IUCrJ最新文献

{"title":"Magnetic order in Tsai-type icosahedral quasicrystals and periodic approximants","authors":"Farid Labib,&nbsp;Ryuji Tamura","doi":"10.1107/S2052252526006263","DOIUrl":"10.1107/S2052252526006263","url":null,"abstract":"<div><div>Quasicrystals (QCs), a class of aperiodic crystals with long-range order and non-crystallographic rotational symmetry, provide a unique platform for exploring emergent magnetism beyond conventional periodic solids. Although theoretical studies have long suggested that magnetic order is compatible with quasi­periodicity, long-range magnetic order in real QCs has only recently been realized through design principles established from their periodic approximants. This review presents three complementary and hierarchical principles for understanding and controlling magnetism in Tsai-type QCs and periodic approximants: (i) tuning the valence electron concentration (<em>e</em>/<em>a</em>) to control the sign and strength of Ruderman–Kittel–Kasuya–Yosida (RKKY) interactions, (ii) exploiting crystal electric field (CEF) anisotropy to select spin orientation and stabilize noncoplanar magnetic textures, and (iii) controlling structural degrees of freedom to manipulate frustration. Together, these principles provide a phenomenological framework for understanding and organizing magnetic phase selection in quasiperiodic materials. They also provide a unified perspective on the contrasting emergence of long-range magnetic order and spin-glass-like freezing in Tsai-type quasicrystals. Critical behaviour near magnetic transitions, emerging opportunities and outstanding challenges are also discussed, highlighting future directions for discovering novel magnetic states in QCs.</div></div><div>Quasicrystals (QCs), a class of aperiodic crystals with long-range order and non-crystallographic rotational symmetry, provide a unique platform for exploring emergent magnetism beyond conventional periodic solids. Although theoretical studies have long suggested that magnetic order is compatible with quasi­periodicity, long-range magnetic order in real QCs has only recently been realized through design principles established from their periodic approximants. This review presents three complementary and hierarchical principles for understanding and controlling magnetism in Tsai-type QCs and periodic approximants: (i) tuning the valence electron concentration (<em>e</em>/<em>a</em>) to control the sign and strength of Ruderman–Kittel–Kasuya–Yosida (RKKY) interactions, (ii) exploiting crystal electric field (CEF) anisotropy to select spin orientation and stabilize noncoplanar magnetic textures, and (iii) controlling structural degrees of freedom to manipulate frustration. Together, these principles provide a phenomenological framework for understanding and organizing magnetic phase selection in quasiperiodic materials. They also provide a unified perspective on the contrasting emergence of long-range magnetic order and spin-glass-like freezing in Tsai-type quasicrystals. Critical behaviour near magnetic transitions, emerging opportunities and outstanding challenges are also discussed, highlighting future directions for discovering novel magnetic states in QCs.</div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 5","pages":"Pages 552-579"},"PeriodicalIF":3.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148887371","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":"Atomic resolution cryo-EM at 200 keV","authors":"Radostin Danev,&nbsp;Haruaki Yanagisawa,&nbsp;Keitaro Yamashita,&nbsp;Fabian Eisenstein,&nbsp;Masahide Kikkawa","doi":"10.1107/S2052252526004100","DOIUrl":"10.1107/S2052252526004100","url":null,"abstract":"<div><div>Atomic resolution in cryo-electron microscopy was first demonstrated six years ago. This was accom­plished using 300 kV electron microscopes equipped with new hardware that provided narrower energy spread, aberration correction and energy filtering. Here, we report the achievement of 1.24 Å atomic resolution on an upgraded 200 kV electron microscope featuring a cold field emission gun, a high-resolution objective lens polepiece and an energy filter. These com­ponents transform the instrument into a cost-effective single-particle cryo-EM platform with performance com­parable to that of significantly more expensive 300 kV systems. The microscope can also be operated at 100 kV and by using a high-speed hybrid-pixel detector we were able to reach sub-2 Å resolution.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 4","pages":"Pages 343-353"},"PeriodicalIF":3.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148217921","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":"Functional role of a tethered domain as a naturally fused cognate partner is demonstrated in a three-domain copper nitrite reductase","authors":"Nopphon Petchyam,&nbsp;Allegra Mbouku,&nbsp;Robert R. Eady,&nbsp;S. Samar Hasnain,&nbsp;Svetlana V. Antonyuk","doi":"10.1107/S2052252526004549","DOIUrl":"10.1107/S2052252526004549","url":null,"abstract":"<div><div>Copper-containing nitrite reductases (CuNiRs) catalyse the reduction of nitrite to nitric oxide and are a key enzyme in the anaerobic ammonium oxidation and denitrification steps of the nitro­gen cycle. The recent recognition of the widespread distribution of three-domain CuNiRs where cognate redox partners are fused to the core NiR enzyme offered the possibility of studying coordinated events (<em>e.g.</em> proton-coupled electron transfer) in a conformationally stable donor–acceptor complex. The C-terminal cytochrome <em>c</em> tethered domain of the CuNiR from <em>Ralstonia pickettii</em> (<em>Rp</em>NiR) has been well studied. Reverse engineering of <em>Rp</em>NiR undertaken to remove the cognate partner domain showed that the presence of the additional domain resulted in significant differences in the apparent <em>K</em>_m for nitrite and the reduction potentials of the Cu centres when compared with the core enzyme. The oxidation state of the haem centre and the position of the tethering linker have also been shown to control access of substrate to the active site. A key feature of this control is a conserved tyrosine residue (Tyr323 in <em>Rp</em>NiR) located in the tethering linker between the fused domain and the core enzyme. To gain insight into this control, we have undertaken targeted mutations of <em>Rp</em>NiR to probe the so-called primary proton channel and perturb putative electron transfer routes from the haem to the ‘gatekeeper’ Tyr323 and to the T1Cu centre. The resolution of our crystallographic data to better than 1.2 Å enabled us to apply unrestrained <em>SHELXL</em> refinement of the structures. Our data provide a significant advance in our understanding of catalysis and modulation of electron transfer in these tethered systems, with wider implications for these fundamental processes in other protein complexes.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 4","pages":"Pages 498-513"},"PeriodicalIF":3.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148251615","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":"Continuous invariant-based asymmetries of periodic crystals quantify deviations from higher symmetry","authors":"Surya Majumder,&nbsp;Daniel Widdowson,&nbsp;Yury Elkin,&nbsp;Olga Anosova,&nbsp;Andrew I. Cooper,&nbsp;Graeme M. Day,&nbsp;Vitaliy A. Kurlin","doi":"10.1107/S2052252526002988","DOIUrl":"10.1107/S2052252526002988","url":null,"abstract":"<div><div>Ideal symmetry is known to break down under almost any noise. One measure of asymmetry in a periodic crystal is the relative multiplicity <em>Z</em>′ of geometrically non-equivalent units. However, <em>Z</em>′ discontinuously changes under almost any displacement of atoms, which can arbitrarily scale up a primitive cell. This discontinuity was recently resolved by a hierarchy of invariant descriptors that continuously change under all small perturbations. We introduce a Continuous Invariant-based Asymmetry (CIA) to quantify (in physically meaningful ångstroms) the deviation of a periodic crystal from a higher-symmetry form. Our experiments on several crystal structure prediction datasets show that about a half of simulated crystals have high values of CIA, while all experimental structures in these datasets have CIA = 0. On another hand, many crystals with high values of <em>Z</em>′ in the Cambridge Structural Database (CSD) turned out to be close to more symmetric forms with <em>Z</em>′ ≤ 1 due to low values of CIAs.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 4","pages":"Pages 456-470"},"PeriodicalIF":3.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148138143","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":"Drop-on-fixed-target reaction initiation approach for serial and time-resolved crystallography","authors":"Jos J. A. G. Kamps,&nbsp;Philip Hinchliffe,&nbsp;Johan Glerup,&nbsp;Emily I. Freeman,&nbsp;Pauline A. Lang,&nbsp;Catherine L. Tooke,&nbsp;Michael Beer,&nbsp;Laura Parkinson,&nbsp;Do-Heon Gu,&nbsp;Sehan Park,&nbsp;Nicholas Devenish,&nbsp;Tiankun Zhou,&nbsp;Anastasya Shilova,&nbsp;Samanpreet Kaur,&nbsp;Patrick Rabe,&nbsp;Christopher J. Schofield,&nbsp;James Spencer,&nbsp;Jaehyun Park,&nbsp;Robin L. Owen,&nbsp;Allen M. Orville,&nbsp;Pierre Aller","doi":"10.1107/S2052252526003489","DOIUrl":"10.1107/S2052252526003489","url":null,"abstract":"<div><div>We describe the design and implementation of a drop-on-fixed-target method for time-resolved serial crystallography at both synchrotron and XFEL facilities. A piezoelectric droplet dispensing pipette is employed for addition of picolitre volume aqueous droplets (∼40–90 pl; ∼40–55 µm diameter sphere), containing (co-)substrate(s) or ligand(s), onto enzyme microcrystals previously loaded into the trapezoidal wells of an etched crystalline silicon fixed-target chip containing 25 600 wells in a high-density, square grid with 125 µm centre-to-centre well spacing. These features demand exquisite accuracy and thereby constrain motion controls to enable robust time-resolved crystallographic studies. The system was tested with three enzyme systems, comprising lysozyme and two β-lactamases, CTX-M-15 and AmpC_EC. Mitigation strategies for cross-well contamination, including the implementation of interleaved controls, are described; the overall performance of the system at synchrotron and X-ray free-electron laser facilities was evaluated. This drop-on-fixed-target method is a reliable framework for time-resolved crystallography and will improve the consistency of measurements across facilities.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 4","pages":"Pages 471-484"},"PeriodicalIF":3.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148163107","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":"Towards light-coupled sample preparation for time-resolved cryoEM studies","authors":"Kyprianos Hadjidemetriou,&nbsp;Sofia Jaho,&nbsp;Pierre Aller,&nbsp;Zhanru Yu,&nbsp;Benedikt M. Kessler,&nbsp;Stephen P. Muench,&nbsp;Nikil Kapur,&nbsp;Gabriel Karras,&nbsp;Robin L. Owen,&nbsp;Peijun Zhang","doi":"10.1107/S2052252526005324","DOIUrl":"10.1107/S2052252526005324","url":null,"abstract":"<div><div>The dynamic nature of protein and macromolecular complexes means that the capture of multiple sequential states along a reaction pathway can provide much greater insight into function than that obtained from a single static structure. We present a set of modular, easy-to-implement tools and workflows for optical excitation, on-grid characterization and tightly coupled rapid vitrification, establishing a proof-of-principle framework for time-resolved cryoEM and cryo-electron tomography (cryoET). We apply this framework to <em>E. coli</em> chemotaxis, in which serine-sensitive chemoreceptors initiate signalling upon ligand binding and undergo critical conformational changes within the chemosensory arrays. Using DMNB-caged serine [<em>O</em>-(4,5-di­meth­oxy-2-nitro­benzyl)-<span>l</span>-serine] as a model trigger, we quantified its photophysical properties and uncaging efficiency using UV–Vis spectroscopy and two-dimensional gas chromatography mass spectrometry (GC×GC-MS). Coupling a femtosecond-pulsed laser to a Vitrobot enabled reproducible reaction-to-vitrification delays of ∼150 ms, yielding intact <em>E. coli</em> minicells with well-preserved chemotaxis arrays suitable for <em>in situ</em> structural analysis by cryoET. This integrated approach provides a robust and generalisable framework for millisecond time-resolved cryoET, laying the groundwork for capturing transient conformational states in their native cellular context.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 4","pages":"Pages 395-408"},"PeriodicalIF":3.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148345498","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":"Atomic structure and formation mechanism of a newly discovered charge density wave in the m = 2 monophosphate tungsten bronze","authors":"Arianna Minelli,&nbsp;Elen Duverger-Nedellec,&nbsp;Olivier Perez,&nbsp;Alain Pautrat,&nbsp;Adrien Girard,&nbsp;Johnathan Bulled,&nbsp;Marek Mihalkovič,&nbsp;Marc de Boissieu,&nbsp;Alexei Bosak","doi":"10.1107/S2052252526002836","DOIUrl":"10.1107/S2052252526002836","url":null,"abstract":"<div><div>The <em>m</em> = 2 member of the monophosphate tungsten bronze family had been thought to be the only one without an electronic instability at low temperature. In this paper, we report the discovery of a charge density wave phase in this compound, with a transition temperature of 290 K and an incommensurate modulation vector <strong>q</strong> = 0.245<strong>b</strong>* + ξ<strong>c</strong>*, which reaches a lock-in with a commensurate vector at 130 K. The presence of this new phase is confirmed by diffraction and resistivity measurements. Pre-transitional dynamics are investigated using diffuse and inelastic X-ray scattering, revealing a clear Kohn anomaly. We analyze both structural and electronic contributions to the phase transition, providing a comprehensive picture of the mechanism driving this newly identified instability.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 4","pages":"Pages 441-455"},"PeriodicalIF":3.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148054557","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":"How cryoEM has advanced our understanding of bacteriophages and bacteriocins targeting Clostridioides difficile","authors":"Per A. Bullough,&nbsp;Jason S. Wilson,&nbsp;Hannah L. Berry,&nbsp;Robert P. Fagan","doi":"10.1107/S2052252526005105","DOIUrl":"10.1107/S2052252526005105","url":null,"abstract":"<div><div>We review the structural and functional characteristics of bacteriophages and bacteriocins (diffocins) that specifically target <em>Clostridioides difficile</em>, a significant healthcare concern due to its role in nosocomial infections. The advent of modern cryogenic electron microscopy (cryoEM) has revolutionized our understanding of these contractile injection systems, providing high-resolution insights into their mechanisms. We compare the structures of <em>C. difficile</em> phages and diffocins, highlighting their adaptations for penetrating the Gram-positive bacterial cell envelope – including the cell membrane, cell wall and protein­aceous surface layer. Diffocins, simpler in structure, utilize a combination of mechanical and enzymatic strategies, while some phages like ΦCD508 may rely on mechanical force alone. This review delves into the assembly and function of key components such as the contractile sheath, baseplate and receptor-binding proteins, offering a framework for engineering precision antimicrobials. We also present new experimental results, including refined cryoEM structures of the ΦCD508 pre- and post-contracted tail, a novel spontaneously contracted conformation and an X-ray crystal structure of a phage receptor-binding protein domain. This work underscores the potential of cryoEM in advancing our understanding of phage biology and its applications in developing targeted therapies against <em>C. difficile</em>.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 4","pages":"Pages 324-342"},"PeriodicalIF":3.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148301670","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":"Phase relationships in homoleptic com­plexes of XeF2","authors":"Lewis A. Clough,&nbsp;Kristian Radan,&nbsp;Dominik Daisenberger,&nbsp;Joseph Hriljac,&nbsp;Nico Giordano,&nbsp;Matic Lozinšek,&nbsp;Simon Parsons","doi":"10.1107/S2052252526003751","DOIUrl":"10.1107/S2052252526003751","url":null,"abstract":"<div><div>The structural behaviour of homoleptic xenon difluoride (XeF₂) com­plexes [<em>M</em>(XeF₂)₆][SbF₆]₂ (<em>M</em> = Cu, Zn) under varying tem­per­a­ture and pressure has been investigated, aiming to resolve the disordered Jahn–Teller distortions in the copper com­plex (<strong>CuSb</strong>). At 200 K, both <strong>CuSb</strong> and its zinc analogue (<strong>ZnSb</strong>) crystallize in a layered CdCl₂-type structure with the space group <em>R</em>3. Upon cooling below 170 (<strong>CuSb</strong>) and 160 K (<strong>ZnSb</strong>), both systems transition to iso­structural phases in <em>P</em>1, with <strong>CuSb</strong> assuming an ordered Jahn–Teller distortion. The transformation is driven by the shortening and optimization of the Xe⋯F inter­molecular contacts, forming stronger and more directional inter­actions, rather than by Jahn–Teller effects alone. This is supported by the observation of similar transitions in the Jahn–Teller-inactive Zn system. High-pressure ex­peri­ments up to ∼2.8 GPa at room tem­per­a­ture show the structural stability of the high-symmetry phases, implicating kinetic barriers to further transformation. Additionally, the synthesis and structural characterization of a novel arsenic analogue, [Zn(XeF₂)₆][AsF₆]₂ (<strong>ZnAs</strong>), reveal similar layered motifs but distinct phase behaviour. Symmetry-mode analyses relate all observed phases through distortions of a common CdCl₂ aristotype.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 4","pages":"Pages 420-432"},"PeriodicalIF":3.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147963657","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":"High-throughput inclined scanning three-dimensional X-ray diffraction microscopy viadual line–beam X-point scanning","authors":"Jaemyung Kim,&nbsp;Yujiro Hayashi,&nbsp;Makina Yabashi","doi":"10.1107/S2052252526004033","DOIUrl":"10.1107/S2052252526004033","url":null,"abstract":"<div><div>Recently developed inclined scanning three-dimensional X-ray diffraction (<em>i</em>-S3DXRD) microscopy enables the non-destructive mapping of crystal orientations in planar-shaped specimens. However, its inherently slow raster-scanning procedure limits its practical applicability. In this work, we achieve a 21-fold reduction in the number of scans, from 51 × 37 to 51 + 37, by introducing a dual line–beam X-point (DLX) scanning mode in <em>i</em>-S3DXRD. Here, 51 and 37 correspond to the numbers of scan steps along the <em>z</em> and <em>x</em> directions under horizontally and vertically elongated X-ray beam illumination, respectively. The DLX approach selectively enhances diffraction peaks corresponding to the inter­section point (X-point) through pixel-wise multiplication of two diffraction images acquired under horizontally and vertically elongated incident beams. Using the reorganized data, we performed multigrain indexing and found that the resulting orientation map agrees with that ob­tained from conventional point–beam raster scanning, demonstrating the validity and time efficiency of the DLX scanning mode.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"13 4","pages":"Pages 433-440"},"PeriodicalIF":3.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147963739","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}