IUCrJ最新文献

{"title":"Structure of an ex vivoDrosophila TOM complex determined by single-particle cryoEM","authors":"Agalya Periasamy ,&nbsp;Pamela Ornelas ,&nbsp;Thomas Bausewein ,&nbsp;Naomi Mitchell ,&nbsp;Jiamin Zhao ,&nbsp;Leonie M. Quinn ,&nbsp;Werner Kuehlbrandt ,&nbsp;Jacqueline M. Gulbis","doi":"10.1107/S2052252524011011","DOIUrl":"10.1107/S2052252524011011","url":null,"abstract":"<div><div>A 3.3 Å resolution map and structural model of the TOM complex from <em>Drosophila melanogaster</em> were determined by single-particle cryoEM. The complex was extracted from native membranes of the fly retina following targeted expression of a Tom40 transgene.</div></div><div><div>Most mitochondrial precursor proteins are encoded in the cell nucleus and synthesized on cytoplasmic ribosomes. The translocase of the outer membrane (TOM) is the main protein-import pore of mitochondria, recognizing nascent precursors of mitochondrially targeted proteins and transferring them across the outer membrane. A 3.3 Å resolution map and molecular model of a TOM complex from <em>Drosophila melanogaster</em>, obtained by single-particle electron cryomicroscopy, is presented. As the first reported structure of a transgenic protein expressed and purified <em>ex vivo</em> from <em>Drosophila</em>, the method provides impetus for parallel structural and genetic analyses of protein complexes linked to human pathology. The core TOM complex extracted from native membranes of the <em>D. melanogaster</em> retina contains transgenic Tom40 co-assembled with four endogenous TOM components: Tom22, Tom5, Tom6 and Tom7. The <em>Drosophila</em> TOM structure presented here shows that the human and <em>Drosophila</em> TOM are very similar, with small conformational changes at two subunit interfaces attributable to variation in lipid-binding residues. The new structure provides an opportunity to pinpoint general features that differentiate the TOM structures of higher and unicellular eukaryotes. While the quaternary fold of the assembly is retained, local nuances of structural elements implicated in precursor import are indicative of subtle evolutionary change.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 1","pages":"Pages 49-61"},"PeriodicalIF":2.9,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11707698/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142687078","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":"Exploiting fourth-generation synchrotron radiation for enzyme and photoreceptor characterization","authors":"Tek Narsingh Malla ,&nbsp;Srinivasan Muniyappan ,&nbsp;David Menendez ,&nbsp;Favour Ogukwe ,&nbsp;Aleksandar N. Dale ,&nbsp;Joseph D. Clayton ,&nbsp;Dominique D. Weatherall ,&nbsp;Prabin Karki ,&nbsp;Shishir Dangi ,&nbsp;Victoria Mandella ,&nbsp;A. Andrew Pacheco ,&nbsp;Emina A. Stojković ,&nbsp;Samuel L. Rose ,&nbsp;Julien Orlans ,&nbsp;Shibom Basu ,&nbsp;Daniele de Sanctis ,&nbsp;Marius Schmidt","doi":"10.1107/S2052252524010868","DOIUrl":"10.1107/S2052252524010868","url":null,"abstract":"<div><div>(Time-resolved) macromolecular crystallography at the new ID29 beamline at the ESRF is described.</div></div><div><div>The upgrade of the European Synchrotron Radiation Facility (ESRF) in Grenoble, France to an Extremely Brilliant Source (EBS) is expected to enable time-resolved synchrotron serial crystallography (SSX) experiments with sub-millisecond time resolution. ID29 is a new beamline dedicated to SSX experiments at ESRF–EBS. Here, we report experiments emerging from the initial phase of user operation at ID29. We first used microcrystals of photoactive yellow protein as a model system to exploit the potential of microsecond pulses for SSX. Subsequently, we investigated microcrystals of cytochrome <em>c</em> nitrite reductase (ccNiR) with microsecond X-ray pulses. CcNiR is a decaheme protein that is ideal for the investigation of radiation damage at the various heme-iron sites. Finally, we performed a proof-of-concept subsecond time-resolved SSX experiment by photoactivating microcrystals of a myxobacterial phytochrome.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 1","pages":"Pages 36-48"},"PeriodicalIF":2.9,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11707700/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142687074","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":"IUCrJ on passing its tenth anniversary and entering its second decade: progress, current status and prospects for the future.","authors":"Andrew J Allen","doi":"10.1107/S205225252401217X","DOIUrl":"10.1107/S205225252401217X","url":null,"abstract":"<p><p>This Editorial briefly celebrates the history and progress of IUCrJ in its first decade, reviews its present status, and suggests some pointers for the future.</p>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":" ","pages":"1-3"},"PeriodicalIF":2.9,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11707694/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142864190","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":"Real-time data processing for serial crystallography experiments","authors":"Thomas White ,&nbsp;Tim Schoof ,&nbsp;Sergey Yakubov ,&nbsp;Aleksandra Tolstikova ,&nbsp;Philipp Middendorf ,&nbsp;Mikhail Karnevskiy ,&nbsp;Valerio Mariani ,&nbsp;Alessandra Henkel ,&nbsp;Bjarne Klopprogge ,&nbsp;Juergen Hannappel ,&nbsp;Dominik Oberthuer ,&nbsp;Ivan De Gennaro Aquino ,&nbsp;Dmitry Egorov ,&nbsp;Anna Munke ,&nbsp;Janina Sprenger ,&nbsp;Guillaume Pompidor ,&nbsp;Helena Taberman ,&nbsp;Andrey Gruzinov ,&nbsp;Jan Meyer ,&nbsp;Johanna Hakanpää ,&nbsp;Martin Gasthuber","doi":"10.1107/S2052252524011837","DOIUrl":"10.1107/S2052252524011837","url":null,"abstract":"<div><div>We report the use of streaming data interfaces to process data in real time from serial crystallography experiments, with a latency of less than 1 s per frame and without requiring intermediate data storage on disk.</div></div><div><div>We report the use of streaming data interfaces to perform fully online data processing for serial crystallography experiments, without storing intermediate data on disk. The system produces Bragg reflection intensity measurements suitable for scaling and merging, with a latency of less than 1 s per frame. Our system uses the <em>CrystFEL</em> software in combination with the ASAP::O data framework. In a series of user experiments at PETRA III, frames from a 16 megapixel Dectris EIGER2 X detector were searched for peaks, indexed and integrated at the maximum full-frame readout speed of 133 frames per second. The computational resources required depend on various factors, most significantly the fraction of non-blank frames (‘hits’). The average single-thread processing time per frame was 242 ms for blank frames and 455 ms for hits, meaning that a single 96-core computing node was sufficient to keep up with the data, with ample headroom for unexpected throughput reductions. Further significant improvements are expected, for example by binning pixel intensities together to reduce the pixel count. We discuss the implications of real-time data processing on the ‘data deluge’ problem from recent and future photon-science experiments, in particular on calibration requirements, computing access patterns and the need for the preservation of raw data.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 1","pages":"Pages 97-108"},"PeriodicalIF":2.9,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11707691/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142877353","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":"Incommensurately modulated structure of Zn4Si2O7(OH)2·H2O at high pressure","authors":"Roman Gajda ,&nbsp;Wojciech Sławiński ,&nbsp;Tomasz Poręba ,&nbsp;Jan Parafiniuk ,&nbsp;Mohamed Mezouar ,&nbsp;Przemysław Dera ,&nbsp;Krzysztof Woźniak","doi":"10.1107/S2052252524011060","DOIUrl":"10.1107/S2052252524011060","url":null,"abstract":"<div><div>Refinement of the hemimorphite crystal structure using single-crystal synchrotron X-ray diffraction data collected at high pressure revealed a structural phase transition into an incommensurately modulated structure, accompanied by the appearance of satellite reflections.</div></div><div><div>High-resolution single-crystal X-ray diffraction experiments on Zn₄Si₂O₇(OH)₂·H₂O hemimorphite were conducted at high pressure using diamond anvil cells at several different synchrotron facilities (ESRF, Elettra, DESY). Experimental data confirmed the existence of a previously reported phase transition and revealed the exact nature of the incommensurate modulation. We report the incommensurately modulated structure described in the (3+1)D space group <em>Pnn</em>2(0, β, 0)000. We have determined the modulation mechanism, which involves the fluctuation of atoms between two main positions, occurring mainly along the [100] direction, perpendicular to the modulation vector. Moreover, our results reveal that the phase transition occurs at lower pressure than previously reported.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 1","pages":"Pages 62-73"},"PeriodicalIF":2.9,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11707689/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142739133","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":"Using high pressure to understand the behavior of organic molecular crystals","authors":"María Guadalupe Vasquez-Ríos","doi":"10.1107/S2052252524012478","DOIUrl":"10.1107/S2052252524012478","url":null,"abstract":"<div><div>In the recent publication by Zhou <em>et al.</em> [(2025). <em>IUCrJ</em>, <strong>12</strong>, 16–22], the crystal structure of benzo[<em>a</em>]pyrene was studied under high pressure up to 28 GPa using single-crystal X-ray diffraction and DFT calculations. This commentary highlights the importance of high pressure for analyzing organic molecular crystals.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 1","pages":"Pages 4-5"},"PeriodicalIF":2.9,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11707696/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142931635","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":"Towards improved accuracy of Hirshfeld atom refinement with an alternative electron density partition","authors":"Michał Chodkiewicz ,&nbsp;Krzysztof Woźniak","doi":"10.1107/S2052252524011242","DOIUrl":"10.1107/S2052252524011242","url":null,"abstract":"<div><div>We demonstrate that applying the alternative electron density partition in a Hirshfeld atom refinement may significantly improve the accuracy of hydrogen atom parameters. The new partition leads to less overlapping atomic densities. As a result, hydrogen atom parameters are less dependent on the structural parameters of their neighbours and their inaccuracies.</div></div><div><div>Hirshfeld atom refinement (HAR) is generally the chosen method for obtaining accurate hydrogen atom parameters from X-ray diffraction data. Still, determination can prove challenging, especially in the case of atomic displacement parameters (ADPs). We demonstrate that such a situation can occur when the ADP values of the bonding partner of the hydrogen atom are not determined accurately. Atomic electron densities partially overlap and inaccuracies in the bonding neighbour ADPs can be partially compensated for with modifications to the hydrogen ADPs. We introduce a modified version of the original Hirshfeld partition: the exponential Hirshfeld partition, parameterized with an adjustable parameter (<em>n</em>) to allow control of the overlap level of the atomic electron densities which, for <em>n</em> = 1, is equivalent to the Hirshfeld partition. The accuracy of the HAR-like procedure using the new partition (expHAR) was tested on a set of organic structures using B3LYP and MP2 electron densities. Applying expHAR improved the hydrogen atom parameters in the majority of the structures (compared with HAR), especially in cases with the highest deviations from the reference neutron values. <em>X</em>—H bond lengths and hydrogen ADPs improved for 9/10 of the structures for B3LYP-based refinement and 8/9 for MP2-based refinement when the ADPs were compared with a newly introduced scale-independent similarity measure.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 1","pages":"Pages 74-87"},"PeriodicalIF":2.9,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11707693/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142854286","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":"Managing negative linear compressibility and thermal expansion through steric hindrance: a case study of 1,2-bis­(4′-pyridyl)­ethane cocrystals","authors":"Ewa Patyk-Kaźmierczak ,&nbsp;Kornelia Szymańska ,&nbsp;Michał Kaźmierczak","doi":"10.1107/S2052252524011734","DOIUrl":"10.1107/S2052252524011734","url":null,"abstract":"<div><div>The negative linear compressibility and negative thermal expansion behaviours of two isostructural 1:1 cocrystals of 1,2-bis­(4′-pyridyl)­ethane with fumaric and succinic acids were revealed and compared, showing surprisingly strong ramifications of a small steric hindrance on the magnitude of both effects.</div></div><div><div>Multicomponent crystals have great scientific potential because of their amenability to crystal engineering in terms of composition and structure, and hence their properties can be easily modified. More and more research areas are employing the design of multicomponent materials to improve the known or induce novel physicochemical properties of crystals, and recently they have been explored as materials with abnormal pressure behaviour. The cocrystal of 1,2-bis­(4′-pyridyl)­ethane and fumaric acid (ETYFUM) exhibits a negative linear compressibility behaviour comparable to that of framework and metal-containing materials, but overcomes many of their deficiencies restricting their use. Herein ETYFUM was investigated at low temperature to reveal negative thermal expansion behaviour. Additionally, a cocrystal isostructural with ETYFUM, based on 1,2-bis­(4′-pyridyl)­ethane and succinic acid (ETYSUC), was exposed to high pressure and low temperature, showing that its behaviour is similar in nature to that of ETYFUM, but significantly differs in the magnitude of both effects. It was revealed that the minor structural difference between the acid molecules does not significantly affect the packing under ambient conditions, but has far-reaching consequences when it comes to the deformation of the structure when exposed to external stimuli.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 1","pages":"Pages 88-96"},"PeriodicalIF":2.9,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11707692/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142864193","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":"FAIR data – the photon and neutron communities move together towards open science","authors":"B. M. Murphy ,&nbsp;A. Götz ,&nbsp;C. Gutt ,&nbsp;C. McGuinness ,&nbsp;H. M. Rønnow ,&nbsp;A. Schneidewind ,&nbsp;S. Deledda ,&nbsp;U. Pietsch","doi":"10.1107/S2052252524011941","DOIUrl":"10.1107/S2052252524011941","url":null,"abstract":"<div><div>The German project DAPHNE4NFDI together with the European Synchrotron and Free Electron Laser User Organization (ESUO), the European Neutron Scattering Association (ENSA), and European synchrotron and neutron facilities continue the development of FAIR data handling procedures laid out by the EU-funded projects PaNOSC and ExPaNDS. Written by members of these organizations, this ‘white paper’ documents the current status of this discussion.</div></div><div><div>The topic of data storage, traceability, and data use and reuse in the years following experiments is becoming an important topic in Europe and across the world. Many scientific communities are striving to create open data by the FAIR principles. This is a requirement from the European Commission for EU-funded projects and experiments at EU-funded research infrastructures (RIs) and from many national funding agencies. This is challenging for users of large-scale RIs such as neutron, photon, synchrotron and free-electron laser facilities. Users of photon and neutron (PaN) RIs employ a wide range of scattering, imaging and spectroscopic methods investigating the behaviour of matter with a broad scientific base across physics, chemistry and biology, including engineering, environmental, cultural heritage and medical applications. They produce large data volumes of up to 1 PByte per day in some cases. To ensure all these data are FAIR requires an enormous effort from PaN RIs. It requires not only the expansion of data storage capacity, but also the development and deployment of software for effective data storage, metadata schemes and implementation of effective data pipelines at each individual experiment across RIs. FAIR data also affect the carbon footprint related to large amounts of data and raise questions related to user authentication, rights of access and cyber security. The RIs alone cannot achieve such a transformational process. For successful open science, cooperation of the user communities is essential as they need to create and utilize existing tools to deliver FAIR data. In this white paper, the European PaN community outline and discuss the role and responsibilities of the users and RIs and their common accountability to achieve FAIR data. This paper shall serve as a starting point for a common user and RI approach on the European scale to achieve FAIR data.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 1","pages":"Pages 8-15"},"PeriodicalIF":2.9,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11707702/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142914802","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":"Quantum refinement in real and reciprocal space using the Phenix and ORCA software","authors":"Kristoffer J. M. Lundgren ,&nbsp;Octav Caldararu ,&nbsp;Esko Oksanen ,&nbsp;Ulf Ryde","doi":"10.1107/S2052252524008406","DOIUrl":"10.1107/S2052252524008406","url":null,"abstract":"<div><div>We present a new implementation of quantum refinement interfacing the widely used <em>Phenix</em> and <em>ORCA</em> software. We show applications on a neutron structure of Mn superoxide dismutase, X-ray structures of V- and Fe-nitrogenase and a cryo-EM structure of particulate methane monooxygenase.</div></div><div><div>X-ray and neutron crystallography, as well as cryogenic electron microscopy (cryo-EM), are the most common methods to obtain atomic structures of biological macromolecules. A feature they all have in common is that, at typical resolutions, the experimental data need to be supplemented by empirical restraints, ensuring that the final structure is chemically reasonable. The restraints are accurate for amino acids and nucleic acids, but often less accurate for substrates, inhibitors, small-molecule ligands and metal sites, for which experimental data are scarce or empirical potentials are harder to formulate. This can be solved using quantum mechanical calculations for a small but interesting part of the structure. Such an approach, called quantum refinement, has been shown to improve structures locally, allow the determination of the protonation and oxidation states of ligands and metals, and discriminate between different interpretations of the structure. Here, we present a new implementation of quantum refinement interfacing the widely used structure-refinement software <em>Phenix</em> and the freely available quantum mechanical software <em>ORCA</em>. Through application to manganese superoxide dismutase and V- and Fe-nitro­genase, we show that the approach works effectively for X-ray and neutron crystal structures, that old results can be reproduced and structural discrimination can be performed. We discuss how the weight factor between the experimental data and the empirical restraints should be selected and how quantum mechanical quality measures such as strain energies should be calculated. We also present an application of quantum refinement to cryo-EM data for particulate methane monooxygenase and show that this may be the method of choice for metal sites in such structures because no accurate empirical restraints are currently available for metals.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 6","pages":"Pages 921-937"},"PeriodicalIF":2.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533993/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142347053","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}