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The structure of Chlamydomonas LOV1 as revealed by time-resolved serial synchrotron crystallography 时间分辨串行同步辐射晶体学揭示的衣藻 LOV1 结构。
IF 2.9 2区 材料科学
IUCrJ Pub Date : 2024-09-01 DOI: 10.1107/S2052252524008327
Marius Schmidt
{"title":"The structure of Chlamydomonas LOV1 as revealed by time-resolved serial synchrotron crystallography","authors":"Marius Schmidt","doi":"10.1107/S2052252524008327","DOIUrl":"10.1107/S2052252524008327","url":null,"abstract":"<div><p>The photo-reaction of the LOV1 domain of the <em>Chlamydomonas reinhardtii</em> phototropin is investigated by room-temperature time-resolved serial crystallography. A covalent adduct forms between the C4a atom of the central flavin-mononucleotide chromophore and a protein cysteine. The structure of the adduct is very similar to that of LOV2 determined 23 years ago from the maidenhair fern Phy3.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 5","pages":"Pages 645-646"},"PeriodicalIF":2.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364020/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142107581","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}
引用次数: 0
Refinement of cryo-EM 3D maps with a self-supervised denoising model: crefDenoiser 利用自监督去噪模型完善冷冻电子显微镜三维图:crefDenoiser。
IF 2.9 2区 材料科学
IUCrJ Pub Date : 2024-09-01 DOI: 10.1107/S2052252524005918
Ishaant Agarwal , Joanna Kaczmar-Michalska , Simon F. Nørrelykke , Andrzej J. Rzepiela
{"title":"Refinement of cryo-EM 3D maps with a self-supervised denoising model: crefDenoiser","authors":"Ishaant Agarwal ,&nbsp;Joanna Kaczmar-Michalska ,&nbsp;Simon F. Nørrelykke ,&nbsp;Andrzej J. Rzepiela","doi":"10.1107/S2052252524005918","DOIUrl":"10.1107/S2052252524005918","url":null,"abstract":"<div><p>State-of-the-art 3D cryo-EM map denoising with a self-supervised neural network model optimized for theoretical noise-free maps is introduced.</p></div><div><p>Cryogenic electron microscopy (cryo-EM) is a pivotal technique for imaging macromolecular structures. However, despite extensive processing of large image sets collected in cryo-EM experiments to amplify the signal-to-noise ratio, the reconstructed 3D protein-density maps are often limited in quality due to residual noise, which in turn affects the accuracy of the macromolecular representation. Here, <em>crefDenoiser</em> is introduced, a denoising neural network model designed to enhance the signal in 3D cryo-EM maps produced with standard processing pipelines. The <em>crefDenoiser</em> model is trained without the need for ‘clean’ ground-truth target maps. Instead, a custom dataset is employed, composed of real noisy protein half-maps sourced from the Electron Microscopy Data Bank repository. Competing with the current state-of-the-art, <em>crefDenoiser</em> is designed to optimize for the theoretical noise-free map during self-supervised training. We demonstrate that our model successfully amplifies the signal across a wide variety of protein maps, outperforming a classic map denoiser and following a network-based sharpening model. Without biasing the map, the proposed denoising method leads to improved visibility of protein structural features, including protein domains, secondary structure elements and modest high-resolution feature restoration.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 5","pages":"Pages 821-830"},"PeriodicalIF":2.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364040/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141788077","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}
引用次数: 0
The crystal structure of olanzapine form III 奥氮平 III 型的晶体结构。
IF 2.9 2区 材料科学
IUCrJ Pub Date : 2024-09-01 DOI: 10.1107/S2052252524007383
Goulielmina Anyfanti , Elena Husanu , Iryna Andrusenko , Danilo Marchetti , Mauro Gemmi
{"title":"The crystal structure of olanzapine form III","authors":"Goulielmina Anyfanti ,&nbsp;Elena Husanu ,&nbsp;Iryna Andrusenko ,&nbsp;Danilo Marchetti ,&nbsp;Mauro Gemmi","doi":"10.1107/S2052252524007383","DOIUrl":"10.1107/S2052252524007383","url":null,"abstract":"<div><p>This paper reports the crystal structure determination of olanzapine form III by 3D electron diffraction, the last unknown anhydrous polymorph in the olanzapine complex polytypism scenario.</p></div><div><p>The antipsychotic drug olanzapine is well known for its complex polymorphism. Although widely investigated, the crystal structure of one of its anhydrous polymorphs, form III, is still unknown. Its appearance, always in concomitance with forms II and I, and the impossibility of isolating it from that mixture, have prevented its structure determination so far. The scenario has changed with the emerging field of 3D electron diffraction (3D ED) and its great advantages in the characterization of polyphasic mixtures of nanosized crystals. In this study, we show how the application of 3D ED allows the <em>ab initio</em> structure determination and dynamical refinement of this elusive crystal structure that remained unknown for more than 20 years. Olanzapine form III is monoclinic and shows a similar but shifted packing with respect to form II. It is remarkably different from the lowest-energy structures predicted by the energy-minimization algorithms of crystal structure prediction.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 5","pages":"Pages 843-848"},"PeriodicalIF":2.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364035/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141788078","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}
引用次数: 0
Capturing the blue-light activated state of the Phot-LOV1 domain from Chlamydomonas reinhardtii using time-resolved serial synchrotron crystallography 利用时间分辨串行同步辐射晶体学捕捉衣藻 Phot-LOV1 结构域的蓝光激活状态。
IF 2.9 2区 材料科学
IUCrJ Pub Date : 2024-09-01 DOI: 10.1107/S2052252524005608
Guillaume Gotthard , Sandra Mous , Tobias Weinert , Raiza Nara Antonelli Maia , Daniel James , Florian Dworkowski , Dardan Gashi , Antonia Furrer , Dmitry Ozerov , Ezequiel Panepucci , Meitian Wang , Gebhard F. X. Schertler , Joachim Heberle , Joerg Standfuss , Przemyslaw Nogly
{"title":"Capturing the blue-light activated state of the Phot-LOV1 domain from Chlamydomonas reinhardtii using time-resolved serial synchrotron crystallography","authors":"Guillaume Gotthard ,&nbsp;Sandra Mous ,&nbsp;Tobias Weinert ,&nbsp;Raiza Nara Antonelli Maia ,&nbsp;Daniel James ,&nbsp;Florian Dworkowski ,&nbsp;Dardan Gashi ,&nbsp;Antonia Furrer ,&nbsp;Dmitry Ozerov ,&nbsp;Ezequiel Panepucci ,&nbsp;Meitian Wang ,&nbsp;Gebhard F. X. Schertler ,&nbsp;Joachim Heberle ,&nbsp;Joerg Standfuss ,&nbsp;Przemyslaw Nogly","doi":"10.1107/S2052252524005608","DOIUrl":"10.1107/S2052252524005608","url":null,"abstract":"<div><p>A crystalline sample of CrLOV1 was optimized for serial crystallography. Time-resolved serial synchrotron crystallography provides high-resolution insights into structural changes of CrLOV1 from Δ<em>t</em> = 2.5 ms up to Δ<em>t</em> = 95 ms post-photoactivation, resolving the geometry of the thio­ether adduct and alteration of the C-terminal region implicated in the signal transduction.</p></div><div><p>Light–oxygen–voltage (LOV) domains are small photosensory flavoprotein modules that allow the conversion of external stimuli (sunlight) into intra­cellular signals responsible for various cell behaviors (<em>e.g.</em> phototropism and chloro­plast relocation). This ability relies on the light-induced formation of a covalent thio­ether adduct between a flavin chromophore and a reactive cysteine from the protein environment, which triggers a cascade of structural changes that result in the activation of a serine/threonine (Ser/Thr) kinase. Recent developments in time-resolved crystallography may allow the activation cascade of the LOV domain to be observed in real time, which has been elusive. In this study, we report a robust protocol for the production and stable delivery of microcrystals of the LOV domain of phototropin Phot-1 from <em>Chlamydomonas reinhardtii</em> (<em>Cr</em>PhotLOV1) with a high-viscosity injector for time-resolved serial synchrotron crystallography (TR-SSX). The detailed process covers all aspects, from sample optimization to data collection, which may serve as a guide for soluble protein preparation for TR-SSX. In addition, we show that the crystals obtained preserve the photoreactivity using infrared spectroscopy. Furthermore, the results of the TR-SSX experiment provide high-resolution insights into structural alterations of <em>Cr</em>PhotLOV1 from Δ<em>t</em> = 2.5 ms up to Δ<em>t</em> = 95 ms post-photoactivation, including resolving the geometry of the thio­ether adduct and the C-terminal region implicated in the signal transduction process.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 5","pages":"Pages 792-808"},"PeriodicalIF":2.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364019/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141734146","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}
引用次数: 0
Texture tomography, a versatile framework to study crystalline texture in 3D 纹理层析技术--研究三维晶体纹理的多功能框架。
IF 2.9 2区 材料科学
IUCrJ Pub Date : 2024-09-01 DOI: 10.1107/S2052252524006547
M. P. K. Frewein , J. Mason , B. Maier , H. Cölfen , A. Medjahed , M. Burghammer , M. Allain , T. A. Grünewald
{"title":"Texture tomography, a versatile framework to study crystalline texture in 3D","authors":"M. P. K. Frewein ,&nbsp;J. Mason ,&nbsp;B. Maier ,&nbsp;H. Cölfen ,&nbsp;A. Medjahed ,&nbsp;M. Burghammer ,&nbsp;M. Allain ,&nbsp;T. A. Grünewald","doi":"10.1107/S2052252524006547","DOIUrl":"10.1107/S2052252524006547","url":null,"abstract":"<div><p>The crystallographic texture is a key feature of crystalline organization in materials, yet no technique exists to locally characterize complex textured materials in 3D. In this manuscript, we present <em>Texture Tomography</em> (<em>TexTOM</em>) as a computational tool to provide full 3D texture information from X-ray diffraction measurements.</p></div><div><p>Crystallographic texture is a key organization feature of many technical and biological materials. In these materials, especially hierarchically structured ones, the preferential alignment of the nano constituents heavily influences the macroscopic behavior of the material. To study local crystallographic texture with both high spatial and angular resolution, we developed <em>Texture Tomography</em> (<em>TexTOM</em>). This approach allows the user to model the diffraction data of polycrystalline materials using the full reciprocal space of the crystal ensemble and describe the texture in each voxel via an orientation distribution function, hence it provides 3D reconstructions of the local texture by measuring the probabilities of all crystal orientations. The <em>TexTOM</em> approach addresses limitations associated with existing models: it correlates the intensities from several Bragg reflections, thus reducing ambiguities resulting from symmetry. Further, it yields quantitative probability distributions of local real space crystal orientations without further assumptions about the sample structure. Finally, its efficient mathematical formulation enables reconstructions faster than the time scale of the experiment. This manuscript presents the mathematical model, the inversion strategy and its current experimental implementation. We show characterizations of simulated data as well as experimental data obtained from a synthetic, inorganic model sample: the silica–witherite biomorph. <em>TexTOM</em> provides a versatile framework to reconstruct 3D quantitative texture information for polycrystalline samples; it opens the door for unprecedented insights into the nanostructural makeup of natural and technical materials.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 5","pages":"Pages 809-820"},"PeriodicalIF":2.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364025/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141751773","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}
引用次数: 0
A predicted model-aided one-step classification–multireconstruction algorithm for X-rayfree-electron laser single-particle imaging 用于 X 射线自由电子激光单粒子成像的预测模型辅助一步分类多重构算法。
IF 2.9 2区 材料科学
IUCrJ Pub Date : 2024-09-01 DOI: 10.1107/S2052252524007851
Zhichao Jiao , Zhi Geng , Wei Ding
{"title":"A predicted model-aided one-step classification–multireconstruction algorithm for X-rayfree-electron laser single-particle imaging","authors":"Zhichao Jiao ,&nbsp;Zhi Geng ,&nbsp;Wei Ding","doi":"10.1107/S2052252524007851","DOIUrl":"10.1107/S2052252524007851","url":null,"abstract":"<div><p>A predicted model-aided one-step classification–multireconstruction algorithm for X-ray free-electron laser single-particle imaging is proposed. The algorithm is capable of processing mixed diffraction patterns from multiple molecules, classifying diffraction patterns by different molecules, determining their orientations and reconstructing multiple 3D diffraction intensities, in one step.</p></div><div><p>Ultrafast, high-intensity X-ray free-electron lasers can perform diffraction imaging of single protein molecules. Various algorithms have been developed to determine the orientation of each single-particle diffraction pattern and reconstruct the 3D diffraction intensity. Most of these algorithms rely on the premise that all diffraction patterns originate from identical protein molecules. However, in actual experiments, diffraction patterns from multiple different molecules may be collected simultaneously. Here, we propose a predicted model-aided one-step classification–multireconstruction algorithm that can handle mixed diffraction patterns from various molecules. The algorithm uses predicted structures of different protein molecules as templates to classify diffraction patterns based on correlation coefficients and determines orientations using a correlation maximization method. Tests on simulated data demonstrated high accuracy and efficiency in classification and reconstruction.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 5","pages":"Pages 891-900"},"PeriodicalIF":2.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364030/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142080327","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}
引用次数: 0
Binding structures of SERF1a with NT17-polyQ peptides of huntingtin exon 1 revealed by SEC-SWAXS, NMR and molecular simulation 通过SEC-SWAXS、核磁共振和分子模拟揭示SERF1a与亨廷基因外显子1的NT17-polyQ肽的结合结构。
IF 2.9 2区 材料科学
IUCrJ Pub Date : 2024-09-01 DOI: 10.1107/S2052252524006341
Tien-Chang Lin , Orion Shih , Tien-Ying Tsai , Yi-Qi Yeh , Kuei-Fen Liao , Bradley W. Mansel , Ying-Jen Shiu , Chi-Fon Chang , An-Chung Su , Yun-Ru Chen , U-Ser Jeng
{"title":"Binding structures of SERF1a with NT17-polyQ peptides of huntingtin exon 1 revealed by SEC-SWAXS, NMR and molecular simulation","authors":"Tien-Chang Lin ,&nbsp;Orion Shih ,&nbsp;Tien-Ying Tsai ,&nbsp;Yi-Qi Yeh ,&nbsp;Kuei-Fen Liao ,&nbsp;Bradley W. Mansel ,&nbsp;Ying-Jen Shiu ,&nbsp;Chi-Fon Chang ,&nbsp;An-Chung Su ,&nbsp;Yun-Ru Chen ,&nbsp;U-Ser Jeng","doi":"10.1107/S2052252524006341","DOIUrl":"10.1107/S2052252524006341","url":null,"abstract":"<div><p>Binding structures of SERF1a with the N-terminal fragment of huntingtin exon 1 and NT17-polyQ peptides are revealed using an integrated analysis of size-exclusion-column-based small- and wide-angle X-ray scattering (SEC-SWAXS), NMR, and molecular simulation.</p></div><div><p>The aberrant fibrillization of huntingtin exon 1 (Httex1) characterized by an expanded polyglutamine (polyQ) tract is a defining feature of Huntington’s disease, a neurodegenerative disorder. Recent investigations underscore the involvement of a small EDRK-rich factor 1a (SERF1a) in promoting Httex1 fibrillization through interactions with its N terminus. By establishing an integrated approach with size-exclusion-column-based small- and wide-angle X-ray scattering (SEC-SWAXS), NMR, and molecular simulations using <em>Rosetta</em>, the analysis here reveals a tight binding of two NT17 fragments of Httex1 (comprising the initial 17 amino acids at the N terminus) to the N-terminal region of SERF1a. In contrast, examination of the complex structure of SERF1a with a coiled NT17-polyQ peptide (33 amino acids in total) indicates sparse contacts of the NT17 and polyQ segments with the N-terminal side of SERF1a. Furthermore, the integrated SEC-SWAXS and molecular-simulation analysis suggests that the coiled NT17 segment can transform into a helical conformation when associated with a polyQ segment exhibiting high helical content. Intriguingly, NT17-polyQ peptides with enhanced secondary structures display diminished interactions with SERF1a. This insight into the conformation-dependent binding of NT17 provides clues to a catalytic association mechanism underlying SERF1a’s facilitation of Httext1 fibrillization.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 5","pages":"Pages 849-858"},"PeriodicalIF":2.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364024/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141906686","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}
引用次数: 0
Exploring serial crystallography for drug discovery 探索用于药物发现的系列晶体学。
IF 2.9 2区 材料科学
IUCrJ Pub Date : 2024-09-01 DOI: 10.1107/S2052252524006134
A. Dunge , C. Phan , O. Uwangue , M. Bjelcic , J. Gunnarsson , G. Wehlander , H. Käck , G. Brändén
{"title":"Exploring serial crystallography for drug discovery","authors":"A. Dunge ,&nbsp;C. Phan ,&nbsp;O. Uwangue ,&nbsp;M. Bjelcic ,&nbsp;J. Gunnarsson ,&nbsp;G. Wehlander ,&nbsp;H. Käck ,&nbsp;G. Brändén","doi":"10.1107/S2052252524006134","DOIUrl":"10.1107/S2052252524006134","url":null,"abstract":"<div><p>In this work, serial crystallography is applied to a drug discovery target and the room-temperature ligand-bound complexes are used to explore temperature-dependent structural differences.</p></div><div><p>Structure-based drug design is highly dependent on the availability of structures of the protein of interest in complex with lead compounds. Ideally, this information can be used to guide the chemical optimization of a compound into a pharmaceutical drug candidate. A limitation of the main structural method used today – conventional X-ray crystallography – is that it only provides structural information about the protein complex in its frozen state. Serial crystallography is a relatively new approach that offers the possibility to study protein structures at room temperature (RT). Here, we explore the use of serial crystallography to determine the structures of the pharmaceutical target, soluble epoxide hydro­lase. We introduce a new method to screen for optimal microcrystallization conditions suitable for use in serial crystallography and present a number of RT ligand-bound structures of our target protein. From a comparison between the RT structural data and previously published cryo-temperature structures, we describe an example of a temperature-dependent difference in the ligand-binding mode and observe that flexible loops are better resolved at RT. Finally, we discuss the current limitations and potential future advances of serial crystallography for use within pharmaceutical drug discovery.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 5","pages":"Pages 831-842"},"PeriodicalIF":2.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364032/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141788076","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}
引用次数: 0
Structure of Aquifex aeolicus lumazine synthase by cryo-electron microscopy to 1.42 Å resolution 通过分辨率为 1.42 Å 的低温电子显微镜观察 Aquifex aeolicus 鲁马嗪合成酶的结构。
IF 2.9 2区 材料科学
IUCrJ Pub Date : 2024-09-01 DOI: 10.1107/S2052252524005530
{"title":"Structure of Aquifex aeolicus lumazine synthase by cryo-electron microscopy to 1.42 Å resolution","authors":"","doi":"10.1107/S2052252524005530","DOIUrl":"10.1107/S2052252524005530","url":null,"abstract":"<div><p>A near-atomic resolution map was obtained for lumazine synthase while benchmarking a new microscope. At this resolution, waters, ligands and hydrogens were visible. A detailed outline of the methods used is presented that can employed for any single-particle cryo-EM experiment.</p></div><div><p>Single-particle cryo-electron microscopy (cryo-EM) has become an essential structural determination technique with recent hardware developments making it possible to reach atomic resolution, at which individual atoms, including hydrogen atoms, can be resolved. In this study, we used the enzyme involved in the penultimate step of riboflavin biosynthesis as a test specimen to benchmark a recently installed microscope and determine if other protein complexes could reach a resolution of 1.5 Å or better, which so far has only been achieved for the iron carrier ferritin. Using state-of-the-art microscope and detector hardware as well as the latest software techniques to overcome microscope and sample limitations, a 1.42 Å map of <em>Aquifex aeolicus</em> lumazine synthase (AaLS) was obtained from a 48 h microscope session. In addition to water molecules and ligands involved in the function of AaLS, we can observe positive density for ∼50% of the hydrogen atoms. A small improvement in the resolution was achieved by Ewald sphere correction which was expected to limit the resolution to ∼1.5 Å for a molecule of this diameter. Our study confirms that other protein complexes can be solved to near-atomic resolution. Future improvements in specimen preparation and protein complex stabilization may allow more flexible macromolecules to reach this level of resolution and should become a priority of study in the field.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 5","pages":"Pages 723-729"},"PeriodicalIF":2.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364023/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141534374","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}
引用次数: 0
Structural characterization of TIR-domain signalosomes through a combination of structural biology approaches 通过结合结构生物学方法确定 TIR-domain信号体的结构特征。
IF 2.9 2区 材料科学
IUCrJ Pub Date : 2024-09-01 DOI: 10.1107/S2052252524007693
Akansha Bhatt , Biswa P. Mishra , Weixi Gu , Mitchell Sorbello , Hongyi Xu , Thomas Ve , Bostjan Kobe
{"title":"Structural characterization of TIR-domain signalosomes through a combination of structural biology approaches","authors":"Akansha Bhatt ,&nbsp;Biswa P. Mishra ,&nbsp;Weixi Gu ,&nbsp;Mitchell Sorbello ,&nbsp;Hongyi Xu ,&nbsp;Thomas Ve ,&nbsp;Bostjan Kobe","doi":"10.1107/S2052252524007693","DOIUrl":"10.1107/S2052252524007693","url":null,"abstract":"<div><p>The TIR (Toll/interleukin-1 receptor) domains are found in proteins with roles in the immune systems of humans, plants and bacteria. A combination of structural methods ranging from X-ray and electron crystallography to cryogenic electron microscopy and nuclear magnetic resonance spectroscopy has been required to understand how these domains contribute to signalling, highlighting the complementarity of different structural approaches.</p></div><div><p>The TIR (Toll/interleukin-1 receptor) domain represents a vital structural element shared by proteins with roles in immunity signalling pathways across phyla (from humans and plants to bacteria). Decades of research have finally led to identifying the key features of the molecular basis of signalling by these domains, including the formation of open-ended (filamentous) assemblies (responsible for the signalling by cooperative assembly formation mechanism, SCAF) and enzymatic activities involving the cleavage of nucleotides. We present a historical perspective of the research that led to this understanding, highlighting the roles that different structural methods played in this process: X-ray crystallography (including serial crystallography), microED (micro-crystal electron diffraction), NMR (nuclear magnetic resonance) spectroscopy and cryo-EM (cryogenic electron microscopy) involving helical reconstruction and single-particle analysis. This perspective emphasizes the complementarity of different structural approaches.</p></div>","PeriodicalId":14775,"journal":{"name":"IUCrJ","volume":"11 5","pages":"Pages 695-707"},"PeriodicalIF":2.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364022/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142080331","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}
引用次数: 0
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