Journal of structural biology最新文献_第7页

Passage of ribosomes through microsprayer increases functional activity – Implications for activity assays in time-resolved cryo-EM 核糖体通过微喷雾器增加功能活性-时间分辨低温电镜活性分析的意义。

IF 3 3区生物学

Journal of structural biology Pub Date : 2025-09-01 Epub Date: 2025-07-04 DOI: 10.1016/j.jsb.2025.108232

Priyanka Garg , Xiangsong Feng , Swastik De , Joachim Frank

引用次数: 0

A generalist deep-learning volume segmentation tool for volume electron microscopy of biological samples 一个通用的深度学习体积分割工具，用于生物样品的体积电子显微镜。

IF 3 3区生物学

Journal of structural biology Pub Date : 2025-09-01 Epub Date: 2025-05-29 DOI: 10.1016/j.jsb.2025.108214

Yuyao Huang , Nickhil Jadav , Georgia Rutter , Lech Szymanski , Mihnea Bostina , Duane P. Harland

引用次数: 0

Improving CryoEM maps of symmetry-mismatched macromolecular assemblies: A case study on the flagellar motor 改进对称错配大分子组装的低温电镜图谱：鞭毛马达的案例研究。

IF 3 3区生物学

Journal of structural biology Pub Date : 2025-06-01 Epub Date: 2025-03-05 DOI: 10.1016/j.jsb.2025.108184

Prashant K. Singh , T.M. Iverson

{"title":"Improving CryoEM maps of symmetry-mismatched macromolecular assemblies: A case study on the flagellar motor","authors":"Prashant K. Singh , T.M. Iverson","doi":"10.1016/j.jsb.2025.108184","DOIUrl":"10.1016/j.jsb.2025.108184","url":null,"abstract":"<div><div>Advances in cryo-electron microscopy instrumentation and sample preparation have significantly improved the ability to collect quality data for biomolecular structures. However, achieving resolutions consistent with data quality remains challenging in structures with symmetry mismatches. As a case study, the bacterial flagellar motor is a large complex essential for bacterial chemotaxis and virulence. This motor contains a smaller membrane-supramembrane ring (MS-ring) and a larger cytoplasmic ring (C-ring). These two features have a 33:34 symmetry mismatch when expressed in <em>E. coli</em>. Because close symmetry mismatches are the most difficult to deconvolute, this makes the flagellar motor an excellent model system to evaluate refinement strategies for symmetry mismatch. We compared the performance of masked refinement, local refinement, and particle subtracted refinement on the same data. We found that particle subtraction prior to refinement was critical for approaching the smaller MS-ring. Additional processing resulted in final resolutions of 3.1 Å for the MS-ring and 3.0 Å for the C-ring, which improves the resolution of the MS-ring by 0.3 Å and the resolution of the C-ring by 1.0 Å as compared to past work. Although particle subtraction is fairly well-established, it is rarely applied to problems of symmetry mismatch, making this case study a valuable demonstration of its utility in this context.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 2","pages":"Article 108184"},"PeriodicalIF":3.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143585985","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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 and biophysical characterization of PadR family protein Rv0047c of Mycobacterium tuberculosis H37Rv 结核分枝杆菌H37Rv PadR家族蛋白Rv0047c的结构与生物物理特性

IF 3 3区生物学

Journal of structural biology Pub Date : 2025-06-01 Epub Date: 2025-05-20 DOI: 10.1016/j.jsb.2025.108211

Md Samsuddin Ansari , Muhammad Zohib , Meera Kumari , Vikash Yadav , Ravi Kant Pal , Sarita Tripathi , Anupam Jain , Bichitra Kumar Biswal , Ashish Arora

{"title":"Structural and biophysical characterization of PadR family protein Rv0047c of Mycobacterium tuberculosis H37Rv","authors":"Md Samsuddin Ansari , Muhammad Zohib , Meera Kumari , Vikash Yadav , Ravi Kant Pal , Sarita Tripathi , Anupam Jain , Bichitra Kumar Biswal , Ashish Arora","doi":"10.1016/j.jsb.2025.108211","DOIUrl":"10.1016/j.jsb.2025.108211","url":null,"abstract":"<div><div>The members of the PadR family of transcriptional regulators are important for cell survival in toxic environments and play an important role in detoxification, pathogenicity, and multi-drug resistance. Rv0047c of <em>Mycobacterium tuberculosis</em> H37Rv is annotated as a PadR family protein. We have characterized the stability and structure of Rv0047c. Rv0047c forms a stable dimer in solution. Its stability is characterized by a thermal melting transition temperature (Tm) of 55.3 °C. The crystal structure of Rv0047c was determined at a resolution of 3.15 Å. The structure indicates the biological unit to be a dimer with each monomer having a characteristic N-terminal winged-helix-turn-helix DNA binding domain and a C-terminal dimerization domain. The N-terminal domain is composed of four helices, α1, α2, α3, and α4 and two beta strands β1 and β2. The C-terminal dimerization domain (CTD) consists two long helices α6 and α7. The two domains are connected by helix α5. A short helical turn (helix αa, residue 89–92), leads to compaction of the α4-α5 loop. Rv0047c exhibits specificity in binding to an upstream region having an inverted repeat sequence. This binding is dependent upon Y18 and Y40 residue of Rv0047c, which are highly conserved among the PadR family. Overall, our results suggest a transcription regulatory role for Rv0047c, similar to other PadR family proteins.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 2","pages":"Article 108211"},"PeriodicalIF":3.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144127989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Structural insights into the RNA binding inhibitors of the C-terminal domain of the SARS-CoV-2 nucleocapsid 对 SARS-CoV-2 核头壳 C 端结构的 RNA 结合抑制剂的结构研究。

IF 3 3区生物学

Journal of structural biology Pub Date : 2025-06-01 Epub Date: 2025-03-18 DOI: 10.1016/j.jsb.2025.108197

Preeti Dhaka, Jai Krishna Mahto, Ankur Singh, Pravindra Kumar, Shailly Tomar

{"title":"Structural insights into the RNA binding inhibitors of the C-terminal domain of the SARS-CoV-2 nucleocapsid","authors":"Preeti Dhaka, Jai Krishna Mahto, Ankur Singh, Pravindra Kumar, Shailly Tomar","doi":"10.1016/j.jsb.2025.108197","DOIUrl":"10.1016/j.jsb.2025.108197","url":null,"abstract":"<div><div>The SARS-CoV-2 nucleocapsid (N) protein is an essential structural element of the virion, playing a crucial role in enclosing the viral genome into a ribonucleoprotein (RNP) assembly, as well as viral replication and transmission. The C-terminal domain of the N-protein (N-CTD) is essential for encapsidation, contributing to the stabilization of the RNP complex. In a previous study, three inhibitors (ceftriaxone, cefuroxime, and ampicillin) were screened for their potential to disrupt the RNA packaging process by targeting the N-protein. However, the binding efficacy, mechanism of RNA binding inhibition, and molecular insights of binding with N-CTD remain unclear. In this study, we evaluated the binding efficacy of these inhibitors using isothermal titration calorimetry (ITC), revealing the affinity of ceftriaxone (18 ± 1.3 μM), cefuroxime (55 ± 4.2 μM), and ampicillin (28 ± 1.2 μM) with the N-CTD. Further inhibition assay and fluorescence polarisation assay demonstrated RNA binding inhibition, with IC<sub>50</sub> ranging from ∼ 12 to 18 μM and K<sub>D</sub> values between 24 μM to 32 μM for the inhibitors, respectively. Additionally, we also determined the inhibitor-bound complex crystal structures of N-CTD-Ceftriaxone (2.0 Å) and N-CTD-Ampicillin (2.2 Å), along with the structure of apo N-CTD (1.4 Å). These crystal structures revealed previously unobserved interaction sites involving residues K261, K266, R293, Q294, and W301 at the oligomerization interface and the predicted RNA-binding region of N-CTD. These findings provide valuable molecular insights into the inhibition of N-CTD, highlighting its potential as an underexplored but promising target for the development of novel antiviral agents against coronaviruses.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 2","pages":"Article 108197"},"PeriodicalIF":3.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143669161","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Three-dimensional reconstruction of Magnetofaba australis strain IT-1: Magnetosome chain position with respect to flagella australis Magnetofaba菌株IT-1的三维重建：磁小体链在鞭毛上的位置。

IF 3 3区生物学

Journal of structural biology Pub Date : 2025-06-01 Epub Date: 2025-02-26 DOI: 10.1016/j.jsb.2025.108181

Eduardo Monteiro , Anderson S. Cabral , Viviana Morillo , Daniel Acosta-Avalos , Ulysses Lins , Fernanda Abreu

{"title":"Three-dimensional reconstruction of Magnetofaba australis strain IT-1: Magnetosome chain position with respect to flagella","authors":"Eduardo Monteiro , Anderson S. Cabral , Viviana Morillo , Daniel Acosta-Avalos , Ulysses Lins , Fernanda Abreu","doi":"10.1016/j.jsb.2025.108181","DOIUrl":"10.1016/j.jsb.2025.108181","url":null,"abstract":"<div><div>Magnetotactic bacteria (MTB) are a broad and diverse group of Gram-negative prokaryotes that biomineralize magnetosomes, organelles composed of a magnetic nanocrystal of magnetite (Fe<sub>3</sub>O<sub>4</sub>) or greigite (Fe<sub>3</sub>S<sub>4</sub>) and enveloped by a biological membrane. Magnetosomes are arranged in one or more chains intracellularly, which impart a magnetic moment to the cell. These structures permit a passive orientation of the MTB with the geomagnetic field lines (GML), which, when associated with swimming propelled by flagella, originate a phenomenon called magneto-aerotaxis, an important life strategy in a chemical stratified environment. There is a classical model based on elongated cells as vibrios and rods that tries to explain the magneto-aerotaxis. Still, this model raises questions when applied to other morphologies other than elongated cells. Here, we observe the spatial disposition of magnetosomes, motility behavior, and influence of magneto-aerotaxis in <em>Magnetofaba australis</em> strain IT-1, an MTB that achieves high swimming speeds and has some peculiarity in its motility. The three-dimensional reconstruction showed that <em>Mf. australis</em> strain IT-1′s magnetosome chain is misaligned with the swimming axis, which makes it impossible to use the classical model to explain magneto-aerotaxis in this MTB. Despite this, <em>Mf. australis</em> strain IT-1 was capable of swimming aligned to the GML. Also, this work studied the influence of the magnetosome and magneto-aerotaxis between populations of <em>Mf. australis</em> strain IT-1 with and without magnetosomes. Our results indicated that the magnetosome presence not only positively influences the movement in <em>Mf.australis</em> strain IT-1 but also can positively impact population growth in these MTB.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 2","pages":"Article 108181"},"PeriodicalIF":3.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143531298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

MRGPRX2 ligandome: Molecular simulations reveal three categories of ligand-receptor interactions MRGPRX2配体：分子模拟揭示了配体与受体相互作用的三种类型。

IF 3 3区生物学

Journal of structural biology Pub Date : 2025-06-01 Epub Date: 2025-03-12 DOI: 10.1016/j.jsb.2025.108193

Philip Maier , Moritz Macht , Silvan Beck , Pavel Kolkhir , Magda Babina , Andreas E. Kremer , Dirk Zahn , Katharina Wolf

{"title":"MRGPRX2 ligandome: Molecular simulations reveal three categories of ligand-receptor interactions","authors":"Philip Maier , Moritz Macht , Silvan Beck , Pavel Kolkhir , Magda Babina , Andreas E. Kremer , Dirk Zahn , Katharina Wolf","doi":"10.1016/j.jsb.2025.108193","DOIUrl":"10.1016/j.jsb.2025.108193","url":null,"abstract":"<div><h3>Introduction</h3><div>Mas-related G protein-coupled receptor (MRGPR) X2 is a mast cell receptor known to be activated by a wide range of ligands of various size, charge and origin. Our aim is to gain a deeper understanding of the binding processes of the different MRGPRX2 ligands and the ligand-receptor interactions in order to identify crucial structural elements for receptor activation.</div></div><div><h3>Materials and methods</h3><div>We used the three-dimensional structure of MRGPRX2 described in <em>Nature</em> in 2021 by Cao et al. and Yang et al. to computationally model the interaction between MRGPRX2 and small molecule ligands under simulated physiological conditions.</div></div><div><h3>Results</h3><div>Docking and post-docking samplings of the MRGPRX2 ligandome within the GPCR binding pocket led to the identification of key structural features for protein–ligand interactions. On the ligand side, we obtained an overlay of different molecular patterns or chemical groups by comparing different ligands plotted on the receptor. These key features include at least one protonated amine moiety of MRGPRX2 ligands contributing to one salt-bridge and one π-cation interaction, as well as an extended non-polar domain of the ligand surface that offer hydrophobic segregation and/or π-stacking interactions. In the receptor, we identified amino acids (GLU164, ASP184, PHE101, PHE170, TRP243, PHE244 and PHE257) that specifically interact via hydrogen bonding, salt-bridges, π-cation interactions and π-π stacking with the ligands to direct binding and ultimately receptor activation.</div></div><div><h3>Discussion</h3><div>Our insights into ligand-receptor interaction obtained by molecular modeling can help to predict mast cell activation via MRGPRX2 including adverse reactions, and facilitate the development of MRGPRX2 antagonists for the treatment of mast cell-mediated diseases.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 2","pages":"Article 108193"},"PeriodicalIF":3.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143630507","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Disulfide bonds enhance thermal stability and thumb region drives activity of the glycoside hydrolase 11 xylanase rMxylcd 二硫键增强热稳定性，拇指区驱动糖苷水解酶11木聚糖酶rMxylcd的活性。

IF 3 3区生物学

Journal of structural biology Pub Date : 2025-06-01 Epub Date: 2025-05-12 DOI: 10.1016/j.jsb.2025.108209

Songna Wu , Nianying Zhang , Qun Wan

{"title":"Disulfide bonds enhance thermal stability and thumb region drives activity of the glycoside hydrolase 11 xylanase rMxylcd","authors":"Songna Wu , Nianying Zhang , Qun Wan","doi":"10.1016/j.jsb.2025.108209","DOIUrl":"10.1016/j.jsb.2025.108209","url":null,"abstract":"<div><div>Thermostable enzymes have significant advantages in industries, yet uncovering novel candidates with superior properties remains a scientific pursuit. This study identified rMxyl<sup>cd</sup>, a glycoside hydrolase 11 family thermophilic xylanase from compost-soil metagenome, which exhibited a high specific activity of 5954 U·mg<sup>−1</sup> at pH 5.5 and 80°C. rMxyl<sup>cd</sup> was crystallized and diffracted to 1.5 Å resolution. Compared to the mesophilic xylanase Xyn II, rMxyl<sup>cd</sup> exhibits a more compact architecture. Notably, B-factor analysis reveals a uniquely flexible thumb region, hinting at its critical role in the enzyme’s catalytic mechanism. rMxyl<sup>cd</sup> contains two disulfide bonds in the thumb and the <em>N</em>-terminal regions. Breaking these disulfide bonds by mutagenesis has dramatically decreased activities and thermostability. Conversely, introducing an extra disulfide bond at the <em>N</em>-terminal region of its α-helix extended its half-life for more than five folds at 80°C. Our studies firmly establish that the disulfide bonds are essential for its high thermal stability and the flexibility of the thumb region is crucial for its activity. Comparing the rMxyl<sup>cd</sup> crystal structure with the AlphaFold2-predicted model shows overall similarity, but the crystal structure offers higher local accuracy, especially in key functional regions. These findings not only deepen our understanding of the structure-function relationship of thermophilic xylanases but also inform a rational design of industrial enzymes.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 2","pages":"Article 108209"},"PeriodicalIF":3.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144078757","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Structural insights into substrate recognition of tri-modular xyloglucanase from Aspergillus oryzae 米曲霉三模木糖葡聚糖酶底物识别的结构研究。

IF 3 3区生物学

Journal of structural biology Pub Date : 2025-06-01 Epub Date: 2025-05-23 DOI: 10.1016/j.jsb.2025.108213

Yusuke Nakamichi , Naoki Shimada , Masahiro Watanabe , Tatsuya Fujii , Katsuro Yaoi , Tomohiko Matsuzawa

引用次数: 0

Allosteric inhibition of cytosolic NADP+-dependent isocitrate dehydrogenase by oxaloacetate 草酰乙酸对胞浆内NADP+依赖性异柠檬酸脱氢酶的变构抑制作用。

IF 3 3区生物学

Journal of structural biology Pub Date : 2025-06-01 Epub Date: 2025-03-08 DOI: 10.1016/j.jsb.2025.108183

Dong Kyu Kim , Ha Yeon Cho , Hyo Je Cho , Beom Sik Kang

{"title":"Allosteric inhibition of cytosolic NADP+-dependent isocitrate dehydrogenase by oxaloacetate","authors":"Dong Kyu Kim , Ha Yeon Cho , Hyo Je Cho , Beom Sik Kang","doi":"10.1016/j.jsb.2025.108183","DOIUrl":"10.1016/j.jsb.2025.108183","url":null,"abstract":"<div><div>NADP<sup>+</sup>-dependent cytosolic isocitrate dehydrogenase (IDH1) plays a crucial role in providing reducing energy in response to oxidative stress through the oxidative decarboxylation of isocitrate. NADPH generated by IDH1 serves as an essential cofactor for fatty acid synthesis. The regulation of IDH1 activity is vital for the biological functions of NADPH within cells, and mutations in IDH1 have been implicated in various cancers. In an effort to identify small regulatory molecules for IDH1, we determined the crystal structures of mouse IDH1 complexed with isocitrate and with oxaloacetate. Each IDH1 comprises large and small domains that form an active site, along with a clasp domain that connects two IDH1 molecules for dimerization. Isocitrate was located at the active site in the presence of a magnesium ion, while oxaloacetate was found at a novel site formed by the two clasp domains, in addition to the active site. The activity of IDH1 was diminished in the presence of oxaloacetate and could not be restored by the addition of isocitrate, indicating the presence of allosteric regulation. The activity of the IDH1 H170A mutant, which is unable to bind oxaloacetate in the clasp domain, was unaffected by oxaloacetate. This allosteric regulatory site may serve as a potential target for novel IDH1 inhibitors.</div></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":"217 2","pages":"Article 108183"},"PeriodicalIF":3.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143597205","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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