3KZ7 | pdb_00003kz7

C-terminal domain of Murine FKBP25 rapamycin complex

• PDB DOI: https://doi.org/10.2210/pdb3KZ7/pdb

• Classification: ISOMERASE/INHIBITOR
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-12-08 Released: 2010-12-15 
• Deposition Author(s): Stura, E.A., Galat, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.222 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Diversified targets of FKBP25 and its complex with rapamycin.

Galat, A., Thai, R., Stura, E.A.

(2014) Int J Biol Macromol 69: 344-352

• PubMed: 24879919 
• DOI: https://doi.org/10.1016/j.ijbiomac.2014.05.060
• Primary Citation Related Structures: 
  3KZ7


• PubMed Abstract: 
  

  FKBP25 is a member of the super-family of peptidylprolyl cis/trans isomerases, which is a high affinity binder for the immunosuppressive antibiotic rapamycin (Rpm). FKBP25 isolated from natural sources, its recombinant murine homologue (mFKBP25) and their complexes with rapamycin bind to diverse DNAs, RNAs and heparin affinity beads. The recombinant mFKBP25/rapamycin complex binds to several proteins including the calcineurin-A/calcineurin-B/calmodulin complex and to elongation factor 1β. We solved the X-ray structure of the C-terminal domain of mFKBP25 bound to rapamycin that has a higher resolution than of its human counterpart, and which clearly illustrates that the positively charged 40s loop is an epitope of the FK506-like binding domain (FKBD) for interactions with various biopolymers.

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Organizational Affiliation: 
• Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Biologie et de Technologies de Saclay, Service d'Ingénierie Moléculaire des Protéines, Gif sur Yvette F-91191, France. Electronic address: [e-mail].
Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Biologie et de Technologies de Saclay, Service d'Ingénierie Moléculaire des Protéines, Gif sur Yvette F-91191, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 14.2 kDa 
• Atom Count: 1,197 
• Modeled Residue Count: 119 
• Deposited Residue Count: 119 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FK506-binding protein 3	A	119	Mus musculus	Mutation(s): 0  Gene Names: Fkbp25, Fkbp3 EC: 5.2.1.8
UniProt
Find proteins for Q62446 (Mus musculus) Explore Q62446  Go to UniProtKB:  Q62446

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RAP	B [auth A]	RAPAMYCIN IMMUNOSUPPRESSANT DRUG C51 H79 N O13 QFJCIRLUMZQUOT-HPLJOQBZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.222 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.649	α = 90
b = 85.649	β = 90
c = 53.09	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
MOLREP	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-15 
Deposition Author(s): Stura, E.A., Galat, A.

Revision History  

• Version 1.0: 2010-12-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-06-18
  Changes: Database references
• Version 1.3: 2014-08-20
  Changes: Database references
• Version 1.4: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description