Acta Crystallographica. Section D, Structural Biology最新文献

{"title":"Optimal 1TEL-target protein linker character is target protein-dependent.","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 Samarwickrama, Ariel Kelsch, Derick Bunn, Cameron Stewart, Wisdom Abiodun, Evan Tsubaki, Seth Brown, Tzanko I Doukov, James D Moody","doi":"10.1107/S2059798326002494","DOIUrl":"10.1107/S2059798326002494","url":null,"abstract":"<p><p>Fusing a variant of the sterile alpha motif domain of the human translocation ETS leukaemia protein (1TEL) to a protein of interest has been shown to significantly enhance its crystallization propensity. 1TEL is a pH-dependent, polymer-forming protein crystallization chaperone which, when covalently fused to a protein of interest, forms a stable, well ordered crystal lattice. However, despite its success, a challenge persists in that crystal quality and diffraction limits appear to be heavily dependent on the choice of linker between 1TEL and the protein of interest, with the identification of a functional linker currently relying on trial-and-error methods. Likewise, previous studies revealed that a ten-histidine tag at the 1TEL N-terminus can either facilitate or hinder the ordered crystallization of target proteins attached via flexible or semi-flexible linkers. To address these challenges, we designed multiple constructs with several types of linkers [rigid (helical fusion), semi-flexible (Pro-Ala and Pro-Ala-Ala) and flexible (Gly-Gly and Gly-Gly-Gly)] of varying lengths to fuse either a designed ankyrin-repeat protein (DARPin) or the thirty-eight-negative kinase-1 ubiquitin-associated (UBA) domain to the 1TEL C-terminus. Semi-flexible and flexible linker constructs were made with and without a ten-histidine tag. Our findings indicate that short semi-flexible and rigid linkers consistently yielded large crystals with a DARPin target protein, but that flexible linkers performed best with a UBA-domain target protein. Removing the ten-histidine tag uniformly enhanced crystallization rates, improved the crystal morphology and increased the crystallization propensity of the semi-flexible and flexible linker constructs. These results suggest that the ideal linker selection primarily depends on the properties of the target protein. Our data support our current recommendation to use a short flexible or semi-flexible linker between 1TEL and the target protein to facilitate protein crystallization and high-resolution structure determination.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"516-532"},"PeriodicalIF":3.8,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13133986/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147632461","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":"ICECREAM: high-fidelity equivariant cryo-electron tomography.","authors":"Vinith Kishore, Valentin Debarnot, Ricardo D Righetto, Benjamin D Engel, Ivan Dokmanić","doi":"10.1107/S2059798326001622","DOIUrl":"10.1107/S2059798326001622","url":null,"abstract":"<p><p>Cryo-electron tomography (cryo-ET) visualizes 3D cellular architecture in its near-native state. The various deep-learning methods have improved denoising and artifact correction, but remain challenged by a very low signal-to-noise ratio, a restricted tilt range (`missing wedge') and the lack of ground truth. Here, we present ICECREAM, which bridges earlier self-supervised methods with the recent equivariant imaging framework [Chen et al. (2021), IEEE/CVF International Conference on Computer Vision (ICCV), pp. 4359-4368]. Across diverse experimental datasets, ICECREAM achieves substantially better denoising and more reliable missing-wedge filling than existing methods. ICECREAM can be applied to any tomography problem that provides two statistically independent views of the volume; in cryo-ET these are obtained by dose splitting or angular partitioning of the tilt series. ICECREAM is openly available at https://github.com/swing-research/icecream.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"295-313"},"PeriodicalIF":3.8,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13044925/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147525322","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":"Molecular structure and nickel-binding capacity of Proteus mirabilis UreE.","authors":"Jiayi Pan, Sarah L Mueller, Nuren Tasneem, Yang Wu, Emily J Furlong","doi":"10.1107/S2059798326001907","DOIUrl":"10.1107/S2059798326001907","url":null,"abstract":"<p><p>UreE is a nickel chaperone that is required for the safe and efficient delivery of nickel to the active site of the metalloenzyme urease, which is a key virulence factor of the urinary-tract pathogen Proteus mirabilis. We investigated the structural features of P. mirabilis UreE (PmUreE) using protein X-ray crystallography and its nickel-binding capacity by inductively coupled plasma mass spectrometry. Here, we report a 2.0 Å resolution crystal structure of homodimeric PmUreE and show that it has the capacity to bind five Ni(II) ions per dimer. Truncation of the histidine-rich C-terminus reduced the nickel-binding capacity by two Ni(II) ions per dimer, and comparison with homologous UreE structures allowed the assignment of putative nickel-binding sites within the PmUreE structure. These findings increase our understanding of how PmUreE binds nickel and ultimately prevents this toxic metal from causing significant cellular damage in P. mirabilis.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"348-357"},"PeriodicalIF":3.8,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13044922/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147462514","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 structures of Fsc1, a novel autophagy factor that mediates autophagosome-vacuole fusion in fission yeast.","authors":"Chidiogo Azuka, Jian Liu, Xiangshu Jin","doi":"10.1107/S205979832600197X","DOIUrl":"10.1107/S205979832600197X","url":null,"abstract":"<p><p>Fsc1 is a recently identified autophagy factor in the fission yeast Schizosaccharomyces pombe that is implicated in the autophagosome-vacuole fusion step during the final stages of autophagy. Despite its critical role, the structural basis of Fsc1 function has remained unknown. Here, we report the first crystal structures of the luminal domain of Fsc1, revealing an elongated, modular architecture composed of five tandem fasciclin (FAS1) domains. Each domain adopts a hallmark β-sandwich fold, and the overall assembly forms a continuous scaffold featuring a conserved surface groove within the FAS1-4 domain. Structural and biochemical analyses demonstrate that Fsc1 forms a homodimer in solution through a shared interface observed in two independent crystal forms, supporting a biologically relevant but potentially low-affinity association. Comparative sequence and structural analyses reveal significant homology between Fsc1 and human fasciclin proteins, including TGFBI and periostin, suggesting similar structural principles underlying their functions. Together, these findings provide the first structural insights into Fsc1 and establish a structural framework for understanding how its modular architecture and context-dependent dimerization may facilitate late-stage membrane fusion during autophagy.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"358-369"},"PeriodicalIF":3.8,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13044898/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147508731","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":"Validated ligand geometries for macromolecular refinement restraints and molecular-mechanics force fields.","authors":"Nigel W Moriarty, David A Case, Dorothee Liebschner, Paul D Adams","doi":"10.1107/S2059798326000975","DOIUrl":"10.1107/S2059798326000975","url":null,"abstract":"<p><p>In macromolecular structure refinement, the low observation-to-parameter ratio and the lack of high-resolution data are countered by using a priori information in the form of restraints. Having accurate geometries of the chemical entities in the sample is paramount for generating accurate chemical restraints and, therefore, accurate macromolecular structures. In particular, it is desirable to have accurate restraints for known and novel ligand entities. Quantum mechanics (QM) can minimize the energy of a ligand by adjusting its geometry, and these geometries can be used to generate restraints for macromolecular refinement. This article describes a library of approximately 37 000 small molecules extracted from the Chemical Component Dictionary in the Protein Data Bank and minimized by density-functional QM. The library includes restraint files for use in crystallography or cryo-EM refinement, along with files suitable for molecular-dynamics simulation. Because the geometries are validated using the Cambridge Structural Database, the restraints library provides users with both functional restraints and minimized geometries. This work also provides procedures for generating new and accurate restraints.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"216-226"},"PeriodicalIF":3.8,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12954859/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146218264","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":"Phosphatidylinositol transfer protein α binds microcolins in its open conformation.","authors":"Andrea Eisenreichova, Martin Klima, Tamas Balla, Evzen Boura","doi":"10.1107/S2059798326000872","DOIUrl":"10.1107/S2059798326000872","url":null,"abstract":"<p><p>Phosphatidylinositol transfer proteins (PITPs) are essential lipid-binding proteins that regulate phosphoinositide signaling, membrane trafficking and autophagy through the transport of phosphatidylinositol and other phospholipids between intracellular membranes. Microcolin compounds have been identified as selective inhibitors of class I PITPs, revealing important roles of PITPs in Hippo signaling and autophagy. Here, we report the crystal structure of human PITPα in complex with microcolin H at 2.0 Å resolution. The structure enables a detailed description of the interaction between microcolin H and the lipid-binding cavity. Besides the expected covalent bond to the Cys94 residue, the structure also reveals an extensive network of hydrogen bonds, water bridges and hydrophobic interactions. Importantly, PITPα remains in the open conformation upon binding to microcolin H. Quantitative cavity analysis confirms that the microcolin-bound structure adopts a volume comparable to that of the unliganded PITPα and is markedly larger than that of the lipid-bound state. These findings demonstrate that microcolins selectively trap PITPα in an open conformation and provide a structural basis for their inhibitory mechanism. Furthermore, our results show that ligand binding can profoundly change protein conformation, which underscores the limitation of docking experiments.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"246-252"},"PeriodicalIF":3.8,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12954856/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146206461","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":"Coupled on-line in crystallo UV-Vis absorption spectroscopy and X-ray crystallography to compare specific radiation damage in metal-containing proteins at room versus cryogenic temperature.","authors":"Nicolas Caramello, Samuel L Rose, Eric Mathieu, Lucas Petit, Ivo Tews, Sylvain Engilberge, Antoine Royant","doi":"10.1107/S2059798326000690","DOIUrl":"10.1107/S2059798326000690","url":null,"abstract":"<p><p>Specific radiation damage (SRD) to proteins is a pertinent issue discovered during the development of cryo-crystallography at synchrotrons, often affecting the macromolecular active site and thus complicating the understanding of mechanistic insights from structural analysis. For proteins with a spectroscopic signature in the visible light spectrum, in crystallo UV-Vis absorption spectroscopy has regularly been used to estimate the dose scale of specific damage build-up and to develop diffraction data-collection strategies to mitigate its effects. Using a coupled spectroscopic and crystallographic approach, here we show that for two metal-containing proteins the structural response to X-ray-induced reduction of metals in their active site is markedly different at room temperature than at cryogenic temperature. This suggests that the use of controlled specific radiation damage to mimic and study a physiological redox transition in a metal-containing protein by X-ray crystallography should preferably be performed at room temperature rather than at cryogenic temperature.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"187-198"},"PeriodicalIF":3.8,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12954861/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146117514","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":"Breaking barriers: transitioning from X-ray crystallography to cryo-EM for structural studies.","authors":"Hassan Zafar, Kiera L Malone, Ajit K Singh, Michael A Cianfrocco, Karen C Glass","doi":"10.1107/S205979832600080X","DOIUrl":"10.1107/S205979832600080X","url":null,"abstract":"<p><p>Cryo-electron microscopy (cryo-EM) has transformed structural biology by enabling near-atomic resolution of large macromolecular complexes without the need for crystallization. Here, we describe our laboratory's transition from X-ray crystallography to single-particle cryo-EM to investigate the ATPase family AAA+ domain-containing protein 2B (ATAD2B), a chromatin regulator implicated in epigenetic signaling. We outline the challenges encountered during protein expression, purification and sample preparation, including co-purification of the chaperonin GroEL, and the strategies employed to overcome these obstacles. Our workflow highlights critical steps in sample optimization, grid vitrification and data processing using CryoSPARC, cisTEM and Topaz, as well as computational requirements for high-resolution reconstructions. We also discuss model-building, refinement and validation approaches, emphasizing best practices for new cryo-EM users. This work provides practical insights for structural biologists adopting cryo-EM, particularly for large, flexible protein complexes, and underscores the importance of integrated approaches combining biochemical, computational and imaging strategies.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"253-273"},"PeriodicalIF":3.8,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12954864/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146218185","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":"SASBDB reaches 5000 data sets: empowering open science and next-generation SAS analysis.","authors":"Clement E Blanchet, Aleksi Sutinen, Melissa A Graewert, Dmytro Soloviov, Timur Tropin","doi":"10.1107/S2059798326000641","DOIUrl":"10.1107/S2059798326000641","url":null,"abstract":"<p><p>The Small-Angle Scattering Biological Data Bank (SASBDB) has recently reached a milestone of 5000 entries, reflecting over a decade of community-driven efforts to support open and reusable biological small-angle scattering data. SASBDB provides curated experimental scattering profiles together with metadata describing samples, experimental conditions and associated structural models, thereby enabling transparent data sharing, reproducibility and comparative analysis. The archive has become an important resource for benchmarking, reanalysis and method development, including the evaluation of structure-based modelling approaches and the integration of solution scattering data with high-resolution predictive models. Its growing content also supports benchmarking, method development, and emerging data-driven and machine-learning approaches that rely on curated collections of real experimental data. This milestone highlights the role of SASBDB as a foundational infrastructure for contemporary and future developments in biological small-angle scattering.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"151-154"},"PeriodicalIF":3.8,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12954860/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146111899","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":"X-ray beam effects on metallo-peptides reflect redox events: insights from X-ray absorption spectroscopy measurements on metal complexes of truncated amyloid-β peptides.","authors":"Bharath Vinjamuri, Enrico Falcone, Emiliano De Santis, Velia Minicozzi, Olivier Proux, Peter Faller, Francesco Stellato","doi":"10.1107/S2059798326001348","DOIUrl":"10.1107/S2059798326001348","url":null,"abstract":"<p><p>The interaction between transition-metal ions and amyloid-β (Aβ) peptides is linked to the pathogenesis of Alzheimer's disease. X-ray absorption spectroscopy is widely used to investigate the coordination of these metal-peptide complexes, but exposure to synchrotron radiation can induce artefacts due to interaction with the X-ray beam. In this work, we examine the effects of X-ray irradiation on Cu(I), Cu(II) and Zn(II) complexes with two truncated Aβ fragments, Aβ_1-6 and Aβ_1-16. Experiments performed at 10 K reveal a marked photoreduction-associated effect: while the spectra of Cu(I)- and Zn(II)-bound peptides remain unchanged, Cu(II) complexes undergo significant spectral modifications. To probe structural relaxation following reduction, we exposed samples at 10 K, raised the temperature to 200 K and then collected additional spectra upon re-cooling. These experiments reveal that higher temperatures promote relaxation processes that are otherwise kinetically limited, and that the extent of relaxation, depending on the metal-binding mode, differs for Aβ_1-6 and Aβ_1-16. Overall, our experiments show that major structural modifications only take place in the presence of X-ray-induced metal reduction and that they are modulated by temperature. Thus, X-ray irradiation can be exploited not only as a probe but also as a trigger to study the redox-associated structural dynamics of copper-Aβ complexes and beyond.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"199-206"},"PeriodicalIF":3.8,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147269391","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}