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Cheng L, Miao Z, Liu S, Li Z, Fu H, Xu C, Hu S, Zhao C, Liu Y, Zhao T, Liu W, Wang H, Liu R, Yan W, Tang X, Liu J, Shao Z, Ke B. Cryo-EM structure of small-molecule agonist bound delta opioid receptor-G i complex enables discovery of biased compound. Nat Commun 2024; 15:8284. [PMID: 39333070 PMCID: PMC11437176 DOI: 10.1038/s41467-024-52601-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 09/12/2024] [Indexed: 09/29/2024] Open
Abstract
Delta opioid receptor (δOR) plays a pivotal role in modulating human sensation and emotion. It is an attractive target for drug discovery since, unlike Mu opioid receptor, it is associated with low risk of drug dependence. Despite its potential applications, the pharmacological properties of δOR, including the mechanisms of activation by small-molecule agonists and the complex signaling pathways it engages, as well as their relation to the potential side effects, remain poorly understood. In this study, we use cryo-electron microscopy (cryo-EM) to determine the structure of the δOR-Gi complex when bound to a small-molecule agonist (ADL5859). Moreover, we design a series of probes to examine the key receptor-ligand interaction site and identify a region involved in signaling bias. Using ADL06 as a chemical tool, we elucidate the relationship between the β-arrestin pathway of the δOR and its biological functions, such as analgesic tolerance and convulsion activities. Notably, we discover that the β-arrestin recruitment of δOR might be linked to reduced gastrointestinal motility. These insights enhance our understanding of δOR's structure, signaling pathways, and biological functions, paving the way for the structure-based drug discovery.
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Grants
- 2023ZYD0168 Department of Science and Technology of Sichuan Province (Sichuan Provincial Department of Science and Technology)
- 2024NSFJQ0052 Department of Science and Technology of Sichuan Province (Sichuan Provincial Department of Science and Technology)
- 82425054, 82273784 National Natural Science Foundation of China (National Science Foundation of China)
- 82271190, 32100965 National Natural Science Foundation of China (National Science Foundation of China)
- 323B2038 National Natural Science Foundation of China (National Science Foundation of China)
- 32371288, 32100988 National Natural Science Foundation of China (National Science Foundation of China)
- 31972916, T2221004, 31972916 National Natural Science Foundation of China (National Science Foundation of China)
- 32330049, 82320108021 National Natural Science Foundation of China (National Science Foundation of China)
- 2019YFA0508800 Ministry of Science,Technology and Research (Ministry of Technology & Research)
- 2021ZD0201900 Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)
- the 1.3.5 Project for Disciplines of Excellence, West China Hospital, Sichuan University,ZYYC21002 and ZYGD23025
- Ministry of Science,Technology and Research (Ministry of Technology & Research)
- Frontiers Medical Center, Tianfu Jincheng Laboratory Foundation, TFJC2023010010; the 1.3.5 Project for Disciplines of Excellence, West China Hospital, Sichuan University, ZYYC20023.
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Affiliation(s)
- Lin Cheng
- Department of Anesthesiology, Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Otolaryngology Head and Neck Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Zhuang Miao
- Department of Anesthesiology, Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Sicen Liu
- Department of Anesthesiology, Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, China
| | - Zhe Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, P. R. China
| | - Hong Fu
- Department of Anesthesiology, Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Chanjuan Xu
- Cellular Signaling Laboratory, International Research Center for Sensory Biology and Technology of MOST, Key Laboratory of Molecular Biophysics of MOE, and College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shilong Hu
- Department of Anesthesiology, Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Chang Zhao
- Department of Anesthesiology, Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yuxuan Liu
- Cellular Signaling Laboratory, International Research Center for Sensory Biology and Technology of MOST, Key Laboratory of Molecular Biophysics of MOE, and College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Tiantian Zhao
- Department of Anesthesiology, Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Wencheng Liu
- Department of Anesthesiology, Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Heli Wang
- Department of Anesthesiology, Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Runduo Liu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, P. R. China
| | - Wei Yan
- Department of Anesthesiology, Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiangdong Tang
- Sleep Medicine Center, Mental Health Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jianfeng Liu
- Cellular Signaling Laboratory, International Research Center for Sensory Biology and Technology of MOST, Key Laboratory of Molecular Biophysics of MOE, and College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Zhenhua Shao
- Department of Anesthesiology, Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
- Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, China.
| | - Bowen Ke
- Department of Anesthesiology, Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
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Fan X, Zhang Q, Zhang H, Zhu J, Ju L, Shi Z, Hu M, Bao C. CryoTRANS: predicting high-resolution maps of rare conformations from self-supervised trajectories in cryo-EM. Commun Biol 2024; 7:1058. [PMID: 39191900 DOI: 10.1038/s42003-024-06739-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 08/14/2024] [Indexed: 08/29/2024] Open
Abstract
Cryogenic electron microscopy (cryo-EM) has revolutionized structural biology, enabling efficient determination of structures at near-atomic resolutions. However, a common challenge arises from the severe imbalance among various conformations of vitrified particles, leading to low-resolution reconstructions in rare conformations due to a lack of particle images in these quasi-stable states. We introduce CryoTRANS, a method that predicts high-resolution maps of rare conformations by constructing a self-supervised pseudo-trajectory between density maps of varying resolutions. This trajectory is represented by an ordinary differential equation parameterized by a deep neural network, ensuring retention of detailed structures from high-resolution density maps. By leveraging a single high-resolution density map, CryoTRANS significantly improves the reconstruction of rare conformations and has been validated on four real-world datasets: alpha-2-macroglobulin, actin-binding protein complexes, SARS-CoV-2 spike glycoprotein, and the 70S ribosome. CryoTRANS can also predict high-resolution structures in cryogenic electron tomography maps using a high-resolution cryo-EM map.
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Affiliation(s)
- Xiao Fan
- Yau Mathematical Sciences Center, Tsinghua University, Beijing, China
| | - Qi Zhang
- School of Life Science, Tsinghua University, Beijing, China
| | - Hui Zhang
- Qiuzhen College, Tsinghua University, Beijing, China
| | - Jianying Zhu
- Yau Mathematical Sciences Center, Tsinghua University, Beijing, China
| | - Lili Ju
- Department of Mathematics, University of South Carolina, Columbia, SC, USA
| | - Zuoqiang Shi
- Yau Mathematical Sciences Center, Tsinghua University, Beijing, China.
- Yanqi Lake Beijing Institute of Mathematical Sciences and Applications, Beijing, China.
| | - Mingxu Hu
- Beijing Frontier Research Center of Biological Structure (Tsinghua University), Beijing, China.
- Beijing Advanced Innovation Center for Structural Biology (Tsinghua University), Beijing, China.
- Institute of Bio-Architecture and Bio-Interactions, Shenzhen Medical Academy of Research and Translation, Shenzhen, China.
| | - Chenglong Bao
- Yau Mathematical Sciences Center, Tsinghua University, Beijing, China.
- Yanqi Lake Beijing Institute of Mathematical Sciences and Applications, Beijing, China.
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing, China.
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He J, Liu G, Kong F, Tan Q, Wang Z, Yang M, He Y, Jia X, Yan C, Wang C, Qian H. Structural basis for the transport and substrate selection of human urate transporter 1. Cell Rep 2024; 43:114628. [PMID: 39146184 DOI: 10.1016/j.celrep.2024.114628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 06/17/2024] [Accepted: 07/30/2024] [Indexed: 08/17/2024] Open
Abstract
High serum urate levels are the major risk factor for gout. URAT1, the primary transporter for urate absorption in the kidneys, is well known as an anti-hyperuricemia drug target. However, the clinical application of URAT1-targeted drugs is limited because of their low specificity and severe side effects. The lack of structural information impedes elucidation of the transport mechanism and the development of new drugs. Here, we present the cryoelectron microscopy (cryo-EM) structures of human URAT1(R477S), its complex with urate, and its closely related homolog OAT4. URAT1(R477S) and OAT4 exhibit major facilitator superfamily (MFS) folds with outward- and inward-open conformations, respectively. Structural comparison reveals a 30° rotation between the N-terminal and C-terminal domains, supporting an alternating access mechanism. A conserved arginine (OAT4-Arg473/URAT1-Arg477) is found to be essential for chloride-mediated inhibition. The URAT1(R477S)-urate complex reveals the specificity of urate recognition. Taken together, our study promotes our understanding of the transport mechanism and substrate selection of URAT1.
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Affiliation(s)
- Jingjing He
- Department of Cardiology, First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Guoyun Liu
- Department of Cardiology, First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Fang Kong
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qiulong Tan
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518107, China
| | - Zhenzhou Wang
- Department of Cardiology, First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Meng Yang
- Department of Cardiology, First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Yonglin He
- Department of Cardiology, First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Xiaoxiao Jia
- Department of Cardiology, First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Chuangye Yan
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Chao Wang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518107, China
| | - Hongwu Qian
- Department of Cardiology, First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.
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4
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Remis J, Petrov PN, Zhang JT, Axelrod JJ, Cheng H, Sandhaus S, Mueller H, Glaeser RM. Cryo-EM phase-plate images reveal unexpected levels of apparent specimen damage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.04.606536. [PMID: 39149370 PMCID: PMC11326166 DOI: 10.1101/2024.08.04.606536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Apoferritin (apoF) is commonly used as a test specimen in single-particle electron cryo-microscopy (cryo-EM), since it consistently produces density maps that go to 3 Å resolution or higher. When we imaged apoF with a laser phase plate (LPP), however, we observed more severe particle-to-particle variation in the images than we had previously thought to exist. Similarly, we found that images of ribulose bisphosphate carboxylase/oxygenase (rubisco) also exhibited a much greater amount of heterogeneity than expected. By comparison to simulations of images, we verified that the heterogeneity is not explained by the known features of the LPP, shot noise, or differences in particle orientation. We also demonstrate that our specimens are comparable to those previously used in the literature, based on using the final-reconstruction resolution as the metric for evaluation. All of this leads us to the hypothesis that the heterogeneity is due to damage that has occurred either during purification of the specimen or during preparation of the grids. It is not, however, our goal to explain the causes of heterogeneity; rather, we report that using the LPP has made the apparent damage too obvious to be ignored. In hindsight, similar heterogeneity can be seen in images of apoF and the 20S proteasome which others had recorded with a Volta phase plate. We therefore conclude that the increased contrast of phase-plate images (at low spatial frequencies) should also make it possible to visualize, on a single-particle basis, various forms of biologically functional heterogeneity in structure that had previously gone unnoticed.
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Affiliation(s)
- Jonathan Remis
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA
| | - Petar N. Petrov
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA
- Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Jessie T, Zhang
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA
- Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Jeremy J. Axelrod
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA
- Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Hang Cheng
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA 94720, USA
| | - Shahar Sandhaus
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA
| | - Holger Mueller
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA
- Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Robert M. Glaeser
- Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
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Zhu J, Zhang Q, Zhang H, Shi Z, Hu M, Bao C. A minority of final stacks yields superior amplitude in single-particle cryo-EM. Nat Commun 2023; 14:7822. [PMID: 38072910 PMCID: PMC10711021 DOI: 10.1038/s41467-023-43555-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023] Open
Abstract
Cryogenic electron microscopy (cryo-EM) is widely used to determine near-atomic resolution structures of biological macromolecules. Due to the low signal-to-noise ratio, cryo-EM relies on averaging many images. However, a crucial question in the field of cryo-EM remains unanswered: how close can we get to the minimum number of particles required to reach a specific resolution in practice? The absence of an answer to this question has impeded progress in understanding sample behavior and the performance of sample preparation methods. To address this issue, we develop an iterative particle sorting and/or sieving method called CryoSieve. Extensive experiments demonstrate that CryoSieve outperforms other cryo-EM particle sorting algorithms, revealing that most particles are unnecessary in final stacks. The minority of particles remaining in the final stacks yield superior high-resolution amplitude in reconstructed density maps. For some datasets, the size of the finest subset approaches the theoretical limit.
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Affiliation(s)
- Jianying Zhu
- Yau Mathematical Sciences Center, Tsinghua University, Beijing, China
| | - Qi Zhang
- Key Laboratory of Protein Sciences (Tsinghua University), Ministry of Education, Beijing, China
- School of Life Science, Tsinghua University, Beijing, China
- Beijing Advanced Innovation Center for Structural Biology, Beijing, China
- Beijing Frontier Research Center for Biological Structure, Beijing, China
| | - Hui Zhang
- Qiuzhen College, Tsinghua University, Beijing, China
| | - Zuoqiang Shi
- Yau Mathematical Sciences Center, Tsinghua University, Beijing, China.
- Yanqi Lake Beijing Institute of Mathematical Sciences and Applications, Beijing, China.
| | - Mingxu Hu
- Key Laboratory of Protein Sciences (Tsinghua University), Ministry of Education, Beijing, China.
- School of Life Science, Tsinghua University, Beijing, China.
- Beijing Advanced Innovation Center for Structural Biology, Beijing, China.
- Beijing Frontier Research Center for Biological Structure, Beijing, China.
- Shenzhen Academy of Research and Translation, Shenzhen, China.
| | - Chenglong Bao
- Yau Mathematical Sciences Center, Tsinghua University, Beijing, China.
- Yanqi Lake Beijing Institute of Mathematical Sciences and Applications, Beijing, China.
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing, China.
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