Pub Date : 2023-07-07DOI: 10.1107/s2053273323097188
Edward H. Snell, E. Garman, Geoff W. Grime, Aina E. Cohen, Sarah E. J. Bowman
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
{"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}
Pub Date : 2023-07-07DOI: 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}
Pub Date : 2023-07-07DOI: 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}
Pub Date : 2023-07-07DOI: 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}
Pub Date : 2023-07-07DOI: 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}
Pub Date : 2023-07-07DOI: 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}
Pub Date : 2023-07-07DOI: 10.1107/s2053273323098492
Carolyn P. Brock
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.
{"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}
Pub Date : 2023-07-07DOI: 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}
Pub Date : 2023-07-07DOI: 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}
Pub Date : 2023-07-07DOI: 10.1107/s2053273323096523
M. Ojha, Deepak Koirala
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.
{"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}
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