Acta crystallographica. Section F, Structural biology communications最新文献_第3页

Helical reconstruction of amyloids in cryoSPARC. 低温sparc中淀粉样蛋白的螺旋重建。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2026-07-01 Epub Date: 2026-06-09 DOI: 10.1107/S2053230X26003675

Jan Hannes Schaefer, Robert T O'Neill, Joseph P Donnelly, Evan T Powers, Jeffery W Kelly, Gabriel C Lander

{"title":"Helical reconstruction of amyloids in cryoSPARC.","authors":"Jan Hannes Schaefer, Robert T O'Neill, Joseph P Donnelly, Evan T Powers, Jeffery W Kelly, Gabriel C Lander","doi":"10.1107/S2053230X26003675","DOIUrl":"10.1107/S2053230X26003675","url":null,"abstract":"Amyloid-mediated proteotoxicity underlies over 50 diseases. Cryo-EM establishes direct links between filament morphologies and pathology, although microbial functional amyloids illustrate that this fold can evolve to serve physiological roles, unlike their pathogenic counterparts. Despite the growing popularity of the processing software cryoSPARC for single-particle analyses, RELION remains the dominant software platform for performing helical reconstruction of amyloid structures, highlighting an area for further development. Here, we present comprehensive processing guidelines for helical reconstruction of helical amyloids using cryoSPARC. Through systematic reprocessing and validation of publicly deposited datasets, we demonstrate the current capabilities and identify the key limitations, emphasizing the need for amyloid-specific parameter optimization within cryoSPARC workflows. Our findings showcase a potential for developing unsupervised processing workflows to meet the demanding throughput requirements of time-resolved in vitro studies and large-scale compound-screening initiatives, thereby accelerating therapeutic drug development. Ultimately, our goal is to shift the focus of amyloid cryo-EM from computationally intensive processing challenges towards addressing fundamental biological questions that enhance our capacity for treatment discovery.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":" ","pages":"252-261"},"PeriodicalIF":1.1,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13335050/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148203793","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

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2026-06-10

引用次数: 0

Crystal structure of the plant GABA aminotransferase AtGABA-T from Arabidopsis thaliana. 拟南芥GABA转氨酶AtGABA-T的晶体结构。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2026-06-01 Epub Date: 2026-05-01 DOI: 10.1107/S2053230X26003456

Naofumi Okoda, Suguru Okuda, Kenta Tsutsumi, Hideaki Itoh, Ken Okamoto, Hiroshi Kawakami, Kaori Sano, Kenji Kobata, Koji Nagata

{"title":"Crystal structure of the plant GABA aminotransferase AtGABA-T from Arabidopsis thaliana.","authors":"Naofumi Okoda, Suguru Okuda, Kenta Tsutsumi, Hideaki Itoh, Ken Okamoto, Hiroshi Kawakami, Kaori Sano, Kenji Kobata, Koji Nagata","doi":"10.1107/S2053230X26003456","DOIUrl":"10.1107/S2053230X26003456","url":null,"abstract":"γ-Aminobutyric acid aminotransferase (GABA-T) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes γ-aminobutyric acid (GABA) degradation in the mitochondrial GABA shunt. Plant GABA-Ts correspond to EC 2.6.1.96 and differ from mammalian and bacterial GABA-Ts (EC 2.6.1.19) in substrate specificity; however, their structural basis has remained unclear. Here, we report the crystal structure of GABA aminotransferase from Arabidopsis thaliana (AtGABA-T) at 2.0 Å resolution. Structural comparison using Foldseek indicates that AtGABA-T belongs to the class III aminotransferase family. Comparison with a class III ω-aminotransferase suggests that Arg423 located in the C-terminal region of AtGABA-T functions as the primary anchor for the carboxyl group of GABA, together with residues forming a tunnel-shaped substrate-access pathway. In contrast to nonplant GABA aminotransferases, which utilize a conserved N-terminal arginine for substrate recognition, AtGABA-T employs a distinct C-terminal arginine. These findings provide direct structural evidence for the classification of AtGABA-T as a class III aminotransferase and reveal a distinct mode of substrate recognition in AtGABA-T.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":" ","pages":"208-215"},"PeriodicalIF":1.1,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13224807/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147809322","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 structures of PCNA1 and PCNA2 from Aeropyrum pernix: implications for a distorted heterotrimeric sliding clamp. 羊角草中PCNA1和PCNA2的晶体结构：畸变异质三聚体滑动钳的意义。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2026-06-01 Epub Date: 2026-05-19 DOI: 10.1107/S2053230X26003687

Tong Wang, Sonoko Ishino, Yoshizumi Ishino, Takuji Oyama

{"title":"Crystal structures of PCNA1 and PCNA2 from Aeropyrum pernix: implications for a distorted heterotrimeric sliding clamp.","authors":"Tong Wang, Sonoko Ishino, Yoshizumi Ishino, Takuji Oyama","doi":"10.1107/S2053230X26003687","DOIUrl":"10.1107/S2053230X26003687","url":null,"abstract":"Aeropyrum pernix is a hyperthermophilic archaeon that possesses three proliferating cell nuclear antigen (PCNA) isoforms (ApePCNA1, ApePCNA2 and ApePCNA3) that form a heterotrimeric sliding clamp. To gain more detailed structural insights into this heterotrimeric assembly, we determined the crystal structures of ApePCNA1 and ApePCNA2. ApePCNA1 was crystallized under a new condition, and the 1.60 Å resolution structure revealed a unique nonproline cis-peptide bond between Arg187 and Arg188, which was not deeply discussed in a previous report. The structure of ApePCNA2 was determined at 2.17 Å resolution, and it forms a typical homotrimeric ring. In the cubic crystal form, its crystal packing shows an intriguing tetrahedral assembly of four trimers. Modeling the ApePCNA1-ApePCNA2-ApePCNA3 heterotrimer based on these structures suggests that the cis-peptide in ApePCNA1 induces significant steric hindrance at the subunit interface, leading to a symmetry-broken or distorted ring conformation rather than the canonical pseudo-threefold-symmetric assembly.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":" ","pages":"216-221"},"PeriodicalIF":1.1,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13224785/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147969450","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

Structural insights into the binding mode of the hypnotic drug vornorexant to orexin receptors. 结构洞察催眠药物与食欲素受体的结合模式。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2026-06-01 Epub Date: 2026-04-30 DOI: 10.1107/S2053230X26003432

Masashi Mima, Chiemi Mishima-Tsumagari, Mayumi Sakata-Sakuta, Ryo Iwaoka, Kunihiko Iwamoto

{"title":"Structural insights into the binding mode of the hypnotic drug vornorexant to orexin receptors.","authors":"Masashi Mima, Chiemi Mishima-Tsumagari, Mayumi Sakata-Sakuta, Ryo Iwaoka, Kunihiko Iwamoto","doi":"10.1107/S2053230X26003432","DOIUrl":"10.1107/S2053230X26003432","url":null,"abstract":"Insomnia is a widespread sleep disorder that significantly impairs quality of life and imposes a societal burden. Although benzodiazepines and Z-drugs are commonly used for treating insomnia, these drugs often have side effects, such as excessive muscle relaxation and dependency. The orexin signaling pathway has emerged as a promising therapeutic target for insomnia, with dual orexin receptor antagonists (DORAs) offering an alternative approach to treatment. To reduce the potential of these drugs for next-day residual effects, we developed vornorexant, a novel DORA with a high receptor affinity and a short elimination half-life. In this study, we investigated the molecular interactions of this drug with human orexin receptors through crystal structure analysis of its binding to orexin type 2 receptor (OX2R) and a docking simulation of the drug with orexin type 1 receptor (OX1R). The crystal structure of the OX2R-vornorexant complex revealed a conserved U-shaped conformation stabilized by hydrophobic and hydrogen-bonding interactions, including key contacts with Asn324, His350 and Pro131. OX1R-vornorexant docking simulations indicated a similar binding mode to OX1R, with no steric hindrance observed, supporting a balanced dual antagonism. These results provide a structural basis for the high-affinity dual antagonism of vornorexant and offer insights for the design of orexin receptor antagonists.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":" ","pages":"201-207"},"PeriodicalIF":1.1,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13224805/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147759393","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

Structural analysis of the flexibility of the Ubl2 domain within the papain-like protease of SARS-CoV-2. SARS-CoV-2木瓜蛋白酶Ubl2结构域柔韧性的结构分析

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2026-06-01 Epub Date: 2026-05-18 DOI: 10.1107/S2053230X26003699

Gian Luca Freiherr von Scholley, Martina Schaefer, Mark D Tully, Marc Andre Hograindleur, Montserrat Soler-López, Roman C Hillig, Christoph Mueller-Dieckmann, Eaazhisai Kandiah

{"title":"Structural analysis of the flexibility of the Ubl2 domain within the papain-like protease of SARS-CoV-2.","authors":"Gian Luca Freiherr von Scholley, Martina Schaefer, Mark D Tully, Marc Andre Hograindleur, Montserrat Soler-López, Roman C Hillig, Christoph Mueller-Dieckmann, Eaazhisai Kandiah","doi":"10.1107/S2053230X26003699","DOIUrl":"10.1107/S2053230X26003699","url":null,"abstract":"The papain-like protease (PLpro) of SARS-CoV-2 is part of the multi-domain nonstructural protein 3 (NSP3) and consists of two domains: a ubiquitin-like domain 2 (Ubl2) and a protease domain. PLpro plays a crucial role in the replication cycle of SARS-CoV-2, facilitating host immune-system evasion and the formation of double-membrane vesicles where replication occurs. While the function of the Ubl2 domain is still not clear, it is critical for the stability and the functional efficiency of PLpro. Despite its predicted inherent flexibility, nearly all SARS-CoV-1 and SARS-CoV-2 PLpro crystal structures deposited in the Protein Data Bank show the Ubl2 domain in a highly similar, closed conformation against the catalytic domain. Here, we present a crystal structure of PLpro exhibiting Ubl2 in two distinct conformations: the well characterized closed state, where Ubl2 is positioned near the PLpro domain, and an as yet uncharacterized open state, where Ubl2 is displaced by 4 Å from the PLpro core. This conformational variability in our structure appears to be related to the occupancy of a zinc ion within the zinc-finger domain. These results provide new insights into the flexibility of Ubl2, suggesting potential avenues for targeting and harnessing this dynamic behaviour for drug discovery.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":" ","pages":"222-230"},"PeriodicalIF":1.1,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13224804/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147961873","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 Plasmodium vivax macrophage migration inhibitory factor. 间日疟原虫巨噬细胞迁移抑制因子的晶体结构。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2026-06-01 Epub Date: 2026-05-05 DOI: 10.1107/S2053230X26003870

Aryana Nair, Matthew Lin, Arav Srivastava, Lijun Liu, Anne Cooper, Kevin Battaile, Elizabeth Harmon, Peter J Myler, Bart L Staker, Scott Lovell, Graham Chakafana, Oluwatoyin A Asojo

引用次数: 0

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2026-05-19

引用次数: 0

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2026-05-18

引用次数: 0

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2026-05-05

引用次数: 0