5WBJ

Crystal structure of the arabidopsis thaliana Raptor in complex with the TOS peptide of human 4EBP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Mechanisms of mTORC1 activation by RHEB and inhibition by PRAS40.

Yang, H.Jiang, X.Li, B.Yang, H.J.Miller, M.Yang, A.Dhar, A.Pavletich, N.P.

(2017) Nature 552: 368-373

  • DOI: 10.1038/nature25023
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The mechanistic target of rapamycin complex 1 (mTORC1) controls cell growth and metabolism in response to nutrients, energy levels, and growth factors. It contains the atypical kinase mTOR and the RAPTOR subunit that binds to the Tor signalling seque ...

    The mechanistic target of rapamycin complex 1 (mTORC1) controls cell growth and metabolism in response to nutrients, energy levels, and growth factors. It contains the atypical kinase mTOR and the RAPTOR subunit that binds to the Tor signalling sequence (TOS) motif of substrates and regulators. mTORC1 is activated by the small GTPase RHEB (Ras homologue enriched in brain) and inhibited by PRAS40. Here we present the 3.0 ångström cryo-electron microscopy structure of mTORC1 and the 3.4 ångström structure of activated RHEB-mTORC1. RHEB binds to mTOR distally from the kinase active site, yet causes a global conformational change that allosterically realigns active-site residues, accelerating catalysis. Cancer-associated hyperactivating mutations map to structural elements that maintain the inactive state, and we provide biochemical evidence that they mimic RHEB relieving auto-inhibition. We also present crystal structures of RAPTOR-TOS motif complexes that define the determinants of TOS recognition, of an mTOR FKBP12-rapamycin-binding (FRB) domain-substrate complex that establishes a second substrate-recruitment mechanism, and of a truncated mTOR-PRAS40 complex that reveals PRAS40 inhibits both substrate-recruitment sites. These findings help explain how mTORC1 selects its substrates, how its kinase activity is controlled, and how it is activated by cancer-associated mutations.


    Organizational Affiliation

    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Regulatory-associated protein of TOR 1
A
1287Arabidopsis thalianaMutation(s): 0 
Gene Names: RAPTOR1 (RAPTOR1B)
Find proteins for Q93YQ1 (Arabidopsis thaliana)
Go to UniProtKB:  Q93YQ1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 4E-binding protein 1
T
20Homo sapiensMutation(s): 0 
Gene Names: EIF4EBP1
Find proteins for Q13541 (Homo sapiens)
Go to Gene View: EIF4EBP1
Go to UniProtKB:  Q13541
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 89.100α = 90.00
b = 113.100β = 90.00
c = 153.500γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
PHASERphasing
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2018-04-18
    Type: Data collection, Database references