Acta crystallographica. Section F, Structural biology communications最新文献_第8页

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2024-11-04

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Multi-species cryoEM calibration and workflow verification standard. 多物种冷冻电镜校准和工作流程验证标准。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2024-11-01 Epub Date: 2024-10-31 DOI: 10.1107/S2053230X24010318

Daija Bobe, Mykhailo Kopylov, Jessalyn Miller, Aaron P Owji, Edward T Eng

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Human transforming growth factor β type I receptor in complex with kinase inhibitor SB505124. 人转化生长因子 β I 型受体与激酶抑制剂 SB505124 的复合物。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2024-11-01 Epub Date: 2024-10-23 DOI: 10.1107/S2053230X24010094

Jhon A Rodriguez Buitrago, Maréne Landström, Magnus Wolf-Watz

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X-ray crystal structure of proliferating cell nuclear antigen 1 from Aeropyrum pernix. 来自 Aeropyrum pernix 的增殖细胞核抗原 1 的 X 射线晶体结构。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2024-11-01 Epub Date: 2024-10-09 DOI: 10.1107/S2053230X24009518

Takahiro Yamauchi, Makiko Kikuchi, Yasuhito Iizuka, Masaru Tsunoda

{"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":"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.","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}

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IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2024-10-23

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Improving the diffraction quality of heat-shock protein 47 crystals 提高热休克蛋白 47 晶体的衍射质量。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2024-10-14 DOI: 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

{"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":"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.","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}

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Crystallization and crystallographic studies of human serine protease inhibitor (serpin) B9 人类丝氨酸蛋白酶抑制剂（serpin）B9 的结晶和晶体学研究。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2024-10-09 DOI: 10.1107/S2053230X24009439

Teng Yan, Aiwu Zhou

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IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2024-10-09

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Welcoming Alejandro Buschiazzo, Dorothee Liebschner and Stephen Muench as Co-editors of Acta Crystallographica F – Structural Biology Communications 欢迎 Alejandro Buschiazzo、Dorothee Liebschner 和 Stephen Muench 成为《结晶学报 F - 结构生物学通讯》的联合编辑。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2024-10-03 DOI: 10.1107/S2053230X24009427

Jon Agirre, Maria Cristina Nonato, Mark J. van Raaij

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First crystal structure of the DUF2436 domain of virulence proteins from Porphyromonas gingivalis. 牙龈卟啉单胞菌毒力蛋白 DUF2436 结构域的首个晶体结构。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2024-10-01 Epub Date: 2024-09-26 DOI: 10.1107/S2053230X24008185

Bogeun Kim, Jisub Hwang, Sehyeok Im, Hackwon Do, Youn Soo Shim, Jun Hyuck Lee

{"title":"First crystal structure of the DUF2436 domain of virulence proteins from Porphyromonas gingivalis.","authors":"Bogeun Kim, Jisub Hwang, Sehyeok Im, Hackwon Do, Youn Soo Shim, Jun Hyuck Lee","doi":"10.1107/S2053230X24008185","DOIUrl":"10.1107/S2053230X24008185","url":null,"abstract":"Porphyromonas gingivalis is a major pathogenic oral bacterium that is responsible for periodontal disease. It is linked to chronic periodontitis, gingivitis and aggressive periodontitis. P. gingivalis exerts its pathogenic effects through mechanisms such as immune evasion and tissue destruction, primarily by secreting various factors, including cysteine proteases such as gingipain K (Kgp), gingipain R (RgpA and RgpB) and PrtH (UniProtKB ID P46071). Virulence proteins comprise multiple domains, including the pro-peptide region, catalytic domain, K domain, R domain and DUF2436 domain. While there is a growing database of knowledge on virulence proteins and domains, there was no prior evidence or information regarding the structure and biological function of the well conserved DUF2436 domain. In this study, the DUF2436 domain of PrtH from P. gingivalis (PgDUF2436) was determined at 2.21 Å resolution, revealing a noncanonical β-jelly-roll sandwich topology with two antiparallel β-sheets and one short α-helix. Although the structure of PgDUF2436 was determined by the molecular-replacement method using an AlphaFold model structure as a template, there were significant differences in the positions of β1 between the AlphaFold model and the experimentally determined PgDUF2436 structure. The Basic Local Alignment Search Tool sequence-similarity search program showed no sequentially similar proteins in the Protein Data Bank. However, DaliLite search results using structure-based alignment revealed that the PgDUF2436 structure has structural similarity Z-scores of 5.9-5.4 with the C-terminal domain of AlgF, the D4 domain of cytolysin, IglE and the extracellular domain structure of PepT2. This study has elucidated the structure of the DUF2436 domain for the first time and a comparative analysis with similar structures has been performed.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":" ","pages":"252-262"},"PeriodicalIF":1.1,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11448926/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142339067","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}

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