4.4 Å Resolution Cryo-EM structure of human mTOR Complex 1
Received date: 20 Oct 2016
Accepted date: 11 Nov 2016
Published date: 24 Jan 2017
Copyright
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.
Key words： mTORC1; structure; cryo-electron microscopy
Huirong Yang , Jia Wang , Mengjie Liu , Xizi Chen , Min Huang , Dan Tan , Meng-Qiu Dong , Catherine C. L. Wong , Jiawei Wang , Yanhui Xu , Hong-Wei Wang . 4.4 Å Resolution Cryo-EM structure of human mTOR Complex 1[J]. Protein & Cell, 2016 , 7(12) : 878 -887 . DOI: 10.1007/s13238-016-0346-6
| 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
|
| 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
|
| 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
|
| 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
|
| 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
|
| 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
|
| 7 |
Dazert E, Hall MN (2011) mTOR signaling in disease. Curr Opin Cell Biol 23:744–755
|
| 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
|
| 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
|
| 10 |
Emsley P, Lohkamp B, Scott W, Cowtan K (2010) Features and development of COOT. Acta Crystallogr D 66:486–501
|
| 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
|
| 12 |
Ginalski K, Zhang H, Grishin NV (2004) Raptor protein contains a caspase-like domain. Trends Biochem Sci 29:522–524
|
| 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
|
| 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
|
| 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
|
| 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
|
| 17 |
Inoki K, Corradetti MN, Guan KL (2005) Dysregulation of the TSCmTOR pathway in human disease. Nat Genet 37:19–24
|
| 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
|
| 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
|
| 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
|
| 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
|
| 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
|
| 23 |
Mindell JA, Grigorieff N (2003) Accurate determination of local defocus and specimen tilt in electron microscopy. J Struct Biol 142:334–347
|
| 24 |
Rossmann MG, Bernal R, Pletnev SV (2001) Combining electron microscopic with X-ray crystallographic structures. J Struct Biol 136:190–200
|
| 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
|
| 26 |
Scheres SH (2012) RELION: implementation of a Bayesian approach to cryo-EM structure determination. J Struct Biol 180:519–530
|
| 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
|
| 28 |
Tee AR, Blenis J(2005) mTOR, translational control and human disease. Semin Cell Dev Biol 16:29–37
|
| 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
|
| 30 |
Vriend G (1990) WHAT IF: a molecular modeling and drug design program. J Mol Graph 8:52–56
|
| 31 |
Wang QS, Yu F, Huang S, Sun B, Zhang KH, Liu K, Wang ZJ, Xu CY, Wang SS, Yang LF
|
| 32 |
Wullschleger S, Loewith R, Hall MN (2006) TOR signaling in growth and metabolism. Cell 124:471–484
|
| 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
|
| 34 |
Yang H, Rudge DG, Koos JD, Vaidialingam B, Yang HJ, Pavletich NP (2013) mTOR kinase structure, mechanism and regulation. Nature 497:217–223
|
| 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
|
| 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
|
| 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
|
/
| 〈 |
|
〉 |