Structure最新文献

Cryogenic electron tomography and elemental analysis of mitochondrial granules in human retinal ganglion cells

IF 5.7 2区生物学

Structure Pub Date : 2025-08-04 DOI: 10.1016/j.str.2025.07.010

Gong-Her Wu, Cathy Hou, Andrew Thron, Hirenkumar Rajendra Patel, Liam Spillane, Sanket Rajan Gupte, Serena Yeung-Levy, Sahil Gulati, Christopher Booth, Yaping Joyce Liao, Wah Chiu

{"title":"Cryogenic electron tomography and elemental analysis of mitochondrial granules in human retinal ganglion cells","authors":"Gong-Her Wu, Cathy Hou, Andrew Thron, Hirenkumar Rajendra Patel, Liam Spillane, Sanket Rajan Gupte, Serena Yeung-Levy, Sahil Gulati, Christopher Booth, Yaping Joyce Liao, Wah Chiu","doi":"10.1016/j.str.2025.07.010","DOIUrl":"https://doi.org/10.1016/j.str.2025.07.010","url":null,"abstract":"Combining three-dimensional (3D) visualization with elemental analysis of vitrified cells can provide crucial insights into subcellular structures and elemental compositions in their native environments. We present a coordinated approach using cryogenic electron energy loss spectroscopy (cryoEELS) and cryogenic electron tomography (cryoET) to characterize the elemental distribution and ultrastructure of vitrified cells. We applied this method to examine calcium disposition in the mitochondria of cultured human retinal ganglion cells (RGCs) exposed to pro-calcifying conditions relevant to optic disc drusen pathology. Our cryoEELS analysis revealed mitochondrial granules with elevated calcium signals, offering direct evidence of mitochondrial calcification. Additionally, cryoET coupled with artificial intelligence-based analysis enabled quantification of the volume and spatial distribution of these calcium granules. This integrated workflow can be broadly applied to various cell types, facilitating the study of ultrastructure and elemental distribution in subcellular structures under diverse physiological and pathological conditions, as well as in response to therapeutic interventions.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"28 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144770104","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 basis of pseudoGTPase-mediated protein-protein interactions 伪tpase介导的蛋白-蛋白相互作用的结构基础

IF 5.7 2区生物学

Structure Pub Date : 2025-08-01 DOI: 10.1016/j.str.2025.07.009

Bing Wang, Rui Yang, Chun Wan, Yuan Tian, Jingyi Wu, Taiwo Scholes Adewole, Sayantan Roy, Suzhao Li, Jingshi Shen, Qian Yin

{"title":"Structural basis of pseudoGTPase-mediated protein-protein interactions","authors":"Bing Wang, Rui Yang, Chun Wan, Yuan Tian, Jingyi Wu, Taiwo Scholes Adewole, Sayantan Roy, Suzhao Li, Jingshi Shen, Qian Yin","doi":"10.1016/j.str.2025.07.009","DOIUrl":"https://doi.org/10.1016/j.str.2025.07.009","url":null,"abstract":"GTPases regulate cellular processes through conformational changes triggered by guanine nucleotide binding. Recently, pseudoGTPases, the catalytically inactive counterparts of GTPases, have been identified across species from bacteria to human, although their functions and mechanisms remain unexplored. Here, we demonstrate that the N-terminal region of the assembly chaperone AAGAB is a class I pseudoGTPase using biochemistry and X-ray crystallography. Furthermore, we discovered that the AAGAB pseudoGTPase domain (psGD) interacts with the σ subunits of AP1 and AP2 adaptor complexes, which are heterotetrameric complexes involved in clathrin-mediated membrane trafficking. AAGAB psGD engages the σ subunits via a unique interface distinct from the conventional GTPase interacting regions. Further biochemical and cell-based assays confirmed the crucial role of the newly identified interface in binding and membrane trafficking. Collectively, our results establish AAGAB pseudoGTPase domain as a critical protein-protein interaction module. These findings offer new insight into the structural basis and molecular mechanisms of pseudoGTPases.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"735 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144756514","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

Crystal structures of PAK2 reveal new insights into its autoinhibitory mechanism PAK2的晶体结构揭示了其自抑制机制的新见解

IF 5.7 2区生物学

Structure Pub Date : 2025-08-01 DOI: 10.1016/j.str.2025.07.008

Hui-Fang Hu, Zhipu Luo, Yikan Zhang, Xianyang Fang, Zhiwen Zhu, Jia-Wei Wu, Zhi-Xin Wang

引用次数: 0

Sub-3 Å resolution protein structure determination by single-particle cryo-EM at 100 keV 亚-3 Å分辨率蛋白质结构测定，单粒子低温电镜在100 keV

IF 5.7 2区生物学

Structure Pub Date : 2025-07-30 DOI: 10.1016/j.str.2025.07.007

Dimple Karia, Adrian F. Koh, Wen Yang, Victoria I. Cushing, Benjamin Basanta, Daniel B. Mihaylov, Sagar Khavnekar, Ondřej Vyroubal, Miloš Malínský, Ondřej Sháněl, Vojtěch Doležal, Jürgen Plitzko, Lingbo Yu, Gabriel C. Lander, A. Radu Aricescu, Basil J. Greber, Abhay Kotecha

{"title":"Sub-3 Å resolution protein structure determination by single-particle cryo-EM at 100 keV","authors":"Dimple Karia, Adrian F. Koh, Wen Yang, Victoria I. Cushing, Benjamin Basanta, Daniel B. Mihaylov, Sagar Khavnekar, Ondřej Vyroubal, Miloš Malínský, Ondřej Sháněl, Vojtěch Doležal, Jürgen Plitzko, Lingbo Yu, Gabriel C. Lander, A. Radu Aricescu, Basil J. Greber, Abhay Kotecha","doi":"10.1016/j.str.2025.07.007","DOIUrl":"https://doi.org/10.1016/j.str.2025.07.007","url":null,"abstract":"Cryoelectron microscopy (cryo-EM) has transformed structural biology by providing high-resolution insights into biological macromolecules. We report sub-3 Å resolution structures using the 100 keV Tundra cryo-TEM, equipped with the Falcon C direct electron detector (DED). This system combines advanced optics, extreme-brightness field emission gun (XFEG), and SP-TWIN lens to enhance coherence and resolution. The semi-automated loader reduced contamination and drift, enabling extended data collection, while the high detective quantum efficiency (DQE) of Falcon C improved signal-to-noise ratio. We validated performance by determining structures of biological samples, including apoferritin (2.1 Å), T20S proteasome (2.7 Å), GABA<sub>A</sub> receptor (2.8 Å), hemoglobin (5.0 Å), transthyretin (3.5 Å), and AAV9 capsid (2.8 Å), spanning 50 kDa–3.9 MDa. This work highlights the potential of 100 keV transmission electron microscopes (TEMs) to make cryo-EM more accessible. It sets a precedent for using lower voltage TEMs not only for screening, but also for high-resolution protein structure determination.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"10 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144737517","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

Antibody-like recognition of a γδ T cell receptor toward a foreign antigen γδ T细胞受体对外来抗原的抗体样识别

IF 5.7 2区生物学

Structure Pub Date : 2025-07-30 DOI: 10.1016/j.str.2025.07.006

Liam Rashleigh, Hariprasad Venugopal, Michael T. Rice, Sachith D. Gunasinghe, Chhon Ling Sok, Nicholas A. Gherardin, Catarina F. Almeida, Ildiko Van Rhijn, D. Branch Moody, Dale I. Godfrey, Jamie Rossjohn, Benjamin S. Gully

{"title":"Antibody-like recognition of a γδ T cell receptor toward a foreign antigen","authors":"Liam Rashleigh, Hariprasad Venugopal, Michael T. Rice, Sachith D. Gunasinghe, Chhon Ling Sok, Nicholas A. Gherardin, Catarina F. Almeida, Ildiko Van Rhijn, D. Branch Moody, Dale I. Godfrey, Jamie Rossjohn, Benjamin S. Gully","doi":"10.1016/j.str.2025.07.006","DOIUrl":"https://doi.org/10.1016/j.str.2025.07.006","url":null,"abstract":"The antigen recognition principles of B cells and αβ T cells have been well described compared to those of the γδ T cell. By way of their specificity conferring receptor (γδTCR), γδ T cells can directly bind proteinaceous antigens. A known γδ T cell and B cell model antigen is phycoerythrin (PE), a light harvesting protein from rhodophytes and cyanobacteria. Here we probed human γδTCR reactivity to PE, in which a Vδ1Vγ5 TCR bound directly to induce proximal signaling and cellular activation. We determined the cryoelectron microscopy (cryo-EM) structure of the γδTCR-phycoerythrin immune complex. We then determined the cryo-EM structures of an antibody fragment and an αβTCR bound to PE. This revealed convergent use of apical aromatic residues to mediate contacts with a common PE epitope. Comparative analyses of the γδTCR revealed multiple antibody-like characteristics, including an enrichment of apical aromatic residues. Our findings reveal further distinct facets of antigen recognition by the γδTCR.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"1 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144737465","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 and thermodynamic classification of amyloid polymorphs 淀粉样多形体的结构和热力学分类

IF 5.7 2区生物学

Structure Pub Date : 2025-07-28 DOI: 10.1016/j.str.2025.07.005

Jack P. Connor, Sheena E. Radford, David J. Brockwell

引用次数: 0

Automated identification of small molecules in cryoelectron microscopy data with density- and energy-guided evaluation 用密度和能量引导评价的低温电子显微镜数据中的小分子的自动鉴定

IF 5.7 2区生物学

Structure Pub Date : 2025-07-25 DOI: 10.1016/j.str.2025.07.002

Andrew Muenks, Daniel P. Farrell, Guangfeng Zhou, Frank DiMaio

引用次数: 0

Cross-species recognition of squirrel ACE2 by the receptor binding domains of SARS-CoV-2, RaTG13, PCoV-GD and PCoV-GX SARS-CoV-2、RaTG13、PCoV-GD和PCoV-GX受体结合域对松鼠ACE2的跨种识别

IF 5.7 2区生物学

Structure Pub Date : 2025-07-25 DOI: 10.1016/j.str.2025.07.003

Chenghai Wang, Xiaoyan Nan, Yang Deng, Shilong Fan, Jun Lan

引用次数: 0

EnsembleFlex: Protein structure ensemble analysis made easy EnsembleFlex：蛋白质结构集成分析变得容易

IF 5.7 2区生物学

Structure Pub Date : 2025-07-25 DOI: 10.1016/j.str.2025.07.001

Melanie Schneider, José Antonio Marquez, Andrew R. Leach

{"title":"EnsembleFlex: Protein structure ensemble analysis made easy","authors":"Melanie Schneider, José Antonio Marquez, Andrew R. Leach","doi":"10.1016/j.str.2025.07.001","DOIUrl":"https://doi.org/10.1016/j.str.2025.07.001","url":null,"abstract":"Proteins exhibit conformational dynamics that underpin function and inform drug design. EnsembleFlex is a computational suite to extract, quantify, and visualize conformational heterogeneity from experimentally determined structure ensembles, thereby enabling both computational and experimental scientists to gain actionable insights into protein dynamics, ligand interactions, and drug-design applications. It performs dual-scale flexibility analysis (backbone and side-chain) via optimized superposition, dimension reduction (principal-component analysis [PCA] and uniform manifold approximation and projection [UMAP]), clustering, automated binding-site frequency mapping, and conserved water detection. Accessible through a no-code graphical interface or scriptable pipelines, EnsembleFlex accepts heterogeneous PDB sets (X-ray, NMR, and cryoelectron microscopy [cryo-EM]) and optionally integrates elastic network-model predictions (anisotropic network model [ANM]/Gaussian network model [GNM]) to complement experimental data. Case studies—including adenylate kinase, hexokinase-1, interleukin-1β (IL-1β) fragment screens, and SARS-CoV-2 main protease ensembles—demonstrate its scalability and utility for high-throughput structural analysis.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"20 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144701417","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

Regulatory mechanisms of PP2A complex assembly driven by physicochemical differences in A-subunit isoforms a亚基异构体的物理化学差异驱动PP2A复合体组装的调控机制

IF 5.7 2区生物学

Structure Pub Date : 2025-07-24 DOI: 10.1016/j.str.2025.06.013

Alexander Day, Wei Huang, Daniel Leonard, Caitlin M. O’Connor, Goutham Narla, Derek J. Taylor

{"title":"Regulatory mechanisms of PP2A complex assembly driven by physicochemical differences in A-subunit isoforms","authors":"Alexander Day, Wei Huang, Daniel Leonard, Caitlin M. O’Connor, Goutham Narla, Derek J. Taylor","doi":"10.1016/j.str.2025.06.013","DOIUrl":"https://doi.org/10.1016/j.str.2025.06.013","url":null,"abstract":"Protein phosphatase 2A (PP2A) is crucial for regulating cellular pathways, with its holoenzyme assembly affecting enzyme function and substrate selection. The PP2A holoenzyme comprises scaffold A-, regulatory B-, and catalytic C-subunits, each with various isoforms. Here, we examine structural and biochemical characteristics of the A-subunit isoforms (Aα and Aβ) and identify different biophysical properties that may promote distinct PP2A functions. Our molecular dynamics simulations and cryo-EM analyses define structural differences in the isoforms that reside primarily at the N-terminus of the A-subunit where it interfaces with regulatory B-subunits. Kinetic analyses show Aβ has a lower binding affinity in complexes with B56 subunits and exhibits unique aggregative properties as a monomeric protein. These findings suggest that the different physicochemical properties between A-subunit isoforms are key to PP2A holoenzyme assembly and function. We predict that the Aβ serves as a reservoir, ensuring that serine-threonine phosphatase activity is maintained during high regulatory demand.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"37 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144693787","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