Acta Crystallographica. Section D, Structural Biology最新文献_第5页

Tomo Live: an on-the-fly reconstruction pipeline to judge data quality for cryo-electron tomography workflows. Tomo Live：用于判断低温电子断层成像工作流程数据质量的即时重建管道。

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-04-01 Epub Date: 2024-03-21 DOI: 10.1107/S2059798324001840

Maxime Comet, Patricia M Dijkman, Reint Boer Iwema, Tilman Franke, Simonas Masiulis, Ruud Schampers, Oliver Raschdorf, Fanis Grollios, Edward E Pryor, Ieva Drulyte

{"title":"Tomo Live: an on-the-fly reconstruction pipeline to judge data quality for cryo-electron tomography workflows.","authors":"Maxime Comet, Patricia M Dijkman, Reint Boer Iwema, Tilman Franke, Simonas Masiulis, Ruud Schampers, Oliver Raschdorf, Fanis Grollios, Edward E Pryor, Ieva Drulyte","doi":"10.1107/S2059798324001840","DOIUrl":"10.1107/S2059798324001840","url":null,"abstract":"Data acquisition and processing for cryo-electron tomography can be a significant bottleneck for users. To simplify and streamline the cryo-ET workflow, Tomo Live, an on-the-fly solution that automates the alignment and reconstruction of tilt-series data, enabling real-time data-quality assessment, has been developed. Through the integration of Tomo Live into the data-acquisition workflow for cryo-ET, motion correction is performed directly after each of the acquired tilt angles. Immediately after the tilt-series acquisition has completed, an unattended tilt-series alignment and reconstruction into a 3D volume is performed. The results are displayed in real time in a dedicated remote web platform that runs on the microscope hardware. Through this web platform, users can review the acquired data (aligned stack and 3D volume) and several quality metrics that are obtained during the alignment and reconstruction process. These quality metrics can be used for fast feedback for subsequent acquisitions to save time. Parameters such as Alignment Accuracy, Deleted Tilts and Tilt Axis Correction Angle are visualized as graphs and can be used as filters to export only the best tomograms (raw data, reconstruction and intermediate data) for further processing. Here, the Tomo Live algorithms and workflow are described and representative results on several biological samples are presented. The Tomo Live workflow is accessible to both expert and non-expert users, making it a valuable tool for the continued advancement of structural biology, cell biology and histology.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"247-258"},"PeriodicalIF":2.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10994173/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140178911","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

XFEL structure of carbonic anhydrase II: a comparative study of XFEL, NMR, X-ray and neutron structures. 碳酸酐酶 II 的 XFEL 结构：XFEL、核磁共振、X 射线和中子结构的比较研究。

IF 2.2 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-03-01 Epub Date: 2024-02-27 DOI: 10.1107/S2059798324000482

Joshua A Hull, Cheol Lee, Jin Kyun Kim, Seon Woo Lim, Jaehyun Park, Sehan Park, Sang Jae Lee, Gisu Park, Intae Eom, Minseok Kim, HyoJung Hyun, Jacob E Combs, Jacob T Andring, Carrie Lomelino, Chae Un Kim, Robert McKenna

引用次数: 0

Characterization of novel mevalonate kinases from the tardigrade Ramazzottius varieornatus and the psychrophilic archaeon Methanococcoides burtonii. 新型甲羟戊酸激酶的表征：来自沙蜥（Ramazzottius varieornatus）和嗜灵古菌（Methanococcoides burtonii）。

IF 2.2 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-03-01 Epub Date: 2024-02-27 DOI: 10.1107/S2059798324001360

Lygie Esquirol, Janet Newman, Tom Nebl, Colin Scott, Claudia Vickers, Frank Sainsbury, Thomas S Peat

引用次数: 0

A service-based approach to cryoEM facility processing pipelines at eBIC. eBIC 的低温电子显微镜设施处理管道采用基于服务的方法。

IF 2.2 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-03-01 Epub Date: 2024-02-20 DOI: 10.1107/S2059798324000986

Anna Horstmann, Stephen Riggs, Yuriy Chaban, Daniel K Clare, Guilherme de Freitas, David Farmer, Andrew Howe, Kyle L Morris, Daniel Hatton

{"title":"A service-based approach to cryoEM facility processing pipelines at eBIC.","authors":"Anna Horstmann, Stephen Riggs, Yuriy Chaban, Daniel K Clare, Guilherme de Freitas, David Farmer, Andrew Howe, Kyle L Morris, Daniel Hatton","doi":"10.1107/S2059798324000986","DOIUrl":"10.1107/S2059798324000986","url":null,"abstract":"Electron cryo-microscopy image-processing workflows are typically composed of elements that may, broadly speaking, be categorized as high-throughput workloads which transition to high-performance workloads as preprocessed data are aggregated. The high-throughput elements are of particular importance in the context of live processing, where an optimal response is highly coupled to the temporal profile of the data collection. In other words, each movie should be processed as quickly as possible at the earliest opportunity. The high level of disconnected parallelization in the high-throughput problem directly allows a completely scalable solution across a distributed computer system, with the only technical obstacle being an efficient and reliable implementation. The cloud computing frameworks primarily developed for the deployment of high-availability web applications provide an environment with a number of appealing features for such high-throughput processing tasks. Here, an implementation of an early-stage processing pipeline for electron cryotomography experiments using a service-based architecture deployed on a Kubernetes cluster is discussed in order to demonstrate the benefits of this approach and how it may be extended to scenarios of considerably increased complexity.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"174-180"},"PeriodicalIF":2.2,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10910546/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139904730","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","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 mycothiol disulfide reductase (Mtr) provides mechanistic insight into the specific low-molecular-weight thiol reductase activity of Actinobacteria. 霉菌硫醇二硫还原酶（Mtr）的晶体结构从机理上揭示了放线菌特异的低分子量硫醇还原酶活性。

IF 2.2 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-03-01 Epub Date: 2024-02-19 DOI: 10.1107/S205979832400113X

Javier Gutiérrez-Fernández, Hans Petter Hersleth, Marta Hammerstad

{"title":"The crystal structure of mycothiol disulfide reductase (Mtr) provides mechanistic insight into the specific low-molecular-weight thiol reductase activity of Actinobacteria.","authors":"Javier Gutiérrez-Fernández, Hans Petter Hersleth, Marta Hammerstad","doi":"10.1107/S205979832400113X","DOIUrl":"10.1107/S205979832400113X","url":null,"abstract":"Low-molecular-weight (LMW) thiols are involved in many processes in all organisms, playing a protective role against reactive species, heavy metals, toxins and antibiotics. Actinobacteria, such as Mycobacterium tuberculosis, use the LMW thiol mycothiol (MSH) to buffer the intracellular redox environment. The NADPH-dependent FAD-containing oxidoreductase mycothiol disulfide reductase (Mtr) is known to reduce oxidized mycothiol disulfide (MSSM) to MSH, which is crucial to maintain the cellular redox balance. In this work, the first crystal structures of Mtr are presented, expanding the structural knowledge and understanding of LMW thiol reductases. The structural analyses and docking calculations provide insight into the nature of Mtrs, with regard to the binding and reduction of the MSSM substrate, in the context of related oxidoreductases. The putative binding site for MSSM suggests a similar binding to that described for the homologous glutathione reductase and its respective substrate glutathione disulfide, but with distinct structural differences shaped to fit the bulkier MSSM substrate, assigning Mtrs as uniquely functioning reductases. As MSH has been acknowledged as an attractive antitubercular target, the structural findings presented in this work may contribute towards future antituberculosis drug development.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"181-193"},"PeriodicalIF":2.2,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10910545/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139899183","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Welcoming five new Co-editors. 欢迎五位新任联合编辑。

IF 2.2 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-03-01 Epub Date: 2024-02-29 DOI: 10.1107/S2059798324002006

Charles S Bond, Elspeth F Garman, Randy J Read

引用次数: 0

Advanced exploitation of unmerged reflection data during processing and refinement with autoPROC and BUSTER. 利用 autoPROC 和 BUSTER，在处理和细化过程中对未合并的反射数据进行高级开发。

IF 2.2 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-03-01 Epub Date: 2024-02-27 DOI: 10.1107/S2059798324001487

Clemens Vonrhein, Claus Flensburg, Peter Keller, Rasmus Fogh, Andrew Sharff, Ian J Tickle, Gérard Bricogne

{"title":"Advanced exploitation of unmerged reflection data during processing and refinement with autoPROC and BUSTER.","authors":"Clemens Vonrhein, Claus Flensburg, Peter Keller, Rasmus Fogh, Andrew Sharff, Ian J Tickle, Gérard Bricogne","doi":"10.1107/S2059798324001487","DOIUrl":"10.1107/S2059798324001487","url":null,"abstract":"The validation of structural models obtained by macromolecular X-ray crystallography against experimental diffraction data, whether before deposition into the PDB or after, is typically carried out exclusively against the merged data that are eventually archived along with the atomic coordinates. It is shown here that the availability of unmerged reflection data enables valuable additional analyses to be performed that yield improvements in the final models, and tools are presented to implement them, together with examples of the results to which they give access. The first example is the automatic identification and removal of image ranges affected by loss of crystal centering or by excessive decay of the diffraction pattern as a result of radiation damage. The second example is the `reflection-auditing' process, whereby individual merged data items showing especially poor agreement with model predictions during refinement are investigated thanks to the specific metadata (such as image number and detector position) that are available for the corresponding unmerged data, potentially revealing previously undiagnosed instrumental, experimental or processing problems. The third example is the calculation of so-called F(early) - F(late) maps from carefully selected subsets of unmerged amplitude data, which can not only highlight the location and extent of radiation damage but can also provide guidance towards suitable fine-grained parametrizations to model the localized effects of such damage.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"148-158"},"PeriodicalIF":2.2,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10910543/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139970604","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Using cryo-EM to understand the assembly pathway of respiratory complex I. 利用低温电子显微镜了解呼吸复合体 I 的组装途径。

IF 2.2 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-03-01 Epub Date: 2024-02-19 DOI: 10.1107/S205979832400086X

Eike Laube, Jonathan Schiller, Volker Zickermann, Janet Vonck

引用次数: 0

Investigation of how gate residues in the main channel affect the catalytic activity of Scytalidium thermophilum catalase. 研究主通道中的门残基如何影响嗜热菌过氧化氢酶的催化活性。

IF 2.2 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-02-01 Epub Date: 2024-01-24 DOI: 10.1107/S2059798323011063

Yonca Yuzugullu Karakus, Gunce Goc, Melis Zengin Karatas, Sinem Balci Unver, Briony A Yorke, Arwen R Pearson

{"title":"Investigation of how gate residues in the main channel affect the catalytic activity of Scytalidium thermophilum catalase.","authors":"Yonca Yuzugullu Karakus, Gunce Goc, Melis Zengin Karatas, Sinem Balci Unver, Briony A Yorke, Arwen R Pearson","doi":"10.1107/S2059798323011063","DOIUrl":"10.1107/S2059798323011063","url":null,"abstract":"Catalase is an antioxidant enzyme that breaks down hydrogen peroxide (H2O2) into molecular oxygen and water. In all monofunctional catalases the pathway that H2O2 takes to the catalytic centre is via the `main channel'. However, the structure of this channel differs in large-subunit and small-subunit catalases. In large-subunit catalases the channel is 15 Å longer and consists of two distinct parts, including a hydrophobic lower region near the heme and a hydrophilic upper region where multiple H2O2 routes are possible. Conserved glutamic acid and threonine residues are located near the intersection of these two regions. Mutations of these two residues in the Scytalidium thermophilum catalase had no significant effect on catalase activity. However, the secondary phenol oxidase activity was markedly altered, with kcat and kcat/Km values that were significantly increased in the five variants E484A, E484I, T188D, T188I and T188F. These variants also showed a lower affinity for inhibitors of oxidase activity than the wild-type enzyme and a higher affinity for phenolic substrates. Oxidation of heme b to heme d did not occur in most of the studied variants. Structural changes in solvent-chain integrity and channel architecture were also observed. In summary, modification of the main-channel gate glutamic acid and threonine residues has a greater influence on the secondary activity of the catalase enzyme, and the oxidation of heme b to heme d is predominantly inhibited by their conversion to aliphatic and aromatic residues.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"101-112"},"PeriodicalIF":2.2,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10836395/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139545257","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket. 以 SARS-CoV-2 主要蛋白酶结合口袋的开放形式为目标的片段筛选。

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-02-01 Epub Date: 2024-01-30 DOI: 10.1107/S2059798324000329

Chia Ying Huang, Alexander Metz, Roland Lange, Nadia Artico, Céline Potot, Julien Hazemann, Manon Müller, Marina Dos Santos, Alain Chambovey, Daniel Ritz, Deniz Eris, Solange Meyer, Geoffroy Bourquin, May Sharpe, Aengus Mac Sweeney

{"title":"Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.","authors":"Chia Ying Huang, Alexander Metz, Roland Lange, Nadia Artico, Céline Potot, Julien Hazemann, Manon Müller, Marina Dos Santos, Alain Chambovey, Daniel Ritz, Deniz Eris, Solange Meyer, Geoffroy Bourquin, May Sharpe, Aengus Mac Sweeney","doi":"10.1107/S2059798324000329","DOIUrl":"10.1107/S2059798324000329","url":null,"abstract":"To identify starting points for therapeutics targeting SARS-CoV-2, the Paul Scherrer Institute and Idorsia decided to collaboratively perform an X-ray crystallographic fragment screen against its main protease. Fragment-based screening was carried out using crystals with a pronounced open conformation of the substrate-binding pocket. Of 631 soaked fragments, a total of 29 hits bound either in the active site (24 hits), a remote binding pocket (three hits) or at crystal-packing interfaces (two hits). Notably, two fragments with a pose that was sterically incompatible with a more occluded crystal form were identified. Two isatin-based electrophilic fragments bound covalently to the catalytic cysteine residue. The structures also revealed a surprisingly strong influence of the crystal form on the binding pose of three published fragments used as positive controls, with implications for fragment screening by crystallography.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"123-136"},"PeriodicalIF":2.6,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10836397/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139641430","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0