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An W, Hall C, Li J, Hung A, Wu J, Park J, Wang L, Bai XC, Choi E. Activation of the insulin receptor by insulin-like growth factor 2. Nat Commun 2024; 15:2609. [PMID: 38521788 PMCID: PMC10960814 DOI: 10.1038/s41467-024-46990-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 03/15/2024] [Indexed: 03/25/2024] Open
Abstract
Insulin receptor (IR) controls growth and metabolism. Insulin-like growth factor 2 (IGF2) has different binding properties on two IR isoforms, mimicking insulin's function. However, the molecular mechanism underlying IGF2-induced IR activation remains unclear. Here, we present cryo-EM structures of full-length human long isoform IR (IR-B) in both the inactive and IGF2-bound active states, and short isoform IR (IR-A) in the IGF2-bound active state. Under saturated IGF2 concentrations, both the IR-A and IR-B adopt predominantly asymmetric conformations with two or three IGF2s bound at site-1 and site-2, which differs from that insulin saturated IR forms an exclusively T-shaped symmetric conformation. IGF2 exhibits a relatively weak binding to IR site-2 compared to insulin, making it less potent in promoting full IR activation. Cell-based experiments validated the functional importance of IGF2 binding to two distinct binding sites in optimal IR signaling and trafficking. In the inactive state, the C-terminus of α-CT of IR-B contacts FnIII-2 domain of the same protomer, hindering its threading into the C-loop of IGF2, thus reducing the association rate of IGF2 with IR-B. Collectively, our studies demonstrate the activation mechanism of IR by IGF2 and reveal the molecular basis underlying the different affinity of IGF2 to IR-A and IR-B.
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Affiliation(s)
- Weidong An
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Catherine Hall
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Jie Li
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Albert Hung
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Jiayi Wu
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Junhee Park
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Liwei Wang
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Eunhee Choi
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA.
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2
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Li J, Canham SM, Wu H, Henault M, Chen L, Liu G, Chen Y, Yu G, Miller HR, Hornak V, Brittain SM, Michaud GA, Tutter A, Broom W, Digan ME, McWhirter SM, Sivick KE, Pham HT, Chen CH, Tria GS, McKenna JM, Schirle M, Mao X, Nicholson TB, Wang Y, Jenkins JL, Jain RK, Tallarico JA, Patel SJ, Zheng L, Ross NT, Cho CY, Zhang X, Bai XC, Feng Y. Activation of human STING by a molecular glue-like compound. Nat Chem Biol 2024; 20:365-372. [PMID: 37828400 PMCID: PMC10907298 DOI: 10.1038/s41589-023-01434-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 09/02/2023] [Indexed: 10/14/2023]
Abstract
Stimulator of interferon genes (STING) is a dimeric transmembrane adapter protein that plays a key role in the human innate immune response to infection and has been therapeutically exploited for its antitumor activity. The activation of STING requires its high-order oligomerization, which could be induced by binding of the endogenous ligand, cGAMP, to the cytosolic ligand-binding domain. Here we report the discovery through functional screens of a class of compounds, named NVS-STGs, that activate human STING. Our cryo-EM structures show that NVS-STG2 induces the high-order oligomerization of human STING by binding to a pocket between the transmembrane domains of the neighboring STING dimers, effectively acting as a molecular glue. Our functional assays showed that NVS-STG2 could elicit potent STING-mediated immune responses in cells and antitumor activities in animal models.
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Affiliation(s)
- Jie Li
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Stephen M Canham
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA.
| | - Hua Wu
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Martin Henault
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Lihao Chen
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Guoxun Liu
- Novartis Institutes for BioMedical Research, San Diego, CA, USA
| | - Yu Chen
- Novartis Institutes for BioMedical Research, San Diego, CA, USA
| | - Gary Yu
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Howard R Miller
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Viktor Hornak
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | | | - Antonin Tutter
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Wendy Broom
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | | | | | - Helen T Pham
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - George S Tria
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Markus Schirle
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Xiaohong Mao
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Yuan Wang
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Rishi K Jain
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Sejal J Patel
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Lianxing Zheng
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Nathan T Ross
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Charles Y Cho
- Novartis Institutes for BioMedical Research, San Diego, CA, USA
| | - Xuewu Zhang
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Yan Feng
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA.
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3
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Bai XC, Zhang X. Applications of cryo-EM in drug development for STING. Curr Opin Struct Biol 2024; 84:102767. [PMID: 38183862 DOI: 10.1016/j.sbi.2023.102767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 01/08/2024]
Abstract
STING is a critical adaptor protein in the cGAS-mediated DNA-sensing innate immune pathway. Binding of the second messenger cGAMP generated by cGAS to STING induces the high-order oligomerization and activation of the STING dimer. STING is a promising target for diseases associated with the cGAS/STING pathway such as cancer and autoimmune diseases. Recent applications of cryo-EM to STING have led to exciting progress in the understanding of its regulatory mechanism. Cryo-EM structures of STING bound to either cGAMP mimetics or novel small molecule ligands not only revealed the action mechanisms of these ligands but also suggested new ways to modulate the activity of STING for therapeutic purposes. Some of these recent studies are highlighted here.
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Affiliation(s)
- Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Xuewu Zhang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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Bai XC, Gonen T, Gronenborn AM, Perrakis A, Thorn A, Yang J. Challenges and opportunities in macromolecular structure determination. Nat Rev Mol Cell Biol 2024; 25:7-12. [PMID: 37848590 DOI: 10.1038/s41580-023-00659-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2023] [Indexed: 10/19/2023]
Affiliation(s)
- Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Tamir Gonen
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA.
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA, USA.
- Department of Physiology, University of California Los Angeles, Los Angeles, CA, USA.
| | | | - Anastassis Perrakis
- Oncode Institute, Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, Netherlands.
| | - Andrea Thorn
- Institute for Nanostructure and Solid State Physics, University of Hamburg, Hamburg, Germany.
| | - Jianyi Yang
- MOE Frontiers Science Center for Nonlinear Expectations, Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao, China.
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Zhang H, Shi Z, Banigan EJ, Kim Y, Yu H, Bai XC, Finkelstein IJ. CTCF and R-loops are boundaries of cohesin-mediated DNA looping. Mol Cell 2023; 83:2856-2871.e8. [PMID: 37536339 DOI: 10.1016/j.molcel.2023.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 05/10/2023] [Accepted: 07/06/2023] [Indexed: 08/05/2023]
Abstract
Cohesin and CCCTC-binding factor (CTCF) are key regulatory proteins of three-dimensional (3D) genome organization. Cohesin extrudes DNA loops that are anchored by CTCF in a polar orientation. Here, we present direct evidence that CTCF binding polarity controls cohesin-mediated DNA looping. Using single-molecule imaging, we demonstrate that a critical N-terminal motif of CTCF blocks cohesin translocation and DNA looping. The cryo-EM structure of the cohesin-CTCF complex reveals that this CTCF motif ahead of zinc fingers can only reach its binding site on the STAG1 cohesin subunit when the N terminus of CTCF faces cohesin. Remarkably, a C-terminally oriented CTCF accelerates DNA compaction by cohesin. DNA-bound Cas9 and Cas12a ribonucleoproteins are also polar cohesin barriers, indicating that stalling may be intrinsic to cohesin itself. Finally, we show that RNA-DNA hybrids (R-loops) block cohesin-mediated DNA compaction in vitro and are enriched with cohesin subunits in vivo, likely forming TAD boundaries.
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Affiliation(s)
- Hongshan Zhang
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Zhubing Shi
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang, China; Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Edward J Banigan
- Department of Physics, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yoori Kim
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu 42988, Republic of Korea
| | - Hongtao Yu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang, China; Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Xiao-Chen Bai
- Department of Biophysics, Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Ilya J Finkelstein
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.
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Abstract
The insulin receptor (IR) is a type II receptor tyrosine kinase that plays essential roles in metabolism, growth, and proliferation. Dysregulation of IR signaling is linked to many human diseases, such as diabetes and cancers. The resolution revolution in cryo-electron microscopy has led to the determination of several structures of IR with different numbers of bound insulin molecules in recent years, which have tremendously improved our understanding of how IR is activated by insulin. Here, we review the insulin-induced activation mechanism of IR, including (a) the detailed binding modes and functions of insulin at site 1 and site 2 and (b) the insulin-induced structural transitions that are required for IR activation. We highlight several other key aspects of the activation and regulation of IR signaling and discuss the remaining gaps in our understanding of the IR activation mechanism and potential avenues of future research.
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Affiliation(s)
- Eunhee Choi
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA;
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, USA;
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Wang L, Hall C, Li J, Choi E, Bai XC. Structural basis of the alkaline pH-dependent activation of insulin receptor-related receptor. Nat Struct Mol Biol 2023; 30:661-669. [PMID: 37055497 PMCID: PMC10465182 DOI: 10.1038/s41594-023-00974-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 03/20/2023] [Indexed: 04/15/2023]
Abstract
The insulin receptor (IR) family is a subfamily of receptor tyrosine kinases that controls metabolic homeostasis and cell growth. Distinct from IR and insulin-like growth factor 1 receptor, whose activation requires ligand binding, insulin receptor-related receptor (IRR)-the third member of the IR family-is activated by alkaline pH. However, the molecular mechanism underlying alkaline pH-induced IRR activation remains unclear. Here, we present cryo-EM structures of human IRR in both neutral pH inactive and alkaline pH active states. Combined with mutagenesis and cellular assays, we show that, upon pH increase, electrostatic repulsion of the pH-sensitive motifs of IRR disrupts its autoinhibited state and promotes a scissor-like rotation between two protomers, leading to a T-shaped active conformation. Together, our study reveals an unprecedented alkaline pH-dependent activation mechanism of IRR, opening up opportunities to understand the structure-function relationship of this important receptor.
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Affiliation(s)
- Liwei Wang
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Catherine Hall
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Jie Li
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Eunhee Choi
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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Xi C, Bai XC, Li C, Wang WN, Tian S, Tang YL, Shen B, Wang J, Sun YM, Zhu YL. Association between Respiratory Function and Motor Function in Different Stages of Parkinson's Disease. Eur Neurol 2023; 86:242-249. [PMID: 37068470 DOI: 10.1159/000530390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/19/2023] [Indexed: 04/19/2023]
Abstract
INTRODUCTION Respiratory dysfunction in patients with Parkinson's disease (PD) could present in the early stage and worsen in the late stages. These changes could be a factor affecting the ability of daily living and quality of life of patients with PD. The primary objective of this study was to assess the respiratory function and its association with motor function in patients with different stages of PD. METHODS This was a cross-sectional study conducted at the Huashan Hospital of Fudan University in Shanghai, China. The study included 65 patients diagnosed with PD (the Hoehn and Yahr scale between 1 and 4) and 20 healthy individuals of similar age, gender, weight, and height. The ventilatory function was assessed using the spirometry. Motor function was evaluated using subscale III of the United Parkinson's disease rating scale (UPDRS-III). After confirming the normality of data distribution, we performed one-way ANOVA with a Tukey's post hoc test. RESULTS Compared with the healthy individuals, there was no statistical significance in forced vital capacity (FVC), forced expiratory volume in 1 s (FEV1), and forced expiratory volume in 1 s/forced vital capacity (FEV1/FVC) in the H&Y 1 group and H&Y 2 group (p > 0.05) but reduced peak expiratory flow (PEF) in the H&Y 2 group (p = 0.002). Reduced FVC, FEV1, and PEF was seen in the H&Y 3 group (p = 0.002, p = 0.001, and p = 0.0001, respectively). Reduced FVC, FEV1, PEF, and FEF25-75% was seen in the H&Y 4 group (p = 0.001, p = 0.0001, p = 0.0001, and p = 0.025, respectively). The correlation analysis revealed that there was a significant negative correlation between FVC and UPDRS-III scores (r = -0.248, p = 0.046), disease duration (r = -0.276, p = 0.026), H&Y scale (r = -0.415, p = 0.001). FEV1 was negatively correlated with UPDRS-III scores (r = -0.277, p = 0.025), disease duration (r = -0.291, p = 0.019), H&Y scale (r = -0.434, p = 0.0001). FEF25-75% was negatively correlated with disease duration (r = -0.247, p = 0.047), H&Y scale (r = -0.278, p = 0.025). CONCLUSION Our findings revealed that respiratory impairment is present in moderate and advanced PD patients, and directly related to the severity of the disease. It is important to conduct respiratory function test in the clinical practice.
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Affiliation(s)
- Chong Xi
- Department of Rehabilitation Medicine, Huashan Hospital, Fudan University, Shanghai, China,
| | - Xiao-Chen Bai
- Department of Rehabilitation Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Ce Li
- Department of Rehabilitation Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Wei-Ning Wang
- Department of Rehabilitation Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Shan Tian
- Department of Rehabilitation Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Yi-Lin Tang
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
| | - Bo Shen
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
| | - Jian Wang
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yi-Min Sun
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yu-Lian Zhu
- Department of Rehabilitation Medicine, Huashan Hospital, Fudan University, Shanghai, China
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Liu S, Chen H, Yin Y, Lu D, Gao G, Li J, Bai XC, Zhang X. Inhibition of FAM46/TENT5 activity by BCCIPα adopting a unique fold. Sci Adv 2023; 9:eadf5583. [PMID: 37018411 PMCID: PMC10075960 DOI: 10.1126/sciadv.adf5583] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
The FAM46 (also known as TENT5) proteins are noncanonical poly(A) polymerases (PAPs) implicated in regulating RNA stability. The regulatory mechanisms of FAM46 are poorly understood. Here, we report that the nuclear protein BCCIPα, but not the alternatively spliced isoform BCCIPβ, binds FAM46 and inhibits their PAP activity. Unexpectedly, our structures of the FAM46A/BCCIPα and FAM46C/BCCIPα complexes show that, despite sharing most of the sequence and differing only at the C-terminal portion, BCCIPα adopts a unique structure completely different from BCCIPβ. The distinct C-terminal segment of BCCIPα supports the adoption of the unique fold but does not directly interact with FAM46. The β sheets in BCCIPα and FAM46 pack side by side to form an extended β sheet. A helix-loop-helix segment in BCCIPα inserts into the active site cleft of FAM46, thereby inhibiting the PAP activity. Our results together show that the unique fold of BCCIPα underlies its interaction with and functional regulation of FAM46.
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Affiliation(s)
- Shun Liu
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hua Chen
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yan Yin
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Defen Lu
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Guoming Gao
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jie Li
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xuewu Zhang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
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Zhao YL, Wang Y, Liu C, Jiang YL, Wei YD, Meng H, Jian S, Zhu XT, Pei LJ, Bai XC, Feng F, Lv Y, Zhou XY, Qi QW, Li JN, Ji W, Ma LS. Impact of the COVID-19 pandemic on congenital diaphragmatic hernia patients: a single-center retrospective study. Pediatr Surg Int 2022; 38:1113-1123. [PMID: 35670846 PMCID: PMC9170880 DOI: 10.1007/s00383-022-05136-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/01/2022] [Indexed: 12/04/2022]
Abstract
PURPOSE To investigate the impact of COVID-19 on the treatment of children with congenital diaphragmatic hernia (CDH). METHODS We retrospectively collected and compared the data of patients with CDH admitted between January 1, 2020 and December 31, 2021(study group) with the CDH patients admitted before the pandemic between January 1, 2018 and December 31, 2019 (control group). RESULTS During the pandemic, 41 patients with CDH diagnosed prenatally were transferred to our hospital, and 40 underwent surgical repair. The number of patients treated in our hospital increased by 24.2% compared with the 33 patients before the pandemic. During the pandemic, the overall survival rate, postoperative survival rate and recurrence rate were 85.4%, 87.5% and 7.3%, respectively, and there were no significant differences compared with the control group (75.8%, 83.3% and 9.1%, respectively). The average length of hospital stay in patients admitted during the pandemic was longer than that in the control group (31 days vs. 16 days, P < 0.001), and the incidence of nosocomial infection was higher than that in the control group (19.5% vs. 3%, P = 0.037). CONCLUSIONS CDH patients confirmed to be SARS-CoV-2 infection-free can receive routine treatment. Our data indicate that the implementation of protective measures during the COVID-19 pandemic, along with appropriate screening and case evaluation, do not have a negative impact on the prognosis of children.
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Affiliation(s)
- Yun-Long Zhao
- Department of Neonatal Surgery, Children's Hospital of Capital Institute of Pediatrics, Graduate School of Peking Union Medical College, Beijing, China
| | - Ying Wang
- Department of Neonatal Surgery, Children's Hospital of Capital Institute of Pediatrics, Beijing, China
| | - Chao Liu
- Department of Neonatal Surgery, Children's Hospital of Capital Institute of Pediatrics, Beijing, China
| | - Yu-Lin Jiang
- Department of Obstetrics, Peking Union Medical College Hospital, Beijing, China
| | - Yan-Dong Wei
- Department of Neonatal Surgery, Children's Hospital of Capital Institute of Pediatrics, Beijing, China
| | - Hua Meng
- Department of Ultrasound, Peking Union Medical College Hospital, Beijing, China
| | - Shan Jian
- Department of Pediatrics, Peking Union Medical College Hospital, Beijing, China
| | - Xi-Ting Zhu
- Everest Clinical Research Corporation, New Jersey, USA
| | - Li-Jian Pei
- Department of Anesthesiology, Peking Union Medical College Hospital, Beijing, China
| | - Xiao-Chen Bai
- Department of Pediatrics, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Feng Feng
- Department of Radiology, Peking Union Medical College Hospital, Beijing, China
| | - Yan Lv
- Department of Obstetrics, Peking Union Medical College Hospital, Beijing, China
| | - Xi-Ya Zhou
- Department of Obstetrics, Peking Union Medical College Hospital, Beijing, China
| | - Qing-Wei Qi
- Department of Obstetrics, Peking Union Medical College Hospital, Beijing, China
| | - Jing-Na Li
- Department of Neonatal Surgery, Children's Hospital of Capital Institute of Pediatrics, Beijing, China
| | - Wei Ji
- Department of Interventional Hemangioma, Children's Hospital of Capital Institute of Pediatrics, Beijing, China
| | - Li-Shuang Ma
- Department of Neonatal Surgery, Children's Hospital of Capital Institute of Pediatrics, Graduate School of Peking Union Medical College, Beijing, China.
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11
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Stepien KP, Xu J, Zhang X, Bai XC, Rizo J. SNARE assembly enlightened by cryo-EM structures of a synaptobrevin-Munc18-1-syntaxin-1 complex. Sci Adv 2022; 8:eabo5272. [PMID: 35731863 PMCID: PMC9216511 DOI: 10.1126/sciadv.abo5272] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/18/2022] [Indexed: 05/16/2023]
Abstract
Munc18-1 forms a template to organize assembly of the neuronal SNARE complex that triggers neurotransmitter release, binding first to a closed conformation of syntaxin-1 where its amino-terminal region interacts with the SNARE motif, and later binding to synaptobrevin. However, the mechanism of SNARE complex assembly remains unclear. Here, we report two cryo-EM structures of Munc18-1 bound to cross-linked syntaxin-1 and synaptobrevin. The structures allow visualization of how syntaxin-1 opens and reveal how part of the syntaxin-1 amino-terminal region can help nucleate interactions between the amino termini of the syntaxin-1 and synaptobrevin SNARE motifs, while their carboxyl termini bind to distal sites of Munc18-1. These observations, together with mutagenesis, SNARE complex assembly experiments, and fusion assays with reconstituted proteoliposomes, support a model whereby these interactions are critical to initiate SNARE complex assembly and multiple energy barriers enable diverse mechanisms for exquisite regulation of neurotransmitter release.
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Affiliation(s)
- Karolina P. Stepien
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Junjie Xu
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xuewu Zhang
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Josep Rizo
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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12
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Lu D, Shang G, Li J, Lu Y, Bai XC, Zhang X. Activation of STING by targeting a pocket in the transmembrane domain. Nature 2022; 604:557-562. [PMID: 35388221 PMCID: PMC9098198 DOI: 10.1038/s41586-022-04559-7] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 02/15/2022] [Indexed: 12/14/2022]
Abstract
Stimulator of interferon genes (STING) is an adaptor protein in innate immunity against DNA viruses or bacteria1-5. STING-mediated immunity could be exploited in the development of vaccines or cancer immunotherapies. STING is a transmembrane dimeric protein that is located in the endoplasmic reticulum or in the Golgi apparatus. STING is activated by the binding of its cytoplasmic ligand-binding domain to cyclic dinucleotides that are produced by the DNA sensor cyclic GMP-AMP (cGAMP) synthase or by invading bacteria1,6,7. Cyclic dinucleotides induce a conformational change in the STING ligand-binding domain, which leads to a high-order oligomerization of STING that is essential for triggering the downstream signalling pathways8,9. However, the cGAMP-induced STING oligomers tend to dissociate in solution and have not been resolved to high resolution, which limits our understanding of the activation mechanism. Here we show that a small-molecule agonist, compound 53 (C53)10, promotes the oligomerization and activation of human STING through a mechanism orthogonal to that of cGAMP. We determined a cryo-electron microscopy structure of STING bound to both C53 and cGAMP, revealing a stable oligomer that is formed by side-by-side packing and has a curled overall shape. Notably, C53 binds to a cryptic pocket in the STING transmembrane domain, between the two subunits of the STING dimer. This binding triggers outward shifts of transmembrane helices in the dimer, and induces inter-dimer interactions between these helices to mediate the formation of the high-order oligomer. Our functional analyses show that cGAMP and C53 together induce stronger activation of STING than either ligand alone.
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Affiliation(s)
- Defen Lu
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Guijun Shang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jie Li
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yong Lu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Xuewu Zhang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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13
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Yu H, Bai XC, Wang W. Characterization of the subunit composition and structure of adult human glycine receptors. Neuron 2021; 109:2707-2716.e6. [PMID: 34473954 DOI: 10.1016/j.neuron.2021.08.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 07/23/2021] [Accepted: 08/16/2021] [Indexed: 11/27/2022]
Abstract
The strychnine-sensitive pentameric glycine receptor (GlyR) mediates fast inhibitory neurotransmission in the mammalian nervous system. Only heteromeric GlyRs mediate synaptic transmission, as they contain the β subunit that permits clustering at the synapse through its interaction with scaffolding proteins. Here, we show that α2 and β subunits assemble with an unexpected 4:1 stoichiometry to produce GlyR with native electrophysiological properties. We determined structures in multiple functional states at 3.6-3.8 Å resolutions and show how 4:1 stoichiometry is consistent with the structural features of α2β GlyR. Furthermore, we show that one single β subunit in each GlyR gives rise to the characteristic electrophysiological properties of heteromeric GlyR, while more β subunits render GlyR non-conductive. A single β subunit ensures a univalent GlyR-scaffold linkage, which means the scaffold alone regulates the cluster properties.
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Affiliation(s)
- Hailong Yu
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Weiwei Wang
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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14
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Kober DL, Radhakrishnan A, Goldstein JL, Brown MS, Clark LD, Bai XC, Rosenbaum DM. Scap structures highlight key role for rotation of intertwined luminal loops in cholesterol sensing. Cell 2021; 184:3689-3701.e22. [PMID: 34139175 PMCID: PMC8277531 DOI: 10.1016/j.cell.2021.05.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/08/2021] [Accepted: 05/14/2021] [Indexed: 11/26/2022]
Abstract
The cholesterol-sensing protein Scap induces cholesterol synthesis by transporting membrane-bound transcription factors called sterol regulatory element-binding proteins (SREBPs) from the endoplasmic reticulum (ER) to the Golgi apparatus for proteolytic activation. Transport requires interaction between Scap's two ER luminal loops (L1 and L7), which flank an intramembrane sterol-sensing domain (SSD). Cholesterol inhibits Scap transport by binding to L1, which triggers Scap's binding to Insig, an ER retention protein. Here we used cryoelectron microscopy (cryo-EM) to elucidate two structures of full-length chicken Scap: (1) a wild-type free of Insigs and (2) mutant Scap bound to chicken Insig without cholesterol. Strikingly, L1 and L7 intertwine tightly to form a globular domain that acts as a luminal platform connecting the SSD to the rest of Scap. In the presence of Insig, this platform undergoes a large rotation accompanied by rearrangement of Scap's transmembrane helices. We postulate that this conformational change halts Scap transport of SREBPs and inhibits cholesterol synthesis.
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Affiliation(s)
- Daniel L Kober
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Molecular Genetics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Arun Radhakrishnan
- Department of Molecular Genetics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Joseph L Goldstein
- Department of Molecular Genetics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Michael S Brown
- Department of Molecular Genetics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lindsay D Clark
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiao-Chen Bai
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Daniel M Rosenbaum
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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15
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Abstract
The c-MET receptor is a receptor tyrosine kinase (RTK) that plays essential roles in normal cell development and motility. Aberrant activation of c-MET can lead to both tumors growth and metastatic progression of cancer cells. C-MET can be activated by either hepatocyte growth factor (HGF), or its natural isoform NK1. Here, we report the cryo-EM structures of c-MET/HGF and c-MET/NK1 complexes in the active state. The c-MET/HGF complex structure reveals that, by utilizing two distinct interfaces, one HGF molecule is sufficient to induce a specific dimerization mode of c-MET for receptor activation. The binding of heparin as well as a second HGF to the 2:1 c-MET:HGF complex further stabilize this active conformation. Distinct to HGF, NK1 forms a stable dimer, and bridges two c-METs in a symmetrical manner for activation. Collectively, our studies provide structural insights into the activation mechanisms of c-MET, and reveal how two isoforms of the same ligand use dramatically different mechanisms to activate the receptor. Activation of c-MET receptor tyrosine kinase involves hepatocyte growth factor (HGF) and glycosaminoglycans, but the molecular mechanism is still under debate. Here, the authors present cryoEM structures of c-MET bound to two HGF splice variants and heparin, revealing the structural basis for c-MET activation.
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Affiliation(s)
- Emiko Uchikawa
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Zhiming Chen
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Guan-Yu Xiao
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Thoracic Head Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xuewu Zhang
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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16
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Abstract
Secreted class 3 semaphorins (Sema3s) form tripartite complexes with the plexin receptor and neuropilin coreceptor, which are both transmembrane proteins that together mediate semaphorin signal for neuronal axon guidance and other processes. Despite extensive investigations, the overall architecture of and the molecular interactions in the Sema3/plexin/neuropilin complex are incompletely understood. Here we present the cryo-EM structure of a near intact extracellular region complex of Sema3A, PlexinA4 and Neuropilin 1 (Nrp1) at 3.7 Å resolution. The structure shows a large symmetric 2:2:2 assembly in which each subunit makes multiple interactions with others. The two PlexinA4 molecules in the complex do not interact directly, but their membrane proximal regions are close to each other and poised to promote the formation of the intracellular active dimer for signaling. The structure reveals a previously unknown interface between the a2b1b2 module in Nrp1 and the Sema domain of Sema3A. This interaction places the a2b1b2 module at the top of the complex, far away from the plasma membrane where the transmembrane regions of Nrp1 and PlexinA4 embed. As a result, the region following the a2b1b2 module in Nrp1 must span a large distance to allow the connection to the transmembrane region, suggesting an essential role for the long non-conserved linkers and the MAM domain in neuropilin in the semaphorin/plexin/neuropilin complex.
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Affiliation(s)
- Defen Lu
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Guijun Shang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiaojing He
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Xuewu Zhang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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17
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Abstract
Nakane et al. and Yip et al., for the first time, demonstrate that, with recent technological advances, atomic-resolution structure determination can be achieved by single-particle cryo-electron microscopy (cryo-EM). This breakthrough opens the door for researchers to apply single-particle cryo-EM to obtain atomic structural information for a wide range of protein complexes.
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Affiliation(s)
- Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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18
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Zhang X, Bai XC, Chen ZJ. Structures and Mechanisms in the cGAS-STING Innate Immunity Pathway. Immunity 2020; 53:43-53. [PMID: 32668227 DOI: 10.1016/j.immuni.2020.05.013] [Citation(s) in RCA: 293] [Impact Index Per Article: 73.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/19/2020] [Accepted: 05/26/2020] [Indexed: 01/29/2023]
Abstract
Besides its role as the blueprint of life, DNA can also alert the cell to the presence of microbial pathogens as well as damaged or malignant cells. A major sensor of DNA that triggers the innate immune response is cyclic guanosine monophosphate (GMP)-adenosine monophosphate (AMP) (cGAMP) synthase (cGAS), which produces the second messenger cGAMP. cGAMP activates stimulator of interferon genes (STING), which activates a signaling cascade leading to the production of type I interferons and other immune mediators. Recent research has demonstrated an expanding role of the cGAS-cGAMP-STING pathway in many physiological and pathological processes, including host defense against microbial infections, anti-tumor immunity, cellular senescence, autophagy, and autoimmune and inflammatory diseases. Biochemical and structural studies have elucidated the mechanism of signal transduction in the cGAS pathway at the atomic resolution. This review focuses on the structural and mechanistic insights into the roles of cGAS and STING in immunity and diseases revealed by these recent studies.
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Affiliation(s)
- Xuewu Zhang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Zhijian J Chen
- Department of Molecular biology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Center for Inflammation Research, University of Texas Southwestern Medical Center, Dallas, TX, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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19
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Abstract
As a ring-shaped adenosine triphosphatase (ATPase) machine, cohesin organizes the eukaryotic genome by extruding DNA loops and mediates sister chromatid cohesion by topologically entrapping DNA. How cohesin executes these fundamental DNA transactions is not understood. Using cryo-electron microscopy (cryo-EM), we determined the structure of human cohesin bound to its loader NIPBL and DNA at medium resolution. Cohesin and NIPBL interact extensively and together form a central tunnel to entrap a 72-base pair DNA. NIPBL and DNA promote the engagement of cohesin's ATPase head domains and ATP binding. The hinge domains of cohesin adopt an "open washer" conformation and dock onto the STAG1 subunit. Our structure explains the synergistic activation of cohesin by NIPBL and DNA and provides insight into DNA entrapment by cohesin.
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Affiliation(s)
- Zhubing Shi
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Haishan Gao
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hongtao Yu
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
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20
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Yin J, Chen KYM, Clark MJ, Hijazi M, Kumari P, Bai XC, Sunahara RK, Barth P, Rosenbaum DM. Structure of a D2 dopamine receptor-G-protein complex in a lipid membrane. Nature 2020; 584:125-129. [PMID: 32528175 PMCID: PMC7415663 DOI: 10.1038/s41586-020-2379-5] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/08/2020] [Indexed: 12/28/2022]
Abstract
The D2 dopamine receptor (DRD2) is a therapeutic target for Parkinson’s disease1 and antipsychotic drugs2. DRD2 is activated by the endogenous neurotransmitter dopamine and synthetic agonist drugs such as bromocriptine3, leading to stimulation of Gi and inhibition of adenylyl cyclase. We used cryo-electron microscopy to elucidate the structure of an agonist-bound activated DRD2-Gi complex reconstituted into a phospholipid membrane. The extracellular ligand binding site of DRD2 is remodeled in response to agonist binding, with conformational changes in extracellular loop 2 (ECL2), transmembrane domain 5 (TM5), TM6, and TM7 propagating to opening of the intracellular Gi binding site. The DRD2-Gi structure represents the first experimental model of a GPCR-G protein complex embedded in a phospholipid bilayer, which serves as a benchmark to validate the interactions seen in previous detergent-bound structures. The structure also reveals interactions that are unique to the membrane-embedded complex, including helix 8 burial in the inner leaflet, ordered lysine and arginine sidechains in the membrane interfacial regions, and lipid anchoring of the G protein in the membrane. Our model of the activated DRD2 will help inform the design of subtype-selective DRD2 ligands for multiple human CNS disorders.
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Affiliation(s)
- Jie Yin
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kuang-Yui M Chen
- Institute of Bioengineering, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Mary J Clark
- Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Mahdi Hijazi
- Institute of Bioengineering, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Punita Kumari
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiao-Chen Bai
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Roger K Sunahara
- Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA, USA.
| | - Patrick Barth
- Institute of Bioengineering, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.
| | - Daniel M Rosenbaum
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, USA.
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21
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Kuo YC, Chen H, Shang G, Uchikawa E, Tian H, Bai XC, Zhang X. Cryo-EM structure of the PlexinC1/A39R complex reveals inter-domain interactions critical for ligand-induced activation. Nat Commun 2020; 11:1953. [PMID: 32327662 PMCID: PMC7181871 DOI: 10.1038/s41467-020-15862-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 04/01/2020] [Indexed: 11/09/2022] Open
Abstract
Plexins are receptors for semaphorins that transduce signals for regulating neuronal development and other processes. Plexins are single-pass transmembrane proteins with multiple domains in both the extracellular and intracellular regions. Semaphorin activates plexin by binding to its extracellular N-terminal Sema domain, inducing the active dimer of the plexin intracellular region. The mechanism underlying this activation process of plexin is incompletely understood. We present cryo-electron microscopic structure of full-length human PlexinC1 in complex with the viral semaphorin mimic A39R. The structure shows that A39R induces a specific dimer of PlexinC1 where the membrane-proximal domains from the two PlexinC1 protomers are placed close to each other, poised to promote the active dimer of the intracellular region. This configuration is imposed by a distinct conformation of the PlexinC1 extracellular region, stabilized by inter-domain interactions among the Sema and membrane-proximal domains. Our mutational analyses support the critical role of this conformation in PlexinC1 activation. Plexins are the receptors for the guidance molecules semaphorins and regulate immunity and the development of the nervous and cardiovascular systems. Here authors present a structure of full-length human PlexinC1 in complex with its ligand A39R, which reveals how inter-domain interactions couple extracellular ligand binding to receptor activation and signaling.
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Affiliation(s)
- Yi-Chun Kuo
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hua Chen
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Guijun Shang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Emiko Uchikawa
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hui Tian
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Xuewu Zhang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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22
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Liu S, Chang S, Han B, Xu L, Zhang M, Zhao C, Yang W, Wang F, Li J, Delpire E, Ye S, Bai XC, Guo J. Cryo-EM structures of the human cation-chloride cotransporter KCC1. Science 2019; 366:505-508. [PMID: 31649201 DOI: 10.1126/science.aay3129] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/26/2019] [Indexed: 11/02/2022]
Abstract
Cation-chloride cotransporters (CCCs) mediate the coupled, electroneutral symport of cations with chloride across the plasma membrane and are vital for cell volume regulation, salt reabsorption in the kidney, and γ-aminobutyric acid (GABA)-mediated modulation in neurons. Here we present cryo-electron microscopy (cryo-EM) structures of human potassium-chloride cotransporter KCC1 in potassium chloride or sodium chloride at 2.9- to 3.5-angstrom resolution. KCC1 exists as a dimer, with both extracellular and transmembrane domains involved in dimerization. The structural and functional analyses, along with computational studies, reveal one potassium site and two chloride sites in KCC1, which are all required for the ion transport activity. KCC1 adopts an inward-facing conformation, with the extracellular gate occluded. The KCC1 structures allow us to model a potential ion transport mechanism in KCCs and provide a blueprint for drug design.
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Affiliation(s)
- Si Liu
- Department of Biophysics, Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Shenghai Chang
- Department of Biophysics, Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Center of Cryo-Electron Microscopy, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Binming Han
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Lingyi Xu
- Department of Biophysics, Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Mingfeng Zhang
- Department of Biophysics, Institute of Neuroscience, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Cheng Zhao
- Department of Biophysics, Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Department of Biophysics, Institute of Neuroscience, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Wei Yang
- Department of Biophysics, Institute of Neuroscience, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Feng Wang
- Wuxi Biortus Biosciences Co. Ltd., 6 Dongsheng West Road, Jiangyin 214437, China
| | - Jingyuan Li
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Hangzhou, Zhejiang 310027, China.
| | - Eric Delpire
- Department of Anesthesiology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
| | - Sheng Ye
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China.
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xiao-Chen Bai
- Departments of Biophysics and Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Jiangtao Guo
- Department of Biophysics, Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.
- Department of Biophysics, Institute of Neuroscience, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou 310058, China
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23
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Abstract
Type 1 insulin-like growth factor receptor (IGF1R) is a receptor tyrosine kinase that regulates cell growth and proliferation, and can be activated by IGF1, IGF2, and insulin. Here, we report the cryo-EM structure of full-length IGF1R–IGF1 complex in the active state. This structure reveals that only one IGF1 molecule binds the Γ-shaped asymmetric IGF1R dimer. The IGF1-binding site is formed by the L1 and CR domains of one IGF1R protomer and the α-CT and FnIII-1 domains of the other. The liganded α-CT forms a rigid beam-like structure with the unliganded α-CT, which hinders the conformational change of the unliganded α-CT required for binding of a second IGF1 molecule. We further identify an L1–FnIII-2 interaction that mediates the dimerization of membrane-proximal domains of IGF1R. This interaction is required for optimal receptor activation. Our study identifies a source of the negative cooperativity in IGF1 binding to IGF1R and reveals the structural basis of IGF1R activation. The activation mechanism of type 1 insulin-like growth factor receptor (IGF1R) is not fully understood. Here, the authors determine the cryo-EM structure of full-length, IGF1-bound IGF1R in the active conformation, providing insights into how IGF1 triggers receptor activation.
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Affiliation(s)
- Jie Li
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Eunhee Choi
- Howard Hughes Medical Institute, Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Hongtao Yu
- Howard Hughes Medical Institute, Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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24
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Wang Y, Nguyen NX, She J, Zeng W, Yang Y, Bai XC, Jiang Y. Structural Mechanism of EMRE-Dependent Gating of the Human Mitochondrial Calcium Uniporter. Cell 2019; 177:1252-1261.e13. [PMID: 31080062 DOI: 10.1016/j.cell.2019.03.050] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 02/09/2019] [Accepted: 03/27/2019] [Indexed: 01/06/2023]
Abstract
Mitochondrial calcium uptake is crucial to the regulation of eukaryotic Ca2+ homeostasis and is mediated by the mitochondrial calcium uniporter (MCU). While MCU alone can transport Ca2+ in primitive eukaryotes, metazoans require an essential single membrane-spanning auxiliary component called EMRE to form functional channels; however, the molecular mechanism of EMRE regulation remains elusive. Here, we present the cryo-EM structure of the human MCU-EMRE complex, which defines the interactions between MCU and EMRE as well as pinpoints the juxtamembrane loop of MCU and extended linker of EMRE as the crucial elements in the EMRE-dependent gating mechanism among metazoan MCUs. The structure also features the dimerization of two MCU-EMRE complexes along an interface at the N-terminal domain (NTD) of human MCU that is a hotspot for post-translational modifications. Thus, the human MCU-EMRE complex, which constitutes the minimal channel components among metazoans, provides a framework for future mechanistic studies on MCU.
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Affiliation(s)
- Yan Wang
- Howard Hughes Medical Institute and Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nam X Nguyen
- Howard Hughes Medical Institute and Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ji She
- Howard Hughes Medical Institute and Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Weizhong Zeng
- Howard Hughes Medical Institute and Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yi Yang
- Howard Hughes Medical Institute and Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Youxing Jiang
- Howard Hughes Medical Institute and Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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25
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Chen Q, Zeng W, She J, Bai XC, Jiang Y. Structural and functional characterization of an otopetrin family proton channel. eLife 2019; 8:46710. [PMID: 30973323 PMCID: PMC6483595 DOI: 10.7554/elife.46710] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 04/11/2019] [Indexed: 12/14/2022] Open
Abstract
The otopetrin (OTOP) proteins were recently characterized as proton channels. Here we present the cryo-EM structure of OTOP3 from Xenopus tropicalis (XtOTOP3) along with functional characterization of the channel. XtOTOP3 forms a homodimer with each subunit containing 12 transmembrane helices that can be divided into two structurally homologous halves; each half assembles as an α-helical barrel that could potentially serve as a proton conduction pore. Both pores open from the extracellular half before becoming occluded at a central constriction point consisting of three highly conserved residues - Gln232/585-Asp262/Asn623-Tyr322/666 (the constriction triads). Mutagenesis shows that the constriction triad from the second pore is less amenable to perturbation than that of the first pore, suggesting an unequal contribution between the two pores to proton transport. We also identified several key residues at the interface between the two pores that are functionally important, particularly Asp509, which confers intracellular pH-dependent desensitization to OTOP channels.
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Affiliation(s)
- Qingfeng Chen
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Weizhong Zeng
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Ji She
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Youxing Jiang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
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26
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She J, Zeng W, Guo J, Chen Q, Bai XC, Jiang Y. Structural mechanisms of phospholipid activation of the human TPC2 channel. eLife 2019; 8:45222. [PMID: 30860481 PMCID: PMC6424560 DOI: 10.7554/elife.45222] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 03/07/2019] [Indexed: 12/21/2022] Open
Abstract
Mammalian two-pore channels (TPCs) regulate the physiological functions of the endolysosome. Here we present cryo-EM structures of human TPC2 (HsTPC2), a phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2)-activated, Na+ selective channel, in the ligand-bound and apo states. The apo structure captures the closed conformation, while the ligand-bound form features the channel in both open and closed conformations. Combined with functional analysis, these structures provide insights into the mechanism of PI(3,5)P2-regulated gating of TPC2, which is distinct from that of TPC1. Specifically, the endolysosome-specific PI(3,5)P2 binds at the first 6-TM and activates the channel – independently of the membrane potential – by inducing a structural change at the pore-lining inner helix (IS6), which forms a continuous helix in the open state but breaks into two segments at Gly317 in the closed state. Additionally, structural comparison to the voltage-dependent TPC1 structure allowed us to identify Ile551 as being responsible for the loss of voltage dependence in TPC2.
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Affiliation(s)
- Ji She
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Weizhong Zeng
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Jiangtao Guo
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, China.,Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qingfeng Chen
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Youxing Jiang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
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27
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She J, Guo J, Chen Q, Zeng W, Jiang Y, Bai XC. Structural insights into the voltage and phospholipid activation of the mammalian TPC1 channel. Nature 2018; 556:130-134. [PMID: 29562233 PMCID: PMC5886804 DOI: 10.1038/nature26139] [Citation(s) in RCA: 137] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 02/19/2018] [Indexed: 01/09/2023]
Abstract
Organellar two-pore channels (TPCs) function as a homodimer with each subunit containing two homologous Shaker-like 6-TM repeats1. They belong to the voltage-gated ion channel superfamily2 and are ubiquitously expressed in animals and plants3,4. Mammalian TPC1 and TPC2 are localized to the endolysosomal membrane and play critical roles in regulating the physiological functions of these acidic organelles5–7. Here we present the cryo-EM structures of mouse TPC1 (MmTPC1), a voltage-dependent, phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2) activated Na+ selective channel, in both the apo closed and ligand-bound open states which, combined with functional analysis, provide comprehensive structural insights into the selectivity and gating mechanisms of mammalian TPC channels. The channel has a coin slot-shaped ion pathway in the filter that defines the selectivity of mammalian TPCs. Only the voltage sensing domain from the second 6-TM domain confers voltage dependence to MmTPC1. Endolysosome-specific PtdIns(3,5)P2 binds to the first 6-TM domain and activates the channel under depolarizing membrane potential. Structural comparison between the apo and PtdIns(3,5)P2-bound structures elucidates the interplay between voltage and ligand in channel activation. In light of the emerging importance of phosphoinositide regulation of ion channels, the MmTPC1 structures exemplify the lipid binding and regulation in a 6-TM voltage-gated channel.
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Affiliation(s)
- Ji She
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390-8816, USA
| | - Jiangtao Guo
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Qingfeng Chen
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390-8816, USA.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA
| | - Weizhong Zeng
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390-8816, USA.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA
| | - Youxing Jiang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390-8816, USA.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390-8816, USA.,Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9039, USA
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28
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Guo J, She J, Zeng W, Chen Q, Bai XC, Jiang Y. Structures of the calcium-activated, non-selective cation channel TRPM4. Nature 2017; 552:205-209. [PMID: 29211714 PMCID: PMC5901961 DOI: 10.1038/nature24997] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 11/03/2017] [Indexed: 12/12/2022]
Abstract
TRPM4 is a calcium-activated, phosphatidylinositol-4,5-bisphosphate (PtdIns(4,5)P2) -modulated, non-selective cation channel that belongs to the family of melastatin-related transient receptor potential (TRPM) channels. Here we present the electron cryo-microscopy structures of the mouse TRPM4 channel with and without ATP. TRPM4 consists of multiple transmembrane and cytosolic domains, which assemble into a three-tiered architecture. The N-terminal nucleotide-binding domain and the C-terminal coiled-coil participate in the tetrameric assembly of the channel; ATP binds at the nucleotide-binding domain and inhibits channel activity. TRPM4 has an exceptionally wide filter but is only permeable to monovalent cations; filter residue Gln973 is essential in defining monovalent selectivity. The S1-S4 domain and the post-S6 TRP domain form the central gating apparatus that probably houses the Ca2+- and PtdIns(4,5)P2-binding sites. These structures provide an essential starting point for elucidating the complex gating mechanisms of TRPM4 and reveal the molecular architecture of the TRPM family.
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Affiliation(s)
- Jiangtao Guo
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390-8816, USA
| | - Ji She
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390-8816, USA
| | - Weizhong Zeng
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390-8816, USA.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA
| | - Qingfeng Chen
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390-8816, USA.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390-8816, USA.,Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9039, USA
| | - Youxing Jiang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390-8816, USA.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA
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29
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Chen Q, She J, Zeng W, Guo J, Xu H, Bai XC, Jiang Y. Structure of mammalian endolysosomal TRPML1 channel in nanodiscs. Nature 2017; 550:415-418. [PMID: 29019981 PMCID: PMC5901962 DOI: 10.1038/nature24035] [Citation(s) in RCA: 176] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 08/24/2017] [Indexed: 12/14/2022]
Abstract
Transient receptor potential mucolipin 1 (TRPML1) is an endo/lysosomal cation channel ubiquitously expressed in mammalian cells1,2 and its loss-of-function mutations are the direct cause of Type IV mucolipidosis (MLIV), an autosomal recessive lysosomal storage disease3-6. Here we present the single particle cryo-electron microscopy (cryo-EM) structure of the mouse TRPML1 channel embedded in nanodiscs. Combined with mutagenesis, the TRPML1 structure reveals that phosphatidylinositol bisphosphate (PIP2) binds to the N-terminus of the channel – distal from the pore – and the helix-turn-helix extension between S2 and S3 likely couples ligand binding to pore opening. The tightly packed selectivity filter contains multiple ion binding sites and the conserved acidic residues form the luminal Ca2+ blocking site that confers luminal pH and Ca2+ modulation on channel conductance. A luminal linker domain forms a fenestrated canopy atop the channel, providing multiple luminal ion passages to the pore and also creating a negative electrostatic trap – preferably for divalent cations at the luminal entrance. The structure also reveals two equally distributed S4-S5 linker conformations in the closed channel, providing structural implication for the S4-S5 linker-mediated PIP2 gating mechanism among TRPML channels7,8.
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Affiliation(s)
- Qingfeng Chen
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390-8816, USA.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA
| | - Ji She
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390-8816, USA
| | - Weizhong Zeng
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390-8816, USA.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA
| | - Jiangtao Guo
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390-8816, USA
| | - Haoxing Xu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109-1048, USA
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390-8816, USA
| | - Youxing Jiang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390-8816, USA.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA
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30
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Boland A, Martin TG, Zhang Z, Yang J, Bai XC, Chang L, Scheres SHW, Barford D. Cryo-EM structure of a metazoan separase-securin complex at near-atomic resolution. Nat Struct Mol Biol 2017; 24:414-418. [PMID: 28263324 PMCID: PMC5385133 DOI: 10.1038/nsmb.3386] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 02/06/2017] [Indexed: 11/09/2022]
Abstract
Separase is a caspase-family protease that initiates chromatid segregation by cleaving the kleisin subunits (Scc1 and Rec8) of cohesin, and regulates centrosome duplication and mitotic spindle function through cleavage of kendrin and Slk19. To understand the mechanisms of securin regulation of separase, we used single-particle cryo-electron microscopy (cryo-EM) to determine a near-atomic-resolution structure of the Caenorhabditis elegans separase-securin complex. Separase adopts a triangular-shaped bilobal architecture comprising an N-terminal tetratricopeptide repeat (TPR)-like α-solenoid domain docked onto the conserved C-terminal protease domain. Securin engages separase in an extended antiparallel conformation, interacting with both lobes. It inhibits separase by interacting with the catalytic site through a pseudosubstrate mechanism, thus revealing that in the inhibited separase-securin complex, the catalytic site adopts a conformation compatible with substrate binding. Securin is protected from cleavage because an aliphatic side chain at the P1 position represses protease activity by disrupting the organization of catalytic site residues.
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Affiliation(s)
| | | | - Ziguo Zhang
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Jing Yang
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | - Leifu Chang
- MRC Laboratory of Molecular Biology, Cambridge, UK
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31
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Wong W, Bai XC, Sleebs BE, Triglia T, Brown A, Thompson JK, Jackson KE, Hanssen E, Marapana DS, Fernandez IS, Ralph SA, Cowman AF, Scheres SH, Baum J. Mefloquine targets the Plasmodium falciparum 80S ribosome to inhibit protein synthesis. Nat Microbiol 2017; 2:17031. [PMID: 28288098 PMCID: PMC5439513 DOI: 10.1038/nmicrobiol.2017.31] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 02/07/2017] [Indexed: 12/26/2022]
Abstract
Malaria control is heavily dependent on chemotherapeutic agents for disease prevention and drug treatment. Defining the mechanism of action for licensed drugs, for which no target is characterized, is critical to the development of their second-generation derivatives to improve drug potency towards inhibition of their molecular targets. Mefloquine is a widely used antimalarial without a known mode of action. Here, we demonstrate that mefloquine is a protein synthesis inhibitor. We solved a 3.2 Å cryo-electron microscopy structure of the Plasmodium falciparum 80S ribosome with the (+)-mefloquine enantiomer bound to the ribosome GTPase-associated centre. Mutagenesis of mefloquine-binding residues generates parasites with increased resistance, confirming the parasite-killing mechanism. Furthermore, structure-guided derivatives with an altered piperidine group, predicted to improve binding, show enhanced parasiticidal effect. These data reveal one possible mode of action for mefloquine and demonstrate the vast potential of cryo-electron microscopy to guide the development of mefloquine derivatives to inhibit parasite protein synthesis.
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Affiliation(s)
- Wilson Wong
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Xiao-Chen Bai
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Brad E. Sleebs
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Tony Triglia
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Alan Brown
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Jennifer K. Thompson
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Katherine E. Jackson
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Eric Hanssen
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Danushka S. Marapana
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Israel S. Fernandez
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Stuart A. Ralph
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Alan F. Cowman
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Sjors H.W. Scheres
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Jake Baum
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, 3010, Australia
- Department of Life Sciences, Imperial College London, South Kensington, London, SW7 2AZ, UK
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32
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Fica SM, Oubridge C, Galej WP, Wilkinson ME, Bai XC, Newman AJ, Nagai K. Structure of a spliceosome remodelled for exon ligation. Nature 2017; 542:377-380. [PMID: 28076345 PMCID: PMC5321579 DOI: 10.1038/nature21078] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 01/04/2017] [Indexed: 12/11/2022]
Abstract
The spliceosome excises introns from pre-mRNAs in two sequential transesterifications – branching and exon ligation1 – catalysed at a single catalytic metal site in U6 snRNA2,3. The recent structures of the spliceosomal C complex4,5 with the cleaved 5’-exon and lariat—3’-exon bound to the catalytic centre revealed that branching-specific factors such as Cwc25 lock the branch helix into position for nucleophilic attack of the branch adenosine at the 5’-splice site. Furthermore, the ATPase Prp16 is positioned to bind and translocate the intron downstream of the branch point to destabilize branching-specific factors and release the branch helix from the active site4. Here we present the 3.8Å cryo-EM structure of a Saccharomyces cerevisiae spliceosome stalled after Prp16-mediated remodelling but prior to exon ligation. While the U6 snRNA catalytic core remains firmly held in the active site cavity of Prp8 by proteins common to both steps, the branch helix has rotated by 75 degrees compared to complex C and is stabilized into a new position by Prp17, Cef1, and the reoriented Prp8 RNaseH domain. This rotation of the branch helix removes the branch adenosine from the catalytic core, creates a space for 3’-exon docking, and restructures the pairing of the 5’-splice site with the U6 snRNA ACAGAGA region. Slu7 and Prp18, which promote exon ligation, bind together to the Prp8 RNaseH domain. The ATPase Prp22, bound to Prp8 in place of Prp16, could interact with the 3’-exon, suggesting a possible basis for mRNA release after exon ligation6,7. Together with the C complex structure4, our new C* complex structure reveals the two major conformations of the spliceosome during the catalytic stages of splicing.
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Affiliation(s)
- Sebastian M Fica
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Chris Oubridge
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Wojciech P Galej
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Max E Wilkinson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Xiao-Chen Bai
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Andrew J Newman
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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33
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Martin TG, Bharat TAM, Joerger AC, Bai XC, Praetorius F, Fersht AR, Dietz H, Scheres SHW. Design of a molecular support for cryo-EM structure determination. Proc Natl Acad Sci U S A 2016; 113:E7456-E7463. [PMID: 27821763 PMCID: PMC5127339 DOI: 10.1073/pnas.1612720113] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite the recent rapid progress in cryo-electron microscopy (cryo-EM), there still exist ample opportunities for improvement in sample preparation. Macromolecular complexes may disassociate or adopt nonrandom orientations against the extended air-water interface that exists for a short time before the sample is frozen. We designed a hollow support structure using 3D DNA origami to protect complexes from the detrimental effects of cryo-EM sample preparation. For a first proof-of-principle, we concentrated on the transcription factor p53, which binds to specific DNA sequences on double-stranded DNA. The support structures spontaneously form monolayers of preoriented particles in a thin film of water, and offer advantages in particle picking and sorting. By controlling the position of the binding sequence on a single helix that spans the hollow support structure, we also sought to control the orientation of individual p53 complexes. Although the latter did not yet yield the desired results, the support structures did provide partial information about the relative orientations of individual p53 complexes. We used this information to calculate a tomographic 3D reconstruction, and refined this structure to a final resolution of ∼15 Å. This structure settles an ongoing debate about the symmetry of the p53 tetramer bound to DNA.
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Affiliation(s)
- Thomas G Martin
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Tanmay A M Bharat
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Andreas C Joerger
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
- German Cancer Consortium (DKTK), Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, 60438 Frankfurt am Main, Germany
| | - Xiao-Chen Bai
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Florian Praetorius
- Physik Department, Walter Schottky Institute, Technische Universität München, 85748 Garching near Munich, Germany
| | - Alan R Fersht
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Hendrik Dietz
- Physik Department, Walter Schottky Institute, Technische Universität München, 85748 Garching near Munich, Germany
| | - Sjors H W Scheres
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom;
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34
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Nguyen THD, Galej WP, Bai XC, Oubridge C, Newman AJ, Scheres SHW, Nagai K. Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 Å resolution. Nature 2016; 530:298-302. [PMID: 26829225 PMCID: PMC4762201 DOI: 10.1038/nature16940] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 12/18/2015] [Indexed: 12/12/2022]
Abstract
U4/U6.U5 tri-snRNP represents a substantial part of the spliceosome before activation. A cryoEM structure of Saccharomyces cerevisiae U4/U6.U5 tri-snRNP at 3.7Å resolution led to an essentially complete atomic model comprising 30 proteins plus U4/U6 and U5 snRNAs. The structure reveals striking interweaving interactions of the protein and RNA components including extended polypeptides penetrating into subunit interfaces. The invariant ACAGAGA sequence of U6 snRNA, which base-pairs with the 5′-splice site during catalytic activation, forms a hairpin stabilised by Dib1 and Prp8 while the adjacent nucleotides interact with the exon binding loop 1 of U5 snRNA. Snu114 harbours GTP but its putative catalytic histidine is held away from the γ-phosphate by hydrogen bonding to a tyrosine in Prp8’s N-terminal domain. Mutation of this histidine to alanine has no detectable effect on yeast growth. The structure provides important new insights into the spliceosome activation process leading to the formation of the catalytic centre.
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Affiliation(s)
| | - Wojciech P Galej
- MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK
| | - Xiao-Chen Bai
- MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK
| | - Chris Oubridge
- MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK
| | - Andrew J Newman
- MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK
| | - Sjors H W Scheres
- MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK
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35
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Zhou M, Li Y, Hu Q, Bai XC, Huang W, Yan C, Scheres SHW, Shi Y. Atomic structure of the apoptosome: mechanism of cytochrome c- and dATP-mediated activation of Apaf-1. Genes Dev 2015; 29:2349-61. [PMID: 26543158 PMCID: PMC4691890 DOI: 10.1101/gad.272278.115] [Citation(s) in RCA: 161] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 10/13/2015] [Indexed: 12/11/2022]
Abstract
In this study, Zhou et al. report the first atomic structure of the mammalian apoptosome, determined at 3.8 Å resolution by cryo-electron microscopy. These findings provide novel insight into how CytC relieves the autoinhibition of Apaf-1 and how dATP triggers Apaf-1 oligomerization. The apoptotic protease-activating factor 1 (Apaf-1) controls the onset of many known forms of intrinsic apoptosis in mammals. Apaf-1 exists in normal cells as an autoinhibited monomer. Upon binding to cytochrome c and dATP, Apaf-1 oligomerizes into a heptameric complex known as the apoptosome, which recruits and activates cell-killing caspases. Here we present an atomic structure of an intact mammalian apoptosome at 3.8 Å resolution, determined by single-particle, cryo-electron microscopy (cryo-EM). Structural analysis, together with structure-guided biochemical characterization, uncovered how cytochrome c releases the autoinhibition of Apaf-1 through specific interactions with the WD40 repeats. Structural comparison with autoinhibited Apaf-1 revealed how dATP binding triggers a set of conformational changes that results in the formation of the apoptosome. Together, these results constitute the molecular mechanism of cytochrome c- and dATP-mediated activation of Apaf-1.
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Affiliation(s)
- Mengying Zhou
- Ministry of Education Protein Science Laboratory, Center for Structural Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yini Li
- Ministry of Education Protein Science Laboratory, Center for Structural Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Qi Hu
- Ministry of Education Protein Science Laboratory, Center for Structural Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiao-Chen Bai
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Weiyun Huang
- Ministry of Education Protein Science Laboratory, Center for Structural Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Chuangye Yan
- Ministry of Education Protein Science Laboratory, Center for Structural Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Sjors H W Scheres
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Yigong Shi
- Ministry of Education Protein Science Laboratory, Center for Structural Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
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36
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Chang C, Verboncoeur J, Guo MN, Zhu M, Song W, Li S, Chen CH, Bai XC, Xie JL. Ultrafast high-power microwave window breakdown: nonlinear and postpulse effects. Phys Rev E Stat Nonlin Soft Matter Phys 2014; 90:063107. [PMID: 25615205 DOI: 10.1103/physreve.90.063107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Indexed: 06/04/2023]
Abstract
The time- and space-dependent optical emissions of nanosecond high-power microwave discharges near a dielectric-air interface have been observed by nanosecond-response four-framing intensified-charged-coupled device cameras. The experimental observations indicate that plasma developed more intensely at the dielectric-air interface than at the free-space region with a higher electric-field amplitude. A thin layer of intense light emission above the dielectric was observed after the microwave pulse. The mechanisms of the breakdown phenomena are analyzed by a three-dimensional electromagnetic-field modeling and a two-dimensional electromagnetic particle-in-cell simulation, revealing the formation of a space-charge microwave sheath near the dielectric surface, accelerated by the normal components of the microwave field, significantly enhancing the local-field amplitude and hence ionization near the dielectric surface. The nonlinear positive feedback of ionization, higher electron mobility, and ultraviolet-driven photoemission due to the elevated electron temperature are crucial for achieving the ultrafast discharge. Following the high-power microwave pulse, the sheath sustains a glow discharge until the sheath collapses.
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Affiliation(s)
- C Chang
- Laboratory on Science and Technology of High Power Microwave, Northwest Institute of Nuclear Technology, Xi'an, Shaanxi 710024, China and Key Laboratory of Physical Electronics and Devices of the Ministry of Education, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China and Department of Engineering Physics, Tsinghua University, Beijing 100084, China
| | - J Verboncoeur
- Department of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, USA
| | - M N Guo
- Laboratory on Science and Technology of High Power Microwave, Northwest Institute of Nuclear Technology, Xi'an, Shaanxi 710024, China
| | - M Zhu
- Laboratory on Science and Technology of High Power Microwave, Northwest Institute of Nuclear Technology, Xi'an, Shaanxi 710024, China
| | - W Song
- Laboratory on Science and Technology of High Power Microwave, Northwest Institute of Nuclear Technology, Xi'an, Shaanxi 710024, China
| | - S Li
- Laboratory on Science and Technology of High Power Microwave, Northwest Institute of Nuclear Technology, Xi'an, Shaanxi 710024, China
| | - C H Chen
- Laboratory on Science and Technology of High Power Microwave, Northwest Institute of Nuclear Technology, Xi'an, Shaanxi 710024, China
| | - X C Bai
- Laboratory on Science and Technology of High Power Microwave, Northwest Institute of Nuclear Technology, Xi'an, Shaanxi 710024, China
| | - J L Xie
- Laboratory on Science and Technology of High Power Microwave, Northwest Institute of Nuclear Technology, Xi'an, Shaanxi 710024, China
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37
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Brown A, Amunts A, Bai XC, Sugimoto Y, Edwards PC, Murshudov G, Scheres SHW, Ramakrishnan V. Structure of the large ribosomal subunit from human mitochondria. Science 2014; 346:718-722. [PMID: 25278503 DOI: 10.1126/science.1258026] [Citation(s) in RCA: 224] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Human mitochondrial ribosomes are highly divergent from all other known ribosomes and are specialized to exclusively translate membrane proteins. They are linked with hereditary mitochondrial diseases and are often the unintended targets of various clinically useful antibiotics. Using single-particle cryogenic electron microscopy, we have determined the structure of its large subunit to 3.4 angstrom resolution, revealing 48 proteins, 21 of which are specific to mitochondria. The structure unveils an adaptation of the exit tunnel for hydrophobic nascent peptides, extensive remodeling of the central protuberance, including recruitment of mitochondrial valine transfer RNA (tRNA(Val)) to play an integral structural role, and changes in the tRNA binding sites related to the unusual characteristics of mitochondrial tRNAs.
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Affiliation(s)
- Alan Brown
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Alexey Amunts
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Xiao-Chen Bai
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Yoichiro Sugimoto
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Patricia C Edwards
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Garib Murshudov
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Sjors H W Scheres
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - V Ramakrishnan
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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38
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Lu P, Bai XC, Ma D, Xie T, Yan C, Sun L, Yang G, Zhao Y, Zhou R, Scheres SHW, Shi Y. Three-dimensional structure of human γ-secretase. Nature 2014; 512:166-170. [PMID: 25043039 DOI: 10.1038/nature13567] [Citation(s) in RCA: 255] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 06/09/2014] [Indexed: 12/12/2022]
Abstract
The γ-secretase complex, comprising presenilin 1 (PS1), PEN-2, APH-1 and nicastrin, is a membrane-embedded protease that controls a number of important cellular functions through substrate cleavage. Aberrant cleavage of the amyloid precursor protein (APP) results in aggregation of amyloid-β, which accumulates in the brain and consequently causes Alzheimer's disease. Here we report the three-dimensional structure of an intact human γ-secretase complex at 4.5 Å resolution, determined by cryo-electron-microscopy single-particle analysis. The γ-secretase complex comprises a horseshoe-shaped transmembrane domain, which contains 19 transmembrane segments (TMs), and a large extracellular domain (ECD) from nicastrin, which sits immediately above the hollow space formed by the TM horseshoe. Intriguingly, nicastrin ECD is structurally similar to a large family of peptidases exemplified by the glutamate carboxypeptidase PSMA. This structure serves as an important basis for understanding the functional mechanisms of the γ-secretase complex.
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Affiliation(s)
- Peilong Lu
- Ministry of Education Key Laboratory of Protein Science, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiao-Chen Bai
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Dan Ma
- Ministry of Education Key Laboratory of Protein Science, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Tian Xie
- Ministry of Education Key Laboratory of Protein Science, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Chuangye Yan
- State Key Laboratory of Bio-membrane and Membrane Biotechnology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Linfeng Sun
- Ministry of Education Key Laboratory of Protein Science, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Guanghui Yang
- State Key Laboratory of Bio-membrane and Membrane Biotechnology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yanyu Zhao
- Ministry of Education Key Laboratory of Protein Science, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Rui Zhou
- Ministry of Education Key Laboratory of Protein Science, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Sjors H W Scheres
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Yigong Shi
- Ministry of Education Key Laboratory of Protein Science, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
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39
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Fernández IS, Bai XC, Murshudov G, Scheres SHW, Ramakrishnan V. Initiation of translation by cricket paralysis virus IRES requires its translocation in the ribosome. Cell 2014; 157:823-31. [PMID: 24792965 PMCID: PMC4017093 DOI: 10.1016/j.cell.2014.04.015] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 03/14/2014] [Accepted: 04/11/2014] [Indexed: 01/04/2023]
Abstract
The cricket paralysis virus internal ribosome entry site (CrPV-IRES) is a folded structure in a viral mRNA that allows initiation of translation in the absence of any host initiation factors. By using recent advances in single-particle electron cryomicroscopy, we have solved the structure of CrPV-IRES bound to the ribosome of the yeast Kluyveromyces lactis in both the canonical and rotated states at overall resolutions of 3.7 and 3.8 Å, respectively. In both states, the pseudoknot PKI of the CrPV-IRES mimics a tRNA/mRNA interaction in the decoding center of the A site of the 40S ribosomal subunit. The structure and accompanying factor-binding data show that CrPV-IRES binding mimics a pretranslocation rather than initiation state of the ribosome. Translocation of the IRES by elongation factor 2 (eEF2) is required to bring the first codon of the mRNA into the A site and to allow the start of translation. The high-resolution structure of CrPV-IRES bound to the ribosome was solved by cryoEM Pseudoknot I of CrPV-IRES binds in the decoding center, thus blocking the A site CrPV-IRES mimics a pretranslocation rather than initiation complex of the ribosome Translocation of CrPV-IRES by eEF2 is required for the start of translation
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Affiliation(s)
- Israel S Fernández
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Xiao-Chen Bai
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Garib Murshudov
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Sjors H W Scheres
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - V Ramakrishnan
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
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40
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Amunts A, Brown A, Bai XC, Llácer JL, Hussain T, Emsley P, Long F, Murshudov G, Scheres SHW, Ramakrishnan V. Structure of the yeast mitochondrial large ribosomal subunit. Science 2014; 343:1485-1489. [PMID: 24675956 DOI: 10.1126/science.1249410] [Citation(s) in RCA: 433] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Mitochondria have specialized ribosomes that have diverged from their bacterial and cytoplasmic counterparts. We have solved the structure of the yeast mitoribosomal large subunit using single-particle cryo-electron microscopy. The resolution of 3.2 angstroms enabled a nearly complete atomic model to be built de novo and refined, including 39 proteins, 13 of which are unique to mitochondria, as well as expansion segments of mitoribosomal RNA. The structure reveals a new exit tunnel path and architecture, unique elements of the E site, and a putative membrane docking site.
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Affiliation(s)
- Alexey Amunts
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Alan Brown
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Xiao-Chen Bai
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Jose L Llácer
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Tanweer Hussain
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Paul Emsley
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Fei Long
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Garib Murshudov
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Sjors H W Scheres
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - V Ramakrishnan
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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41
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Fernández IS, Bai XC, Hussain T, Kelley AC, Lorsch JR, Ramakrishnan V, Scheres SHW. Molecular architecture of a eukaryotic translational initiation complex. Science 2013; 342:1240585. [PMID: 24200810 DOI: 10.1126/science.1240585] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The last step in eukaryotic translational initiation involves the joining of the large and small subunits of the ribosome, with initiator transfer RNA (Met-tRNA(i)(Met)) positioned over the start codon of messenger RNA in the P site. This step is catalyzed by initiation factor eIF5B. We used recent advances in cryo-electron microscopy (cryo-EM) to determine a structure of the eIF5B initiation complex to 6.6 angstrom resolution from <3% of the population, comprising just 5143 particles. The structure reveals conformational changes in eIF5B, initiator tRNA, and the ribosome that provide insights into the role of eIF5B in translational initiation. The relatively high resolution obtained from such a small fraction of a heterogeneous sample suggests a general approach for characterizing the structure of other dynamic or transient biological complexes.
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Affiliation(s)
- Israel S Fernández
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, CB2 0QH, United Kingdom
| | - Xiao-Chen Bai
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, CB2 0QH, United Kingdom
| | - Tanweer Hussain
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, CB2 0QH, United Kingdom
| | - Ann C Kelley
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, CB2 0QH, United Kingdom
| | - Jon R Lorsch
- Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD, USA
| | - V Ramakrishnan
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, CB2 0QH, United Kingdom
| | - Sjors H W Scheres
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, CB2 0QH, United Kingdom
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42
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Bai XC, Fernandez IS, McMullan G, Scheres SHW. Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles. eLife 2013; 2:e00461. [PMID: 23427024 PMCID: PMC3576727 DOI: 10.7554/elife.00461] [Citation(s) in RCA: 313] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 01/15/2013] [Indexed: 11/13/2022] Open
Abstract
Although electron cryo-microscopy (cryo-EM) single-particle analysis has become an important tool for structural biology of large and flexible macro-molecular assemblies, the technique has not yet reached its full potential. Besides fundamental limits imposed by radiation damage, poor detectors and beam-induced sample movement have been shown to degrade attainable resolutions. A new generation of direct electron detectors may ameliorate both effects. Apart from exhibiting improved signal-to-noise performance, these cameras are also fast enough to follow particle movements during electron irradiation. Here, we assess the potentials of this technology for cryo-EM structure determination. Using a newly developed statistical movie processing approach to compensate for beam-induced movement, we show that ribosome reconstructions with unprecedented resolutions may be calculated from almost two orders of magnitude fewer particles than used previously. Therefore, this methodology may expand the scope of high-resolution cryo-EM to a broad range of biological specimens.DOI:http://dx.doi.org/10.7554/eLife.00461.001.
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Affiliation(s)
- Xiao-Chen Bai
- Medical Research Council Laboratory of Molecular Biology , Cambridge , United Kingdom
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43
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Chang LF, Chen S, Liu CC, Pan X, Jiang J, Bai XC, Xie X, Wang HW, Sui SF. Structural characterization of full-length NSF and 20S particles. Nat Struct Mol Biol 2012; 19:268-75. [PMID: 22307055 DOI: 10.1038/nsmb.2237] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2011] [Accepted: 12/20/2011] [Indexed: 11/09/2022]
Abstract
The 20S particle, which is composed of the N-ethylmaleimide-sensitive factor (NSF), soluble NSF attachment proteins (SNAPs) and the SNAP receptor (SNARE) complex, has an essential role in intracellular vesicle fusion events. Using single-particle cryo-EM and negative stain EM, we reconstructed four related three-dimensional structures: Chinese hamster NSF hexamer in the ATPγS, ADP-AlFx and ADP states, and the 20S particle. These structures reveal a parallel arrangement between the D1 and D2 domains of the hexameric NSF and characterize the nucleotide-dependent conformational changes in NSF. The structure of the 20S particle shows that it holds the SNARE complex at two interaction interfaces around the C terminus and N-terminal half of the SNARE complex, respectively. These findings provide insight into the molecular mechanism underlying disassembly of the SNARE complex by NSF.
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Affiliation(s)
- Lei-Fu Chang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing, China
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44
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Abstract
Exosomes play important roles in many physiological and pathological processes. However, the exosome-cell interaction mode and the intracellular trafficking pathway of exosomes in their recipient cells remain unclear. Here, we report that exosomes derived from K562 or MT4 cells are internalized more efficiently by phagocytes than by non-phagocytic cells. Most exosomes were observed attached to the plasma membrane of non-phagocytic cells, while in phagocytic cells these exosomes were found to enter via phagocytosis. Specifically, they moved to phagosomes together with phagocytic polystyrene carboxylate-modified latex beads (biospheres) and were further sorted into phagolysosomes. Moreover, exosome internalization was dependent on the actin cytoskeleton and phosphatidylinositol 3-kinase, and could be inhibited by the knockdown of dynamin2 or overexpression of a dominant-negative form of dynamin2. Further, antibody pretreatment assays demonstrated that tim4 but not tim1 was involved in exosomes uptake. We also found that exosomes did not enter the internalization pathway involving caveolae, macropinocytosis and clathrin-coated vesicles. Our observation that the cellular uptake of exosomes occurs through phagocytosis has important implications for exosome-cell interactions and the exosome intracellular trafficking pathway.
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Affiliation(s)
- Du Feng
- School of Life Sciences, State Key Laboratory of Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing, PR China
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45
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Tan Y, Lv ZP, Bai XC, Liu XY, Zhang XF. Traditional Chinese medicine Bao Gan Ning increase phosphorylation of CREB in liver fibrosis in vivo and in vitro. J Ethnopharmacol 2006; 105:69-75. [PMID: 16293380 DOI: 10.1016/j.jep.2005.09.040] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2004] [Revised: 09/24/2005] [Accepted: 09/30/2005] [Indexed: 05/05/2023]
Abstract
Previous studies have demonstrated that traditional Chinese medicine Bao Gan Ning, which contains six different drugs: Trionyx sinensis Wiegmann shell, Prunus persica (L.) Batsch seed, Salvia miltiorrhiza Bge. root, Mallotus opelta (Lour.) Muell-Arg root, Astragalus membranaceus (Fisch.) Bge. var. mongho-licus (Bge.) Hsiao root and Scutellaria baicalensis Georgi root, was able to protect liver against fibrosis in CCL4 models. In an effort to elucidate molecular mechanisms by which Bao Gan Ning exerts its anti-fibrosis activity, effects of Bao Gan Ning on liver fibrosis and cAMP response element binding protein (CREB), an important transcription factor involved in liver fibrosis, were evaluated in animal and cell models in this work. Results showed that Bao Gan Ning (2.16 or 4.32 g/kg/day) significantly decreased alanine aminotransferase (ALT) and hyaluronidase levels and reversed liver fibrosis in rat liver fibrosis models. The proliferation of HSC-T6, a hepatic stellate cell line, was also significantly inhibited by incubation with serums that were prepared from rats fed with Bao Gan Ning. Most interestingly, results from Western blot, immunohistochemistry and electrophoretic mobility shift assay (EMSA) showed that Bao Gan Ning up-regulated CREB phosphorylation both in rat liver fibrosis models and in HSC-T6 cells, but did not affect protein level of CREB and the DNA binding activity of CREB. These results suggested that up-regulation of CREB phosphorylation may be involved in anti-fibrosis activity of Chinese medicine Bao Gan Ning.
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Affiliation(s)
- Y Tan
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
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46
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Bai XC, Luo SQ, Bai J, Deng F, Zheng WS, Ji QS. Up-regulation of Phosphatidylinositol-3 Kinase Signaling in plcg1 Gene Null Fibroblasts. Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai) 2002; 33:677-681. [PMID: 12035061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Phospholipase C-gamma1(PLC-gamma1) and phosphatidylinositol-3 kinase(PI-3K) play crucial role in growth factor-induced cell growth and proliferation. To investigate the complementary mechanism of PLC-gamma1 in cell growth and epidermal growth factor (EGF)-induced mitogenic signaling, PLC-gamma1 deficient mouse embryonic fibroblasts(PLC-gamma1(-/-)) and its wild type(PLC-gamma1(+/+)) were exposed to U73122, a phospholipase C-specific inhibitor, or wortmannin, a PI-3K inhibitor then the clonogenicity, viability, EGF-induced DNA synthesis of the two cell lines were determined by cloning formation, MTT method and (3)H -thymidine incorporation assay. Results showed that either U73122 or wortmannin inhibited PLC-gamma1(-/-) and PLC-gamma1(+/+) cells in terms of EGF-induced DNA synthesis, cloning formation and cell viability, but PLC-gamma1(-/-) cells were more dependent on PI-3K and less dependent on PLC compared with wild types. The PLC-gamma1 signaling pathway of PLC-gamma1(-/-) cells might be complemented by PI-3K pathway, because after EGF stimulation, the tyrosine phospholation of p85alpha PI-3K increased significantly in PLC-gamma1(-/-), but not in PLC-gamma2(-/-), as Western blotting showed that there was neither complementary PLC-gamma2 expression in PLC-gamma1(-/-) cells, nor other PLC isozymes such as PLC-beta and PLC-delta. These results suggest the redundancy of EGF-mediated signaling and the complementary mechanism of PLC-gamma1 pathway.
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Affiliation(s)
- X C Bai
- Department of Cell Biology and Medical Genetics, the First Military Medical University, Guangzhou 510515, China.
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Bai XC, Bao YD. [Zinc modulation of GABA receptors expressed in Xenopus oocytes injected with carp brain poly(A)+ RNA]. Sheng Li Xue Bao 1998; 50:268-74. [PMID: 11324566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Two types of GABA receptors, GABAA receptors (approximately 85%) and GABAC-like receptors (approximately 15%), were expressed in Xenopus oocytes after injection of Poly(A)+ RNA with carp (Carassius carassius) brain. Using voltage-clamp technique and pharmacological methods, the effects of zinc on the two receptors were studied. It was found that zinc modulation of both GABAA and GABAC-like receptors by zinc was inhibitory and reversible with the former being stronger than the latter as indicated by a value of IC50 of 48.4 +/- 10.1 mumol/L against 255.6 +/- 21.5 mumol/L.
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Affiliation(s)
- X C Bai
- Shanghai Institute of Physiology, Chinese Academy of Sciences, Shanghai 200031
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48
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Tong QS, Xia GJ, Yao WX, Jiang MX, Bai XC, Bao YD. [Blocking effects of benzyltetrahydropalmatine on delayed rectified K+ currents expressed in Xenopus oocytes and in toad oocytes]. Yao Xue Xue Bao 1996; 31:867-71. [PMID: 9863258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
The effects of benzyltetrahydropalmatine (BTHP) on delayed rectified K+ currents (Ik) expressed in Xenopus oocytes and Ik of toad (Bufo bufo gargarizans) oocytes were studied. The Ik expressed in Xenopus oocytes was measured after microinjection of mRNA isolated from carp fish (C anratus L.) brains with double -microelectrode voltage clamp technique. The maximum and mean value of Ik expressed in Xenopus oocytes were 600 nA and 360 +/- 104 nA, respectively. BTHP reduced the current amplitude of Ik expressed in Xenopus oocytes in 10-1000 mumol.L-1 dose-dependently, EC50 was 29 mumol.L-1. Also, the reduction of Ik of toad oocytes was 9.1%, 29.1%, 54.7% and 68.6% by BTHP 10, 30, 100 and 1000 mumol.L-1, respectively, EC50 was 33 mumol.L-1. The results showed that BTHP possesses an inhibitory effect on Ik, the main ion mechanism of antiarrhythmic action of BTHP.
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Affiliation(s)
- Q S Tong
- Department of Pharmacology, School of Basic Medical Science, Tongji Medical University, Wuhan
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