IUCrJ最新文献

{"title":"Structure of the bacteriophage PhiKZ non-virion RNA polymerase bound to a p119L open promoter analogue","authors":"Chao-Sheng Chen ,&nbsp;Natàlia de Martín Garrido ,&nbsp;Maria Yakunina ,&nbsp;Christopher H. S. Aylett","doi":"10.1107/S2052252525009273","DOIUrl":"10.1107/S2052252525009273","url":null,"abstract":"<div><div>Bacteriophage ΦKZ is a massive bacterial virus with potential as a therapy for <em>Pseudomonas aeruginosa</em>, which forms a bacteriophage nucleus in infected cells to exclude the host immune system, and transcribes its genes with its own, non-canonical multi-subunit RNA polymerase. The structure of this polymerase in the process of binding an analogue of its cognate promoter is resolved, revealing an unanticipated method of promoter consensus recognition involving the β-like, rather than the σ-factor-like subunit.</div></div><div><div>Bacteriophage ΦKZ (PhiKZ) was the first identified member of a family of massive bacterial viruses. ΦKZ infects <em>Pseudomonas aeruginosa</em>, which kills tens of thousands every year, and it therefore has potential as a bacteriophage therapy. On infection, ΦKZ forms a ‘nucleus’ to protect its genome by excluding host immune systems. This barrier means that it has had to become independent of the host transcriptional apparatus; it cannot simply recruit the host RNA polymerase (RNAP) to its promoters as it is excluded from the viral DNA, and therefore it expresses and imports its own non-virion RNA polymerase (nvRNAP). The ΦKZ nvRNAP, and related jumbo-phage RNAPs including that from bacteriophage AR9, are particularly noteworthy. Unlike typical viral RNAPs which are formed as only a single subunit, it is a non-canonical multi-subunit RNAP directly related to those from eubacteria, and more distantly eukaryotes and archaea. It encompasses four proteins representing patchwork homologues of the eubacterial β/β′ subunits, and a fifth that appears to have evolved from a σ factor, but no homologues of the α or ω subunits required for formation of a catalytically active complex in eubacterial RNAPs. Its mechanism of promoter recognition is also highly divergent; transcription is initiated from a site marked only by a tiny four-base consensus sequence co-located with the start site. We have resolved the structure of the ΦKZ nvRNAP bound to an open analogue of its cognate promoter, p119L, revealing that while the σ-factor-like subunit GP68 is involved in bubble stabilization, the sequence-specific promoter consensus sequence is bound between the lobe of the β-subunit homologue GP123 and the enzymatic core of the complex. Our results shed light on the differences between mechanisms of promoter recognition in the ΦKZ nvRNAP and canonical eubacterial RNAPs, and on the uniquely specialized features of bacteriophage transcriptional apparatuses in general.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 1","pages":"Pages 31-43"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145482101","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The relationship between the Ewald sphere and exit wave explored using focal series electron micrographs","authors":"J. Bernard Heymann","doi":"10.1107/S2052252525010796","DOIUrl":"10.1107/S2052252525010796","url":null,"abstract":"<div><div>The Ewald sphere is inherent in image formation in the electron microscope and must therefore be part of the reconstruction of cryoEM maps. This study examines linear image-formation theory to show how Ewald sphere information derives from focal series micrographs and relates to the exit wave. It concludes by suggesting the proper way to correct for the contrast transfer function for cryoEM reconstruction.</div></div><div><div>CryoEM reconstructions must be performed along the Ewald spheres to achieve resolutions beyond the projection approximation limit. The linear theory of image formation models the scattering from the specimen and focusing by the objective lens as two conjugate Ewald spheres that correspond to the two halves of the contrast transfer function (CTF). A focal series of micrographs mimics the focal gradient inherent in the Ewald wavefront, and its 3D Fourier transform provides a visual representation of the conjugate Ewald spheres. To better understand the nature of the Ewald spheres, focal series of graphene oxide as a thin specimen and platinum–iridium as a strongly scattering specimen were acquired. An algorithm was developed to fit and correct the CTF of the whole focal series. Correcting for the one half of the CTF flattens one of the Ewald spheres in the 3D transform, while doubling the curvature of the other. This yields the best representation of the Ewald sphere and thus the ‘exit wave’, and can be performed on every single micrograph. The 2D reconstruction as the sum of the partial CTF corrected transforms recovers missing information in the individual micrographs and increases the signal-to-noise ratio. Iterative refinement of the reconstructed image against the amplitudes of the original focal series recovers the second Ewald sphere only at frequencies where the two spheres overlap, but introduces artifacts. The conclusion is that the correct way to account for the Ewald spheres in cryoEM is to apply the two halves of the CTF to a particle image and incorporate the two results into their corresponding spheres within the cryoEM reconstruction.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 1","pages":"Pages 77-93"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145793928","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"AutoLEI: A step towards automatic 3D ED data processing","authors":"Shitao Wu ,&nbsp;Yanhang Ma","doi":"10.1107/S2052252525011108","DOIUrl":"10.1107/S2052252525011108","url":null,"abstract":"<div><div>A user-friendly interface has been developed for <em>XDS</em>, enabling efficient real-time and batch processing of 3D ED data to accelerate structure determination.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 1","pages":"Pages 6-7"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145889059","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Crystal structure of di­acet­y­lene unveiled by X-ray and neutron diffraction, Raman spectroscopy and periodic DFT","authors":"Larissa Lopes Cavalcante ,&nbsp;Helen E. Maynard-Casely ,&nbsp;Morgan L. Cable ,&nbsp;Samuel G. Duyker ,&nbsp;Edith C. Fayolle ,&nbsp;Robert Hodyss ,&nbsp;Brendan J. Kennedy ,&nbsp;Tuan H. Vu ,&nbsp;Courtney Ennis","doi":"10.1107/S2052252525010486","DOIUrl":"10.1107/S2052252525010486","url":null,"abstract":"<div><div>The crystal structure and thermal expansion behaviour of di­acet­y­lene were determined <em>via</em> diffraction methods and supplemented by spectroscopic techniques. The similarities to the structure of acetylene and implications for Titan <em>in situ</em> exploration are discussed.</div></div><div><div>Combining powder X-ray and neutron diffraction, the first crystallographic characterization of di­acet­y­lene (IUPAC designation 1,3-butadiyne) is presented and supplemented by Raman spectroscopy and periodic-DFT calculations. The structure is described in the space group <em>Pnma</em>, with <em>a</em> = 9.348 (2), <em>b</em> = 5.9890 (6), <em>c</em> = 5.6746 (11) Å and <em>V</em> = 317.69 (6) ų at 5 K, with four molecules in the unit cell resulting in a density of 1.0466 g cm⁻³. The di­acet­y­lene molecules are arranged in a layered structure dominated by C—H⋯π interactions, which leads to anisotropic thermal expansion behaviour. No structural phase transitions were observed across the 5–220 K tem­per­a­ture range at ambient pressure. The structural similarity with acetylene identifies it as a potential cocrystal component of particular importance for Titan’s surface chemistry in view of the upcoming NASA Dragonfly mission.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 1","pages":"Pages 94-104"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145804591","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural insights into the antiviral efficacy of AG7404 against human rhinovirus 3C proteases","authors":"Juyeon Lee ,&nbsp;Hye Lim Lee ,&nbsp;Hyojin Kim ,&nbsp;Yeji Gil ,&nbsp;Sang-Ho Lee ,&nbsp;Young-Sik Jung ,&nbsp;Jin Soo Shin ,&nbsp;Inseong Jo","doi":"10.1107/S2052252525008929","DOIUrl":"10.1107/S2052252525008929","url":null,"abstract":"<div><div>This study presents the crystal structure of human rhinovirus (hRV)-B14 3C protease bound to AG7404, a broad-spectrum antiviral inhibitor, at a resolution of 2.11 Å. Antiviral assays and <em>in silico</em> studies provide structural insights into AG7404’s efficacy and binding mechanism against hRV-B14, hRV-A16 and hRV-A21 3C proteases.</div></div><div><div>Human rhinoviruses (hRVs) are major causative agents of the common cold and contribute to lower respiratory tract infections. Although extensive research efforts continue to explore potential therapeutic interventions, no clinically approved antiviral treatment currently exists for hRV infections. This study provides the structural basis of hRV 3C protease inhibition in several serotypes by AG7404, a modified rupintrivir derivative. AG7404 showed potent antiviral activity against hRV-B14, hRV-A16 and hRV-A21 with EC₅₀ values of 0.108, 0.191 and 0.187 µ<em>M</em>, respectively, and directly inhibited purified hRV-B14 3C protease with an IC₅₀ of 0.046 µ<em>M</em>. The 2.11 Å crystal structure of hRV-B14 3C protease in complex with AG7404 revealed covalent binding to the catalytic Cys146 and occupation of the substrate-binding pockets by the ligand. Comparative structural analyses incorporating ligand-free hRV-B14 3C protease structures as well as rupintrivir-bound 3C protease structures from other hRV serotypes revealed significant conformational variability of the βcII–βdII region. Molecular dynamics simulations of the structural models of hRV-A16 and hRV-A21 3C proteases showed that the binding interactions of AG7404, including critical water-mediated networks, are conserved across serotypes despite sequence variations. These findings offer structural insights into the binding mode of AG7404 and establish a foundation for the rational design of broad-spectrum antivirals targeting hRV 3C proteases.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 1","pages":"Pages 19-30"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145482027","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A survey of crystallographic quality metrics from CIFs in the Cambridge Structural Database","authors":"Clare A. Tovee ,&nbsp;Seth B. Wiggin ,&nbsp;Natalie T. Johnson ,&nbsp;Philip I. Andrews ,&nbsp;Matthew P. Lightfoot","doi":"10.1107/S2052252525007134","DOIUrl":"10.1107/S2052252525007134","url":null,"abstract":"<div><div>This study examines data extracted from Crystallographic Information Files (CIFs) deposited at the Cambridge Crystallographic Data Centre (CCDC) to gain insight into patterns and trends seen in the quality of structural models obtained from structure refinements. From the results of over 1 300 000 individual datasets, this work aims to show what can be considered as typical values over a variety of experimental conditions.</div></div><div><div>The Cambridge Structural Database (CSD) is a comprehensive repository of over 1.3 million unique crystallographic datasets, compiled from data deposited at the Cambridge Crystallographic Data Centre (CCDC). Given the vast size of this collection, identifying datasets suitable for reuse in a particular area of study is critical. Traditionally, the <em>R</em> factor has been used as an indicator of structure refinement quality; however, numerous additional metrics can provide valuable insights into the refinement and structural model. Some of these metrics have been extracted from data in the deposited Crystallographic Information Files (CIFs) and added to the CSD. This study surveys these selected crystallographic data items and explores the variability in them between different types of structures. Through a statistical analysis of their values, this work aims to assist with the selection of relevant structures for future reuse.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 6","pages":"Pages 647-657"},"PeriodicalIF":3.6,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145113357","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantum Crystallography: the 100-year revolution.","authors":"Malcolm J Cooper","doi":"10.1107/S2052252524007164","DOIUrl":"10.1107/S2052252524007164","url":null,"abstract":"<p><p>The IUCr's close association with quantum crystallography, rightly celebrated by this focused anniversary issue, has its origins in regular meetings of experimentalists and theoreticians interested in electron charge and spin density back in the 1960s. That ad hoc group was adopted by the IUCr in the 1970s, when a Commission was created and latterly it has been renamed as the Commission on Quantum Crystallography. The history is summarized in this foreword to the issue.</p>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":" ","pages":"614-615"},"PeriodicalIF":3.6,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12573919/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145372814","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Magellon – an extensible platform for cryo-EM data visualization, management and processing","authors":"Behdad Khoshbin ,&nbsp;Puneeth Damodar ,&nbsp;Rupali R. Garje ,&nbsp;Frank H. Schotanus ,&nbsp;Nandagopal Nair ,&nbsp;Lai Wei ,&nbsp;Jan-Hannes Schäfer ,&nbsp;Gabriel C. Lander ,&nbsp;Michael A. Cianfrocco ,&nbsp;Scott M. Stagg","doi":"10.1107/S2052252525007432","DOIUrl":"10.1107/S2052252525007432","url":null,"abstract":"<div><div>This work presents a new cyberinfrastructure framework for cryo-EM structure determination, <em>Magellon</em>, which offers a robust and flexible approach to cryo-EM data management. We show the power of this platform by building a frontend web interface, <em>Magellon Viewer</em>, on top of <em>Magellon</em>.</div></div><div><div>Single-particle cryo-electron microscopy (cryo-EM) has revolutionized structural biology by enabling high-resolution determination of macromolecular structures. However, the field faces challenges in data management, processing workflow integration and software extensibility. We present <em>Magellon</em>, an innovative cryo-EM software platform that addresses these challenges through a modern microservices architecture. <em>Magellon</em> consists of an extensible backend with a web based frontend that we call <em>Magellon Viewer</em>. Together, these combine high-performance computing capabilities with an intuitive user interface, enabling researchers to efficiently process and analyze cryo-EM data. The platform’s distinguishing features include a plugin based architecture, distributed processing capabilities, comprehensive monitoring systems, and a novel approach to data organization and visualization. A key philosophy of the approach is that the <em>Magellon</em> backend provides a platform that uses robust industry-standard libraries to orchestrate computational tasks while offering users and developers flexibility in selecting the computational resources for performing calculations. <em>Magellon</em> represents a significant advancement in cryo-EM software infrastructure, offering flexibility, scalability and extensibility while maintaining ease of use.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 6","pages":"Pages 637-646"},"PeriodicalIF":3.6,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145000632","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Testing the limits: serial crystallography using unpatterned fixed targets","authors":"Alexander Gorel ,&nbsp;Robert L. Shoeman ,&nbsp;Elisabeth Hartmann ,&nbsp;Stanislaw Nizinski ,&nbsp;Martin V. Appleby ,&nbsp;Emma V. Beale ,&nbsp;Florian Dworkowski ,&nbsp;Guillaume C. Gotthard ,&nbsp;John H. Beale ,&nbsp;James Holton ,&nbsp;R. Bruce Doak ,&nbsp;Thomas R. M. Barends ,&nbsp;Ilme Schlichting","doi":"10.1107/S2052252525008371","DOIUrl":"10.1107/S2052252525008371","url":null,"abstract":"<div><div>The influence of the X-ray step size on radiation damage occurring in serial data collection from a metalloprotein using sheet-on-sheet fixed-target chips was investigated at fourth-generation synchrotron and XFEL beamlines.</div></div><div><div>Sheet-on-sheet (SOS) fixed-target chips are arguably the most versatile, cheapest and simplest sample-delivery method for ambient-temperature data acquisition using serial crystallography approaches at synchrotrons and X-ray free-electron lasers (XFELs). Their defining feature, the absence of any hard-patterned restrictions around crystals, is their strength as it removes limitations on crystal sizes or environments. However, it is also their weakness when it comes to limiting undesired effects on yet-to-be-irradiated crystals due to diffusing heat, radicals or gas originating from previous exposures. We explored whether SOS chips can be used for damage-free serial data collection on the new ID29 beamline at the ESRF-EBS, a fourth-generation synchrotron light source, as well as at the new Cristallina-MX station at SwissFEL. We collected serial data sets from microcrystals of the hemoprotein DtpAa, which was reported to have a highly radiation-sensitive iron–water bond length. The data sets differ in step size between exposures within and between lines of a serpentine-like data-acquisition scan. We observe no significant changes in the distance of the water ligand of the heme in the structures obtained from the ID29 SSX data. However, when compared with those collected at Cristallina-MX, the diffraction intensities collected at ID29 suggest global damage akin to Bragg termination occurring during the 90 µs exposure at ID29. Moreover, differences in the heme geometry and the proximal histidine–iron bond length point to local damage in all ID29 data sets regardless of the X-ray spacing. SFX data collected at Cristallina-MX show a phase transition of the DtpAa crystal lattice for X-ray step sizes of ≤20 µm. This phase transition might be caused by heating and/or hydrogen-gas-induced crystal dehydration. Vigilance remains required to safeguard against radiation damage at fourth-generation synchrotrons and XFELs.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 6","pages":"Pages 692-709"},"PeriodicalIF":3.6,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145280355","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"‘Mix-it-up’: accessible time-resolved cryo-EM on the millisecond timescale","authors":"Lauren Alexandrescu ,&nbsp;William Lessin ,&nbsp;Gabriel C. Lander","doi":"10.1107/S2052252525008838","DOIUrl":"10.1107/S2052252525008838","url":null,"abstract":"<div><div>The development of methods for low-cost time-resolved cryo-EM using an on-grid mixing strategy is described.</div></div><div><div>Biological reactions often involve macromolecules that undergo substrate-induced conformational changes in under a second, yet capturing these transient states remains challenging. While high-resolution structural techniques such as X-ray crystallography and cryo-electron microscopy (cryo-EM) have advanced our mechanistic understanding of protein–substrate interactions, traditional sample-preparation methods are too slow to capture rapid biochemical events. Time-resolved cryo-EM has emerged as a promising approach to visualize structural dynamics on microsecond-to-millisecond timescales, but its widespread adoption has been limited by costly equipment and challenges in achieving rapid mixing, application and vitrification of samples in a reproducible manner. To address these limitations, we developed ‘Mix-it-up’ (MIU), a modified spray device designed for rapid on-grid mixing and vitrification of cryo-EM samples. By manually applying one sample onto the EM grid, blotting and subsequently spraying the second sample, we achieve on-grid mixing with a vitrification delay of as low as ∼120 ms. We demonstrate MIU’s time-resolved capabilities through high-resolution structure determination of mixed samples, pH-induced viral capsid contraction and ligand-dependent complex formation. These findings establish MIU as a cost-effective, versatile tool for studying rapid biochemical processes and lay the groundwork for future applications to time-resolved cryo-EM.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 6","pages":"Pages 710-724"},"PeriodicalIF":3.6,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145372884","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}