Acta Crystallographica. Section D, Structural Biology最新文献_第10页

Cryo-EM structure of adeno-associated virus 4 at 2.2 Å resolution. 分辨率为 2.2 Å 的腺相关病毒 4 的冷冻电镜结构。

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2023-02-01 Epub Date: 2023-01-20 DOI: 10.1107/S2059798322012190

Grant Zane, Mark Silveria, Nancy Meyer, Tommi White, Rui Duan, Xiaoqin Zou, Michael Chapman

{"title":"Cryo-EM structure of adeno-associated virus 4 at 2.2 Å resolution.","authors":"Grant Zane, Mark Silveria, Nancy Meyer, Tommi White, Rui Duan, Xiaoqin Zou, Michael Chapman","doi":"10.1107/S2059798322012190","DOIUrl":"10.1107/S2059798322012190","url":null,"abstract":"Adeno-associated virus (AAV) is the vector of choice for several approved gene-therapy treatments and is the basis for many ongoing clinical trials. Various strains of AAV exist (referred to as serotypes), each with their own transfection characteristics. Here, a high-resolution cryo-electron microscopy structure (2.2 Å) of AAV serotype 4 (AAV4) is presented. The receptor responsible for transduction of the AAV4 clade of AAV viruses (including AAV11, AAV12 and AAVrh32.33) is unknown. Other AAVs interact with the same cell receptor, adeno-associated virus receptor (AAVR), in one of two different ways. AAV5-like viruses interact exclusively with the polycystic kidney disease-like 1 (PKD1) domain of AAVR, while most other AAVs interact primarily with the PKD2 domain. A comparison of the present AAV4 structure with prior corresponding structures of AAV5, AAV2 and AAV1 in complex with AAVR provides a foundation for understanding why the AAV4-like clade is unable to interact with either PKD1 or PKD2 of AAVR. The conformation of the AAV4 capsid in variable regions I, III, IV and V on the viral surface appears to be sufficiently different from AAV2 to ablate binding with PKD2. Differences between AAV4 and AAV5 in variable region VII appear to be sufficient to exclude binding with PKD1.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":"79 Pt 2","pages":"140-153"},"PeriodicalIF":2.6,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9912921/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9479460","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

30 years of Acta D. 《医学学报》30年

IF 2.2 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2023-02-01 DOI: 10.1107/S2059798323001006

Elspeth F Garman, Randy J Read, Charles S Bond

引用次数: 0

The LH-DH module of bacterial replicative helicases is the common binding site for DciA and other helicase loaders. 细菌复制螺旋酶的 LH-DH 模块是 DciA 和其他螺旋酶加载器的共同结合位点。

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2023-02-01 Epub Date: 2023-02-06 DOI: 10.1107/S2059798323000281

Claire Cargemel, Stéphanie Marsin, Magali Noiray, Pierre Legrand, Halil Bounoua, Inès Li de la Sierra-Gallay, Hélène Walbott, Sophie Quevillon-Cheruel

{"title":"The LH-DH module of bacterial replicative helicases is the common binding site for DciA and other helicase loaders.","authors":"Claire Cargemel, Stéphanie Marsin, Magali Noiray, Pierre Legrand, Halil Bounoua, Inès Li de la Sierra-Gallay, Hélène Walbott, Sophie Quevillon-Cheruel","doi":"10.1107/S2059798323000281","DOIUrl":"10.1107/S2059798323000281","url":null,"abstract":"During the initiation step of bacterial genome replication, replicative helicases depend on specialized proteins for their loading onto oriC. DnaC and DnaI were the first loaders to be characterized. However, most bacteria do not contain any of these genes, which are domesticated phage elements that have replaced the ancestral and unrelated loader gene dciA several times during evolution. To understand how DciA assists the loading of DnaB, the crystal structure of the complex from Vibrio cholerae was determined, in which two VcDciA molecules interact with a dimer of VcDnaB without changing its canonical structure. The data showed that the VcDciA binding site on VcDnaB is the conserved module formed by the linker helix LH of one monomer and the determinant helix DH of the second monomer. Interestingly, DnaC from Escherichia coli also targets this module onto EcDnaB. Thanks to their common target site, it was shown that VcDciA and EcDnaC could be functionally interchanged in vitro despite sharing no structural similarity. This represents a milestone in understanding the mechanism employed by phage helicase loaders to hijack bacterial replicative helicases during evolution.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":"79 Pt 2","pages":"177-187"},"PeriodicalIF":2.6,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9912922/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9267038","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

Crystal structure of a polyglycine hydrolase determined using a RoseTTAFold model. 使用 RoseTTAFold 模型测定的聚甘氨酸水解酶晶体结构。

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2023-02-01 Epub Date: 2023-02-06 DOI: 10.1107/S2059798323000311

Nicole V Dowling, Todd A Naumann, Neil P J Price, David R Rose

{"title":"Crystal structure of a polyglycine hydrolase determined using a RoseTTAFold model.","authors":"Nicole V Dowling, Todd A Naumann, Neil P J Price, David R Rose","doi":"10.1107/S2059798323000311","DOIUrl":"10.1107/S2059798323000311","url":null,"abstract":"Polyglycine hydrolases (PGHs) are secreted fungal proteases that cleave the polyglycine linker of Zea mays ChitA, a defensive chitinase, thus overcoming one mechanism of plant resistance to infection. Despite their importance in agriculture, there has been no previous structural characterization of this family of proteases. The objective of this research was to investigate the proteolytic mechanism and other characteristics by structural and biochemical means. Here, the first atomic structure of a polyglycine hydrolase was identified. It was solved by X-ray crystallography using a RoseTTAFold model, taking advantage of recent technical advances in structure prediction. PGHs are composed of two domains: the N- and C-domains. The N-domain is a novel tertiary fold with an as-yet unknown function that is found across all kingdoms of life. The C-domain shares structural similarities with class C β-lactamases, including a common catalytic nucleophilic serine. In addition to insights into the PGH family and its relationship to β-lactamases, the results demonstrate the power of complementing experimental structure determination with new computational techniques.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":"79 Pt 2","pages":"168-176"},"PeriodicalIF":2.6,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9912923/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9282726","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

Right-handed Z-DNA at ultrahigh resolution: a tale of two hands and the power of the crystallographic method. 超高分辨率的右手 Z-DNA：两只手的故事和晶体学方法的力量。

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2023-02-01 Epub Date: 2023-01-20 DOI: 10.1107/S2059798322011937

Pawel Drozdzal, Tomasz Manszewski, Miroslaw Gilski, Krzysztof Brzezinski, Mariusz Jaskolski

{"title":"Right-handed Z-DNA at ultrahigh resolution: a tale of two hands and the power of the crystallographic method.","authors":"Pawel Drozdzal, Tomasz Manszewski, Miroslaw Gilski, Krzysztof Brzezinski, Mariusz Jaskolski","doi":"10.1107/S2059798322011937","DOIUrl":"10.1107/S2059798322011937","url":null,"abstract":"The self-complementary L-d(CGCGCG)2 purine/pyrimidine hexanucleotide was crystallized in complex with the polyamine cadaverine and potassium cations. Since the oligonucleotide contained the enantiomeric 2'-deoxy-L-ribose, the Z-DNA duplex is right-handed, as confirmed by the ultrahigh-resolution crystal structure determined at 0.69 Å resolution. Although the X-ray diffraction data were collected at a very short wavelength (0.7085 Å), where the anomalous signal of the P and K atoms is very weak, the signal was sufficiently outstanding to clearly indicate the wrong hand when the structure was mistakenly solved assuming the presence of 2'-deoxy-D-ribose. The electron density clearly shows the entire cadaverinium dication, which has an occupancy of 0.53 and interacts with one Z-DNA duplex. The K+ cation, with an occupancy of 0.32, has an irregular coordination sphere that is formed by three OP atoms of two symmetry-related Z-DNA duplexes and one O5' hydroxyl O atom, and is completed by three water sites, one of which is twofold disordered. The K+ site is complemented by a partial water molecule, the hydrogen bonds of which have the same lengths as the K-O bonds. The sugar-phosphate backbone assumes two conformations, but the base pairs do not show any sign of disorder.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":"79 Pt 2","pages":"133-139"},"PeriodicalIF":2.6,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9912920/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9282727","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

Protein model refinement for cryo-EM maps using AlphaFold2 and the DAQ score. 使用 AlphaFold2 和 DAQ 分数完善低温电子显微镜图的蛋白质模型。

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2023-01-01 DOI: 10.1107/S2059798322011676

Genki Terashi, Xiao Wang, Daisuke Kihara

{"title":"Protein model refinement for cryo-EM maps using AlphaFold2 and the DAQ score.","authors":"Genki Terashi, Xiao Wang, Daisuke Kihara","doi":"10.1107/S2059798322011676","DOIUrl":"10.1107/S2059798322011676","url":null,"abstract":"As more protein structure models have been determined from cryogenic electron microscopy (cryo-EM) density maps, establishing how to evaluate the model accuracy and how to correct models in cases where they contain errors is becoming crucial to ensure the quality of the structural models deposited in the public database, the PDB. Here, a new protocol is presented for evaluating a protein model built from a cryo-EM map and applying local structure refinement in the case where the model has potential errors. Firstly, model evaluation is performed using a deep-learning-based model-local map assessment score, DAQ, that has recently been developed. The subsequent local refinement is performed by a modified AlphaFold2 procedure, in which a trimmed template model and a trimmed multiple sequence alignment are provided as input to control which structure regions to refine while leaving other more confident regions of the model intact. A benchmark study showed that this protocol, DAQ-refine, consistently improves low-quality regions of the initial models. Among 18 refined models generated for an initial structure, DAQ shows a high correlation with model quality and can identify the best accurate model for most of the tested cases. The improvements obtained by DAQ-refine were on average larger than other existing methods.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":"79 Pt 1","pages":"10-21"},"PeriodicalIF":2.6,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9815095/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9441470","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

Drosophila melanogaster frataxin: protein crystal and predicted solution structure with identification of the iron-binding regions. 黑腹果蝇 frataxin：蛋白质晶体和预测溶液结构以及铁结合区域的鉴定。

IF 2.2 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2023-01-01 DOI: 10.1107/S2059798322011639

Andria V Rodrigues, Sharon Batelu, Tiara V Hinton, John Rotondo, Lindsey Thompson, Joseph S Brunzelle, Timothy L Stemmler

{"title":"Drosophila melanogaster frataxin: protein crystal and predicted solution structure with identification of the iron-binding regions.","authors":"Andria V Rodrigues, Sharon Batelu, Tiara V Hinton, John Rotondo, Lindsey Thompson, Joseph S Brunzelle, Timothy L Stemmler","doi":"10.1107/S2059798322011639","DOIUrl":"10.1107/S2059798322011639","url":null,"abstract":"Friedreich's ataxia (FRDA) is a hereditary cardiodegenerative and neurodegenerative disease that affects 1 in 50 000 Americans. FRDA arises from either a cellular inability to produce sufficient quantities or the production of a nonfunctional form of the protein frataxin, a key molecule associated with mitochondrial iron-sulfur cluster biosynthesis. Within the mitochondrial iron-sulfur cluster (ISC) assembly pathway, frataxin serves as an allosteric regulator for cysteine desulfurase, the enzyme that provides sulfur for [2Fe-2S] cluster assembly. Frataxin is a known iron-binding protein and is also linked to the delivery of ferrous ions to the scaffold protein, the ISC molecule responsible for the direct assembly of [2Fe-2S] clusters. The goal of this report is to provide structural details of the Drosophila melanogaster frataxin ortholog (Dfh), using both X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy, in order to provide the foundational insight needed to understand the structure-function correlation of the protein. Additionally, NMR iron(II) titrations were used to provide metal contacts on the protein to better understand how it binds iron and aids its delivery to the ISC scaffold protein. Here, the structural and functional similarities of Dfh to its orthologs are also outlined. Structural data show that bacterial, yeast, human and Drosophila frataxins are structurally similar, apart from a structured C-terminus in Dfh that is likely to aid in protein stability. The iron-binding location on helix 1 and strand 1 of Dfh is also conserved across orthologs.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":"79 Pt 1","pages":"22-30"},"PeriodicalIF":2.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9815096/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10869849","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: 1

Crystal structure of a covalently linked Aurora-A-MYCN complex. 共价连接的 Aurora-A-MYCN 复合物的晶体结构。

IF 2.6 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2023-01-01 DOI: 10.1107/S2059798322011433

Mathias Diebold, Lars Schönemann, Martin Eilers, Christoph Sotriffer, Hermann Schindelin

引用次数: 0

Structural insights into the effects of glycerol on ligand binding to cytochrome P450. 甘油对配体结合细胞色素P450的影响的结构见解。

IF 2.2 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2023-01-01 DOI: 10.1107/S2059798322011019

Sergey Bukhdruker, Tatsiana Varaksa, Philipp Orekhov, Irina Grabovec, Egor Marin, Ivan Kapranov, Kirill Kovalev, Roman Astashkin, Leonid Kaluzhskiy, Alexis Ivanov, Alexey Mishin, Andrey Rogachev, Valentin Gordeliy, Andrei Gilep, Natallia Strushkevich, Valentin Borshchevskiy

{"title":"Structural insights into the effects of glycerol on ligand binding to cytochrome P450.","authors":"Sergey Bukhdruker, Tatsiana Varaksa, Philipp Orekhov, Irina Grabovec, Egor Marin, Ivan Kapranov, Kirill Kovalev, Roman Astashkin, Leonid Kaluzhskiy, Alexis Ivanov, Alexey Mishin, Andrey Rogachev, Valentin Gordeliy, Andrei Gilep, Natallia Strushkevich, Valentin Borshchevskiy","doi":"10.1107/S2059798322011019","DOIUrl":"https://doi.org/10.1107/S2059798322011019","url":null,"abstract":"New antitubercular drugs are vital due to the spread of resistant strains. Carbethoxyhexyl imidazole (CHImi) inhibits cytochrome P450 CYP124, which is a steroid-metabolizing enzyme that is important for the survival of Mycobacterium tuberculosis in macrophages. The available crystal structure of the CYP124-CHImi complex reveals two glycerol molecules in the active site. A 1.15 Å resolution crystal structure of the glycerol-free CYP124-CHimi complex reported here shows multiple conformations of CHImi and the CYP124 active site which were previously restricted by glycerol. Complementary molecular dynamics simulations show coherence of the ligand and enzyme conformations. Spectrophotometric titration confirmed the influence of glycerol on CHImi binding: the affinity decreases more than tenfold in glycerol-containing buffer. In addition, it also showed that glycerol has a similar effect on other azole and triazole CYP124 ligands. Together, these data show that glycerol may compromise structural-functional studies and impede rational drug-design campaigns.","PeriodicalId":7116,"journal":{"name":"Acta Crystallographica. Section D, Structural Biology","volume":"79 Pt 1","pages":"66-77"},"PeriodicalIF":2.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10481492","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

A scoring function for the prediction of protein complex interfaces based on the neighborhood preferences of amino acids. 基于氨基酸邻域偏好预测蛋白质复合物界面的评分函数。

IF 2.2 4区生物学

Acta Crystallographica. Section D, Structural Biology Pub Date : 2023-01-01 DOI: 10.1107/S2059798322011858

Mulpuri Nagaraju, Haiguang Liu

引用次数: 0