1M63

Crystal structure of calcineurin-cyclophilin-cyclosporin shows common but distinct recognition of immunophilin-drug complexes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.260 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Crystal Structure of Calcineurin-Cyclophilin-Cyclosporin Shows Common But Distinct Recognition of Immunophilin-Drug Complexes

Huai, Q.Kim, H.-Y.Liu, Y.Zhao, Y.Mondragon, A.Liu, J.O.Ke, H.

(2002) Proc.Natl.Acad.Sci.USA 99: 12037

  • DOI: 10.1073/pnas.192206699

  • PubMed Abstract: 
  • Calcineurin, a Ca2+/calmodulin-dependent protein phosphatase, is the common target for two immunophilin-immunosuppressant complexes, cyclophilin A-cyclosporin A (CyPA-CsA) and FKBP-FK506. How the two structurally distinct immunophilin-drug complexes ...

    Calcineurin, a Ca2+/calmodulin-dependent protein phosphatase, is the common target for two immunophilin-immunosuppressant complexes, cyclophilin A-cyclosporin A (CyPA-CsA) and FKBP-FK506. How the two structurally distinct immunophilin-drug complexes bind the same target has remained unknown. We report the crystal structure of calcineurin (CN) in complex with CyPA-CsA at 2.8-A resolution. The CyPA-CsA complex binds to a composite surface formed by the catalytic and regulatory subunits of CN, where the complex of FK506 and its binding protein FKBP also binds. While the majority of the CN residues involved in the binding are common for both immunophilin-immunosuppressant complexes, a significant number of the residues are distinct. Unlike FKBP-FK506, CyPA-CsA interacts with Arg-122 at the active site of CN, implying direct involvement of CyPA-CsA in the regulation of CN catalysis. The simultaneous interaction of CyPA with both the composite surface and the active site of CN suggests that the composite surface may serve as a substrate recognition site responsible for the narrow substrate specificity of CN. The comparison of CyPA-CsA-CN with FKBP-FK506-CN significantly contributes to understanding the molecular basis of regulation of CN activity by the immunophilin-immunosuppressant.


    Organizational Affiliation

    Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599-7260, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SERINE/THREONINE PROTEIN PHOSPHATASE 2B CATALYTIC SUBUNIT, ALPHA ISOFORM
A, E
372Homo sapiensMutation(s): 0 
Gene Names: PPP3CA (CALNA, CNA)
EC: 3.1.3.16
Find proteins for Q08209 (Homo sapiens)
Go to Gene View: PPP3CA
Go to UniProtKB:  Q08209
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CALCINEURIN B SUBUNIT ISOFORM 1
B, F
169Homo sapiensMutation(s): 0 
Gene Names: PPP3R1 (CNA2, CNB)
Find proteins for P63098 (Homo sapiens)
Go to Gene View: PPP3R1
Go to UniProtKB:  P63098
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A
C, G
165Homo sapiensMutation(s): 0 
Gene Names: PPIA (CYPA)
EC: 5.2.1.8
Find proteins for P62937 (Homo sapiens)
Go to Gene View: PPIA
Go to UniProtKB:  P62937
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
CYCLOSPORIN A
D, H
11N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, E
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
B, F
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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Download CCD File 
A, E
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000142
Query on PRD_000142
D,HCyclosporin ACyclic peptide / Immunosuppressant

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.260 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 108.657α = 90.00
b = 108.657β = 90.00
c = 316.590γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-09-25
    Type: Initial release
  • Version 1.1: 2011-06-14
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-07-27
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 1.4: 2012-12-12
    Type: Other
  • Version 1.5: 2017-11-01
    Type: Derived calculations