Acta Crystallographica. Section D, Structural Biology最新文献_第7页

A database overview of metal-coordination distances in metalloproteins. 金属蛋白中金属配位距离的数据库概览。

IF 2.2 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-05-01 Epub Date: 2024-04-29 DOI: 10.1107/S2059798324003152

Milana Bazayeva, Claudia Andreini, Antonio Rosato

{"title":"A database overview of metal-coordination distances in metalloproteins.","authors":"Milana Bazayeva, Claudia Andreini, Antonio Rosato","doi":"10.1107/S2059798324003152","DOIUrl":"https://doi.org/10.1107/S2059798324003152","url":null,"abstract":"Metalloproteins are ubiquitous in all living organisms and take part in a very wide range of biological processes. For this reason, their experimental characterization is crucial to obtain improved knowledge of their structure and biological functions. The three-dimensional structure represents highly relevant information since it provides insight into the interaction between the metal ion(s) and the protein fold. Such interactions determine the chemical reactivity of the bound metal. The available PDB structures can contain errors due to experimental factors such as poor resolution and radiation damage. A lack of use of distance restraints during the refinement and validation process also impacts the structure quality. Here, the aim was to obtain a thorough overview of the distribution of the distances between metal ions and their donor atoms through the statistical analysis of a data set based on more than 115 000 metal-binding sites in proteins. This analysis not only produced reference data that can be used by experimentalists to support the structure-determination process, for example as refinement restraints, but also resulted in an improved insight into how protein coordination occurs for different metals and the nature of their binding interactions. In particular, the features of carboxylate coordination were inspected, which is the only type of interaction that is commonly present for nearly all metals.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":"80 Pt 5","pages":"362-376"},"PeriodicalIF":2.2,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11066882/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140848506","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

Mononuclear binding and catalytic activity of europium(III) and gadolinium(III) at the active site of the model metalloenzyme phosphotriesterase. 铕（III）和钆（III）在模型金属酶磷酸三酯酶活性位点的单核结合和催化活性。

IF 4.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-04-01 Epub Date: 2024-03-21 DOI: 10.1107/S2059798324002316

Callum W Breeze, Yuji Nakano, Eleanor C Campbell, Rebecca L Frkic, David W Lupton, Colin J Jackson

引用次数: 0

Efficient in situ screening of and data collection from microcrystals in crystallization plates. 对结晶板中的微晶体进行高效的原位筛选和数据采集。

IF 4.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-04-01 Epub Date: 2024-03-15 DOI: 10.1107/S2059798324001955

Amy J Thompson, Juan Sanchez-Weatherby, Lewis J Williams, Halina Mikolajek, James Sandy, Jonathan A R Worrall, Michael A Hough

引用次数: 0

AlphaFold-assisted structure determination of a bacterial protein of unknown function using X-ray and electron crystallography. 利用 X 射线和电子晶体学技术，在 AlphaFold 辅助下确定一种功能未知的细菌蛋白质的结构。

IF 2.2 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-04-01 Epub Date: 2024-03-07 DOI: 10.1107/S205979832400072X

Justin E Miller, Matthew P Agdanowski, Joshua L Dolinsky, Michael R Sawaya, Duilio Cascio, Jose A Rodriguez, Todd O Yeates

{"title":"AlphaFold-assisted structure determination of a bacterial protein of unknown function using X-ray and electron crystallography.","authors":"Justin E Miller, Matthew P Agdanowski, Joshua L Dolinsky, Michael R Sawaya, Duilio Cascio, Jose A Rodriguez, Todd O Yeates","doi":"10.1107/S205979832400072X","DOIUrl":"10.1107/S205979832400072X","url":null,"abstract":"Macromolecular crystallography generally requires the recovery of missing phase information from diffraction data to reconstruct an electron-density map of the crystallized molecule. Most recent structures have been solved using molecular replacement as a phasing method, requiring an a priori structure that is closely related to the target protein to serve as a search model; when no such search model exists, molecular replacement is not possible. New advances in computational machine-learning methods, however, have resulted in major advances in protein structure predictions from sequence information. Methods that generate predicted structural models of sufficient accuracy provide a powerful approach to molecular replacement. Taking advantage of these advances, AlphaFold predictions were applied to enable structure determination of a bacterial protein of unknown function (UniProtKB Q63NT7, NCBI locus BPSS0212) based on diffraction data that had evaded phasing attempts using MIR and anomalous scattering methods. Using both X-ray and micro-electron (microED) diffraction data, it was possible to solve the structure of the main fragment of the protein using a predicted model of that domain as a starting point. The use of predicted structural models importantly expands the promise of electron diffraction, where structure determination relies critically on molecular replacement.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"270-278"},"PeriodicalIF":2.2,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10994174/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140048526","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

Structural determination and modeling of ciliary microtubules. 纤毛微管的结构测定和建模。

IF 2.2 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-04-01 Epub Date: 2024-03-07 DOI: 10.1107/S2059798324001815

Travis Walton, Matthew H Doran, Alan Brown

引用次数: 0

VitroJet: new features and case studies. VitroJet：新功能和案例研究。

IF 2.2 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2024-04-01 Epub Date: 2024-03-15 DOI: 10.1107/S2059798324001852

Rene J M Henderikx, Daniel Mann, Aušra Domanska, Jing Dong, Saba Shahzad, Behnam Lak, Aikaterini Filopoulou, Damian Ludig, Martin Grininger, Jeffrey Momoh, Elina Laanto, Hanna M Oksanen, Kyrylo Bisikalo, Pamela A Williams, Sarah J Butcher, Peter J Peters, Bart W A M M Beulen

{"title":"VitroJet: new features and case studies.","authors":"Rene J M Henderikx, Daniel Mann, Aušra Domanska, Jing Dong, Saba Shahzad, Behnam Lak, Aikaterini Filopoulou, Damian Ludig, Martin Grininger, Jeffrey Momoh, Elina Laanto, Hanna M Oksanen, Kyrylo Bisikalo, Pamela A Williams, Sarah J Butcher, Peter J Peters, Bart W A M M Beulen","doi":"10.1107/S2059798324001852","DOIUrl":"10.1107/S2059798324001852","url":null,"abstract":"Single-particle cryo-electron microscopy has become a widely adopted method in structural biology due to many recent technological advances in microscopes, detectors and image processing. Before being able to inspect a biological sample in an electron microscope, it needs to be deposited in a thin layer on a grid and rapidly frozen. The VitroJet was designed with this aim, as well as avoiding the delicate manual handling and transfer steps that occur during the conventional grid-preparation process. Since its creation, numerous technical developments have resulted in a device that is now widely utilized in multiple laboratories worldwide. It features plasma treatment, low-volume sample deposition through pin printing, optical ice-thickness measurement and cryofixation of pre-clipped Autogrids through jet vitrification. This paper presents recent technical improvements to the VitroJet and the benefits that it brings to the cryo-EM workflow. A wide variety of applications are shown: membrane proteins, nucleosomes, fatty-acid synthase, Tobacco mosaic virus, lipid nanoparticles, tick-borne encephalitis viruses and bacteriophages. These case studies illustrate the advancement of the VitroJet into an instrument that enables accurate control and reproducibility, demonstrating its suitability for time-efficient cryo-EM structure determination.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":" ","pages":"232-246"},"PeriodicalIF":2.2,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10994172/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140130476","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

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 2.6 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