4JT6

structure of mTORDeltaN-mLST8-PI-103 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

mTOR kinase structure, mechanism and regulation.

Yang, H.Rudge, D.G.Koos, J.D.Vaidialingam, B.Yang, H.J.Pavletich, N.P.

(2013) Nature 497: 217-223

  • DOI: 10.1038/nature12122
  • Primary Citation of Related Structures:  
    4JT6, 4JSV, 4JSX, 4JSN, 4JSP, 4JT5

  • PubMed Abstract: 
  • The mammalian target of rapamycin (mTOR), a phosphoinositide 3-kinase-related protein kinase, controls cell growth in response to nutrients and growth factors and is frequently deregulated in cancer. Here we report co-crystal structures of a complex ...

    The mammalian target of rapamycin (mTOR), a phosphoinositide 3-kinase-related protein kinase, controls cell growth in response to nutrients and growth factors and is frequently deregulated in cancer. Here we report co-crystal structures of a complex of truncated mTOR and mammalian lethal with SEC13 protein 8 (mLST8) with an ATP transition state mimic and with ATP-site inhibitors. The structures reveal an intrinsically active kinase conformation, with catalytic residues and a catalytic mechanism remarkably similar to canonical protein kinases. The active site is highly recessed owing to the FKBP12-rapamycin-binding (FRB) domain and an inhibitory helix protruding from the catalytic cleft. mTOR-activating mutations map to the structural framework that holds these elements in place, indicating that the kinase is controlled by restricted access. In vitro biochemistry shows that the FRB domain acts as a gatekeeper, with its rapamycin-binding site interacting with substrates to grant them access to the restricted active site. Rapamycin-FKBP12 inhibits the kinase by directly blocking substrate recruitment and by further restricting active-site access. The structures also reveal active-site residues and conformational changes that underlie inhibitor potency and specificity.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
mTORAB1174Homo sapiensMutation(s): 0 
Gene Names: MTORFRAPFRAP1FRAP2RAFT1RAPT1
EC: 2.7.11.1
Find proteins for P42345 (Homo sapiens)
Explore P42345 
Go to UniProtKB:  P42345
NIH Common Fund Data Resources
PHAROS  P42345
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
mLST8CD326Homo sapiensMutation(s): 0 
Gene Names: MLST8GBLLST8
Find proteins for Q9BVC4 (Homo sapiens)
Explore Q9BVC4 
Go to UniProtKB:  Q9BVC4
NIH Common Fund Data Resources
PHAROS  Q9BVC4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
X6K
Query on X6K

Download CCD File 
A, B
3-(4-MORPHOLIN-4-YLPYRIDO[3',2':4,5]FURO[3,2-D]PYRIMIDIN-2-YL)PHENOL
C19 H16 N4 O3
TUVCWJQQGGETHL-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
X6KIC50:  20   nM  BindingDB
X6KIC50:  19   nM  BindingDB
X6KIC50:  38   nM  BindingDB
X6KIC50:  5.300000190734863   nM  BindingDB
X6KIC50:  16   nM  BindingDB
X6KIC50:  1.100000023841858   nM  BindingDB
X6KIC50:  8.800000190734863   nM  BindingDB
X6KIC50:  31   nM  BindingDB
X6KKi:  19   nM  BindingDB
X6KKi:  20   nM  BindingDB
X6KKd:  12   nM  BindingDB
X6KIC50:  82   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.4α = 90
b = 163.2β = 90
c = 207.8γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-08
    Type: Initial release
  • Version 1.1: 2013-05-29
    Changes: Database references