4DRH

Co-crystal structure of the PPIase domain of FKBP51, Rapamycin and the FRB fragment of mTOR at low pH

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Large FK506-Binding Proteins Shape the Pharmacology of Rapamycin.

Marz, A.M., Fabian, A.K., Kozany, C., Bracher, A., Hausch, F.

(2013) Mol.Cell.Biol. 33: 1357-1367

  • DOI: 10.1128/MCB.00678-12
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The immunosuppressant and anticancer drug rapamycin works by inducing inhibitory protein complexes with the kinase mTOR, an important regulator of growth and proliferation. The obligatory accessory partner of rapamycin is believed to be FK506-binding ...

    The immunosuppressant and anticancer drug rapamycin works by inducing inhibitory protein complexes with the kinase mTOR, an important regulator of growth and proliferation. The obligatory accessory partner of rapamycin is believed to be FK506-binding protein 12 (FKBP12). Here we show that rapamycin complexes of larger FKBP family members can tightly bind to mTOR and potently inhibit its kinase activity. Cocrystal structures with FKBP51 and FKBP52 reveal the modified molecular binding mode of these alternative ternary complexes in detail. In cellular model systems, FKBP12 can be functionally replaced by larger FKBPs. When the rapamycin dosage is limiting, mTOR inhibition of S6K phosphorylation can be enhanced by FKBP51 overexpression in mammalian cells, whereas FKBP12 is dispensable. FKBP51 could also enable the rapamycin-induced hyperphosphorylation of Akt, which depended on higher FKBP levels than rapamycin-induced inhibition of S6K phosphorylation. These insights provide a mechanistic rationale for preferential mTOR inhibition in specific cell or tissue types by engaging specific FKBP homologs.

    Organizational Affiliation: 

    Max Planck Institute of Psychiatry, Department of Chemical Genomics, Munich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase FKBP5
A, D
144Homo sapiensMutation(s): 0 
Gene Names: FKBP5 (AIG6, FKBP51)
EC: 5.2.1.8
Find proteins for Q13451 (Homo sapiens)
Go to Gene View: FKBP5
Go to UniProtKB:  Q13451
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase mTOR
B, E
98Homo 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
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A, B, D, E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
RAP
Query on RAP
Download SDF File 
Download CCD File 
A, D
RAPAMYCIN IMMUNOSUPPRESSANT DRUG
C51 H79 N O13
QFJCIRLUMZQUOT-HPLJOQBZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RAPKi: 3 nM (100) BINDINGDB
RAPIC50: 0.1 - 3.5 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.187 
  • Space Group: P 31 1 2
Unit Cell:
Length (Å)Angle (°)
a = 103.678α = 90.00
b = 103.678β = 90.00
c = 106.543γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
PDB_EXTRACTdata extraction
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-06
    Type: Initial release
  • Version 1.1: 2013-03-27
    Type: Database references