1FKK

ATOMIC STRUCTURE OF FKBP12, AN IMMUNOPHILIN BINDING PROTEIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Comparative X-ray structures of the major binding protein for the immunosuppressant FK506 (tacrolimus) in unliganded form and in complex with FK506 and rapamycin.

Wilson, K.P.Yamashita, M.M.Sintchak, M.D.Rotstein, S.H.Murcko, M.A.Boger, J.Thomson, J.A.Fitzgibbon, M.J.Black, J.R.Navia, M.A.

(1995) Acta Crystallogr.,Sect.D 51: 511-521

  • DOI: 10.1107/S0907444994014514
  • Primary Citation of Related Structures:  1FKJ, 1FKL

  • PubMed Abstract: 
  • FK506 (tacrolimus) is a natural product now approved in the US and Japan for organ transplantation. FK506, in complex with its 12 kDa cytosolic receptor (FKBP12), is a potent agonist of immunosuppression through the inhibition of the phosphatase acti ...

    FK506 (tacrolimus) is a natural product now approved in the US and Japan for organ transplantation. FK506, in complex with its 12 kDa cytosolic receptor (FKBP12), is a potent agonist of immunosuppression through the inhibition of the phosphatase activity of calcineurin. Rapamycin (sirolimus), which is itself an immunosuppressant by a different mechanism, completes with FK506 for binding to FKBP12 and thereby acts as an antagonist of calcineurin inhibition. We have solved the X-ray structure of unliganded FKBP12 and of FKBP12 in complex with FK506 and with rapamycin; these structures show localized differences in conformation and mobility in those regions of the protein that are known, by site-directed mutagenesis, to be involved in calcineurin inhibition. A comparison of 16 additional X-ray structures of FKBP12 in complex with FKBP12-binding ligands, where those structures were determined from different crystal forms with distinct packing arrangements, lends significance to the observed structural variability and suggests that it represents an intrinsic functional characteristic of the protein. Similar differences have been observed for FKBP12 before, but were considered artifacts of crystal-packing interactions. We suggest that immunosuppressive ligands express their differential effects in part by modulating the conformation of FKBP12, in agreement with mutagenesis experiments on the protein, and not simply through differences in the ligand structures themselves.


    Related Citations: 
    • X-Ray Structure of Calcineurin Inhibited by the Immunophilin-Immunosuppressant Fkbp12-Fk506 Complex
      Griffith, J.P.,Kim, J.L.,Kim, E.E.,Sintchak, M.D.,Thomson, J.A.,Fitzgibbon, M.J.,Fleming, M.A.,Caron, P.R.,Hsiao, K.,Navia, M.A.
      (1995) Cell 82: 507
    • Fk-506-Binding Protein: Three-Dimensional Structure of the Complex with the Antagonist L-685,818
      Becker, J.W.,Rotonda, J.,Mckeever, B.M.,Chan, H.K.,Marcy, A.I.,Wiederrecht, G.,Hermes, J.D.,Springer, J.P.
      (1993) J.Mol.Biol. 268: 11335
    • Improved Calcineurin Inhibition by Yeast Fkbp12-Drug Complexes
      Rotonda, J.,Burbaum, J.J.,Chan, H.K.,Marcy, A.I.,Becker, J.W.
      (1993) J.Biol.Chem. 268: 7607
    • Atomic Structure of the Rapamycin Human Immunophilin Fkbp-12 Complex
      Van Duyne, G.D.,Standaert, R.F.,Schreiber, S.L.,Clardy, J.
      (1991) J.Am.Chem.Soc. 113: 7433
    • Atomic Structure of Fkbp-Fk506, an Immunophilin-Immunosuppressant Complex
      Van Duyne, G.D.,Standaert, R.F.,Karplus, P.A.,Schreiber, S.L.,Clardy, J.
      (1991) Science 252: 839
    • Atomic Structures of Human Immunophilin Fkbp12 Complexes with Fk506 and Rapamycin
      Van Duyne, G.D.,Standaert, R.F.,Karplus, P.A.,Schreiber, S.L.,Clardy, J.
      (1993) J.Mol.Biol. 229: 105


    Organizational Affiliation

    Vertex Pharmaceuticals Incorporated, Cambridge, MA 02139-4211, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FK506 BINDING PROTEIN
A
107Bos taurusGene Names: FKBP1A (FKBP1)
EC: 5.2.1.8
Find proteins for P18203 (Bos taurus)
Go to Gene View: FKBP1A
Go to UniProtKB:  P18203
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 0.158 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 34.100α = 90.00
b = 34.100β = 90.00
c = 202.200γ = 90.00
Software Package:
Software NamePurpose
MANUFACTURERdata reduction
X-PLORrefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-12-07
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance