ASC-1 homology (ASCH) domain family proteins are believed to play essential roles in RNA metabolism, but detailed structural and functional information is limited. Research has shown that the E. coli enzyme YqfB, which contains an ASCH domain, has amidohydrolase activity, converting N4-acetylcytidine (ac4C) RNA nucleoside into cytidine. Here, we present the crystal structures of EcYqfB both in its unbound state and bound to a substrate. Our analysis reveals how the substrate interacts with the enzyme, offering insights into its catalytic mechanism. In vivo experiments further show that deleting EcYqfB does not change overall ac4C levels across various RNA types, indicating that EcYqfB specifically functions in ac4C nucleoside metabolism. We also determined the structures of two homologous proteins: mouse EOLA1 and the human TRIP4-ASCH domain, highlighting differences in their substrate preferences. These findings offer important insights for future research into the structure and function of the ASCH domain protein family.
{"title":"Structural analysis of ASCH domain-containing proteins and their implications for nucleotide processing","authors":"Chunyan Meng, Xiaoyan Shi, Wenting Guo, Xing Jian, Jie Zhao, Yan Wen, Ruiqi Wang, Yu Li, Sha Xu, Haitao Chen, Jiayu Zhang, Mingjia Chen, Hao Chen, Baixing Wu","doi":"10.1016/j.str.2025.08.015","DOIUrl":"https://doi.org/10.1016/j.str.2025.08.015","url":null,"abstract":"ASC-1 homology (ASCH) domain family proteins are believed to play essential roles in RNA metabolism, but detailed structural and functional information is limited. Research has shown that the <em>E. coli</em> enzyme YqfB, which contains an ASCH domain, has amidohydrolase activity, converting <em>N</em><sup>4</sup>-acetylcytidine (ac<sup>4</sup>C) RNA nucleoside into cytidine. Here, we present the crystal structures of <em>Ec</em>YqfB both in its unbound state and bound to a substrate. Our analysis reveals how the substrate interacts with the enzyme, offering insights into its catalytic mechanism. <em>In vivo</em> experiments further show that deleting <em>Ec</em>YqfB does not change overall ac<sup>4</sup>C levels across various RNA types, indicating that <em>Ec</em>YqfB specifically functions in ac<sup>4</sup>C nucleoside metabolism. We also determined the structures of two homologous proteins: mouse EOLA1 and the human TRIP4-ASCH domain, highlighting differences in their substrate preferences. These findings offer important insights for future research into the structure and function of the ASCH domain protein family.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"24 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145043309","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-08DOI: 10.1016/j.str.2025.08.013
Chang Wang, Amin Khosrozadeh, Ioan Iacovache, Benoît Zuber
Cryo-electron tomography (cryoET) provides 3D datasets of organelles and proteins at nanometer and sub-nanometer resolution. However, locating target proteins in live cells remains a significant challenge. Conventional labeling methods, such as fluorescent protein tagging and immunogold labeling, are unsuitable for small structures in vitrified samples at molecular resolution. Directly linking large, visually identifiable proteins to target proteins may alter their structure, localization, and function. To overcome this, we employed a rapamycin-induced oligomer formation system involving two tags, FK506 binding protein (FKBP) and FKBP-rapamycin binding (FRB), which bind in the presence of rapamycin. FKBP is linked to the target protein, while FRB is linked to ferritin, a large (10–12 nm) iron-binding complex that creates strong contrast in cryoET. Upon adding rapamycin to the cell medium, the iron-loaded ferritin accurately marks the target protein location. As in situ cryoET with subtomogram averaging advances, our method addresses the persistent challenge of locating target proteins in live cells.
{"title":"Genetically encoded FerriTag as a specific label for cryo-electron tomography","authors":"Chang Wang, Amin Khosrozadeh, Ioan Iacovache, Benoît Zuber","doi":"10.1016/j.str.2025.08.013","DOIUrl":"https://doi.org/10.1016/j.str.2025.08.013","url":null,"abstract":"Cryo-electron tomography (cryoET) provides 3D datasets of organelles and proteins at nanometer and sub-nanometer resolution. However, locating target proteins in live cells remains a significant challenge. Conventional labeling methods, such as fluorescent protein tagging and immunogold labeling, are unsuitable for small structures in vitrified samples at molecular resolution. Directly linking large, visually identifiable proteins to target proteins may alter their structure, localization, and function. To overcome this, we employed a rapamycin-induced oligomer formation system involving two tags, FK506 binding protein (FKBP) and FKBP-rapamycin binding (FRB), which bind in the presence of rapamycin. FKBP is linked to the target protein, while FRB is linked to ferritin, a large (10–12 nm) iron-binding complex that creates strong contrast in cryoET. Upon adding rapamycin to the cell medium, the iron-loaded ferritin accurately marks the target protein location. As <em>in situ</em> cryoET with subtomogram averaging advances, our method addresses the persistent challenge of locating target proteins in live cells.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"69 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145009471","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-05DOI: 10.1016/j.str.2025.08.012
Hao Xu, Yimin Zhang, Qinru Bai, Linli He, Qihao Chen, Yunlong Qiu, Renjie Li, Jie Yu, Jun Zhao, Yan Zhao
GABA (g-aminobutyric acid) transporter 3 (GAT3) is primarily found in glial cells and is essential for regulating GABA homeostasis in the central nervous system by mediating GABA uptake. Consequently, GAT3 has emerged as a significant therapeutic target for the treatment of epilepsy. In this study, we present the cryoelectron microscopy (cryo-EM) structures of GAT3 bound to its substrate GABA, the selective inhibitor SNAP-5114, and in the substrate-free state. GAT3 binds to GABA in an inward-facing conformation, while SNAP-5114 occupies the GABA-binding pocket and is stabilized by extensive interactions with surrounding residues. Functional studies reveal that E66 plays a pivotal role in determining the substrate-binding mode and specificity of SNAP-5114 binding. Taken together, our study clarifies the GABA binding mechanism of GAT3 and reveals the molecular basis for the specific inhibition of SNAP-5114, offering valuable insights for developing GAT3 subtypes selective inhibitors, which hold potential as a treatment for epilepsy.
{"title":"Substrate and inhibitor binding of human GABA transporter 3","authors":"Hao Xu, Yimin Zhang, Qinru Bai, Linli He, Qihao Chen, Yunlong Qiu, Renjie Li, Jie Yu, Jun Zhao, Yan Zhao","doi":"10.1016/j.str.2025.08.012","DOIUrl":"https://doi.org/10.1016/j.str.2025.08.012","url":null,"abstract":"GABA (g-aminobutyric acid) transporter 3 (GAT3) is primarily found in glial cells and is essential for regulating GABA homeostasis in the central nervous system by mediating GABA uptake. Consequently, GAT3 has emerged as a significant therapeutic target for the treatment of epilepsy. In this study, we present the cryoelectron microscopy (cryo-EM) structures of GAT3 bound to its substrate GABA, the selective inhibitor SNAP-5114, and in the substrate-free state. GAT3 binds to GABA in an inward-facing conformation, while SNAP-5114 occupies the GABA-binding pocket and is stabilized by extensive interactions with surrounding residues. Functional studies reveal that E66 plays a pivotal role in determining the substrate-binding mode and specificity of SNAP-5114 binding. Taken together, our study clarifies the GABA binding mechanism of GAT3 and reveals the molecular basis for the specific inhibition of SNAP-5114, offering valuable insights for developing GAT3 subtypes selective inhibitors, which hold potential as a treatment for epilepsy.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"39 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144996090","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-04DOI: 10.1016/j.str.2025.08.005
Zhenmei Xu, Yuanzheng He
Rhodopsins typically harness light energy through the covalently bound retinal cofactor. However, some rhodopsins have lost this ability during evolution. In this issue of Structure, Kovalev et al.1 present the cryo-electron microscopy (cryo-EM) structure of a retinal-free flotillin-associated rhodopsin (FArhodopsin), providing new insights into their architecture and potential non-photochemical functions.
{"title":"Structural insights into retinal-free microbial rhodopsins","authors":"Zhenmei Xu, Yuanzheng He","doi":"10.1016/j.str.2025.08.005","DOIUrl":"https://doi.org/10.1016/j.str.2025.08.005","url":null,"abstract":"Rhodopsins typically harness light energy through the covalently bound retinal cofactor. However, some rhodopsins have lost this ability during evolution. In this issue of <em>Structure</em>, Kovalev et al.<span><span><sup>1</sup></span></span> present the cryo-electron microscopy (cryo-EM) structure of a retinal-free flotillin-associated rhodopsin (FArhodopsin), providing new insights into their architecture and potential non-photochemical functions.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"29 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144987575","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-04DOI: 10.1016/j.str.2025.08.006
Kevin D. Corbett, Amar Deep
The structural maintenance of chromosomes (SMC)-family Wadjet complex restricts plasmid transformation in bacteria through a distinctive mechanism coupling DNA loop extrusion and cleavage. In this issue of Structure, Roisné-Hamelin et al.1 report the biochemical reconstitution and structure of a type II Wadjet complex, revealing a shared overall mechanism and notable architectural differences compared to related type I complexes.
{"title":"Wadjet—Keeping a watchful eye on circular DNA","authors":"Kevin D. Corbett, Amar Deep","doi":"10.1016/j.str.2025.08.006","DOIUrl":"https://doi.org/10.1016/j.str.2025.08.006","url":null,"abstract":"The structural maintenance of chromosomes (SMC)-family Wadjet complex restricts plasmid transformation in bacteria through a distinctive mechanism coupling DNA loop extrusion and cleavage. In this issue of <em>Structure,</em> Roisné-Hamelin et al.<span><span><sup>1</sup></span></span> report the biochemical reconstitution and structure of a type II Wadjet complex, revealing a shared overall mechanism and notable architectural differences compared to related type I complexes.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"47 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144987587","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-03DOI: 10.1016/j.str.2025.08.011
Daria Trofimova, Caitlin Doubleday, Byron Hunter, Jesus Danilo Serrano Arevalo, Emma Davison, Eric Wen, Kim Munro, John S. Allingham
Kinesin-8 motors regulate kinetochore-microtubule dynamics and control spindle length and positioning. Certain isoforms achieve this by traversing microtubules, accumulating at plus-ends, and depolymerizing terminal αβ-tubulin subunits. While the kinesin-8 motor domain is well characterized, the tail domain regions are less understood. Using the Candida albicans Kip3 protein as a model for fungal kinesin-8, we present an X-ray crystal structure and hydrodynamic analysis of its motor-proximal tail segment, revealing its role in motor dimerization. This segment forms a compact, 92 Å-long four-helix bundle, rather than an elongated coiled-coil stalk seen in most kinesins. The bundle is stabilized primarily by interactions between helices one and three, with additional support from helices two and four. A flexible hinge bisects the bundle into two lobules, imparting mechanical pliability and asymmetric exterior surfaces. These unique features may facilitate interactions with regulatory elements or contribute to the functional versatility of kinesin-8 motors.
{"title":"Fungal kinesin-8 motors dimerize by folding their proximal tail domain into a compact helical bundle","authors":"Daria Trofimova, Caitlin Doubleday, Byron Hunter, Jesus Danilo Serrano Arevalo, Emma Davison, Eric Wen, Kim Munro, John S. Allingham","doi":"10.1016/j.str.2025.08.011","DOIUrl":"https://doi.org/10.1016/j.str.2025.08.011","url":null,"abstract":"Kinesin-8 motors regulate kinetochore-microtubule dynamics and control spindle length and positioning. Certain isoforms achieve this by traversing microtubules, accumulating at plus-ends, and depolymerizing terminal αβ-tubulin subunits. While the kinesin-8 motor domain is well characterized, the tail domain regions are less understood. Using the <em>Candida albicans</em> Kip3 protein as a model for fungal kinesin-8, we present an X-ray crystal structure and hydrodynamic analysis of its motor-proximal tail segment, revealing its role in motor dimerization. This segment forms a compact, 92 Å-long four-helix bundle, rather than an elongated coiled-coil stalk seen in most kinesins. The bundle is stabilized primarily by interactions between helices one and three, with additional support from helices two and four. A flexible hinge bisects the bundle into two lobules, imparting mechanical pliability and asymmetric exterior surfaces. These unique features may facilitate interactions with regulatory elements or contribute to the functional versatility of kinesin-8 motors.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"11 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144930865","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-02DOI: 10.1016/j.str.2025.08.009
Evan Billings, Zixing Fan, Moloud Aflaki Sooreshjani, James C. Gumbart, Nicholas Noinaj
N. gonorrhoeae (Ngo) causes the sexually transmitted infection gonorrhea with ∼106 million infections worldwide annually. Ngo infections can result in an increased risk of acquiring HIV, infertility, and blindness. To combat Ngo infections, we report the cryoelectron microscopy (cryo-EM) structure of the Ngo β-barrel assembly machinery (NgBAM), which is responsible for the biogenesis of β-barrel outer membrane proteins (OMPs). NgBAM was observed in an inward-open state; however, the polypeptide transport-associated (POTRA) domains more closely match those found in the outward-open state in E. coli β-barrel assembly machinery (BAM). The barrel seam of NgBamA consists of partial pairing of strand β1 with β16; no outward-open state of NgBAM was observed. Molecular dynamics (MD) simulations reveal unique overall dynamics and interplay between the POTRA domains of NgBamA and NgBamD. We propose that in Ngo, initial recognition occurs in the inward-open state where the last strand of the OMP partially pairs with β1 of NgBamA and must compete off β16.
{"title":"Structural insights into outer membrane protein biogenesis in pathogenic Neisseria","authors":"Evan Billings, Zixing Fan, Moloud Aflaki Sooreshjani, James C. Gumbart, Nicholas Noinaj","doi":"10.1016/j.str.2025.08.009","DOIUrl":"https://doi.org/10.1016/j.str.2025.08.009","url":null,"abstract":"<em>N.</em> g<em>onorrhoeae</em> (Ngo) causes the sexually transmitted infection gonorrhea with ∼106 million infections worldwide annually. Ngo infections can result in an increased risk of acquiring HIV, infertility, and blindness. To combat Ngo infections, we report the cryoelectron microscopy (cryo-EM) structure of the Ngo β-barrel assembly machinery (<em>Ng</em>BAM), which is responsible for the biogenesis of β-barrel outer membrane proteins (OMPs). <em>Ng</em>BAM was observed in an inward-open state; however, the polypeptide transport-associated (POTRA) domains more closely match those found in the outward-open state in <em>E</em>. <em>coli</em> β-barrel assembly machinery (BAM). The barrel seam of <em>Ng</em>BamA consists of partial pairing of strand β1 with β16; no outward-open state of <em>Ng</em>BAM was observed. Molecular dynamics (MD) simulations reveal unique overall dynamics and interplay between the POTRA domains of <em>Ng</em>BamA and <em>Ng</em>BamD. We propose that in Ngo, initial recognition occurs in the inward-open state where the last strand of the OMP partially pairs with β1 of <em>Ng</em>BamA and must compete off β16.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"14 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144928517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-01DOI: 10.1016/j.str.2025.08.008
Claire Overly Cottom, Eva Heinz, Satchal Erramilli, Anthony Kossiakoff, Daniel J. Slade, Nicholas Noinaj
F. nucleatum is a Gram-negative bacteria that causes oral infections and is linked to colorectal cancer. Pathogenicity relies on a type of β-barrel outer membrane protein (OMP) called an autotransporter. The biogenesis of OMPs is typically mediated by the barrel assembly machinery (BAM) complex. In this study, we investigate the evolution, composition, and structure of the OMP biogenesis machinery in F. nucleatum. Our bioinformatics and proteomics analyses indicate that OMP biogenesis in F. nucleatum is mediated solely by the core component BamA. The structure of FnBamA highlights distinct features, including four POTRA domains and a C-terminal 16-stranded β-barrel domain observed as an inverted dimer. FnBamA represents the original composition of the assembly machinery, and a duplication event that resulted in BamA and TamA occurred after the split of other lineages, including the Proteobacteria, from the Fusobacteria. FnBamA, therefore, likely serves a singular role in the biogenesis of all OMPs.
{"title":"Characterization of the OMP biogenesis machinery in Fusobacterium nucleatum","authors":"Claire Overly Cottom, Eva Heinz, Satchal Erramilli, Anthony Kossiakoff, Daniel J. Slade, Nicholas Noinaj","doi":"10.1016/j.str.2025.08.008","DOIUrl":"https://doi.org/10.1016/j.str.2025.08.008","url":null,"abstract":"F. <em>nucleatum</em> is a Gram-negative bacteria that causes oral infections and is linked to colorectal cancer. Pathogenicity relies on a type of β-barrel outer membrane protein (OMP) called an autotransporter. The biogenesis of OMPs is typically mediated by the barrel assembly machinery (BAM) complex. In this study, we investigate the evolution, composition, and structure of the OMP biogenesis machinery in <em>F. nucleatum</em>. Our bioinformatics and proteomics analyses indicate that OMP biogenesis in <em>F. nucleatum</em> is mediated solely by the core component BamA. The structure of <em>Fn</em>BamA highlights distinct features, including four POTRA domains and a C-terminal 16-stranded β-barrel domain observed as an inverted dimer. <em>Fn</em>BamA represents the original composition of the assembly machinery, and a duplication event that resulted in BamA and TamA occurred after the split of other lineages, including the <em>Proteobacteria</em>, from the <em>Fusobacteria</em>. <em>Fn</em>BamA, therefore, likely serves a singular role in the biogenesis of all OMPs.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"25 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144924259","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-01DOI: 10.1016/j.str.2025.08.007
Daniel R. Fox, Cyntia Taveneau, Janik Clement, Rhys Grinter, Gavin J. Knott
The application of artificial intelligence to structural biology has transformed protein design from a conceptual challenge into a practical approach for creating new-to-nature proteins. By leveraging machine learning, researchers can now computationally design proteins with tailored architectures and binding specificities. This has enabled the rapid in silico generation of high-affinity binders to diverse and previously intractable targets. This approach dramatically reduces binder development time and resource requirements, compared to traditional experimental approaches, while improving hit rates and designability. Recent successes include the creation of binding proteins that neutralize toxins, modulate immune pathways, and engage disordered targets with high affinity and specificity. Improvements in model accuracy are expanding the scope of what can be designed, while characterization in preclinical models is paving the way for therapeutic development. De novo binder design represents a paradigm shift in protein engineering, where custom binders can now be programmed to meet specific biological challenges.
{"title":"Code to complex: AI-driven de novo binder design","authors":"Daniel R. Fox, Cyntia Taveneau, Janik Clement, Rhys Grinter, Gavin J. Knott","doi":"10.1016/j.str.2025.08.007","DOIUrl":"https://doi.org/10.1016/j.str.2025.08.007","url":null,"abstract":"The application of artificial intelligence to structural biology has transformed protein design from a conceptual challenge into a practical approach for creating new-to-nature proteins. By leveraging machine learning, researchers can now computationally design proteins with tailored architectures and binding specificities. This has enabled the rapid <em>in silico</em> generation of high-affinity binders to diverse and previously intractable targets. This approach dramatically reduces binder development time and resource requirements, compared to traditional experimental approaches, while improving hit rates and designability. Recent successes include the creation of binding proteins that neutralize toxins, modulate immune pathways, and engage disordered targets with high affinity and specificity. Improvements in model accuracy are expanding the scope of what can be designed, while characterization in preclinical models is paving the way for therapeutic development. <em>De novo</em> binder design represents a paradigm shift in protein engineering, where custom binders can now be programmed to meet specific biological challenges.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"31 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144924257","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
SPO1-related bacteriophages are promising candidates for phage therapy. We present the 3.0 Å cryo-electron microscopy (cryo-EM) structure of the SPO1 capsid with a triangulation number T = 16, enabling the construction of an atomic model comprising the major capsid protein and three types of minor capsid proteins: gp29.2, gp2.7, and gp36.3. These minor capsid proteins adopt novel folds. They might stabilize the capsid and determine its curvature. Gp29.2 monomers contain a three-blade propeller fold and are located at the 3-fold and quasi-three-fold axes. Gp2.7 forms pentamers atop pentameric capsomers, while gp36.3 binds to the capsid’s inner surface, forming star-shaped structures increasing connections between pentameric and hexameric capsomers. The surface exposed regions of gp29.2 and gp2.7 make SPO1 of interest as a nanocage for phage display. Our findings advance the understanding of capsid architecture, stabilization, and local curvature determination for SPO1-related bacteriophages.
{"title":"Capsid structure of phage SPO1 reveals novel minor capsid proteins and insights into capsid stabilization","authors":"Xinyue Zhao, Aohan Wang, Yueting Wang, Yue Kang, Qianqian Shao, Lin Li, Yaqi Zheng, Hongli Hu, Xiangyun Li, Hongling Fan, Can Cai, Bing Liu, Qianglin Fang","doi":"10.1016/j.str.2025.08.004","DOIUrl":"https://doi.org/10.1016/j.str.2025.08.004","url":null,"abstract":"SPO1-related bacteriophages are promising candidates for phage therapy. We present the 3.0 Å cryo-electron microscopy (cryo-EM) structure of the SPO1 capsid with a triangulation number T = 16, enabling the construction of an atomic model comprising the major capsid protein and three types of minor capsid proteins: gp29.2, gp2.7, and gp36.3. These minor capsid proteins adopt novel folds. They might stabilize the capsid and determine its curvature. Gp29.2 monomers contain a three-blade propeller fold and are located at the 3-fold and quasi-three-fold axes. Gp2.7 forms pentamers atop pentameric capsomers, while gp36.3 binds to the capsid’s inner surface, forming star-shaped structures increasing connections between pentameric and hexameric capsomers. The surface exposed regions of gp29.2 and gp2.7 make SPO1 of interest as a nanocage for phage display. Our findings advance the understanding of capsid architecture, stabilization, and local curvature determination for SPO1-related bacteriophages.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"8 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144915925","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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