6BCU

Cryo-EM structure of the activated RHEB-mTORC1 refined to 3.4 angstrom


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 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
Serine/threonine-protein kinase mTOR,Serine/threonine-protein kinase mTOR
A, B
2549Homo sapiensMutation(s): 0 
Gene Names: MTOR (FRAP, FRAP1, FRAP2, RAFT1, RAPT1)
EC: 2.7.11.1
Find proteins for P42345 (Homo sapiens)
Go to Gene View: MTOR
Go to UniProtKB:  P42345
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Target of rapamycin complex subunit LST8
D, E
326Homo sapiensMutation(s): 0 
Gene Names: MLST8 (GBL, LST8)
Find proteins for Q9BVC4 (Homo sapiens)
Go to Gene View: MLST8
Go to UniProtKB:  Q9BVC4
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Regulatory-associated protein of mTOR,Regulatory-associated protein of mTOR
W, Y
1343Homo sapiensMutation(s): 0 
Gene Names: RPTOR (KIAA1303, RAPTOR)
Find proteins for Q8N122 (Homo sapiens)
Go to Gene View: RPTOR
Go to UniProtKB:  Q8N122
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 4E-binding protein 1
X, Z
122Homo sapiensMutation(s): 0 
Gene Names: EIF4EBP1
Find proteins for Q13541 (Homo sapiens)
Go to Gene View: EIF4EBP1
Go to UniProtKB:  Q13541
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
GTP-binding protein Rheb
S, R
188Homo sapiensMutation(s): 0 
Gene Names: RHEB (RHEB2)
Find proteins for Q15382 (Homo sapiens)
Go to Gene View: RHEB
Go to UniProtKB:  Q15382
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, B
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
GTP
Query on GTP

Download SDF File 
Download CCD File 
R, S
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, R, S
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
A, B
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical InstituteUnited States--

Revision History 

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2018-01-17
    Type: Author supporting evidence
  • Version 1.2: 2018-01-24
    Type: Database references
  • Version 1.3: 2018-10-03
    Type: Data collection, Refinement description