Acta Crystallographica. Section D, Structural Biology最新文献

{"title":"Structure of the Arabidopsis receptor kinase SRF6 ectodomain determined from crystals obtained using the LRR crystallization screen.","authors":"Alberto Caregnato, Ulrich Hohmann, Michael Hothorn","doi":"10.1107/S2059798326005498","DOIUrl":"10.1107/S2059798326005498","url":null,"abstract":"<p><p>Plant-specific membrane receptor kinases with structurally diverse extracellular domains regulate key processes in plant growth, development, immunity and symbiosis. Structural studies of these glycoproteins are often hampered by the limited quantities in which they can be obtained. Here, we describe the leucine-rich repeat (LRR) crystallization screen, which has enabled the successful crystallization and structure determination of multiple receptor kinase ectodomains, including ligand- and co-receptor-bound complexes. As an example, we report the 1.5 Å resolution crystal structure of the LRR domain of STRUBBELIG-RECEPTOR FAMILY 6 (SRF6) from Arabidopsis thaliana. The SRF6 ectodomain contains seven LRRs and a disulfide-bond-stabilized N-terminal capping domain but lacks the canonical C-terminal cap and the N-glycosylation pattern typically found in other family members. Previously reported protein-protein interactions between the SRF6 and SRF7 ectodomains and the receptor kinases BRI1, BRL1, BRL3, SERK3 and BIR1-BIR3 could not be confirmed by quantitative isothermal titration calorimetry and grating-coupled interferometry assays, suggesting that these structurally conserved LRR receptor kinases may have signalling functions outside the brassinosteroid pathway.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"800-812"},"PeriodicalIF":4.3,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13317683/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148222564","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":"Simulating neutron protein crystallography experiments: applications to the development of the NMX instrument at ESS.","authors":"Mads Bertelsen, Peter K Willendrup, Sunyoung Yoo, Adriano Meligrana, David McDonagh, Justin Bergmann, Esko Oksanen, Aaron D Finke","doi":"10.1107/S205979832600584X","DOIUrl":"10.1107/S205979832600584X","url":null,"abstract":"<p><p>Monte Carlo neutron ray-tracing simulations of time-of-flight (TOF)-Laue neutron macromolecular crystal diffraction (n-MX) using the McStas software package were performed for the upcoming NMX Macromolecular Diffractometer at the European Spallation Source. Splitting neutron rays that arrive at the crystal leads to dramatic improvements in event formation with minimal computational overhead. The simulated event-probability data were sampled using a new single-pass weighted reservoir-sampling method, and processed like real n-MX data using DIALS. The effects of air and beamstop scatter on simulated data were investigated.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"751-760"},"PeriodicalIF":4.3,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13317687/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148293105","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":"It started off as a Cys, how did it end up like this? Identifying the extent of unmodelled oxidatively modified cysteines within the Protein Data Bank.","authors":"Samuel P Foster, Anna J Warren, C Alistair Siebert, Jaswir Basran, Peter C E Moody","doi":"10.1107/S2059798326003943","DOIUrl":"10.1107/S2059798326003943","url":null,"abstract":"<p><p>Radiation damage to macromolecular structures remains a significant challenge for accurate structure solution by X-ray crystallography, leading to incorrect structural and chemical interpretation of the data. Site-specific radiation damage is insidious, typically unidentifiable solely from summary statistics, and is primarily discussed with reference to the predominant forms: disulfide-bond cleavage, metal-centre reduction and decarboxylation of acidic residues. A method is presented for identifying potentially oxidatively damaged cysteines by interrogating the accuracy of the built model within the electron density and the geometry of the difference density peaks surrounding a cysteine. We also highlight that cysteines located within protein active sites or that are in hydrolases are predisposed to this damage.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"700-714"},"PeriodicalIF":4.3,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13317685/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148136373","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 VI. The extended use of the information contained in the Patterson map.","authors":"Maria Cristina Burla, Giovanni Luca Cascarano, Carmelo Giacovazzo, Giampiero Polidori","doi":"10.1107/S2059798326004419","DOIUrl":"10.1107/S2059798326004419","url":null,"abstract":"<p><p>In the previous articles in this series, it was shown how the use of the Patterson map as a priori information significantly improves the estimation of triplet invariants and makes possible the ab initio solution of macromolecular structures with data resolutions up to 2.2 Å, provided that heavy atoms are present in the unit cell. For the above estimation, the position and intensity of the most representative Patterson peaks were used. No effort towards Patterson deconvolution is necessary. Triplet invariants, however, depend not only on individual Patterson peaks, but also on pairs of interatomic vectors that start or converge on the same atom. Such pairs presuppose the presence of a third interatomic vector, and therefore in this article we legitimately speak of Patterson peak triples. The new mathematical formulation allows their algebra to be described: the informative contribution coming from them has been incorporated into the technique of joint probability distribution functions, and the result is a concentration factor that significantly improves the estimation of triplet invariants. Experimental tests on proteins and nucleic acids show that structural complexity and non-atomic resolution are no longer an unsurpassable obstacle for crystal structure solution.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"763-775"},"PeriodicalIF":4.3,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148142185","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":"Assessing protein-specific radiation damage in time-resolved X-ray solution-scattering experiments at high-brilliance synchrotrons using fast detector readout.","authors":"Fatemeh Sabzian-Molaei, Tomás S Plivelic, Magnus Andersson","doi":"10.1107/S2059798326005164","DOIUrl":"10.1107/S2059798326005164","url":null,"abstract":"<p><p>Time-resolved X-ray solution scattering (TR-XSS) enables tracking of protein structural dynamics but can suffer from radiation damage when performed with continuous X-ray beam exposure at multipurpose small-angle X-ray scattering (SAXS) beamlines. Here, we systematically assess how protein concentration, exposure time, X-ray dose and beam focusing influence the stability of adenylate kinase (AdK) during TR-XSS at CoSAXS at the MAX IV Laboratory. Static SAXS measurements from 2.5 to 21 mg ml^-1 showed only minor interparticle effects, establishing suitable concentrations for TR-XSS. Under detector-focused conditions, AdK irradiated at room temperature remained stable up to 3.13 kGy, with consistent absolute and difference scattering profiles over 50 ms. In contrast, focusing the beam directly on the sample increased the absorbed dose to 21.3 kGy and produced clear signatures of radiation damage, which included low-q intensity loss and increasing deviation from the low-dose condition. These results identify practical system-specific dose limits and highlight beam focusing as a key determinant of sample integrity. The workflow presented here provides general guidelines for minimizing radiation artifacts in TR-XSS on multipurpose SAXS beamlines.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"715-726"},"PeriodicalIF":4.3,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13317681/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148222540","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":"Cefdinir binding to a class A β-lactamase revealed by serial cryo-crystallography.","authors":"Gargi Gore, Andreas Prester, Kim Bartels, David von Stetten, Eike C Schulz","doi":"10.1107/S2059798326003992","DOIUrl":"10.1107/S2059798326003992","url":null,"abstract":"<p><p>One of the most common resistance mechanisms against antibiotics employed by Gram-negative bacteria involves the production of β-lactamases, resulting in rapid hydrolysis of the antibiotic. Extensive use of the early-generation cephalosporins led to the rise of extended-spectrum β-lactamases such as CTX-Ms. Cefdinir is an extended-spectrum third-generation cephalosporin administered since the late 1990s; despite this, there is no reported 3D structure of the antibiotic bound to any β-lactamase or penicillin-binding protein in the PDB. Here, we report the X-ray crystallographic structure of cefdinir-bound CTX-M-14 E166A mutant obtained via serial cryo-crystallography.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"672-682"},"PeriodicalIF":4.3,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13224927/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147969501","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":"Rational acquisition of laboratory equipment: an accurate mathematical model to estimate the trade-offs in shared and nonshared equipment.","authors":"C O S Sorzano, J M Carazo","doi":"10.1107/S2059798326003608","DOIUrl":"10.1107/S2059798326003608","url":null,"abstract":"<p><p>Scientific equipment, such as high-end electron microscopes, entails considerable costs for acquisition, maintenance and operation. Efficient use of these instruments requires thoughtful allocation of access among multiple users. This task may be aided by a thorough statistical analysis that combines cost modelling and queueing theory. In this work, we propose a framework for estimating the hourly access cost and the average waiting time, based on equipment characteristics (price, lifespan and operating hours), user patterns (cycle and acquisition times) and staffing assumptions. In this way, we derive expressions that help estimate the optimal number of users and service congestion levels. The methodology is general and applicable to many types of shared scientific infrastructure. We illustrate its use with realistic cryo-electron microscopy scenarios. To facilitate adoption, we provide an open-access online calculator implementing the model at https://i2pc.es/coss/Programs/equipmentCost.html. This tool can support evidence-based decision-making in equipment planning and policy design.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"638-645"},"PeriodicalIF":4.3,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13224926/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147832227","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":"Definition of the catalytic cleft and product profile of a GH5_5 cellulase from Thermoascus aurantiacus.","authors":"Laetitia Collet, Agathe Denys, Yamina Oudjama, Kawtar Sifennasr, Corinne Vander Wauven, Raphaël Dutoit","doi":"10.1107/S2059798326003578","DOIUrl":"10.1107/S2059798326003578","url":null,"abstract":"<p><p>Glycoside hydrolases (GHs) achieve glycan breakdown through glycosidic bond hydrolysis. Some retaining GHs can also transglycosylate, which could be useful for glycosynthesis. Improving GHs for either glycan degradation or synthesis requires a deep understanding of the residues involved in catalysis and substrate binding. This study characterizes in detail the activity and structure of Ta_Cel5A, a cellulase in glycoside hydrolase family 5, subfamily 5 (GH5_5) from the thermophilic ascomycete Thermoascus aurantiacus. While its hydrolytic activity was confirmed, Ta_Cel5A was also found to exhibit a weak transglycosylase activity with cellopentaose as a substrate. Transglycosylation products were detected within the first minutes of reaction at 25°C, far below its optimal temperature. The structures of catalytically impaired variants were solved in complex with oligosaccharides. The entire catalytic cleft was defined, consisting of seven glucose-binding subsites, five negative subsites and two positive subsites, from the nonreducing end to the reducing end. The fifth negative subsite could not be inferred in silico, showing the limitation in predicting distal subsites based on structural analogy. The structure of the glycosyl-enzyme intermediate was also obtained, revealing the displacement of key residues in the active site. The covalent binding of a glycosidic molecule triggers a major displacement of the nucleophilic residue, Glu244, changing its interaction network. The acid/base residue, Glu133, and a conserved tyrosine residue, Tyr201, are also displaced during glycosyl-enzyme intermediate formation, hinting at their role in the deglycosylation step.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"626-637"},"PeriodicalIF":4.3,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147832209","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":"A novel fusion tool to enable G protein-coupled receptor structure determination.","authors":"Nita R Shah, Mathieu Oosterlaken, Claudine Bisson, Mattia Bertinelli, Alicia M Churchill-Angus, Andrew Hutchin, Jola Kopec, Vadim Kotov, Ciaran R McFarlane, Erika Griss Pascualli, Ana Pavic, Matthias Zebisch, Cédric Fiez-Vandal, Edoardo Fabini, Stéphanie Duclos","doi":"10.1107/S2059798326003785","DOIUrl":"10.1107/S2059798326003785","url":null,"abstract":"<p><p>Structure determination of G protein-coupled receptors (GPCRs) plays an important role in accelerating drug development against this medically important protein family. This study outlines the development of a new fusion tool to enable structure determination of GPCRs in inactive conformations by cryo-EM. Initially, a PDB mining approach was applied to select eight naturally occurring proteins with the intention of fusing them into the intracellular loop 3 (ICL3) of GPCRs to create a suitable fiducial marker for cryo-EM workflows. During the selection process, candidates with known high-affinity protein binders were prioritized to enable a further increase in the protein mass of the fiducial marker. Fusion constructs were generated with adenosine receptor A_2A (A_2AR) and were assessed for expression and aggregation levels. For the two best-performing new fusion constructs, ligand binding was characterized to ensure that the fusion tag did not significantly affect protein behaviour. A_2AR with a β-lactamase fusion in ICL3 and binding partner β-lactamase inhibitory protein II (BLIPII) was then selected to solve an antagonist-bound structure. The overall map was resolved to an average of 3.2 Å resolution with continuous helices connecting the β-lactamase to helices 5 and 6 of A_2AR. Focused refinement of the A_2AR region improved the local resolution and map detail in the orthosteric site, thereby allowing confident modelling of the antagonist ligand, ZM241385, which matches previously described X-ray crystallographic structures. This new fusion provides an alternative option for GPCR structure determination, with several potential benefits compared with existing tools, such as a more favourable position relative to the GPCR to reduce potential clashes.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"655-663"},"PeriodicalIF":4.3,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13224925/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147947433","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":"Structural insights into urocanate reductase using room-temperature X-ray crystallography.","authors":"Swati Aggarwal, Nitisha Gurav, Esko Oksanen, Karin Lindkvist-Petersson, Raminta Venskutonytė","doi":"10.1107/S2059798326003360","DOIUrl":"10.1107/S2059798326003360","url":null,"abstract":"<p><p>Urocanate reductase (UrdA) is a bacterial enzyme that converts urocanic acid to imidazole propionate. Its catalytic residue Arg411 undergoes a large conformational change in the substrate-bound versus product-bound states. In contrast to previously studied cryo-conditions, the room-temperature X-ray data of UrdA presented here show that the occupancy distribution of Arg411 is affected by crystal cryocooling. We further provide evidence that a phosphate ion stabilizes the substrate complex and can bias the conformation of Arg411. Both room-temperature and cryogenic X-ray datasets were essential to elucidate the dynamic nature of the UrdA active site, highlighting the importance of collecting data at both temperatures, as each may reveal distinct conformational states.</p>","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"603-614"},"PeriodicalIF":4.3,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13224921/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147832170","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}