4.4 Å Resolution Cryo-EM structure of human mTOR Complex 1

doi:10.1007/s13238-016-0346-6

Protein Cell

2016, Vol. 7

Issue (12) : 878-887 https://doi.org/10.1007/s13238-016-0346-6

RESEARCH ARTICLE

4.4 Å Resolution Cryo-EM structure of human mTOR Complex 1

Huirong Yang^1,^2,³,Jia Wang⁴,Mengjie Liu^1,^2,³,Xizi Chen^1,^2,³,Min Huang⁵,Dan Tan⁶,Meng-Qiu Dong⁶,Catherine C. L. Wong⁵,Jiawei Wang⁴(

),Yanhui Xu^1,^2,³(

),Hong-Wei Wang⁴(

)

¹. Fudan University Shanghai Cancer Center, Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
². Key Laboratory of Molecular Medicine, Ministry of Education, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
³. State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
⁴. Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
⁵. National Center for Protein Science, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
⁶. National Institute of Biological Sciences, Beijing 102206, China

Download: PDF(2817 KB)
Export: BibTeX | EndNote | Reference Manager | ProCite | RefWorks

Abstract

Mechanistic target of rapamycin (mTOR) complex 1 (mTORC1) integrates signals from growth factors, cellular energy levels, stress and amino acids to control cell growth and proliferation through regulating translation, autophagy and metabolism. Here we determined the cryo-electron microscopy structure of human mTORC1 at 4.4 Å resolution. The mTORC1 comprises a dimer of heterotrimer (mTOR-Raptor-mLST8) mediated by the mTOR protein. The complex adopts a hollow rhomboid shape with 2-fold symmetry. Notably, mTORC1 shows intrinsic conformational dynamics. Within the complex, the conserved N-terminal caspaselike domain of Raptor faces toward the catalytic cavity of the kinase domain of mTOR. Raptor shows no caspase activity and therefore may bind to TOS motif for substrate recognition. Structural analysis indicates that FKBP12-Rapamycin may generate steric hindrance for substrate entry to the catalytic cavity of mTORC1. The structure provides a basis to understand the assembly of mTORC1 and a framework to characterize the regulatory mechanism of mTORC1 pathway.

Keywords mTORC1 structure cryo-electron microscopy

Corresponding Author(s): Jiawei Wang,Yanhui Xu,Hong-Wei Wang

Issue Date: 24 January 2017

Cite this article:

Huirong Yang,Jia Wang,Mengjie Liu, et al. 4.4 Å Resolution Cryo-EM structure of human mTOR Complex 1[J]. Protein Cell, 2016, 7(12): 878-887.

URL:

https://academic.hep.com.cn/pac/EN/10.1007/s13238-016-0346-6
https://academic.hep.com.cn/pac/EN/Y2016/V7/I12/878

1	Adams PD, Afonine PV, Bunkóczi G,Chen VB, Davis IW, Echols N, Headd JJ, Hung L-W, Kapral GJ, Grosse-Kunstleve RW (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D 66:213–221 https://doi.org/10.1107/S0907444909052925
2	Aylett CH, Sauer E, Imseng S, Boehringer D, Hall MN, Ban N, Maier T (2016) Architecture of human mTOR complex 1. Science 351:48–52 https://doi.org/10.1126/science.aaa3870
3	Baretic D, Berndt A, Ohashi Y, Johnson CM, Williams RL (2016) Tor forms a dimer through an N-terminal helical solenoid with a complex topology. Nat Commun 7:11016 https://doi.org/10.1038/ncomms11016
4	Benjamin D, Colombi M, Moroni C, Hall MN (2011) Rapamycin passes the torch: a new generation of mTOR inhibitors. Nat Rev Drug Discov 10:868–880 https://doi.org/10.1038/nrd3531
5	Chen SX, McMullan G, Faruqi AR, Murshudov GN, Short JM, Scheres SHW, Henderson R (2013) High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy. Ultramicroscopy 135:24–35 https://doi.org/10.1016/j.ultramic.2013.06.004
6	Choi J, Chen J, Schreiber SL, Clardy J (1996) Structure of the FKBP12-rapamycin complex interacting with the binding domain of human FRAP. Science (NY) 273:239–242 https://doi.org/10.1126/science.273.5272.239
7	Dazert E, Hall MN (2011) mTOR signaling in disease. Curr Opin Cell Biol 23:744–755 https://doi.org/10.1016/j.ceb.2011.09.003
8	Dunlop EA, Hunt DK, Acosta-Jaquez HA, Fingar DC, Tee AR (2014) ULK1 inhibits mTORC1 signaling, promotes multisite Raptor phosphorylation and hinders substrate binding. Autophagy 7:737–747 https://doi.org/10.4161/auto.7.7.15491
9	Ellisen LW, Ramsayer KD, Johannessen CM,Yang A, Beppu H, Minda K, Oliner JD, McKeon F, Haber DA (2002) REDD1, a developmentally regulated transcriptional target of p63 and p53, links p63 to regulation of reactive oxygen species. Mol Cell 10:995–1005 https://doi.org/10.1016/S1097-2765(02)00706-2
10	Emsley P, Lohkamp B, Scott W, Cowtan K (2010) Features and development of COOT. Acta Crystallogr D 66:486–501 https://doi.org/10.1107/S0907444910007493
11	Garami A, Zwartkruis FJ, Nobukuni T, Joaquin M, Roccio M, Stocker H, Kozma SC, Hafen E, Bos JL, Thomas G (2003) Insulin activation of Rheb, a mediator of mTOR/S6K/4E-BP signaling, is inhibited by TSC1 and 2. Mol Cell 11:1457–1466 https://doi.org/10.1016/S1097-2765(03)00220-X
12	Ginalski K, Zhang H, Grishin NV (2004) Raptor protein contains a caspase-like domain. Trends Biochem Sci 29:522–524 https://doi.org/10.1016/j.tibs.2004.08.006
13	Gingras AC, Gygi SP, Raught B, Polakiewicz RD, Abraham RT, Hoekstra MF, Aebersold R, Sonenberg N (1999) Regulation of 4E-BP1 phosphorylation: a novel two-step mechanism. Genes Dev 13:1422–1437 https://doi.org/10.1101/gad.13.11.1422
14	Holz MK, Blenis J (2005) Identification of S6 kinase 1 as a novel mammalian target of rapamycin (mTOR)-phosphorylating kinase. J Biol Chem 280:26089–26093 https://doi.org/10.1074/jbc.M504045200
15	Holz MK, Ballif BA, Gygi SP, Blenis J (2005) mTOR and S6K1 mediate assembly of the translation preinitiation complex through dynamic protein interchange and ordered phosphorylation events. Cell 123:569–580 https://doi.org/10.1016/j.cell.2005.10.024
16	Inoki K, Li Y, Xu T, Guan KL (2003) Rheb GTPase is a direct target of TSC2 GAP activity and regulates mTOR signaling. Genes Dev 17:1829–1834 https://doi.org/10.1101/gad.1110003
17	Inoki K, Corradetti MN, Guan KL (2005) Dysregulation of the TSCmTOR pathway in human disease. Nat Genet 37:19–24 https://doi.org/10.1038/ng1494
18	Kim DH, Sarbassov DD, Ali SM, King JE, Latek RR, Erdjument-Bromage H, Tempst P, Sabatini DM (2002) mTOR interacts with raptor to form a nutrient-sensitive complex that signals to the cell growth machinery. Cell 110:163–175 https://doi.org/10.1016/S0092-8674(02)00808-5
19	Kim E, Goraksha-Hicks P, Li L, Neufeld TP, Guan KL (2008) Regulation of TORC1 by Rag GTPases in nutrient response. Nat Cell Biol 10:935–945 https://doi.org/10.1038/ncb1753
20	Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26:283–291 https://doi.org/10.1107/S0021889892009944
21	Li X, Mooney P, Zheng S, Booth CR, Braunfeld MB, Gubbens S, Agard DA, Cheng Y (2013) Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nat Methods 10:584–590 https://doi.org/10.1038/nmeth.2472
22	Loewith R, Jacinto E, Wullschleger S, Lorberg A, Crespo JL, Bonenfant D, Oppliger W, Jenoe P, Hall MN (2002) Two TOR complexes, only one of which is rapamycin sensitive, have distinct roles in cell growth control. Mol Cell 10:457–468 https://doi.org/10.1016/S1097-2765(02)00636-6
23	Mindell JA, Grigorieff N (2003) Accurate determination of local defocus and specimen tilt in electron microscopy. J Struct Biol 142:334–347 https://doi.org/10.1016/S1047-8477(03)00069-8
24	Rossmann MG, Bernal R, Pletnev SV (2001) Combining electron microscopic with X-ray crystallographic structures. J Struct Biol 136:190–200 https://doi.org/10.1006/jsbi.2002.4435
25	Sarbassov DD, Ali SM, Kim DH, Guertin DA, Latek RR, Erdjument-Bromage H, Tempst P, Sabatini DM (2004) Rictor, a novel binding partner of mTOR, defines a rapamycin-insensitive and raptorindependent pathway that regulates the cytoskeleton. Curr Biol 14:1296–1302 https://doi.org/10.1016/j.cub.2004.06.054
26	Scheres SH (2012) RELION: implementation of a Bayesian approach to cryo-EM structure determination. J Struct Biol 180:519–530 https://doi.org/10.1016/j.jsb.2012.09.006
27	Stretton C, Hoffmann TM, Munson MJ, Prescott A, Taylor PM, Ganley IG, Hundal HS (2015) GSK3-mediated raptor phosphorylation supports amino-acid-dependent mTORC1-directed signalling. Biochem J 470:207–221 https://doi.org/10.1042/BJ20150404
28	Tee AR, Blenis J(2005) mTOR, translational control and human disease. Semin Cell Dev Biol 16:29–37 https://doi.org/10.1016/j.semcdb.2004.11.005
29	Tee AR, Manning BD, Roux PP, Cantley LC, Blenis J(2003) Tuberous sclerosis complex gene products, Tuberin and Hamartin, control mTOR signaling by acting as a GTPase-activating protein complex toward Rheb. Curr Biol 13:1259–1268 https://doi.org/10.1016/S0960-9822(03)00506-2
30	Vriend G (1990) WHAT IF: a molecular modeling and drug design program. J Mol Graph 8:52–56 https://doi.org/10.1016/0263-7855(90)80070-V
31	Wang QS, Yu F, Huang S, Sun B, Zhang KH, Liu K, Wang ZJ, Xu CY, Wang SS, Yang LF (2015) The macromolecular crystallography beamline of SSRF. Nucl Sci Technol 26:12–17
32	Wullschleger S, Loewith R, Hall MN (2006) TOR signaling in growth and metabolism. Cell 124:471–484 https://doi.org/10.1016/j.cell.2006.01.016
33	Xu Y, Xing Y, Chen Y, Chao Y, Lin Z, Fan E, Yu JW, Strack S, Jeffrey PD, Shi Y (2006) Structure of the protein phosphatase 2A holoenzyme. Cell 127:1239–1251 https://doi.org/10.1016/j.cell.2006.11.033
34	Yang H, Rudge DG, Koos JD, Vaidialingam B, Yang HJ, Pavletich NP (2013) mTOR kinase structure, mechanism and regulation. Nature 497:217–223 https://doi.org/10.1038/nature12122
35	Yip CK, Murata K, Walz T, Sabatini DM, Kang SA (2010) Structure of the human mTOR complex I and its implications for rapamycin inhibition. Mol Cell 38:768–774 https://doi.org/10.1016/j.molcel.2010.05.017
36	Yuan HX, Wang Z, Yu FX, Li F, Russell RC, Jewell JL, Guan KL (2015) NLK phosphorylates Raptor to mediate stress-induced mTORC1 inhibition. Genes Dev 29:2362–2376 https://doi.org/10.1101/gad.265116.115
37	Zoncu R, Efeyan A, Sabatini DM (2011) mTOR: from growth signal integration to cancer, diabetes and ageing. Nat Rev Mol Cell Biol 12:21–35 https://doi.org/10.1038/nrm3025

[1]	PAC-0878-16229-XYH_suppl_1	Download
[2]	PAC-0878-16229-XYH_suppl_2	Download
[3]	PAC-0878-16229-XYH_suppl_3	Download

[1]	Meng Wu, Jinke Gu, Shuai Zong, Runyu Guo, Tianya Liu, Maojun Yang. Research journey of respirasome[J]. Protein Cell, 2020, 11(5): 318-338.
[2]	Jinbo Han, Yiguo Wang. mTORC1 signaling in hepatic lipid metabolism[J]. Protein Cell, 2018, 9(2): 145-151.
[3]	Vsevolod V. Gurevich, Eugenia V. Gurevich, Vladimir N. Uversky. Arrestins: structural disorder creates rich functionality[J]. Protein Cell, 2018, 9(12): 986-1003.
[4]	Yusuke Mimura, Toshihiko Katoh, Radka Saldova, Roisin O’Flaherty, Tomonori Izumi, Yuka Mimura-Kimura, Toshiaki Utsunomiya, Yoichi Mizukami, Kenji Yamamoto, Tsuneo Matsumoto, Pauline M. Rudd. Glycosylation engineering of therapeutic IgG antibodies: challenges for the safety, functionality and efficacy[J]. Protein Cell, 2018, 9(1): 47-62.
[5]	Weiyun Huang, Minhao Liu, S. Frank Yan, Nieng Yan. Structure-based assessment of diseaserelated mutations in human voltage-gated sodium channels[J]. Protein Cell, 2017, 8(6): 401-438.
[6]	Hongliang Tian,Xiaoyun Ji,Xiaoyun Yang,Zhongxin Zhang,Zuokun Lu,Kailin Yang,Cheng Chen,Qi Zhao,Heng Chi,Zhongyu Mu,Wei Xie,Zefang Wang,Huiqiang Lou,Haitao Yang,Zihe Rao. Structural basis of Zika virus helicase in recognizing its substrates[J]. Protein Cell, 2016, 7(8): 562-570.
[7]	Runyu Guo,Jinke Gu,Meng Wu,Maojun Yang. Amazing structure of respirasome: unveiling the secrets of cell respiration[J]. Protein Cell, 2016, 7(12): 854-865.
[8]	Hong Shan,Zihao Wang,Fa Zhang,Yong Xiong,Chang-Cheng Yin,Fei Sun. A local-optimization refinement algorithm in single particle analysis for macromolecular complex with multiple rigid modules[J]. Protein Cell, 2016, 07(1): 46-62.
[9]	Mingyang Wang,Michael Veit. Hemagglutinin-esterase-fusion (HEF) protein of influenza C virus[J]. Protein Cell, 2016, 7(1): 28-45.
[10]	Chengying Ma,Kaige Yan,Dan Tan,Ningning Li,Yixiao Zhang,Yi Yuan,Zhifei Li,Meng-Qiu Dong,Jianlin Lei,Ning Gao. Structural dynamics of the yeast Shwachman-Diamond syndrome protein (Sdo1) on the ribosome and its implication in the 60S subunit maturation[J]. Protein Cell, 2016, 07(03): 187-200.
[11]	Shishang Dong,Peng Yang,Guobang Li,Baocheng Liu,Wenming Wang,Xiang Liu,Boran Xia,Cheng Yang,Zhiyong Lou,Yu Guo,Zihe Rao. Insight into the Ebola virus nucleocapsid assembly mechanism: crystal structure of Ebola virus nucleoprotein core domain at 1.8 ? resolution[J]. Protein Cell, 2015, 6(5): 351-362.
[12]	Ping Wang,Chang Sun,Tingting Zhu,Yanhui Xu. Structural insight into mechanisms for dynamic regulation of PKM2[J]. Protein Cell, 2015, 6(4): 275-287.
[13]	Wenzhi Feng,Tong Wu,Xiaoyu Dan,Yuling Chen,Lin Li,She Chen,Di Miao,Haiteng Deng,Xinqi Gong,Li Yu. Phosphorylation of Atg31 is required for autophagy[J]. Protein Cell, 2015, 6(4): 288-296.
[14]	Ning Hao,Yutao Chen,Ming Xia,Ming Tan,Wu Liu,Xiaotao Guan,Xi Jiang,Xuemei Li,Zihe Rao. Crystal structures of GI.8 Boxer virus P dimers in complex with HBGAs, a novel evolutionary path selected by the Lewis epitope[J]. Protein Cell, 2015, 6(2): 101-116.
[15]	Chenjun Jia,Mei Li,Jianjun Li,Jingjing Zhang,Hongmei Zhang,Peng Cao,Xiaowei Pan,Xuefeng Lu,Wenrui Chang. Structural insights into the catalytic mechanism of aldehyde-deformylating oxygenases[J]. Protein Cell, 2015, 6(1): 55-67.

Viewed

Full text

Abstract

Cited

Shared

Discussed