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Three-dimensional structures of Vibrio cholerae typing podophage VP1 in two states 霍乱弧菌分型荚膜 VP1 在两种状态下的三维结构
IF 5.7 2区 生物学
Structure Pub Date : 2024-10-28 DOI: 10.1016/j.str.2024.10.005
Hao Pang, Fenxia Fan, Jing Zheng, Hao Xiao, Zhixue Tan, Jingdong Song, Biao Kan, Hongrong Liu
{"title":"Three-dimensional structures of Vibrio cholerae typing podophage VP1 in two states","authors":"Hao Pang, Fenxia Fan, Jing Zheng, Hao Xiao, Zhixue Tan, Jingdong Song, Biao Kan, Hongrong Liu","doi":"10.1016/j.str.2024.10.005","DOIUrl":"https://doi.org/10.1016/j.str.2024.10.005","url":null,"abstract":"Lytic podophages (VP1–VP5) play crucial roles in subtyping <em>Vibrio cholerae</em> O1 biotype El Tor. However, until now no structures of these phages have been available, which hindered our understanding of the molecular mechanisms of infection and DNA release. Here, we determined the cryoelectron microscopy (cryo-EM) structures of mature and DNA-ejected VP1 structures at near-atomic and subnanometer resolutions, respectively. The VP1 head is composed of 415 copies of the major capsid protein gp7 and 11 turret-shaped spikes. The VP1 tail consists of an adapter, a nozzle, a slender ring, and a tail needle, and is flanked by three extended fibers I and six trimeric fibers II. Conformational changes of fiber II in DNA-ejected VP1 may cause the release of the tail needle and core proteins, forming an elongated tail channel. Our structures provide insights into the molecular mechanisms of infection and DNA release for podophages with a tail needle.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"101 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142519519","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}
引用次数: 0
Structural requirements for the specific binding of CRABP2 to cyclin D3 CRABP2 与细胞周期蛋白 D3 特异性结合的结构要求
IF 5.7 2区 生物学
Structure Pub Date : 2024-10-26 DOI: 10.1016/j.str.2024.10.027
Martyna W. Pastok, Charles W.E. Tomlinson, Shannon Turberville, Abbey M. Butler, Arnaud Baslé, Martin E.M. Noble, Jane A. Endicott, Ehmke Pohl, Natalie J. Tatum
{"title":"Structural requirements for the specific binding of CRABP2 to cyclin D3","authors":"Martyna W. Pastok, Charles W.E. Tomlinson, Shannon Turberville, Abbey M. Butler, Arnaud Baslé, Martin E.M. Noble, Jane A. Endicott, Ehmke Pohl, Natalie J. Tatum","doi":"10.1016/j.str.2024.10.027","DOIUrl":"https://doi.org/10.1016/j.str.2024.10.027","url":null,"abstract":"(Structure <em>32</em>, 1–15; December 5, 2024)","PeriodicalId":22168,"journal":{"name":"Structure","volume":"14 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142490568","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}
引用次数: 0
ANTIPASTI: Interpretable prediction of antibody binding affinity exploiting normal modes and deep learning ANTIPASTI：利用正常模式和深度学习对抗体结合亲和力进行可解释的预测
IF 5.7 2区 生物学
Structure Pub Date : 2024-10-25 DOI: 10.1016/j.str.2024.10.001
Kevin Michalewicz, Mauricio Barahona, Barbara Bravi
{"title":"ANTIPASTI: Interpretable prediction of antibody binding affinity exploiting normal modes and deep learning","authors":"Kevin Michalewicz, Mauricio Barahona, Barbara Bravi","doi":"10.1016/j.str.2024.10.001","DOIUrl":"https://doi.org/10.1016/j.str.2024.10.001","url":null,"abstract":"The high binding affinity of antibodies toward their cognate targets is key to eliciting effective immune responses, as well as to the use of antibodies as research and therapeutic tools. Here, we propose ANTIPASTI, a convolutional neural network model that achieves state-of-the-art performance in the prediction of antibody binding affinity using as input a representation of antibody-antigen structures in terms of normal mode correlation maps derived from elastic network models. This representation captures not only structural features but energetic patterns of local and global residue fluctuations. The learnt representations are interpretable: they reveal similarities of binding patterns among antibodies targeting the same antigen type, and can be used to quantify the importance of antibody regions contributing to binding affinity. Our results show the importance of the antigen imprint in the normal mode landscape, and the dominance of cooperative effects and long-range correlations between antibody regions to determine binding affinity.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"194 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142489632","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}
引用次数: 0
Exploiting cryo-EM structures of actomyosin-5a to reveal the physical properties of its lever 利用肌动蛋白-5a 的低温电子显微镜结构揭示其杠杆的物理特性
IF 5.7 2区 生物学
Structure Pub Date : 2024-10-24 DOI: 10.1016/j.str.2024.09.025
Molly S.C. Gravett, David P. Klebl, Oliver G. Harlen, Daniel J. Read, Stephen P. Muench, Sarah A. Harris, Michelle Peckham
{"title":"Exploiting cryo-EM structures of actomyosin-5a to reveal the physical properties of its lever","authors":"Molly S.C. Gravett, David P. Klebl, Oliver G. Harlen, Daniel J. Read, Stephen P. Muench, Sarah A. Harris, Michelle Peckham","doi":"10.1016/j.str.2024.09.025","DOIUrl":"https://doi.org/10.1016/j.str.2024.09.025","url":null,"abstract":"Myosin 5a (Myo5a) is a dimeric processive motor protein that transports cellular cargos along filamentous actin (F-actin). Its long lever is responsible for its large power-stroke, step size, and load-bearing ability. Little is known about the levers’ structure and physical properties, and how they contribute to walking mechanics. Using cryoelectron microscopy (cryo-EM) and molecular dynamics (MD) simulations, we resolved the structure of monomeric Myo5a, comprising the motor domain and full-length lever, bound to F-actin. The range of its lever conformations revealed its physical properties, how stiffness varies along its length and predicts a large, 35 nm, working stroke. Thus, the newly released trail head in a dimeric Myo5a would only need to perform a small diffusive search for its new binding site on F-actin, and stress would only be generated across the dimer once phosphate is released from the lead head, revealing new insight into the walking behavior of Myo5a.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"40 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142489057","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}
引用次数: 0
The mechanism of allosteric activation of SYK kinase derived from multiple phospho-ITAM-bound structures 从多个磷酸-ITAM 结合结构得出的 SYK 激酶异位激活机制
IF 5.7 2区 生物学
Structure Pub Date : 2024-10-22 DOI: 10.1016/j.str.2024.09.024
William J. Bradshaw, Gemma Harris, Opher Gileadi, Vittorio L. Katis
{"title":"The mechanism of allosteric activation of SYK kinase derived from multiple phospho-ITAM-bound structures","authors":"William J. Bradshaw, Gemma Harris, Opher Gileadi, Vittorio L. Katis","doi":"10.1016/j.str.2024.09.024","DOIUrl":"https://doi.org/10.1016/j.str.2024.09.024","url":null,"abstract":"Spleen tyrosine kinase (SYK) is central to adaptive and innate immune signaling. It features a regulatory region containing tandem SH2 (tSH2) domains separated by a helical “hinge” segment keeping SYK inactive by associating with the kinase domain. SYK activation is triggered when the tSH2 domains bind to a phosphorylated immunoreceptor tyrosine-based activation motif (ITAM) found on receptor tails. Past mutational studies have indicated that ITAM binding disrupts the hinge-kinase interaction, leading to SYK phosphorylation and activation. However, the mechanism of this process is unclear, as the ITAM interaction occurs far from the hinge region. We have determined crystal structures of three phospho-ITAMs in complex with the tSH2 domains, revealing a highly conserved binding mechanism. These structures, together with mutational studies and biophysical analyses, reveal that phospho-ITAM binding restricts SH2 domain movement and causes allosteric changes in the hinge region. These changes are not compatible with the association of the kinase domain, leading to kinase activation.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"67 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142486612","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}
引用次数: 0
Insights into the distinct membrane targeting mechanisms of WDR91 family proteins 深入了解 WDR91 家族蛋白的不同膜靶向机制
IF 5.7 2区 生物学
Structure Pub Date : 2024-10-18 DOI: 10.1016/j.str.2024.09.023
Xinli Ma, Jian Li, Nan Liu, Surajit Banerjee, Xiaotong Hu, Xiaoyu Wang, Jianshu Dong, Kangdong Liu, Chonglin Yang, Zigang Dong
{"title":"Insights into the distinct membrane targeting mechanisms of WDR91 family proteins","authors":"Xinli Ma, Jian Li, Nan Liu, Surajit Banerjee, Xiaotong Hu, Xiaoyu Wang, Jianshu Dong, Kangdong Liu, Chonglin Yang, Zigang Dong","doi":"10.1016/j.str.2024.09.023","DOIUrl":"https://doi.org/10.1016/j.str.2024.09.023","url":null,"abstract":"WDR91 and SORF1, members of the WD repeat-containing protein 91 family, control phosphoinositide conversion by inhibiting phosphatidylinositol 3-kinase activity on endosomes, which promotes endosome maturation. Here, we report the crystal structure of the human WDR91 WD40 domain complexed with Rab7 that has an unusual interface at the C-terminus of the Rab7 switch II region. WDR91 is highly selective for Rab7 among the tested GTPases. A LIS1 homology (LisH) motif within the WDR91 N-terminal domain (NTD) mediates self-association and may contribute partly to the augmented interaction between full-length WDR91 and Rab7. Both the Rab7 binding site and the LisH motif are indispensable for WDR91 function in endocytic trafficking. For the WDR91 orthologue SORF1 lacking the C-terminal WD40 domain, a C-terminal amphipathic helix (AH) mediates strong interactions with liposomes containing acidic lipids. During evolution the human WDR91 ancestor gene might have acquired a WD40 domain to replace the AH for endosomal membrane targeting.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"11 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142448832","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}
引用次数: 0
Structural insights into the DNA-binding mechanism of BCL11A: The integral role of ZnF6 对 BCL11A DNA 结合机制的结构性认识：ZnF6 的重要作用
IF 5.7 2区 生物学
Structure Pub Date : 2024-10-17 DOI: 10.1016/j.str.2024.09.022
Thibault Viennet, Maolu Yin, Abhilash Jayaraj, Woojin Kim, Zhen-Yu J. Sun, Yuko Fujiwara, Kevin Zhang, Davide Seruggia, Hyuk-Soo Seo, Sirano Dhe-Paganon, Stuart H. Orkin, Haribabu Arthanari
{"title":"Structural insights into the DNA-binding mechanism of BCL11A: The integral role of ZnF6","authors":"Thibault Viennet, Maolu Yin, Abhilash Jayaraj, Woojin Kim, Zhen-Yu J. Sun, Yuko Fujiwara, Kevin Zhang, Davide Seruggia, Hyuk-Soo Seo, Sirano Dhe-Paganon, Stuart H. Orkin, Haribabu Arthanari","doi":"10.1016/j.str.2024.09.022","DOIUrl":"https://doi.org/10.1016/j.str.2024.09.022","url":null,"abstract":"The transcription factor BCL11A is a critical regulator of the switch from fetal hemoglobin (HbF: α<sub>2</sub>γ<sub>2</sub>) to adult hemoglobin (HbA: α<sub>2</sub>β<sub>2</sub>) during development. BCL11A binds at a cognate recognition site (TGACCA) in the γ-globin gene promoter and represses its expression. DNA-binding is mediated by a triple zinc finger domain, designated ZnF456. Here, we report comprehensive investigation of ZnF456, leveraging X-ray crystallography and NMR to determine the structures in both the presence and absence of DNA. We delve into the dynamics and mode of interaction with DNA. Moreover, we discovered that the last zinc finger of BCL11A (ZnF6) plays a different role compared to ZnF4 and 5, providing a positive entropic contribution to DNA binding and γ-globin gene repression. Comprehending the DNA binding mechanism of BCL11A opens avenues for the strategic, structure-based design of novel therapeutics targeting sickle cell disease and β-thalassemia.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"21 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142444185","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}
引用次数: 0
ATTRv-V30M amyloid fibrils from heart and nerves exhibit structural homogeneity 来自心脏和神经的 ATTRv-V30M 淀粉样蛋白纤维在结构上具有同质性
IF 5.7 2区 生物学
Structure Pub Date : 2024-10-17 DOI: 10.1016/j.str.2024.09.021
Binh An Nguyen, Shumaila Afrin, Anna Yakubovska, Virender Singh, Rose Pedretti, Parker Bassett, Maja Pekala, Jaime Vaquer Alicea, Peter Kunach, Lanie Wang, Andrew Lemoff, Barbara Kluve-Beckerman, Lorena Saelices
{"title":"ATTRv-V30M amyloid fibrils from heart and nerves exhibit structural homogeneity","authors":"Binh An Nguyen, Shumaila Afrin, Anna Yakubovska, Virender Singh, Rose Pedretti, Parker Bassett, Maja Pekala, Jaime Vaquer Alicea, Peter Kunach, Lanie Wang, Andrew Lemoff, Barbara Kluve-Beckerman, Lorena Saelices","doi":"10.1016/j.str.2024.09.021","DOIUrl":"https://doi.org/10.1016/j.str.2024.09.021","url":null,"abstract":"Amyloidogenic transthyretin (ATTR) amyloidosis is a systemic disease characterized by the deposition of amyloid fibrils made of transthyretin. Transthyretin is primarily produced in tetrameric form by the liver, but also by retinal epithelium and choroid plexus. The deposition of these fibrils in the myocardium and peripheral nerves causes cardiomyopathies and neuropathies, respectively. Using cryoelectron microscopy (cryo-EM), we investigated fibrils extracted from cardiac and nerve tissues of an ATTRv-V30M patient. We found consistent fibril structures from both tissues, similar to cardiac fibrils previously described, but different from vitreous humor fibrils of the same genotype. Our findings, along with previous ATTR fibrils structural studies, suggest a uniform fibrillar architecture across different tissues when transthyretin originates from the liver. This study advances our understanding of how deposition and production sites influence fibril structure in ATTRv-V30M amyloidosis.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"32 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142444186","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}
引用次数: 0
Ribosome-inactivation by a class of widely distributed C-tail anchored membrane proteins 一类广泛分布的 C 尾锚定膜蛋白的核糖体失活作用
IF 5.7 2区 生物学
Structure Pub Date : 2024-10-16 DOI: 10.1016/j.str.2024.09.019
Robert Karari Njenga, Julian Boele, Friedel Drepper, Kasturica Sinha, Eirini Marouda, Pitter F. Huesgen, Crysten Blaby-Haas, Hans-Georg Koch
{"title":"Ribosome-inactivation by a class of widely distributed C-tail anchored membrane proteins","authors":"Robert Karari Njenga, Julian Boele, Friedel Drepper, Kasturica Sinha, Eirini Marouda, Pitter F. Huesgen, Crysten Blaby-Haas, Hans-Georg Koch","doi":"10.1016/j.str.2024.09.019","DOIUrl":"https://doi.org/10.1016/j.str.2024.09.019","url":null,"abstract":"Ribosome hibernation is a commonly used strategy that protects ribosomes under unfavorable conditions and regulates developmental processes. Multiple ribosome-hibernation factors have been identified in all domains of life, but due to their structural diversity and the lack of a common inactivation mechanism, it is currently unknown how many different hibernation factors exist. Here, we show that the YqjD/ElaB/YgaM paralogs, initially discovered as membrane-bound ribosome binding proteins in <em>E. coli</em>, constitute an abundant class of ribosome-hibernating proteins, which are conserved across all proteobacteria and some other bacterial phyla. Our data demonstrate that they inhibit <em>in vitro</em> protein synthesis by interacting with the 50S ribosomal subunit. <em>In vivo</em> cross-linking combined with mass spectrometry revealed their specific interactions with proteins surrounding the ribosomal tunnel exit and even their penetration into the ribosomal tunnel. Thus, YqjD/ElaB/YgaM inhibit translation by blocking the ribosomal tunnel and thus mimic the activity of antimicrobial peptides and macrolide antibiotics.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"13 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142440034","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}
引用次数: 0
Structural requirements for the specific binding of CRABP2 to cyclin D3 CRABP2 与细胞周期蛋白 D3 特异性结合的结构要求
IF 5.7 2区 生物学
Structure Pub Date : 2024-10-16 DOI: 10.1016/j.str.2024.09.020
Martyna W. Pastok, Charles W.E. Tomlinson, Shannon Turberville, Abbey M. Butler, Arnaud Baslé, Martin E.M. Noble, Jane A. Endicott, Ehmke Pohl, Natalie J. Tatum
{"title":"Structural requirements for the specific binding of CRABP2 to cyclin D3","authors":"Martyna W. Pastok, Charles W.E. Tomlinson, Shannon Turberville, Abbey M. Butler, Arnaud Baslé, Martin E.M. Noble, Jane A. Endicott, Ehmke Pohl, Natalie J. Tatum","doi":"10.1016/j.str.2024.09.020","DOIUrl":"https://doi.org/10.1016/j.str.2024.09.020","url":null,"abstract":"Cellular retinoic acid binding protein 2 (CRABP2) transports retinoic acid from the cytoplasm to the nucleus where it then transfers its cargo to retinoic acid receptor-containing complexes leading to activation of gene transcription. We demonstrate using purified proteins that CRABP2 is also a cyclin D3-specific binding protein and that the CRABP2 cyclin D3 binding site and the proposed CRABP2 nuclear localization sequence overlap. Both sequences are within the helix-loop-helix motif that forms a lid to the retinoic acid binding pocket. Mutations within this sequence that block both cyclin D3 and retinoic acid binding promote formation of a CRABP2 structure in which the retinoic acid binding pocket is occupied by an alternative lid conformation. Structural and functional analysis of CRABP2 and cyclin D3 mutants combined with AlphaFold models of the ternary CDK4/6-cyclin D3-CRABP2 complex supports the identification of an α-helical protein binding site on the cyclin D3 C-terminal cyclin box fold.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"59 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142440035","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}
引用次数: 0
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