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

Molecular assemblies built with the artificial protein Pizza 用人造蛋白披萨构建的分子组装

IF 2.9

Journal of Structural Biology: X Pub Date : 2020-01-01 DOI: 10.1016/j.yjsbx.2020.100027

Jeroen P.M. Vrancken , Jana Aupič , Christine Addy , Roman Jerala , Jeremy R.H. Tame , Arnout R.D. Voet

{"title":"Molecular assemblies built with the artificial protein Pizza","authors":"Jeroen P.M. Vrancken , Jana Aupič , Christine Addy , Roman Jerala , Jeremy R.H. Tame , Arnout R.D. Voet","doi":"10.1016/j.yjsbx.2020.100027","DOIUrl":"10.1016/j.yjsbx.2020.100027","url":null,"abstract":"<div><p>Recently an artificial protein named Pizza6 was reported, which possesses six identical tandem repeats and adopts a monomeric <span><math><mrow><mi>β</mi></mrow></math></span>-propeller fold with sixfold structural symmetry. Pizza2, a truncated form that consists of a double tandem repeat, self-assembles into a trimer reconstructing the same propeller architecture as Pizza6. The ability of pizza proteins to self-assemble to form complete propellers makes them interesting building blocks to engineer larger symmetrical protein complexes such as symmetric nanoparticles. Here we have explored the self-assembly of Pizza2 fused to homo-oligomerizing peptides. In total, we engineered five different fusion proteins, of which three appeared to assemble successfully into larger complexes. Further characterization of these proteins showed one monodisperse designer protein with a structure close to the intended design. This protein was further fused to eGFP to investigate functionalization of the nanoparticle. The fusion protein was stable and could be expressed in high yield, showing that Pizza-based nanoparticles may be further decorated with functional domains</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.2020.100027","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38137189","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: 7

A Monte Carlo framework for missing wedge restoration and noise removal in cryo-electron tomography 低温电子断层扫描中缺失楔形恢复和噪声去除的蒙特卡罗框架

IF 2.9

Journal of Structural Biology: X Pub Date : 2020-01-01 DOI: 10.1016/j.yjsbx.2019.100013

Emmanuel Moebel, Charles Kervrann

引用次数: 14

Cryo-EM structure of the prefusion state of canine distemper virus fusion protein ectodomain 犬瘟热病毒融合蛋白外结构域融合前状态的低温电镜结构

IF 2.9

Journal of Structural Biology: X Pub Date : 2020-01-01 DOI: 10.1016/j.yjsbx.2020.100021

David Kalbermatter , Neeta Shrestha , Flavio M. Gall , Marianne Wyss , Rainer Riedl , Philippe Plattet , Dimitrios Fotiadis

{"title":"Cryo-EM structure of the prefusion state of canine distemper virus fusion protein ectodomain","authors":"David Kalbermatter , Neeta Shrestha , Flavio M. Gall , Marianne Wyss , Rainer Riedl , Philippe Plattet , Dimitrios Fotiadis","doi":"10.1016/j.yjsbx.2020.100021","DOIUrl":"10.1016/j.yjsbx.2020.100021","url":null,"abstract":"<div><p>Measles virus (MeV) and canine distemper virus (CDV), two members of the <em>Morbillivirus</em> genus, are still causing important global diseases of humans and animals, respectively. To enter target cells, morbilliviruses rely on an envelope-anchored machinery, which is composed of two interacting glycoproteins: a tetrameric receptor binding (H) protein and a trimeric fusion (F) protein. To execute membrane fusion, the F protein initially adopts a metastable, prefusion state that refolds into a highly stable postfusion conformation as the result of a finely coordinated activation process mediated by the H protein. Here, we employed cryo-electron microscopy (cryo-EM) and single particle reconstruction to elucidate the structure of the prefusion state of the CDV F protein ectodomain (solF) at 4.3 Å resolution. Stabilization of the prefusion solF trimer was achieved by fusing the GCNt trimerization sequence at the C-terminal protein region, and expressing and purifying the recombinant protein in the presence of a morbilliviral fusion inhibitor class compound. The three-dimensional cryo-EM map of prefusion CDV solF in complex with the inhibitor clearly shows density for the ligand at the protein binding site suggesting common mechanisms of membrane fusion activation and inhibition employed by different morbillivirus members.</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.2020.100021","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38137185","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

Sub-2 Angstrom resolution structure determination using single-particle cryo-EM at 200 keV 在200 keV下使用单粒子低温电镜进行亚2埃分辨率结构测定

IF 2.9

Journal of Structural Biology: X Pub Date : 2020-01-01 DOI: 10.1016/j.yjsbx.2020.100020

Mengyu Wu , Gabriel C. Lander , Mark A. Herzik Jr.

{"title":"Sub-2 Angstrom resolution structure determination using single-particle cryo-EM at 200 keV","authors":"Mengyu Wu , Gabriel C. Lander , Mark A. Herzik Jr.","doi":"10.1016/j.yjsbx.2020.100020","DOIUrl":"10.1016/j.yjsbx.2020.100020","url":null,"abstract":"<div><p>Although the advent of direct electron detectors (DEDs) and software developments have enabled the routine use of single-particle cryogenic electron microscopy (cryo-EM) for structure determination of well-behaved specimens to high-resolution, there nonetheless remains a discrepancy between the resolutions attained for biological specimens and the information limits of modern transmission electron microscopes (TEMs). Instruments operating at 300 kV equipped with DEDs are the current paradigm for high-resolution single-particle cryo-EM, while 200 kV TEMs remain comparatively underutilized for purposes beyond sample screening. Here, we expand upon our prior work and demonstrate that one such 200 kV microscope, the Talos Arctica, equipped with a K2 DED is capable of determining structures of macromolecules to as high as ∼1.7 Å resolution. At this resolution, ordered water molecules are readily assigned and holes in aromatic residues can be clearly distinguished in the reconstructions. This work emphasizes the utility of 200 kV electrons for high-resolution single-particle cryo-EM and applications such as structure-based drug design.</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.2020.100020","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38137268","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: 35

Improvements on marker-free images alignment for electron tomography 电子断层扫描无标记图像对准的改进

IF 2.9

Journal of Structural Biology: X Pub Date : 2020-01-01 DOI: 10.1016/j.yjsbx.2020.100037

C.O.S. Sorzano , F. de Isidro-Gómez , E. Fernández-Giménez , D. Herreros , S. Marco , J.M. Carazo , C. Messaoudi

{"title":"Improvements on marker-free images alignment for electron tomography","authors":"C.O.S. Sorzano , F. de Isidro-Gómez , E. Fernández-Giménez , D. Herreros , S. Marco , J.M. Carazo , C. Messaoudi","doi":"10.1016/j.yjsbx.2020.100037","DOIUrl":"10.1016/j.yjsbx.2020.100037","url":null,"abstract":"<div><p>Electron tomography is a technique to obtain three-dimensional structural information of samples. However, the technique is limited by shifts occurring during acquisition that need to be corrected before the reconstruction process. In 2009, we proposed an approach for post-acquisition alignment of tilt series images. This approach was marker-free, based on patch tracking and integrated in free software. Here, we present improvements to the method to make it more reliable, stable and accurate. In addition, we modified the image formation model underlying the alignment procedure to include different deformations occurring during acquisition. We propose a new way to correct these computed deformations to obtain reconstructions with reduced artifacts. The new approach has demonstrated to improve the quality of the final 3D reconstruction, giving access to better defined structures for different transmission electron tomography methods: resin embedded STEM-tomography and cryo-TEM tomography. The method is freely available in TomoJ software.</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.2020.100037","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38461302","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

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