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The mythical metal – insights on the accuracy of metal identification in structural biology 神秘的金属--对结构生物学中金属识别准确性的见解
Acta Crystallographica Section A Foundations and Advances Pub Date : 2023-07-07 DOI: 10.1107/s2053273323097188
Edward H. Snell, E. Garman, Geoff W. Grime, Aina E. Cohen, Sarah E. J. Bowman
{"title":"The mythical metal – insights on the accuracy of metal identification in structural biology","authors":"Edward H. Snell, E. Garman, Geoff W. Grime, Aina E. Cohen, Sarah E. J. Bowman","doi":"10.1107/s2053273323097188","DOIUrl":"https://doi.org/10.1107/s2053273323097188","url":null,"abstract":"The Protein Data Bank (PDB) contains information on more than 200,000 proteins. Some 25 - 50% of all proteins contain one or more metals or metal co-factors playing a key structural or catalytic role. Metalloproteins can be difficult targets for structural studies because the specific metals required for enzymatic activity are not always those with the highest binding affinity. To incorporate uncompetitive metals into an enzyme active site, cells have evolved sophisticated machinery, including metal transporters and chaperones, which are often bypassed during protein production in the laboratory. The problem of metal promiscuity is compounded by the difficulty of accurately identifying incorporated metals. In many cases, the small sample volumes available confound the issue. Using","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361625","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The National Center for Cryo-EM Access and Training – establishing a cross-facility accepted training curriculum 国家低温电子显微镜使用和培训中心--建立跨机构的公认培训课程
Acta Crystallographica Section A Foundations and Advances Pub Date : 2023-07-07 DOI: 10.1107/s2053273323099977
Edward T. Eng, Elina Kopylov, Charlie Dubbeldam, Cathleen Castello, Christina Zimanyi
{"title":"The National Center for Cryo-EM Access and Training – establishing a cross-facility accepted training curriculum","authors":"Edward T. Eng, Elina Kopylov, Charlie Dubbeldam, Cathleen Castello, Christina Zimanyi","doi":"10.1107/s2053273323099977","DOIUrl":"https://doi.org/10.1107/s2053273323099977","url":null,"abstract":"","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"26 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361642","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Bicalutamide polymorphism: solid-state NMR characterization of two crystalline forms 比卡鲁胺的多态性：两种结晶形式的固态核磁共振表征
Acta Crystallographica Section A Foundations and Advances Pub Date : 2023-07-07 DOI: 10.1107/s2053273323096377
Shubha S Gunaga, Janice Rusli, David L. Bryce
{"title":"Bicalutamide polymorphism: solid-state NMR characterization of two crystalline forms","authors":"Shubha S Gunaga, Janice Rusli, David L. Bryce","doi":"10.1107/s2053273323096377","DOIUrl":"https://doi.org/10.1107/s2053273323096377","url":null,"abstract":"","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361655","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Hot and bothered: perturbing protein dynamics with temperature jump for time-resolved crystallography experiments 热热闹闹：用温度跃迁扰动蛋白质动力学，进行时间分辨晶体学实验
Acta Crystallographica Section A Foundations and Advances Pub Date : 2023-07-07 DOI: 10.1107/s2053273323097334
Michael C. Thompson
{"title":"Hot and bothered: perturbing protein dynamics with temperature jump for time-resolved crystallography experiments","authors":"Michael C. Thompson","doi":"10.1107/s2053273323097334","DOIUrl":"https://doi.org/10.1107/s2053273323097334","url":null,"abstract":"","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361707","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Structural characterization of spermidine methyltransferase, a novel member of the plant aminopropyltransferase family from Erythroxylum coca 来自 Erythroxylum coca 的植物氨丙基转移酶家族新成员--亚精胺甲基转移酶的结构特征
Acta Crystallographica Section A Foundations and Advances Pub Date : 2023-07-07 DOI: 10.1107/s2053273323096912
Charles E. Stewart, Benjamin G Chavez, John C. D'Auria
{"title":"Structural characterization of spermidine methyltransferase, a novel member of the plant aminopropyltransferase family from Erythroxylum coca","authors":"Charles E. Stewart, Benjamin G Chavez, John C. D'Auria","doi":"10.1107/s2053273323096912","DOIUrl":"https://doi.org/10.1107/s2053273323096912","url":null,"abstract":"","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"46 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361711","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Structural studies of the human particulate guanylyl cyclase receptor A (Pgc-A) to support therapeutics for cardiovascular diseases 人类微粒鸟苷酸环化酶受体 A（Pgc-A）的结构研究为心血管疾病治疗提供支持
Acta Crystallographica Section A Foundations and Advances Pub Date : 2023-07-07 DOI: 10.1107/s2053273323096286
Kohilan Jeyasothy, Shangji Zhang, J. Martin-Garcia, Domingo M. Aguilar, Debra T. Hansen, Petra Fromme, John C Burnett Jr
{"title":"Structural studies of the human particulate guanylyl cyclase receptor A (Pgc-A) to support therapeutics for cardiovascular diseases","authors":"Kohilan Jeyasothy, Shangji Zhang, J. Martin-Garcia, Domingo M. Aguilar, Debra T. Hansen, Petra Fromme, John C Burnett Jr","doi":"10.1107/s2053273323096286","DOIUrl":"https://doi.org/10.1107/s2053273323096286","url":null,"abstract":"","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"82 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361734","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Approximate symmetry in p2 and c2 organic structures p2 和 c2 有机结构的近似对称性
Acta Crystallographica Section A Foundations and Advances Pub Date : 2023-07-07 DOI: 10.1107/s2053273323098492
Carolyn P. Brock
{"title":"Approximate symmetry in p2 and c2 organic structures","authors":"Carolyn P. Brock","doi":"10.1107/s2053273323098492","DOIUrl":"https://doi.org/10.1107/s2053273323098492","url":null,"abstract":"The crystal packing in well - determined, organic, Z* ≥ 1 † structures in groups #3 ( P 2) and #5 ( C 2/ A 2/ I 2) has been analyzed. The study completes the survey of packing in organic structures archived in the CSD that have R ≤ 0.050 and that were reported in low - symmetry (SG# ≤ 8), low - frequency (< 5000 entries) space groups. Surveys of the structures described in P 11 and in group #7 ( Pc / Pn / Pa ) 2 have already been published. There are only 6 such structures in group #6 ( Pm ) and only 12 in #8 ( Cm ), with a number of those being either suspicious or very inorganic.","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"77 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361807","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Octahedral tilting, cation ordering and hydrogen bonding in layered hybrid halide perovskites 层状混合卤化物过磷酸盐中的八面体倾斜、阳离子排序和氢键
Acta Crystallographica Section A Foundations and Advances Pub Date : 2023-07-07 DOI: 10.1107/s2053273323098194
Patrick M. Woodward, Noah P. Holzapfel, Tianyu Liu, Joe Race
{"title":"Octahedral tilting, cation ordering and hydrogen bonding in layered hybrid halide perovskites","authors":"Patrick M. Woodward, Noah P. Holzapfel, Tianyu Liu, Joe Race","doi":"10.1107/s2053273323098194","DOIUrl":"https://doi.org/10.1107/s2053273323098194","url":null,"abstract":"","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361855","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Advancing crystallography research: the latest progress and future directions of NE-CAT beamlines at the Advanced Photon Source 推进晶体学研究：先进光子源 NE-CAT 光束线的最新进展和未来方向
Acta Crystallographica Section A Foundations and Advances Pub Date : 2023-07-07 DOI: 10.1107/s205327332309616x
Ali Kaya, Malcom Capel, I. Kourinov, A. Lynch, Frank Murphy, David Neau, Kay Perry, Jonanthan Schuermamm, Narayasnasami Sukumar, J. Withrow, Steve Ealick
{"title":"Advancing crystallography research: the latest progress and future directions of NE-CAT beamlines at the Advanced Photon Source","authors":"Ali Kaya, Malcom Capel, I. Kourinov, A. Lynch, Frank Murphy, David Neau, Kay Perry, Jonanthan Schuermamm, Narayasnasami Sukumar, J. Withrow, Steve Ealick","doi":"10.1107/s205327332309616x","DOIUrl":"https://doi.org/10.1107/s205327332309616x","url":null,"abstract":"","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361876","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The crystal structure of a PTE RNA element from a cactus virus that binds human eIF4E 与人类 eIF4E 结合的仙人掌病毒 PTE RNA 元件的晶体结构
Acta Crystallographica Section A Foundations and Advances Pub Date : 2023-07-07 DOI: 10.1107/s2053273323096523
M. Ojha, Deepak Koirala
{"title":"The crystal structure of a PTE RNA element from a cactus virus that binds human eIF4E","authors":"M. Ojha, Deepak Koirala","doi":"10.1107/s2053273323096523","DOIUrl":"https://doi.org/10.1107/s2053273323096523","url":null,"abstract":"The 3ꞌ cap -independent translation enhancers (3ꞌ - CITEs) at the 3ꞌ untranslated region (UTR) of tombusvirus genomes promote translation of viral RNA genome that bypass the requirement of 5ꞌ -cap to recruit various host translation initiation factors through the cap-independent mechanism. In the absence of a 5' - cap, they have been proposed to participate in long-range interaction with 5' UTR to circularize the mRNA and hence prepare the genome for translation. These 3ꞌ - CITEs are known to bind the ribosomal subunits or translation initiation factors. However, the lack of a high-resolution, three -dimensional structure has limited our understanding of how these structured RNA elements mimic the 5ꞌ -cap to recruit the eukaryotic initiation factors. In this study, we have determined the crystal structure of a PTE (Panicum Mosaic Virus - like 3ꞌ - CITE) from the Saguaro Cactus Virus (SCV) genome which was made possible by a Fab chaperone - assisted crystallography. Our structure reveals a T -shaped three-way junction that constitutes an unusual pseudoknot architecture between the G-rich bulge and the pyrimidine-rich domain. Consistent with the previous biochemical studies, the hypermodified G18 nucleotide fl ips from the rest of the PTE structure to create the binding site for eIF4E. The similar crystal structures of G18C, G18A, and G18U mutants compared to the wild -type structure demonstrate that the PTE structure is preorganized. Furthermore, despite being a plant virus, the binding of PTE with human eIF4E shown by our isothermal titration calorimetry (ITC) and gel electrophoresis mobili ty shift assays supports the hypothesis that this PTE domain represents a structured RNA mimic of the mRNA 5′cap.","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"56 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361885","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","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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