Pub Date : 2024-11-01Epub Date: 2024-10-31DOI: 10.1107/S2053230X24010318
Daija Bobe, Mykhailo Kopylov, Jessalyn Miller, Aaron P Owji, Edward T Eng
Cryogenic electron microscopy (cryoEM) is a rapidly growing structural biology modality that has been successful in revealing molecular details of biological systems. However, unlike established biophysical and analytical techniques with calibration standards, cryoEM has lacked comprehensive biological test samples. Here, a cryoEM calibration sample consisting of a mixture of compatible macromolecules is introduced that can not only be used for resolution optimization, but also provides multiple reference points for evaluating instrument performance, data quality and image-processing workflows in a single experiment. This combined test specimen provides researchers with a reference point for validating their cryoEM pipeline, benchmarking their methodologies and testing new algorithms.
{"title":"Multi-species cryoEM calibration and workflow verification standard.","authors":"Daija Bobe, Mykhailo Kopylov, Jessalyn Miller, Aaron P Owji, Edward T Eng","doi":"10.1107/S2053230X24010318","DOIUrl":"10.1107/S2053230X24010318","url":null,"abstract":"<p><p>Cryogenic electron microscopy (cryoEM) is a rapidly growing structural biology modality that has been successful in revealing molecular details of biological systems. However, unlike established biophysical and analytical techniques with calibration standards, cryoEM has lacked comprehensive biological test samples. Here, a cryoEM calibration sample consisting of a mixture of compatible macromolecules is introduced that can not only be used for resolution optimization, but also provides multiple reference points for evaluating instrument performance, data quality and image-processing workflows in a single experiment. This combined test specimen provides researchers with a reference point for validating their cryoEM pipeline, benchmarking their methodologies and testing new algorithms.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"80 Pt 11","pages":"320-327"},"PeriodicalIF":1.1,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533365/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142567186","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}
Pub Date : 2024-11-01Epub Date: 2024-10-23DOI: 10.1107/S2053230X24010094
Jhon A Rodriguez Buitrago, Maréne Landström, Magnus Wolf-Watz
The crystal structure of the intracellular domain of transforming growth factor β type I receptor (TβR1) in complex with the competitive inhibitor SB505124 is presented. The study provides insights into the structure and function of TβR1 in complex with SB505124, and as such offers molecular-level understanding of the inhibition of this critical signalling pathway. The potential of SB505124 as an avenue for therapy in cancer treatment is discussed on basis of the results.
{"title":"Human transforming growth factor β type I receptor in complex with kinase inhibitor SB505124.","authors":"Jhon A Rodriguez Buitrago, Maréne Landström, Magnus Wolf-Watz","doi":"10.1107/S2053230X24010094","DOIUrl":"10.1107/S2053230X24010094","url":null,"abstract":"<p><p>The crystal structure of the intracellular domain of transforming growth factor β type I receptor (TβR1) in complex with the competitive inhibitor SB505124 is presented. The study provides insights into the structure and function of TβR1 in complex with SB505124, and as such offers molecular-level understanding of the inhibition of this critical signalling pathway. The potential of SB505124 as an avenue for therapy in cancer treatment is discussed on basis of the results.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":" ","pages":"314-319"},"PeriodicalIF":1.1,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533363/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142492755","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}
Proliferating cell nuclear antigen (PCNA) plays a critical role in DNA replication by enhancing the activity of various proteins involved in replication. In this study, the crystal structure of ApePCNA1, one of three PCNAs from the thermophilic archaeon Aeropyrum pernix, was elucidated. ApePCNA1 was cloned and expressed in Escherichia coli and the protein was purified and crystallized. The resulting crystal structure determined at 2.00 Å resolution revealed that ApePCNA1 does not form a trimeric ring, unlike PCNAs from other domains of life. It has unique structural features, including a long interdomain-connecting loop and a PIP-box-like sequence at the N-terminus, indicating potential interactions with other proteins. These findings provide insights into the functional mechanisms of PCNAs in archaea and their evolutionary conservation across different domains of life. A modified medium and protocol were used to express recombinant protein containing the lac operon. The expression of the target protein increased and the total incubation time decreased when using this system compared with those of previous expression protocols.
增殖细胞核抗原(PCNA)通过增强参与复制的各种蛋白质的活性,在 DNA 复制过程中发挥着至关重要的作用。本研究阐明了嗜热古生物 Aeropyrum pernix 的三种 PCNA 之一 ApePCNA1 的晶体结构。ApePCNA1 被克隆并在大肠杆菌中表达,蛋白质被纯化并结晶。以 2.00 Å 分辨率测定的晶体结构显示,与其他生命领域的 PCNA 不同,ApePCNA1 并未形成三聚环。它具有独特的结构特征,包括一个长的域间连接环和位于 N 端的 PIP-box 样序列,这表明它可能与其他蛋白质发生相互作用。这些发现有助于深入了解古菌中 PCNA 的功能机制及其在不同生命领域中的进化保护。使用改良的培养基和方案来表达含有 lac 操作子的重组蛋白。与之前的表达方案相比,使用该系统时目标蛋白的表达量增加,总孵育时间缩短。
{"title":"X-ray crystal structure of proliferating cell nuclear antigen 1 from Aeropyrum pernix.","authors":"Takahiro Yamauchi, Makiko Kikuchi, Yasuhito Iizuka, Masaru Tsunoda","doi":"10.1107/S2053230X24009518","DOIUrl":"10.1107/S2053230X24009518","url":null,"abstract":"<p><p>Proliferating cell nuclear antigen (PCNA) plays a critical role in DNA replication by enhancing the activity of various proteins involved in replication. In this study, the crystal structure of ApePCNA1, one of three PCNAs from the thermophilic archaeon Aeropyrum pernix, was elucidated. ApePCNA1 was cloned and expressed in Escherichia coli and the protein was purified and crystallized. The resulting crystal structure determined at 2.00 Å resolution revealed that ApePCNA1 does not form a trimeric ring, unlike PCNAs from other domains of life. It has unique structural features, including a long interdomain-connecting loop and a PIP-box-like sequence at the N-terminus, indicating potential interactions with other proteins. These findings provide insights into the functional mechanisms of PCNAs in archaea and their evolutionary conservation across different domains of life. A modified medium and protocol were used to express recombinant protein containing the lac operon. The expression of the target protein increased and the total incubation time decreased when using this system compared with those of previous expression protocols.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":" ","pages":"294-301"},"PeriodicalIF":1.1,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11533367/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142387126","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}
Pub Date : 2024-10-14DOI: 10.1107/S2053230X24009233
Kevin Kish, Stephen Cobell, Nicolas Szapiel, Chunhong Yan, John A. Newitt, Jeffrey Tredup, Iyoncy Rodrigo, Elizabeth Tomasco, Mian Gao, Frank Marsilio, John Haugner, Dasa Lipovšek, Bi Deng, Patrick Bousquet, Yihong Zhang, Holly Schmidt, Steven Sheriff
Heat-shock protein 47 (HSP47) is a potential target for inhibitors that ameliorate fibrosis by reducing collagen assembly. In an effort to develop a structure-based drug-design system, it was not possible to replicate a previous literature result (PDB entry 4au4) for apo dog HSP47; instead, crystal forms were obtained in which pairs of dog HSP47 molecules interacted through a noncleavable C-terminal His-tag to build up tetramers, all of which had multiple molecules of HSP47 in the asymmetric unit and none of which diffracted as well as the literature precedent. To overcome these difficulties, a two-pronged approach was followed: (i) the His-tag was moved from the C-terminus to the N-terminus and was made cleavable, and (ii) Adnectin (derived from the tenth domain of human fibronectin type III) crystallization chaperones were developed. Both approaches provided well diffracting crystals, but the latter approach yielded crystal forms with only one or two HSP47 complexes per asymmetric unit, which made model building less onerous.
热休克蛋白 47(HSP47)是抑制剂的潜在靶点,抑制剂可通过减少胶原组装来改善纤维化。在开发基于结构的药物设计系统的过程中,我们无法复制之前文献中关于 apo dog HSP47 的结果(PDB 条目 4au4);相反,我们获得了一些晶体形式,其中成对的 dog HSP47 分子通过不可清除的 C 端 His-tag 相互作用,形成了四聚体,所有这些四聚体的不对称单元中都有多个 HSP47 分子,而且它们的衍射效果都不如文献中的先例。为了克服这些困难,我们采取了双管齐下的方法:(i) 将 His 标记从 C 端移至 N 端,并使其可裂解;(ii) 开发了 Adnectin(源自人类 III 型纤连蛋白的第十个结构域)结晶伴侣。这两种方法都能得到衍射良好的晶体,但后一种方法得到的晶体形式每个不对称单元只有一个或两个 HSP47 复合物,因此建立模型的难度较小。
{"title":"Improving the diffraction quality of heat-shock protein 47 crystals","authors":"Kevin Kish, Stephen Cobell, Nicolas Szapiel, Chunhong Yan, John A. Newitt, Jeffrey Tredup, Iyoncy Rodrigo, Elizabeth Tomasco, Mian Gao, Frank Marsilio, John Haugner, Dasa Lipovšek, Bi Deng, Patrick Bousquet, Yihong Zhang, Holly Schmidt, Steven Sheriff","doi":"10.1107/S2053230X24009233","DOIUrl":"10.1107/S2053230X24009233","url":null,"abstract":"<p>Heat-shock protein 47 (HSP47) is a potential target for inhibitors that ameliorate fibrosis by reducing collagen assembly. In an effort to develop a structure-based drug-design system, it was not possible to replicate a previous literature result (PDB entry 4au4) for apo dog HSP47; instead, crystal forms were obtained in which pairs of dog HSP47 molecules interacted through a noncleavable C-terminal His-tag to build up tetramers, all of which had multiple molecules of HSP47 in the asymmetric unit and none of which diffracted as well as the literature precedent. To overcome these difficulties, a two-pronged approach was followed: (i) the His-tag was moved from the C-terminus to the N-terminus and was made cleavable, and (ii) Adnectin (derived from the tenth domain of human fibronectin type III) crystallization chaperones were developed. Both approaches provided well diffracting crystals, but the latter approach yielded crystal forms with only one or two HSP47 complexes per asymmetric unit, which made model building less onerous.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"80 11","pages":"302-313"},"PeriodicalIF":1.1,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142455525","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}