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Acta crystallographica. Section F, Structural biology communications最新文献

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IF 1.1 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2024-07-03
{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141536711","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}
引用次数: 0
IF 1.1 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2024-07-03
{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141536713","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}
引用次数: 0
The structure of a pectin-active family 1 polysaccharide lyase from the marine bacterium Pseudoalteromonas fuliginea. 海洋假交替单胞菌（Pseudoalteromonas fuliginea）果胶活性家族 1 多糖裂解酶的结构。
IF 1.1 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2024-07-01 Epub Date: 2024-06-27 DOI: 10.1107/S2053230X2400596X
Joanne K Hobbs, Alisdair B Boraston
{"title":"The structure of a pectin-active family 1 polysaccharide lyase from the marine bacterium Pseudoalteromonas fuliginea.","authors":"Joanne K Hobbs, Alisdair B Boraston","doi":"10.1107/S2053230X2400596X","DOIUrl":"10.1107/S2053230X2400596X","url":null,"abstract":"<p><p>Pseudoalteromonas fuliginea sp. PS47 is a recently identified marine bacterium that has extensive enzymatic machinery to metabolize polysaccharides, including a locus that targets pectin-like substrates. This locus contains a gene (locus tag EU509_03255) that encodes a pectin-degrading lyase, called PfPL1, that belongs to polysaccharide lyase family 1 (PL1). The 2.2 Å resolution X-ray crystal structure of PfPL1 reveals the compact parallel β-helix fold of the PL1 family. The back side of the core parallel β-helix opposite to the active site is a meandering set of five α-helices joined by lengthy loops. A comparison of the active site with those of other PL1 enzymes suggests a catalytic mechanism that is independent of metal ions, such as Ca<sup>2+</sup>, but that substrate recognition may require metal ions. Overall, this work provides the first structural insight into a pectinase of marine origin and the first structure of a PL1 enzyme in subfamily 2.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11229556/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141465354","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 impact of exchanging the light and heavy chains on the structures of bovine ultralong antibodies. 交换轻链和重链对牛超长抗体结构的影响。
IF 1.1 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2024-07-01 DOI: 10.1107/S2053230X2400606X
John D Clarke, Alice Douangamath, Halina Mikolajek, Marie Bonnet-Di Placido, Jingshan Ren, Elizabeth E Fry, Dave I Stuart, John A Hammond, Raymond J Owens
{"title":"The impact of exchanging the light and heavy chains on the structures of bovine ultralong antibodies.","authors":"John D Clarke, Alice Douangamath, Halina Mikolajek, Marie Bonnet-Di Placido, Jingshan Ren, Elizabeth E Fry, Dave I Stuart, John A Hammond, Raymond J Owens","doi":"10.1107/S2053230X2400606X","DOIUrl":"10.1107/S2053230X2400606X","url":null,"abstract":"<p><p>The third complementary-determining regions of the heavy-chain (CDR3H) variable regions (VH) of some cattle antibodies are highly extended, consisting of 48 or more residues. These `ultralong' CDR3Hs form β-ribbon stalks that protrude from the surface of the antibody with a disulfide cross-linked knob region at their apex that dominates antigen interactions over the other CDR loops. The structure of the Fab fragment of a naturally paired bovine ultralong antibody (D08), identified by single B-cell sequencing, has been determined to 1.6 Å resolution. By swapping the D08 native light chain with that of an unrelated antigen-unknown ultralong antibody, it is shown that interactions between the CDR3s of the variable domains potentially affect the fine positioning of the ultralong CDR3H; however, comparison with other crystallographic structures shows that crystalline packing is also a major contributor. It is concluded that, on balance, the exact positioning of ultralong CDR3H loops is most likely to be due to the constraints of crystal packing.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11229553/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141490482","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
Preliminary X-ray diffraction and ligand-binding analyses of the N-terminal domain of hypothetical protein Rv1421 from Mycobacterium tuberculosis H37Rv. 结核分枝杆菌 H37Rv 假想蛋白 Rv1421 N 端结构域的初步 X 射线衍射和配体结合分析。
IF 1.1 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2024-07-01 Epub Date: 2024-06-27 DOI: 10.1107/S2053230X24005831
Jihyun Park, Yu Jeong Cheon, Yoon Chae Jeong, Ki Seog Lee
{"title":"Preliminary X-ray diffraction and ligand-binding analyses of the N-terminal domain of hypothetical protein Rv1421 from Mycobacterium tuberculosis H37Rv.","authors":"Jihyun Park, Yu Jeong Cheon, Yoon Chae Jeong, Ki Seog Lee","doi":"10.1107/S2053230X24005831","DOIUrl":"10.1107/S2053230X24005831","url":null,"abstract":"<p><p>Mycobacterium tuberculosis can reside and persist in deep tissues; latent tuberculosis can evade immune detection and has a unique mechanism to convert it into active disease through reactivation. M. tuberculosis Rv1421 (MtRv1421) is a hypothetical protein that has been proposed to be involved in nucleotide binding-related metabolism in cell-growth and cell-division processes. However, due to a lack of structural information, the detailed function of MtRv1421 remains unclear. In this study, a truncated N-terminal domain (NTD) of MtRv1421, which contains a Walker A/B-like motif, was purified and crystallized using PEG 400 as a precipitant. The crystal of MtRv1421-NTD diffracted to a resolution of 1.7 Å and was considered to belong to either the C-centered monoclinic space group C2 or the I-centered orthorhombic space group I222, with unit-cell parameters a = 124.01, b = 58.55, c = 84.87 Å, β = 133.12° or a = 58.53, b = 84.86, c = 90.52 Å, respectively. The asymmetric units of the C2 or I222 crystals contained two or one monomers, respectively. In terms of the binding ability of MtRv1421-NTD to various ligands, uridine diphosphate (UDP) and UDP-N-acetylglucosamine significantly increased the melting temperature of MtRv1421-NTD, which indicates structural stabilization through the binding of these ligands. Altogether, the results reveal that a UDP moiety may be required for the interaction of MtRv1421-NTD as a nucleotide-binding protein with its ligand.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11229554/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141465352","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 importance of international collaborations in science and structural biology 科学和结构生物学国际合作的重要性。
IF 1.1 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2024-06-20 DOI: 10.1107/S2053230X24005545
Maria Cristina Nonato, Mark J. van Raaij, Jon Agirre
{"title":"The importance of international collaborations in science and structural biology","authors":"Maria Cristina Nonato,&nbsp;Mark J. van Raaij,&nbsp;Jon Agirre","doi":"10.1107/S2053230X24005545","DOIUrl":"10.1107/S2053230X24005545","url":null,"abstract":"<p>The <i>Acta Cryst. F – Structural Biology Communications</i> Editors explain how important international collaborations are in science and structural biology.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141431116","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}
引用次数: 0
Room-temperature serial synchrotron crystallography structure of Spinacia oleracea RuBisCO. 菠菜 RuBisCO 的室温串行同步辐射晶体学结构。
IF 1.1 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2024-06-01 Epub Date: 2024-05-29 DOI: 10.1107/S2053230X24004643
Monika Bjelčić, Oskar Aurelius, Jie Nan, Richard Neutze, Thomas Ursby
{"title":"Room-temperature serial synchrotron crystallography structure of Spinacia oleracea RuBisCO.","authors":"Monika Bjelčić, Oskar Aurelius, Jie Nan, Richard Neutze, Thomas Ursby","doi":"10.1107/S2053230X24004643","DOIUrl":"10.1107/S2053230X24004643","url":null,"abstract":"<p><p>Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is the enzyme responsible for the first step of carbon dioxide (CO<sub>2</sub>) fixation in plants, which proceeds via the carboxylation of ribulose 1,5-biphosphate. Because of the enormous importance of this reaction in agriculture and the environment, there is considerable interest in the mechanism of fixation of CO<sub>2</sub> by RuBisCO. Here, a serial synchrotron crystallography structure of spinach RuBisCO is reported at 2.3 Å resolution. This structure is consistent with earlier single-crystal X-ray structures of this enzyme and the results are a good starting point for a further push towards time-resolved serial synchrotron crystallography in order to better understand the mechanism of the reaction.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11189101/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141160097","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
IF 1.1 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2024-05-31
{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141435643","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}
引用次数: 0
Cryo-EM structure and functional analysis of the chromatin remodeler RSF 染色质重塑器 RSF 的冷冻电镜结构和功能分析。
IF 1.1 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2024-05-31 DOI: 10.1107/S2053230X24004655
Jiale Zhang, Heyu Zhao, Binqian Zou, Huadong Li, Shuqi Dong, Jiali Guan, Chi Wang, Weijie Li, Yutong Liu, Yingying Chen, Nadia Rasheed, Jun He
{"title":"Cryo-EM structure and functional analysis of the chromatin remodeler RSF","authors":"Jiale Zhang,&nbsp;Heyu Zhao,&nbsp;Binqian Zou,&nbsp;Huadong Li,&nbsp;Shuqi Dong,&nbsp;Jiali Guan,&nbsp;Chi Wang,&nbsp;Weijie Li,&nbsp;Yutong Liu,&nbsp;Yingying Chen,&nbsp;Nadia Rasheed,&nbsp;Jun He","doi":"10.1107/S2053230X24004655","DOIUrl":"10.1107/S2053230X24004655","url":null,"abstract":"<p>The RSF complex belongs to the ISWI chromatin-remodeling family and is composed of two subunits: RSF1 (remodeling and spacing factor 1) and SNF2h (sucrose nonfermenting protein 2 homolog). The RSF complex participates in nucleosome spacing and assembly, and subsequently promotes nucleosome maturation. Although SNF2h has been extensively studied in the last few years, the structural and functional properties of the remodeler RSF1 still remain vague. Here, a cryo-EM structure of the RSF–nucleosome complex is reported. The 3D model shows a two-lobe architecture of RSF, and the structure of the RSF–nucleosome (flanked with linker DNA) complex shows that the RSF complex moves the DNA away from the histone octamer surface at the DNA-entry point. Additionally, a nucleosome-sliding assay and a restriction-enzyme accessibility assay show that the RSF1 subunit may cause changes in the chromatin-remodeling properties of SNF2h. As a `nucleosome ruler', the results of an RSF–dinucleosome binding affinity test led to the proposal that the critical distance that RSF `measures' between two nucleosomes is about 24 base pairs.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141178459","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}
引用次数: 0
IF 0.9 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2024-05-20
{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":null,"pages":null},"PeriodicalIF":0.9,"publicationDate":"2024-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141164865","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}
引用次数: 0
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