Brucella melitensis bacterioferritin.","authors":"Tanguy Scaillet, Clément Champagne, Johan Wouters","doi":"10.1107/S2059798326006625","DOIUrl":"10.1107/S2059798326006625","url":null,"abstract":"<p><p>Bacterioferritin from Brucella melitensis (BmBfr) is a protein that plays essential roles in oxidative stress management and metal homeostasis in the bacterium. It presents itself as a 24-mer forming a spherical nanocage, allowing further applications such as drug delivery and nanoparticle synthesis. Studying the oligomerization process is thus important for a deeper understanding of the protein. In this work, two forms of the protein were studied: with the heme cofactor (holo BmBfr) and without the cofactor (apo BmBfr). Analyses were performed using size-exclusion chromatography, thermal shift analysis and structure determination of apo BmBfr by X-ray crystallography. This revealed that oligomerization is not possible with the apo form, since the heme is essential for dimer formation, which is the first oligomerization step. Further oligomerization can occur at a pH above 5.0, where interface interactions are favorable, to form a highly stable 24-mer state. Those findings allowed us to suggest an oligomerization mechanism for BmBfr.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"1062-1071"},"PeriodicalIF":4.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13532695/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148700368","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":"Room-temperature crystal structure of a metal-dependent W-formate dehydrogenase by serial synchrotron crystallography.","authors":"Guilherme Vilela-Alves, Guilherme Martins, David von Stetten, Pedram Mehrabi, Inês A C Pereira, Maria João Romão, Arwen R Pearson, Cristiano Mota","doi":"10.1107/S2059798326006923","DOIUrl":"10.1107/S2059798326006923","url":null,"abstract":"<p><p>Metal-dependent formate dehydrogenases (Fdhs) are a promising research target in efforts to mitigate climate change by developing active, efficient, selective and safe industrial catalysts for CO₂ reduction. Here, we report the room-temperature (RT) serial synchrotron X-ray crystallography (SSX) structure of Nitratidesulfovibrio vulgaris formate dehydrogenase AB and compare this structure with previously reported cryogenic structures. The comparison reveals structural differences likely arising from the absence of cryoprotectants, differences in data-collection temperature and the much lower radiation dose accumulated by each crystal during the SSX experiments. The RT-SSX structure provides the first step towards time-resolved serial crystallography experiments targeting possible catalytic intermediates in order to fully understand the catalytic mechanism of metal-dependent Fdhs.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"1072-1081"},"PeriodicalIF":4.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13532692/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148700343","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":"Direct deposition on pre-cooled grids: a new approach to sub-millisecond cryoEM grid preparation.","authors":"David P Klebl, Robert W Kay, Sean McMillan, Frank Sobott, Nikil Kapur, Stephen P Muench","doi":"10.1107/S2059798326007126","DOIUrl":"10.1107/S2059798326007126","url":null,"abstract":"<p><p>There has been a rapid expansion in new approaches to sample preparation for single-particle cryoEM. One drive has been around speeding up the process both for the application of time-resolved studies and in outrunning some of the negative effects which may come from the sample interacting with the air-water interface, such as degradation and preferred orientation. Here, we set out to significantly improve the speed of grid preparation by removing the plunging stage and directly spraying onto pre-cooled grids which are situated in the cryogen, allowing us to produce grids where two samples are mixed and frozen on the grid in less than 1 ms. We have previously shown a preliminary proof of principle with this new approach and here we provide a detailed description of the approach taken and the methodology behind it. This approach allows us to move beyond the millisecond timescale to open up more systems to time-resolved EM and potentially improve samples.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"1056-1061"},"PeriodicalIF":4.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13532694/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148704999","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":"Decision making in macromolecular crystallography: how to be a productive structural biologist.","authors":"Helen M Ginn, Nicholas M Pearce, Clemens Vonrhein","doi":"10.1107/S2059798326006856","DOIUrl":"10.1107/S2059798326006856","url":null,"abstract":"<p><p>The Guest Editors introduce the special issue based on talks at the CCP4 Study Weekend 2024. The virtual issue is available at https://journals.iucr.org/special_issues/2026/CCP42024/.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"1012-1015"},"PeriodicalIF":4.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148719669","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":"Replacement soaking for human tankyrase 2 enables studies on substrate analogues and inhibitors.","authors":"Johan Pääkkönen, Sven T Sowa, Chiara Bosetti, Lari Lehtiö","doi":"10.1107/S2059798326006868","DOIUrl":"10.1107/S2059798326006868","url":null,"abstract":"<p><p>Crystallography has facilitated the development of inhibitors in modern drug discovery. Complex structures are traditionally obtained by co-crystallization or soaking methods, but they are not always successful; co-crystallization may lead to selective crystallization of the apoprotein, and compounds cannot necessarily be soaked into preformed crystals. Successful endeavours in this field include human tankyrases TNKS1 and TNKS2, which are promising drug targets controlling a wide range of signalling events. In the case of TNKS2, apo crystals have a closed conformation in the donor loop, delineating the NAD⁺-binding active site, and compound soaking requires a large conformational change, which often damages the crystals and deteriorates the diffraction quality. This work describes a crystal form of TNKS2 that can be used efficiently in replacement soaking (also known as cross-soaking) when TNKS2 is co-crystallized with a low-affinity inhibitor. Replacement soaking is demonstrated with recently described nanomolar inhibitors as well as a nonhydrolysable analogue of NAD⁺, which all occupy the substrate-binding site. The obtained complex structures offer new insight into the binding modes of the inhibitors and the substrate NAD⁺, and comparison to previously published complex structures of closely related PARP proteins with NAD⁺ analogues reveals key characteristics of the NAD⁺-binding site of TNKS2. In cases where traditional methods fail to yield complex structures, the replacement soaking method provides an alternative method, which was demonstrated here to be necessary for elucidating the complex structures.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"998-1008"},"PeriodicalIF":4.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13431646/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148597322","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":"Advances in the nanostructure characterization of biological hydrogels formed by the prion-like domain of EARLY FLOWERING 3.","authors":"Stephanie Hutin, Pedro L O Filho, Anton M Popov, Petra Pernot, Chloe Zubieta, Mark D Tully","doi":"10.1107/S2059798326006698","DOIUrl":"10.1107/S2059798326006698","url":null,"abstract":"<p><p>Hydrogels exhibit traits of both liquids and solids, forming a 3D structural network with generally high water content, high porosity and increasing stability over time. However, probing the structure of hydrogels is challenging due to the semi-disordered nature of their internal molecular organization and the presence of multiple species with varying dynamics. Small-angle X-ray scattering (SAXS) is well suited to study materials of this nature due to its ability to probe different length scales and to provide information as to the structure and conformation of different molecular species within the hydrogel. Here, we used the prion-like domain from the plant thermosensory protein EARLY FLOWERING 3 (ELF3) as a model hydrogel for structural characterization by SAXS. To overcome sample-handling challenges, we developed an X-ray- and vacuum-compatible sample cell for hydrogel manipulation that allows direct measurement in the X-ray beam. Furthermore, by using a three-component model, which gathers the scattering contributions from the different species in the hydrogel, which arise from individual and aggregated oligomers as well as from their stacking into a loose lamellar phase, we were able to satisfactorily fit the experimental data and provide a full description of the nanostructure of the ELF3 hydrogel.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"940-946"},"PeriodicalIF":4.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13431640/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148597562","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":"Optimal 1TEL-target protein linker character is target protein-dependent. Corrigendum.","authors":"Maria J Pedroza Romo, Alihikaua Keliiliki, Jacob C Averett, Joseph F Gonzalez, Ethan Noakes, Elijah W Wilson, Conrad Smith, Blake Averett, Dalton Hansen, Riley Nickles, Miles Bradford, Sara Soleimani, Tobin Smith, Supeshala Nawarathnage, Prasadika Samarawickrama, Ariel Kelsch, Derick Bunn, Cameron Stewart, Wisdom Abiodun, Evan Tsubaki, Seth Brown, Tzanko I Doukov, James D Moody","doi":"10.1107/S2059798326007102","DOIUrl":"10.1107/S2059798326007102","url":null,"abstract":"<p><p>The name of one of the authors in the article by Pedroza Romo et al. [(2026), Acta Cryst. D82, 516-532] is corrected.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"1009"},"PeriodicalIF":4.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13431638/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148417690","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":"Crystal structure of pilus-specific sortase from Enterococcus faecalis reveals both open and closed conformations: insights into loop dynamics and substrate recognition.","authors":"Vinay Sharma, Sumit Murmu, Rajendra Prasad Roy, Vengadesan Krishnan","doi":"10.1107/S2059798326006066","DOIUrl":"10.1107/S2059798326006066","url":null,"abstract":"<p><p>Pilus-specific or class C sortases (SrtCs) catalyze pilus polymerization in Gram-positive bacteria and possess a critical lid near the active site that is in a closed or open conformation. The crystal structure of SrtC, which polymerizes endocarditis and biofilm-associated pili in Enterococcus faecalis, presented here at 1.9 Å resolution (PDB entry 24rr), reveals the flexible lid in both conformations. Two molecules in the asymmetric unit exhibit different lid conformations stabilized by distinct sets of contacts. The DPX motif from the lid at the active site stabilizes the closed conformation, while the TPY motif within the conserved TP(Y/L)XIN(S/T)H motif of the β7-β8 loop from the asymmetric mate pointing towards the active site stabilizes the open conformation. For the first time, proline cis-trans isomerization, likely acting as a molecular switch in SrtC, was captured, regulating the access of secondary substrate to the active-site cleft by toggling between two states at the β7-β8 loop. Lid movement regulates primary-substrate (LPXTG sorting motif) binding and harmonizes conformational changes at the β7-β8 loop for secondary-substrate (YPKN pilin motif) binding. In silico analysis and RP-HPLC-based assays helped to map residues within sorting motifs near the scissile bond, providing insights into enzyme-substrate recognition. Removing the N-terminal lid region enhances E. faecalis SrtC activity. The unprecedented structural snapshots of both open and closed lid conformations, synchronized with the proline switch in the β7-β8 loop, captured in the same crystal structure, advance the understanding of sortase-mediated virulence in enterococci and provide a framework for the development of antivirulence strategies.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"947-961"},"PeriodicalIF":4.3,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148597400","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}