1
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Kochańczyk T, Hann ZS, Lux MC, Delos Reyes AMV, Ji C, Tan DS, Lima CD. Structural basis for transthiolation intermediates in the ubiquitin pathway. Nature 2024; 633:216-223. [PMID: 39143218 PMCID: PMC11374688 DOI: 10.1038/s41586-024-07828-9] [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: 03/26/2024] [Accepted: 07/12/2024] [Indexed: 08/16/2024]
Abstract
Transthiolation (also known as transthioesterification) reactions are used in the biosynthesis of acetyl coenzyme A, fatty acids and polyketides, and for post-translational modification by ubiquitin (Ub) and ubiquitin-like (Ubl) proteins1-3. For the Ub pathway, E1 enzymes catalyse transthiolation from an E1~Ub thioester to an E2~Ub thioester. Transthiolation is also required for transfer of Ub from an E2~Ub thioester to HECT (homologous to E6AP C terminus) and RBR (ring-between-ring) E3 ligases to form E3~Ub thioesters4-6. How isoenergetic transfer of thioester bonds is driven forward by enzymes in the Ub pathway remains unclear. Here we isolate mimics of transient transthiolation intermediates for E1-Ub(T)-E2 and E2-Ub(T)-E3HECT complexes (where T denotes Ub in a thioester or Ub undergoing transthiolation) using a chemical strategy with native enzymes and near-native Ub to capture and visualize a continuum of structures determined by single-particle cryo-electron microscopy. These structures and accompanying biochemical experiments illuminate conformational changes in Ub, E1, E2 and E3 that are coordinated with the chemical reactions to facilitate directional transfer of Ub from each enzyme to the next.
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Affiliation(s)
- Tomasz Kochańczyk
- Structural Biology Program, Sloan Kettering Institute, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
| | - Zachary S Hann
- Structural Biology Program, Sloan Kettering Institute, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michaelyn C Lux
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Chemical Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Avelyn Mae V Delos Reyes
- Chemical Biology Program, Sloan Kettering Institute, New York, NY, USA
- Pharmacology Graduate Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Cheng Ji
- Chemical Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Derek S Tan
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Chemical Biology Program, Sloan Kettering Institute, New York, NY, USA.
- Pharmacology Graduate Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Christopher D Lima
- Structural Biology Program, Sloan Kettering Institute, New York, NY, USA.
- Howard Hughes Medical Institute, New York, NY, USA.
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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2
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Gül E, Huuskonen J, Abi Younes A, Maurer L, Enz U, Zimmermann J, Sellin ME, Bakkeren E, Hardt WD. Salmonella T3SS-2 virulence enhances gut-luminal colonization by enabling chemotaxis-dependent exploitation of intestinal inflammation. Cell Rep 2024; 43:113925. [PMID: 38460128 DOI: 10.1016/j.celrep.2024.113925] [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: 06/23/2023] [Revised: 01/12/2024] [Accepted: 02/20/2024] [Indexed: 03/11/2024] Open
Abstract
Salmonella Typhimurium (S.Tm) utilizes the chemotaxis receptor Tsr to exploit gut inflammation. However, the characteristics of this exploitation and the mechanism(s) employed by the pathogen to circumvent antimicrobial effects of inflammation are poorly defined. Here, using different naturally occurring S.Tm strains (SL1344 and 14028) and competitive infection experiments, we demonstrate that type-three secretion system (T3SS)-2 virulence is indispensable for the beneficial effects of Tsr-directed chemotaxis. The removal of the 14028-specific prophage Gifsy3, encoding virulence effectors, results in the loss of the Tsr-mediated fitness advantage in that strain. Surprisingly, without T3SS-2 effector secretion, chemotaxis toward the gut epithelium using Tsr becomes disadvantageous for either strain. Our findings reveal that luminal neutrophils recruited as a result of NLRC4 inflammasome activation locally counteract S.Tm cells exploiting the byproducts of the host immune response. This work highlights a mechanism by which S.Tm exploitation of gut inflammation for colonization relies on the coordinated effects of chemotaxis and T3SS activities.
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Affiliation(s)
- Ersin Gül
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland.
| | - Jemina Huuskonen
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Andrew Abi Younes
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Luca Maurer
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Ursina Enz
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Jakob Zimmermann
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for Biomedical Research, University of Bern, Bern, Switzerland
| | - Mikael E Sellin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden; Science for Life Laboratory, Uppsala, Sweden
| | - Erik Bakkeren
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Wolf-Dietrich Hardt
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland.
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3
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Roberts CG, Franklin TG, Pruneda JN. Ubiquitin-targeted bacterial effectors: rule breakers of the ubiquitin system. EMBO J 2023; 42:e114318. [PMID: 37555693 PMCID: PMC10505922 DOI: 10.15252/embj.2023114318] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/10/2023] [Accepted: 07/18/2023] [Indexed: 08/10/2023] Open
Abstract
Regulation through post-translational ubiquitin signaling underlies a large portion of eukaryotic biology. This has not gone unnoticed by invading pathogens, many of which have evolved mechanisms to manipulate or subvert the host ubiquitin system. Bacteria are particularly adept at this and rely heavily upon ubiquitin-targeted virulence factors for invasion and replication. Despite lacking a conventional ubiquitin system of their own, many bacterial ubiquitin regulators loosely follow the structural and mechanistic rules established by eukaryotic ubiquitin machinery. Others completely break these rules and have evolved novel structural folds, exhibit distinct mechanisms of regulation, or catalyze foreign ubiquitin modifications. Studying these interactions can not only reveal important aspects of bacterial pathogenesis but also shed light on unexplored areas of ubiquitin signaling and regulation. In this review, we discuss the methods by which bacteria manipulate host ubiquitin and highlight aspects that follow or break the rules of ubiquitination.
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Affiliation(s)
- Cameron G Roberts
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
| | - Tyler G Franklin
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
| | - Jonathan N Pruneda
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
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4
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Li Q, Qi Z, Fu D, Tang B, Song X, Shao Y, Tu J, Qi K. EspE3 plays a role in the pathogenicity of avian pathogenic Escherichia coli. Vet Res 2023; 54:70. [PMID: 37644523 PMCID: PMC10463865 DOI: 10.1186/s13567-023-01202-9] [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: 04/28/2023] [Accepted: 07/04/2023] [Indexed: 08/31/2023] Open
Abstract
APEC encodes multiple virulence factors that have complex pathogenic mechanisms. In this study, we report a virulence factor named EspE3, which can be secreted from APEC. This protein was predicted to have a leucine-rich repeat domain (LRR) and may have a similar function to IpaH class effectors of the type III secretion system (T3SS). For further exploration, the regulatory correlation between the espE3 and ETT2 genes in APEC was analysed. We then assessed the pathogenicity of EspE3, detected it in APEC secretion proteins and screened the proteins of EspE3 that interact with chicken trachea epithelial cells. This study provides data on a new virulence factor for further exploring the pathogenic mechanism of APEC.
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Affiliation(s)
- Qianwen Li
- Anhui Province Key Laboratory of Veterinary and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China.
- Anhui Province Engineering Laboratory for Animal Food Quality and Biosafety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China.
- Institute of Veterinary Immunology & Engineering, Jiangsu Academy of Agricultural Sciences, Nanjing, China.
- National Research Center of Veterinary Bioproduct Engineering and Technology, Jiangsu Academy of Agricultural Science, Nanjing, China.
- Guotai (Taizhou) Veterinary Biotechnology Innovation Center, Jiangsu Academy of Agricultural Science, Nanjing, China.
| | - Zhao Qi
- Anhui Province Key Laboratory of Veterinary and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China
- Anhui Province Engineering Laboratory for Animal Food Quality and Biosafety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China
| | - Dandan Fu
- Anhui Province Key Laboratory of Veterinary and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China
- Anhui Province Engineering Laboratory for Animal Food Quality and Biosafety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China
| | - Bo Tang
- Institute of Veterinary Immunology & Engineering, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- National Research Center of Veterinary Bioproduct Engineering and Technology, Jiangsu Academy of Agricultural Science, Nanjing, China
- Guotai (Taizhou) Veterinary Biotechnology Innovation Center, Jiangsu Academy of Agricultural Science, Nanjing, China
| | - Xiangjun Song
- Anhui Province Key Laboratory of Veterinary and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China
- Anhui Province Engineering Laboratory for Animal Food Quality and Biosafety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China
| | - Ying Shao
- Anhui Province Key Laboratory of Veterinary and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China
- Anhui Province Engineering Laboratory for Animal Food Quality and Biosafety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China
| | - Jian Tu
- Anhui Province Key Laboratory of Veterinary and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China
- Anhui Province Engineering Laboratory for Animal Food Quality and Biosafety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China
| | - Kezong Qi
- Anhui Province Key Laboratory of Veterinary and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China.
- Anhui Province Engineering Laboratory for Animal Food Quality and Biosafety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China.
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5
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Pillay TD, Hettiarachchi SU, Gan J, Diaz-Del-Olmo I, Yu XJ, Muench JH, Thurston TL, Pearson JS. Speaking the host language: how Salmonella effector proteins manipulate the host. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001342. [PMID: 37279149 PMCID: PMC10333799 DOI: 10.1099/mic.0.001342] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 05/10/2023] [Indexed: 06/08/2023]
Abstract
Salmonella injects over 40 virulence factors, termed effectors, into host cells to subvert diverse host cellular processes. Of these 40 Salmonella effectors, at least 25 have been described as mediating eukaryotic-like, biochemical post-translational modifications (PTMs) of host proteins, altering the outcome of infection. The downstream changes mediated by an effector's enzymatic activity range from highly specific to multifunctional, and altogether their combined action impacts the function of an impressive array of host cellular processes, including signal transduction, membrane trafficking, and both innate and adaptive immune responses. Salmonella and related Gram-negative pathogens have been a rich resource for the discovery of unique enzymatic activities, expanding our understanding of host signalling networks, bacterial pathogenesis as well as basic biochemistry. In this review, we provide an up-to-date assessment of host manipulation mediated by the Salmonella type III secretion system injectosome, exploring the cellular effects of diverse effector activities with a particular focus on PTMs and the implications for infection outcomes. We also highlight activities and functions of numerous effectors that remain poorly characterized.
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Affiliation(s)
- Timesh D. Pillay
- Centre for Bacterial Resistance Biology, Department of Infectious Disease, Imperial College, London SW7 2AZ, UK
- The Francis Crick Institute, London NW1 1AT, UK
| | - Sahampath U. Hettiarachchi
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Jiyao Gan
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
| | - Ines Diaz-Del-Olmo
- Centre for Bacterial Resistance Biology, Department of Infectious Disease, Imperial College, London SW7 2AZ, UK
| | - Xiu-Jun Yu
- Centre for Bacterial Resistance Biology, Department of Infectious Disease, Imperial College, London SW7 2AZ, UK
| | - Janina H. Muench
- Centre for Bacterial Resistance Biology, Department of Infectious Disease, Imperial College, London SW7 2AZ, UK
- The Francis Crick Institute, London NW1 1AT, UK
| | - Teresa L.M. Thurston
- Centre for Bacterial Resistance Biology, Department of Infectious Disease, Imperial College, London SW7 2AZ, UK
- The Francis Crick Institute, London NW1 1AT, UK
| | - Jaclyn S. Pearson
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
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6
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Bullones-Bolaños A, Bernal-Bayard J, Ramos-Morales F. The NEL Family of Bacterial E3 Ubiquitin Ligases. Int J Mol Sci 2022; 23:7725. [PMID: 35887072 PMCID: PMC9320238 DOI: 10.3390/ijms23147725] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 12/16/2022] Open
Abstract
Some pathogenic or symbiotic Gram-negative bacteria can manipulate the ubiquitination system of the eukaryotic host cell using a variety of strategies. Members of the genera Salmonella, Shigella, Sinorhizobium, and Ralstonia, among others, express E3 ubiquitin ligases that belong to the NEL family. These bacteria use type III secretion systems to translocate these proteins into host cells, where they will find their targets. In this review, we first introduce type III secretion systems and the ubiquitination process and consider the various ways bacteria use to alter the ubiquitin ligation machinery. We then focus on the members of the NEL family, their expression, translocation, and subcellular localization in the host cell, and we review what is known about the structure of these proteins, their function in virulence or symbiosis, and their specific targets.
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Affiliation(s)
| | | | - Francisco Ramos-Morales
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Sevilla, Spain; (A.B.-B.); (J.B.-B.)
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7
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James EI, Murphree TA, Vorauer C, Engen JR, Guttman M. Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems. Chem Rev 2021; 122:7562-7623. [PMID: 34493042 PMCID: PMC9053315 DOI: 10.1021/acs.chemrev.1c00279] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Solution-phase hydrogen/deuterium
exchange (HDX) coupled to mass
spectrometry (MS) is a widespread tool for structural analysis across
academia and the biopharmaceutical industry. By monitoring the exchangeability
of backbone amide protons, HDX-MS can reveal information about higher-order
structure and dynamics throughout a protein, can track protein folding
pathways, map interaction sites, and assess conformational states
of protein samples. The combination of the versatility of the hydrogen/deuterium
exchange reaction with the sensitivity of mass spectrometry has enabled
the study of extremely challenging protein systems, some of which
cannot be suitably studied using other techniques. Improvements over
the past three decades have continually increased throughput, robustness,
and expanded the limits of what is feasible for HDX-MS investigations.
To provide an overview for researchers seeking to utilize and derive
the most from HDX-MS for protein structural analysis, we summarize
the fundamental principles, basic methodology, strengths and weaknesses,
and the established applications of HDX-MS while highlighting new
developments and applications.
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Affiliation(s)
- Ellie I James
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Taylor A Murphree
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Clint Vorauer
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - John R Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
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8
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Ye Y, Xiong Y, Huang H. Substrate-binding destabilizes the hydrophobic cluster to relieve the autoinhibition of bacterial ubiquitin ligase IpaH9.8. Commun Biol 2020; 3:752. [PMID: 33303953 PMCID: PMC7728815 DOI: 10.1038/s42003-020-01492-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 11/17/2020] [Indexed: 12/21/2022] Open
Abstract
IpaH enzymes are bacterial E3 ligases targeting host proteins for ubiquitylation. Two autoinhibition modes of IpaH enzymes have been proposed based on the relative positioning of the Leucine-rich repeat domain (LRR) with respect to the NEL domain. In mode 1, substrate-binding competitively displaces the interactions between theLRR and NEL to relieve autoinhibition. However, the molecular basis for mode 2 is unclear. Here, we present the crystal structures of Shigella IpaH9.8 and the LRR of IpaH9.8 in complex with the substrate of human guanylate-binding protein 1 (hGBP1). A hydrophobic cluster in the C-terminus of IpaH9.8LRR forms a hydrophobic pocket involved in binding the NEL domain, and the binding is important for IpaH9.8 autoinhibition. Substrate-binding destabilizes the hydrophobic cluster by inducing conformational changes of IpaH9.8LRR. Arg166 and Phe187 in IpaH9.8LRR function as sensors for substrate-binding. Collectively, our findings provide insights into the molecular mechanisms for the actication of IpaH9.8 in autoinhibition mode 2. Ye, Xiong et al. present crystal structures of bacterial E3 ubiquitin ligase IpaH9.8 and IpaH9.8LRR–hGBP1. They find that substrate-binding destabilizes the hydrophobic cluster to relieve the autoinhibition of IpaH9.8. This study provides insights into the mechanisms underlying substrate-induced activation of IpaH9.8.
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Affiliation(s)
- Yuxin Ye
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, 518055, Shenzhen, China. .,Shenzhen Bay Laboratory Pingshan Translational Medicine Center, Shenzhen, China. .,Laboratory of Structural Biology and Drug Discovery, Peking University Shenzhen Graduate School, 518055, Shenzhen, China.
| | - Yuxian Xiong
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, 518055, Shenzhen, China.,Laboratory of Structural Biology and Drug Discovery, Peking University Shenzhen Graduate School, 518055, Shenzhen, China
| | - Hao Huang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, 518055, Shenzhen, China. .,Laboratory of Structural Biology and Drug Discovery, Peking University Shenzhen Graduate School, 518055, Shenzhen, China.
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