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: 2.30 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

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:  
    4DRJ, 4DRH, 4DRI

  • 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 pro ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase FKBP5 A, D144Homo sapiensMutation(s): 0 
Gene Names: AIG6, FKBP5, FKBP51
EC: 5.2.1.8
Find proteins for Q13451 (Homo sapiens)
Explore Q13451 
Go to UniProtKB:  Q13451
NIH Common Fund Data Resources
PHAROS:  Q13451
GTEx:  ENSG00000096060
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase mTOR B, E98Homo sapiensMutation(s): 0 
Gene Names: FRAP, FRAP1, FRAP2, MTOR, RAFT1, RAPT1
EC: 2.7.11.1
Find proteins for P42345 (Homo sapiens)
Explore P42345 
Go to UniProtKB:  P42345
NIH Common Fund Data Resources
PHAROS:  P42345
GTEx:  ENSG00000198793
Protein Feature View
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  • Reference Sequence
Small Molecules
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RAPIC50:  0.44999998807907104   nM  BindingDB
RAPKi:  3   nM  BindingDB
RAPIC50:  0.10000000149011612   nM  BindingDB
RAPKd:  0.6000000238418579   nM  BindingDB
RAPIC50:  3.5   nM  BindingDB
RAPIC50:  430   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 31 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.678α = 90
b = 103.678β = 90
c = 106.543γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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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
    Changes: Database references