IUCrJ最新文献

{"title":"Microcrystals in structural biology: small samples, big insights","authors":"Dominik Oberthür","doi":"10.1107/S2052252525003653","DOIUrl":"10.1107/S2052252525003653","url":null,"abstract":"<div><div>Microcrystals are transforming structural biology by enabling high-resolution structures and time-resolved insights from samples once deemed too small. This commentary highlights recent advances in microfocus X-ray and MicroED methods, emphasizing their growing role as powerful and complementary tools in modern macromolecular crystallography.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 3","pages":"Pages 259-261"},"PeriodicalIF":2.9,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143902097","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":"Additive-driven microwave crystallization of tyramine polymorphs and salts: a quantum crystallography perspective","authors":"Szymon Grabowski ,&nbsp;Klaudia Nowakowska ,&nbsp;Helena Butkiewicz ,&nbsp;Anna Hoser ,&nbsp;Aleksandra Wesełucha-Birczyńska ,&nbsp;Tomasz Seidler ,&nbsp;Paulina Moskal ,&nbsp;Marlena Gryl","doi":"10.1107/S2052252525002210","DOIUrl":"10.1107/S2052252525002210","url":null,"abstract":"<div><div>This study reveals how additives and microwave radiation influence the crystallization of new tyramine polymorphs and their cocrystallization with barbital. The findings provide insights into polymorph stability and offer potential applications in molecular encapsulation and optical materials.</div></div><div><div>Polymorphism – the ability of a compound to exist in multiple crystalline forms – needs to be carefully considered in the design of functional materials, particularly in the context of cocrystallization. Tyramine, a biogenic amine, is a promising candidate for polymorph exploration due to its conformational flexibility and ability to form salts. In this study, we investigate the crystallization of tyramine polymorphs using additives and microwave-assisted techniques. Our findings reveal the formation of a new tyramine polymorph and two distinct salts, highlighting the impact of microwave radiation and additive-driven crystallization on polymorph stability and molecular encapsulation. The study demonstrates that the triclinic tyramine polymorph (T2) is thermodynamically more stable due to its lower electronic energy, whereas the monoclinic form (T1) features slightly stronger intermolecular interactions. Over time, in solution, crystals of barbital–tyramine salts (C1 and C2) begin to form, providing an opportunity to assess structural evolution. Optical properties calculations show significant maximum linear birefringence values (0.164 and 0.255) for two polymorphs of tyramine, whereas for C1, this value decreases to 0.095.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 3","pages":"Pages 403-416"},"PeriodicalIF":2.9,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143901999","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":"Instrumentation and methods for efficient time-resolved X-ray crystallography of biomolecular systems with sub-10 ms time resolution","authors":"John A. Indergaard ,&nbsp;Kashfia Mahmood ,&nbsp;Leo Gabriel ,&nbsp;Gary Zhong ,&nbsp;Adam Lastovka ,&nbsp;Matthew J. McLeod ,&nbsp;Robert E. Thorne","doi":"10.1107/S205225252500288X","DOIUrl":"10.1107/S205225252500288X","url":null,"abstract":"<div><div>Methods and instrumentation for reaction initiation via mixing followed by rapid cooling allow sample-efficient time-resolved crystallographic studies with sub-10 ms time resolution. The instrumentation is robust, amenable to diverse samples, cost-effective and enables the remote collection of time-resolved X-ray data using standard sample supports and high-throughput cryocrystallography beamlines.</div></div><div><div>Time-resolved X-ray crystallography has great promise to illuminate structure–function relations and key steps of enzymatic reactions with atomic resolution. The dominant methods for chemically-initiated reactions require complex instrumentation at the X-ray beamline, significant effort to operate and maintain this instrumentation, and enormous numbers (∼10⁵–10⁹) of crystals per time point. We describe instrumentation and methods that enable high-throughput time-resolved study of biomolecular systems using standard crystallography sample supports and mail-in X-ray data collection at standard high-throughput cryocrystallography synchrotron beamlines. The instrumentation allows rapid reaction initiation by mixing of crystals and substrate/ligand solution, rapid capture of structural states via thermal quenching with no pre-cooling perturbations, and yields time resolutions in the single-millisecond range, comparable to the best achieved by any non-photo-initiated method in both crystallography and cryo-electron microscopy. Our approach to reaction initiation has the advantages of simplicity, robustness, low cost, adaptability to diverse ligand solutions and small minimum volume requirements, making it well suited to routine laboratory use and to high-throughput screening. We report the detailed characterization of instrument performance, present structures of binding of <em>N</em>-acetylglucosamine to lysozyme at time points from 8 ms to 2 s determined using only one crystal per time point, and discuss additional improvements that will push time resolution toward 1 ms.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 3","pages":"Pages 372-383"},"PeriodicalIF":2.9,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143902093","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":"Peptide bonds strike back","authors":"Ashwin Chari","doi":"10.1107/S2052252525003604","DOIUrl":"10.1107/S2052252525003604","url":null,"abstract":"<div><div>Recent advances in protein design and protein structure prediction have questioned whether experimental structural biology still has a role to play in research today. The article by Panjikar and Weiss [(2025). <em>IUCrJ</em>, <strong>12</strong>, 307–321] partially answers this question and alludes to a role still to be played by structural biology. Several properties of peptide bonds, likely important for function, are described that are absent in protein design and predicted protein structures, and that have largely been overlooked by the structural biology community.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 3","pages":"Pages 257-258"},"PeriodicalIF":2.9,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143902098","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":"Accurate temperature dependence of structure factors of l-alanine and taurine for quantum crystallography","authors":"Mibuki Hayashi ,&nbsp;Takashi Nishioka ,&nbsp;Hidetaka Kasai ,&nbsp;Eiji Nishibori","doi":"10.1107/S2052252525002647","DOIUrl":"10.1107/S2052252525002647","url":null,"abstract":"<div><div>The temperature dependence of accurate structure factors of <span>l</span>-alanine and taurine was measured at the SPring-8 BL02B1 beamline. The quality of the structure factors is evaluated by charge density and quantum crystallographic studies. The effects of small amounts of twinning on the charge density study for taurine are also described.</div></div><div><div>Multi-temperature high-quality structure factors of <span>l</span>-alanine and taurine were re-measured at the SPring-8 BL02B1 beamline for method development in quantum crystallography. The quality of the data was evaluated by comparison with previous studies. In the case of taurine, we found that the data quality was highly affected by small amounts of twinning. Residual electron density around the sulfur atoms observed in a previous study [Hibbs <em>et al.</em> (2003). <em>Chem. A Eur. J.</em><strong>9</strong>, 1075–1084] disappeared with the re-measured data. X-ray wavefunction refinements were carried out on these data. The difference electron density between the X-ray constrained wavefunction (XCW) results and the Hartree–Fock charge density showed a positive difference electron density around the nucleus and a negative difference electron density between the bonds. These features were consistent with those reported [Hupf <em>et al.</em> (2023). <em>J. Chem. Phys.</em><strong>158</strong>, 124103]. It was found that the deformation density around the nucleus and between bonds due to electron correlations and electronic polarization could be confirmed by the XCW method using the present structure factors.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 3","pages":"Pages 384-392"},"PeriodicalIF":2.9,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143902102","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":"Small but mighty: the power of microcrystals in structural biology","authors":"Courtney J. Tremlett ,&nbsp;Jack Stubbs ,&nbsp;William S. Stuart ,&nbsp;Patrick D. Shaw Stewart ,&nbsp;Jonathan West ,&nbsp;Allen M. Orville ,&nbsp;Ivo Tews ,&nbsp;Nicholas J. Harmer","doi":"10.1107/S2052252525001484","DOIUrl":"10.1107/S2052252525001484","url":null,"abstract":"<div><div>Developments in macromolecular crystallography now allow the use of microcrystals for structural analysis through advanced beamlines and techniques such as microcrystal electron diffraction and room-temperature crystallography. This review addresses methods of matching microcrystal preparation and sample delivery. The use of microcrystals enhances the possibilities in fields such as time-resolved crystallography.</div></div><div><div>Advancements in macromolecular crystallography, driven by improved sources and cryocooling techniques, have enabled the use of increasingly smaller crystals for structure determination, with microfocus beamlines now widely accessible. Initially developed for challenging samples, these techniques have culminated in advanced beamlines such as VMXm. Here, an <em>in vacuo</em> sample environment improves the signal-to-noise ratio in X-ray diffraction experiments, and thus enables the use of submicrometre crystals. The advancement of techniques such as microcrystal electron diffraction (MicroED) for atomic-level insights into charged states and hydrogen positions, along with room-temperature crystallography to observe physiological states via serial crystallography, has driven a resurgence in the use of microcrystals. Reproducibly preparing small crystals, especially from samples that typically yield larger crystals, requires considerable effort, as no one singular approach guarantees optimal crystals for every technique. This review discusses methods for generating such small crystals, including mechanical crushing and batch crystallization with seeding, and evaluates their compatibility with microcrystal data-collection modalities. Additionally, we examine sample-delivery methods, which are crucial for selecting appropriate crystallization strategies. Establishing reliable protocols for sample preparation and delivery opens new avenues for macromolecular crystallography, particularly in the rapidly progressing field of time-resolved crystallography.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 3","pages":"Pages 262-279"},"PeriodicalIF":2.9,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143624589","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 origin of synthons and supramolecular motifs: beyond atoms and functional groups","authors":"Rahul Shukla ,&nbsp;Emmanuel Aubert ,&nbsp;Mariya Brezgunova ,&nbsp;Sébastien Lebègue ,&nbsp;Marc Fourmigué ,&nbsp;Enrique Espinosa","doi":"10.1107/S2052252525001447","DOIUrl":"10.1107/S2052252525001447","url":null,"abstract":"&lt;div&gt;&lt;div&gt;This study establishes that hydrogen-, halogen- and chalcogen-bonding intermolecular and non-covalent intramolecular interactions are driven by a face-to-face orientation of electrophilic (charge-depleted) and nucleophilic (charge-concentrated) regions, which is the origin of the specific geometries found in synthons and supramolecular motifs.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;div&gt;A four-membered &lt;em&gt;R&lt;/em&gt;&lt;sub&gt;2&lt;/sub&gt;&lt;sup&gt;2&lt;/sup&gt;(4) supramolecular motif formed by S⋯S and S⋯I chalcogen-bonding interactions in the crystal structure of 4-iodo-1,3-di­thiol-2-one (C&lt;sub&gt;3&lt;/sub&gt;HIOS&lt;sub&gt;2&lt;/sub&gt;, IDT) is analysed and compared with a similar &lt;em&gt;R&lt;/em&gt;&lt;sub&gt;2&lt;/sub&gt;&lt;sup&gt;2&lt;/sup&gt;(4) motif (stabilized by Se⋯Se and Se⋯O chalcogen bonds) observed in the previously reported crystal structure of selena­phthalic anhydride (C&lt;sub&gt;8&lt;/sub&gt;H&lt;sub&gt;4&lt;/sub&gt;O&lt;sub&gt;2&lt;/sub&gt;Se, SePA) through detailed charge density analysis. Our investigation reveals that the chalcogen-bonding interactions participating in the &lt;em&gt;R&lt;/em&gt;&lt;sub&gt;2&lt;/sub&gt;&lt;sup&gt;2&lt;/sup&gt;(4) motifs observed in the two structures have the same characteristic orientation of local electrostatic electrophilic⋯nucleophilic interactions while involving different types of atoms. We carried out Cambridge Structural Database searches for synthons and supramolecular motifs involving chalcogen-, halogen- and hydrogen-bonding (ChB, XB and HB) interactions. Geometrical characterizations and topological analyses of the electron density ρ(&lt;strong&gt;r&lt;/strong&gt;) and its negative Laplacian function [&lt;em&gt;L&lt;/em&gt;(&lt;strong&gt;r&lt;/strong&gt;) = −∇&lt;sup&gt;2&lt;/sup&gt;ρ(&lt;strong&gt;r&lt;/strong&gt;)] indicate that all the bonding interactions forming the motifs are driven by local electrophilic⋯nucleophilic interactions between complementary charge concentration (CC) and charge depletion (CD) sites present in the valence shells of the atoms, regardless of the atoms and functional groups involved. The graph-set assignment &lt;em&gt;G&lt;/em&gt;&lt;sub&gt;&lt;em&gt;d&lt;/em&gt;&lt;/sub&gt;&lt;sup&gt;&lt;em&gt;a&lt;/em&gt;&lt;/sup&gt;(&lt;em&gt;n&lt;/em&gt;) (&lt;em&gt;G&lt;/em&gt; = &lt;em&gt;C&lt;/em&gt;, &lt;em&gt;R&lt;/em&gt;, &lt;em&gt;D&lt;/em&gt; or &lt;em&gt;S&lt;/em&gt;), formerly developed by Etter [&lt;em&gt;Acc. Chem. Res.&lt;/em&gt; (1990), &lt;strong&gt;23&lt;/strong&gt;, 120–126] for HB interactions, is a convenient way to describe the connectivity in supramolecular motifs based on electrophilic⋯nucleophilic interactions (such as ChB, XB and HB interactions), exchanging the number of atomic acceptors (&lt;em&gt;a&lt;/em&gt;) and donors (&lt;em&gt;d&lt;/em&gt;) with the number of nucleophilic (&lt;em&gt;n&lt;/em&gt;: CC) and electrophilic (&lt;em&gt;e&lt;/em&gt;: CD) sites, and the number of atoms building the motif &lt;em&gt;n&lt;/em&gt; by &lt;em&gt;m&lt;/em&gt;, leading to the new graph-set assignment &lt;em&gt;G&lt;/em&gt;&lt;sub&gt;&lt;em&gt;e&lt;/em&gt;&lt;/sub&gt;&lt;sup&gt;&lt;em&gt;n&lt;/em&gt;&lt;/sup&gt;(&lt;em&gt;m&lt;/em&gt;) (&lt;em&gt;G&lt;/em&gt; = &lt;em&gt;C&lt;/em&gt;, &lt;em&gt;R&lt;/em&gt;, &lt;em&gt;D&lt;/em&gt; or &lt;em&gt;S&lt;/em&gt;). Geometrical preferences in the molecular assembly of synthons and other supramolecular motifs are governed by the relative positions of CC and CD sites through CC⋯CD interactions that, in most cases, align with the internuclear directions within a &lt;15° range de","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 3","pages":"Pages 334-357"},"PeriodicalIF":2.9,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143795300","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":"Code dependence of calculated crystalline electron densities. Possible lessons for quantum crystallography","authors":"Bruno Landeros-Rivera ,&nbsp;Julia Contreras-García ,&nbsp;Ángel Martín Pendás","doi":"10.1107/S2052252525001721","DOIUrl":"10.1107/S2052252525001721","url":null,"abstract":"<div><div>The development of quantum crystallography depends on the availability of reliable theoretical electron densities. This work demonstrates a non-negligible code dependence of these densities and warns against their blind use.</div></div><div><div>The use of electronic structure methods in crystallographic data analysis, the now well known field of quantum crystallography, aids in the solution of several problems in X-ray diffraction refinement, as well as opening new avenues to access a whole new set of experimentally available observables. A key ingredient in quantum crystallography is the theoretically derived electron density, ρ, obtained from standard electronic structure codes. Here, we introduce a factor that has not been carefully considered until now. As we demonstrate, theoretically derived ρ values depend not only on the set of computational conditions used to obtain them but also on the particular computational code selected for this task. We recommend that all quantum crystallographers carefully check the convergence of ρ before undertaking any serious study.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 3","pages":"Pages 295-306"},"PeriodicalIF":2.9,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143730036","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":"Solid-state calculations for iterative refinement in quantum crystallography using the multipole model","authors":"Michael Patzer ,&nbsp;Christian W. Lehmann","doi":"10.1107/S2052252525002040","DOIUrl":"10.1107/S2052252525002040","url":null,"abstract":"<div><div>This work presents a new iterative refinement method, comparable to Hirshfeld atom refinement, using the Hansen–Coppens multipole model charge density description to obtain accurate atomic coordinates and atomic displacements based on <em>CRYSTAL17</em> periodic boundary calculations. The refinement, performed using the Python code <em>ReCrystal</em>, allows the user to explore the full periodic charge density in the crystalline solid state for charge density analysis of weak interactions.</div></div><div><div>A quantum crystallographic refinement methodology has been developed using theoretical multipole parameters generated directly from solid-state calculations using the <em>CRYSTAL17</em> program. This refinement method is comparable to other transferable form factor approaches, such as the Invariom model, but in contrast to the Hirshfeld atom refinement, it uses theoretical multipole parameters to describe the electron density from a solid-state calculation performed with <em>CRYSTAL17</em> in an iterative refinement procedure. For this purpose, a Python3 code named <em>ReCrystal</em> has been developed. To start <em>ReCrystal</em>, a CIF, a Gaussian basis set, a DFT functional and the number of CPUs must be defined. The Pack–Monkhorst and Gilat shrinking factors, which define a lattice in the first Brillouin zone, must also be specified. After <em>k</em>-point sampling, <em>CRYSTAL17</em> calculates structure factors directly from the static electron density. Multipole parameters are generated from these structure factors using the <em>XD</em> program and are fixed during least-squares refinement. The refinement of the xylitol molecular crystal has shown that the hydrogen atom positions can be determined with reasonable agreement to those obtained in the neutron diffraction experiment. This indicates that the periodic boundary condition in <em>ReCrystal</em> is an improvement over gas phase refinement with HAR. The multipole parameters obtained from <em>ReCrystal</em> can be used for further charge density studies especially if weak interactions are the focus. In this work, we demonstrate the performance of <em>ReCrystal</em> on molecular crystals of the small molecules <span>d</span>/<span>l</span>-serine and xylitol with weak hydrogen-bonding motifs using multipole refinement. The advantage of this approach is that multipole parameters can be obtained from high-resolution calculated diffraction data, no database is required, and errors due to the model and errors resulting from the experiment are clearly separated.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 3","pages":"Pages 322-333"},"PeriodicalIF":2.9,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143780089","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 large, general and modular DARPin–apoferritin scaffold enables the visualization of small proteins by cryo-EM","authors":"Xin Lu ,&nbsp;Ming Yan ,&nbsp;Yang Cai ,&nbsp;Xi Song ,&nbsp;Huan Chen ,&nbsp;Mengtan Du ,&nbsp;Zhenyi Wang ,&nbsp;Jia’an Li ,&nbsp;Liwen Niu ,&nbsp;Fuxing Zeng ,&nbsp;Quan Hao ,&nbsp;Hongmin Zhang","doi":"10.1107/S2052252525003021","DOIUrl":"10.1107/S2052252525003021","url":null,"abstract":"<div><div>This study introduces a modular scaffold strategy utilizing designed ankyrin-repeat proteins (DARPins) and a symmetric apoferritin base to overcome size limitations in single-particle cryo-EM, enabling near-atomic-resolution structural determination of medium-sized proteins like GFP and MBP. The high-symmetry, near-spherical scaffold not only resolves the common preferred-orientation challenges in single-particle cryo-EM but also reduces data-processing demands, offering a versatile platform for structural analysis of diverse proteins.</div></div><div><div>Single-particle cryo-electron microscopy (cryo-EM) has emerged as an indispensable technique in structural biology that is pivotal for deciphering protein architectures. However, the medium-sized proteins (30–40 kDa) that are prevalent in both eukaryotic and prokaryotic organisms often elude the resolving capabilities of contemporary cryo-EM methods. To address this challenge, we engineered a scaffold strategy that securely anchors proteins of interest to a robust, symmetric base via a selective adapter. Our most efficacious constructs, namely models 4 and 6c, feature a designed ankyrin-repeat protein (DARPin) rigidly linked to an octahedral human apoferritin via a helical linker. By utilizing these large, highly symmetric scaffolds (∼1 MDa), we achieved near-atomic-resolution cryo-EM structures of green fluorescent protein (GFP) and maltose-binding protein (MBP), revealing nearly all side-chain densities of GFP and the distinct structural features of MBP. The modular design of our scaffold allows the adaptation of new DARPins through minor amino-acid-sequence modifications, enabling the binding and visualization of a diverse array of proteins. The high symmetry and near-spherical shape of the scaffold not only mitigates the prevalent challenge of preferred particle orientation in cryo-EM but also significantly reduces the demands of image collection and data processing. This approach presents a versatile solution, breaking through the size constraints that have traditionally limited single-particle cryo-EM.</div></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"12 3","pages":"Pages 393-402"},"PeriodicalIF":2.9,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143902094","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}