4DRH | pdb_00004drh

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

• PDB DOI: https://doi.org/10.2210/pdb4DRH/pdb

• Classification: Isomerase/Transferase
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-02-17 Released: 2013-02-06 
• Deposition Author(s): Maerz, A.M., Bracher, A., Hausch, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.226 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

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

• PubMed: 23358420 
• DOI: https://doi.org/10.1128/MCB.00678-12
• Primary Citation Related Structures: 
  4DRH, 4DRI, 4DRJ


• 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 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.

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Organizational Affiliation: 
• Max Planck Institute of Psychiatry, Department of Chemical Genomics, Munich, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 58.73 kDa 
• Atom Count: 3,841 
• Modeled Residue Count: 447 
• Deposited Residue Count: 484 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase FKBP5	A, C [auth D]	144	Homo sapiens	Mutation(s): 0  Gene Names: AIG6, FKBP5, FKBP51 EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q13451 (Homo sapiens) Explore Q13451  Go to UniProtKB:  Q13451
PHAROS:  Q13451 GTEx:  ENSG00000096060

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase mTOR	B, D [auth E]	98	Homo sapiens	Mutation(s): 0  Gene Names: FRAP, FRAP1, FRAP2, MTOR, RAFT1, RAPT1 EC: 2.7.11.1 (PDB Primary Data), 2.7.10.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P42345 (Homo sapiens) Explore P42345  Go to UniProtKB:  P42345
PHAROS:  P42345 GTEx:  ENSG00000198793

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RAP	E [auth A], Q [auth D]	RAPAMYCIN IMMUNOSUPPRESSANT DRUG C51 H79 N O13 QFJCIRLUMZQUOT-HPLJOQBZSA-N
SO4	AA [auth E], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth B], N [auth B], O [auth B], P [auth B], R [auth D], S [auth D], T [auth D], U [auth D], V [auth E], W [auth E], X [auth E], Y [auth E], Z [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.226 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.678	α = 90
b = 103.678	β = 90
c = 106.543	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-06 
Deposition Author(s): Maerz, A.M., Bracher, A., Hausch, F.

Revision History  

• Version 1.0: 2013-02-06
  Type: Initial release
  
• Version 1.1: 2013-03-27
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description