Journal of Structural Biology: X最新文献_第10页

Validation tests for cryo-EM maps using an independent particle set 使用独立粒子集的低温电镜图验证测试

IF 2.9

Journal of Structural Biology: X Pub Date : 2020-01-01 DOI: 10.1016/j.yjsbx.2020.100032

Sebastian Ortiz , Luka Stanisic , Boris A Rodriguez , Markus Rampp , Gerhard Hummer , Pilar Cossio

{"title":"Validation tests for cryo-EM maps using an independent particle set","authors":"Sebastian Ortiz , Luka Stanisic , Boris A Rodriguez , Markus Rampp , Gerhard Hummer , Pilar Cossio","doi":"10.1016/j.yjsbx.2020.100032","DOIUrl":"10.1016/j.yjsbx.2020.100032","url":null,"abstract":"<div><p>Cryo-electron microscopy (cryo-EM) has revolutionized structural biology by providing 3D density maps of biomolecules at near-atomic resolution. However, map validation is still an open issue. Despite several efforts from the community, it is possible to overfit 3D maps to noisy data. Here, we develop a novel methodology that uses a small independent particle set (not used during the 3D refinement) to validate the maps. The main idea is to monitor how the map probability evolves over the control set during the 3D refinement. The method is complementary to the gold-standard procedure, which generates two reconstructions at each iteration. We low-pass filter the two reconstructions for different frequency cutoffs, and we calculate the probability of each filtered map given the control set. For high-quality maps, the probability should increase as a function of the frequency cutoff and the refinement iteration. We also compute the similarity between the densities of probability distributions of the two reconstructions. As higher frequencies are included, the distributions become more dissimilar. We optimized the BioEM package to perform these calculations, and tested it over systems ranging from quality data to pure noise. Our results show that with our methodology, it possible to discriminate datasets that are constructed from noise particles. We conclude that validation against a control particle set provides a powerful tool to assess the quality of cryo-EM maps.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.yjsbx.2020.100032","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38218712","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Crystallographic and cryogenic electron microscopic structures and enzymatic characterization of sulfur oxygenase reductase from Sulfurisphaera tokodaii 硫加氧酶还原酶的晶体学和低温电镜结构及酶学性质

IF 2.9

Journal of Structural Biology: X Pub Date : 2020-01-01 DOI: 10.1016/j.yjsbx.2020.100030

Yuta Sato , Takashi Yabuki , Naruhiko Adachi , Toshio Moriya , Takatoshi Arakawa , Masato Kawasaki , Chihaya Yamada , Toshiya Senda , Shinya Fushinobu , Takayoshi Wakagi

{"title":"Crystallographic and cryogenic electron microscopic structures and enzymatic characterization of sulfur oxygenase reductase from Sulfurisphaera tokodaii","authors":"Yuta Sato , Takashi Yabuki , Naruhiko Adachi , Toshio Moriya , Takatoshi Arakawa , Masato Kawasaki , Chihaya Yamada , Toshiya Senda , Shinya Fushinobu , Takayoshi Wakagi","doi":"10.1016/j.yjsbx.2020.100030","DOIUrl":"https://doi.org/10.1016/j.yjsbx.2020.100030","url":null,"abstract":"<div><p>Sulfur oxygenase reductases (SORs) are present in thermophilic and mesophilic archaea and bacteria, and catalyze oxygen-dependent oxygenation and disproportionation of elemental sulfur. SOR has a hollow, spherical homo-24-mer structure and reactions take place at active sites inside the chamber. The crystal structures of SORs from <em>Acidianus</em> species have been reported. However, the states of the active site components (mononuclear iron and cysteines) and the entry and exit paths of the substrate and products are still in dispute. Here, we report the biochemical and structural characterizations of SORs from the thermoacidophilic archaeon <em>Sulfurisphaera tokodaii</em> (StSOR) and present high-resolution structures determined by X-ray crystallography and cryogenic electron microscopy (cryo-EM). The crystal structure of StSOR was determined at 1.73 Å resolution. At the catalytic center, iron is ligated to His86, His90, Glu114, and two water molecules. Three conserved cysteines in the cavity are located 9.5–13 Å from the iron and were observed as free thiol forms. A mutational analysis indicated that the iron and one of the cysteines (Cys31) were essential for both activities. The cryo-EM structure was determined at 2.24 Å resolution using an instrument operating at 200 kV. The two structures determined by different methodologies showed similar main chain traces, but the maps exhibited different features at catalytically important components. A possible role of StSOR in the sulfur metabolism of <em>S. tokodaii</em> (an obligate aerobe) is discussed based on this study. Given the high resolution achieved in this study, StSOR was shown to be a good benchmark sample for cryo-EM.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.yjsbx.2020.100030","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72113476","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Type I beta turns make a new twist in pentapeptide repeat proteins: Crystal structure of Alr5209 from Nostoc sp. PCC 7120 determined at 1.7 angström resolution I型β旋转在五肽重复蛋白中产生新的扭曲:Nostoc sp. PCC 7120的Alr5209的晶体结构在1.7 angström分辨率下测定

IF 2.9

Journal of Structural Biology: X Pub Date : 2019-07-01 DOI: 10.1016/j.yjsbx.2019.100010

Ruojing Zhang, Shuisong Ni, Michael A. Kennedy

{"title":"Type I beta turns make a new twist in pentapeptide repeat proteins: Crystal structure of Alr5209 from Nostoc sp. PCC 7120 determined at 1.7 angström resolution","authors":"Ruojing Zhang, Shuisong Ni, Michael A. Kennedy","doi":"10.1016/j.yjsbx.2019.100010","DOIUrl":"10.1016/j.yjsbx.2019.100010","url":null,"abstract":"<div><p>Pentapeptide repeat proteins (PRPs) are found abundantly in cyanobacteria, numbering in the dozens in some genomes, e.g. in Nostoc sp. PCC 7120. PRPs, comprised of a repeating consensus sequence of five amino acids, adopt a distinctive right-handed quadrilateral β-helical structure, also referred to as a repeat five residue (Rfr) fold, made up of stacks of coils formed by four consecutive pentapeptide repeats. The right-handed quadrilateral β-helical PRP structure is constructed by repeating β turns at each of four corners in a given coil, each causing a 90° change in direction of the polypeptide chain. Until now, all PRP structures have consisted either of type II and IV β turns or exclusively of type II β turns. Here, we report the first structure of a PRP comprised of type I and II β turns, Alr5209 from Nostoc sp. PCC 7120. The <em>alr5209</em> gene encodes 129 amino acids containing 16 tandem pentapeptide repeats. The Alr5209 structure was analyzed in comparison to all other PRPs to determine how type I β turns can be accommodated in Rfr folds and the consequences of type I β turns on the right-handed quadrilateral β-helical structure. Given that Alr5209 represents the first PRP structure containing type I β turns, the PRP consensus sequence was reevaluated and updated. Despite a growing number of PRP structural investigations, their function remains largely unknown. Genome analysis indicated that <em>alr5209</em> resides in a five-gene operon (<em>alr5208</em>-<em>alr5212</em>) with Alr5211 annotated to be a NADH dehydrogenase indicating Alr5209 may be involved in oxidative phosphorylation.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2019-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.yjsbx.2019.100010","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38137261","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Inactivation in the potassium channel KcsA 钾离子通道KcsA失活

IF 2.9

Journal of Structural Biology: X Pub Date : 2019-07-01 DOI: 10.1016/j.yjsbx.2019.100009

Yunyao Xu, Ann E. McDermott

引用次数: 13

Structural insights into the activity and regulation of human Josephin-2 人类Josephin-2活性和调控的结构见解

IF 2.9

Journal of Structural Biology: X Pub Date : 2019-07-01 DOI: 10.1016/j.yjsbx.2019.100011

Kimberly C. Grasty, Stephen D. Weeks , Patrick J. Loll

引用次数: 10

Parsing the functional specificity of Siderocalin/Lipocalin 2/NGAL for siderophores and related small-molecule ligands 解析铁载体/脂钙蛋白2/NGAL对铁载体及相关小分子配体的功能特异性

IF 2.9

Journal of Structural Biology: X Pub Date : 2019-04-01 DOI: 10.1016/j.yjsbx.2019.100008

Matthew C. Clifton , Peter B. Rupert , Trisha M. Hoette , Kenneth N. Raymond , Rebecca J. Abergel , Roland K. Strong

{"title":"Parsing the functional specificity of Siderocalin/Lipocalin 2/NGAL for siderophores and related small-molecule ligands","authors":"Matthew C. Clifton , Peter B. Rupert , Trisha M. Hoette , Kenneth N. Raymond , Rebecca J. Abergel , Roland K. Strong","doi":"10.1016/j.yjsbx.2019.100008","DOIUrl":"10.1016/j.yjsbx.2019.100008","url":null,"abstract":"<div><p>Siderocalin/Lipocalin 2/Neutrophil Gelatinase Associated Lipocalin/24p3 is an innate immune system protein with bacteriostatic activity, acting by tightly binding and sequestering diverse catecholate and mixed-type ferric siderophores from enteric bacteria and mycobacteria. Bacterial virulence achieved through siderophore modifications, or utilization of alternate siderophores, can be explained by evasion of Siderocalin binding. Siderocalin has also been implicated in a wide variety of disease processes, though often in seemingly contradictory ways, and has been proposed to bind to a broader array of ligands beyond siderophores. Using structural, directed mutational, and binding studies, we have sought to rigorously test, and fully elucidate, the Siderocalin recognition mechanism. Several proposed ligands fail to meet rigorous binding criteria, including the bacterial siderophore pyochelin, the iron-chelating catecholamine hormone norepinephrine, and the bacterial second messenger cyclic diguanylate monophosphate. While possessing a remarkably rigid structure, in principle simplifying analyses of ligand recognition, understanding Scn recognition is complicated by the observed conformational and stoichiometric plasticity, and instability, of its <em>bona fide</em> siderophore ligands. Since the role of Siderocalin at the early host/pathogen interface is to compete for bacterial ferric siderophores, we also analyzed how bacterial siderophore binding proteins and enzymes alternately recognize siderophores that efficiently bind to, or evade, Siderocalin sequestration – including determining the crystal structure of <em>Bacillus cereus</em> YfiY bound to schizokinen. These studies combine to refine the potential physiological functions of Siderocalin by defining its multiplexed recognition mechanism.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2019-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.yjsbx.2019.100008","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38137862","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 17

SmartBac, a new baculovirus system for large protein complex production SmartBac是一种新的杆状病毒系统，用于生产大的蛋白质复合物

IF 2.9

Journal of Structural Biology: X Pub Date : 2019-01-01 DOI: 10.1016/j.yjsbx.2019.100003

Yujia Zhai , Danyang Zhang , Leiye Yu , Fang Sun , Fei Sun

引用次数: 17

Growth and regrowth of adult sea urchin spines involve hydrated and anhydrous amorphous calcium carbonate precursors 成年海胆棘的生长和再生涉及水合和无水无定形碳酸钙前体

IF 2.9

Journal of Structural Biology: X Pub Date : 2019-01-01 DOI: 10.1016/j.yjsbx.2019.100004

Marie Albéric , Cayla A. Stifler , Zhaoyong Zou , Chang-Yu Sun , Christopher E. Killian , Sergio Valencia , Mohamad-Assaad Mawass , Luca Bertinetti , Pupa U.P.A. Gilbert , Yael Politi

{"title":"Growth and regrowth of adult sea urchin spines involve hydrated and anhydrous amorphous calcium carbonate precursors","authors":"Marie Albéric , Cayla A. Stifler , Zhaoyong Zou , Chang-Yu Sun , Christopher E. Killian , Sergio Valencia , Mohamad-Assaad Mawass , Luca Bertinetti , Pupa U.P.A. Gilbert , Yael Politi","doi":"10.1016/j.yjsbx.2019.100004","DOIUrl":"10.1016/j.yjsbx.2019.100004","url":null,"abstract":"<div><p>In various mineralizing marine organisms, calcite or aragonite crystals form through the initial deposition of amorphous calcium carbonate (ACC) phases with different hydration levels. Using X-ray PhotoEmission Electron spectroMicroscopy (X-PEEM), ACCs with varied spectroscopic signatures were previously identified. In particular, ACC type I and II were recognized in embryonic sea urchin spicules. ACC type I was assigned to hydrated ACC based on spectral similarity with synthetic hydrated ACC. However, the identity of ACC type II has never been unequivocally determined experimentally. In the present study we show that synthetic anhydrous ACC and ACC type II identified here in sea urchin spines, have similar Ca <em>L</em><sub>2,3</sub>-edge spectra. Moreover, using X-PEEM chemical mapping, we revealed the presence of ACC-H<sub>2</sub>O and anhydrous ACC in growing stereom and septa regions of sea urchin spines, supporting their role as precursor phases in both structures. However, the distribution and the abundance of the two ACC phases differ substantially between the two growing structures, suggesting a variation in the crystal growth mechanism; in particular, ACC dehydration, in the two-step reaction ACC-H<sub>2</sub>O → ACC → calcite, presents different kinetics, which are proposed to be controlled biologically.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.yjsbx.2019.100004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38137859","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 22

Structural and biochemical characterization of the pleckstrin homology domain of the RhoGEF P-Rex2 and its regulation by PIP3 RhoGEF P-Rex2的pleckstrin同源结构域的结构和生化特性及其对PIP3的调控

IF 2.9

Journal of Structural Biology: X Pub Date : 2019-01-01 DOI: 10.1016/j.yjsbx.2018.100001

Jennifer N. Cash , Prateek V. Sharma , John J.G. Tesmer

{"title":"Structural and biochemical characterization of the pleckstrin homology domain of the RhoGEF P-Rex2 and its regulation by PIP3","authors":"Jennifer N. Cash , Prateek V. Sharma , John J.G. Tesmer","doi":"10.1016/j.yjsbx.2018.100001","DOIUrl":"https://doi.org/10.1016/j.yjsbx.2018.100001","url":null,"abstract":"<div><p>P-Rex family Rho guanine-nucleotide exchange factors are important regulators of cell motility through their activation of a subset of small GTPases. Both P-Rex1 and P-Rex2 have also been implicated in the progression of certain cancers, including breast cancer and melanoma. Although these molecules display a high level of homology, differences exist in tissue distribution, physiological function, and regulation at the molecular level. Here, we sought to compare the P-Rex2 pleckstrin homology (PH) domain structure and ability to interact with PIP<sub>3</sub> with those of P-Rex1. The 1.9 Å crystal structure of the P-Rex2 PH domain reveals conformational differences in the loop regions, yet biochemical studies indicate that the interaction of the P-Rex2 PH domain with PIP<sub>3</sub> is very similar to that of P-Rex1. Binding of the PH domain to PIP<sub>3</sub> is critical for P-Rex2 activity but not membrane localization, as previously demonstrated for P-Rex1. These studies serve as a starting point in the identification of P-Rex structural features that are divergent between isoforms and could be exploited for the design of P-Rex selective compounds.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.yjsbx.2018.100001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72085746","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

3D mapping of native extracellular matrix reveals cellular responses to the microenvironment 原生细胞外基质的三维映射揭示了细胞对微环境的反应

IF 2.9

Journal of Structural Biology: X Pub Date : 2019-01-01 DOI: 10.1016/j.yjsbx.2018.100002

Zipora Lansky , Yael Mutsafi , Lothar Houben , Tal Ilani , Gad Armony , Sharon G. Wolf , Deborah Fass

{"title":"3D mapping of native extracellular matrix reveals cellular responses to the microenvironment","authors":"Zipora Lansky , Yael Mutsafi , Lothar Houben , Tal Ilani , Gad Armony , Sharon G. Wolf , Deborah Fass","doi":"10.1016/j.yjsbx.2018.100002","DOIUrl":"10.1016/j.yjsbx.2018.100002","url":null,"abstract":"<div><p>Cells and extracellular matrix (ECM) are mutually interdependent: cells guide self-assembly of ECM precursors, and the resulting ECM architecture supports and instructs cells. Though bidirectional signaling between ECM and cells is fundamental to cell biology, it is challenging to gain high-resolution structural information on cellular responses to the matrix microenvironment. Here we used cryo-scanning transmission electron tomography (CSTET) to reveal the nanometer- to micron-scale organization of major fibroblast ECM components in a native-like context, while simultaneously visualizing internal cell ultrastructure including organelles and cytoskeleton. In addition to extending current models for collagen VI fibril organization, three-dimensional views of thick cell regions and surrounding matrix showed how ECM networks impact the structures and dynamics of intracellular organelles and how cells remodel ECM. Collagen VI and fibronectin were seen to distribute in fundamentally different ways in the cell microenvironment and perform distinct roles in supporting and interacting with cells. This work demonstrates that CSTET provides a new perspective for the study of ECM in cell biology, highlighting labeled extracellular elements against a backdrop of unlabeled but morphologically identifiable cellular features with nanometer resolution detail.</p></div>","PeriodicalId":17238,"journal":{"name":"Journal of Structural Biology: X","volume":null,"pages":null},"PeriodicalIF":2.9,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.yjsbx.2018.100002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37642500","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 18