1M63

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.260 

wwPDB Validation   3D Report Full Report


This is version 1.6 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 U S A 99: 12037

  • DOI: https://doi.org/10.1073/pnas.192206699
  • Primary Citation of Related Structures:  
    1M63

  • 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 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SERINE/THREONINE PROTEIN PHOSPHATASE 2B CATALYTIC SUBUNIT, ALPHA ISOFORM
A, E
372Homo sapiensMutation(s): 0 
Gene Names: CNA ALPHA
EC: 3.1.3.16
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Find proteins for Q08209 (Homo sapiens)
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Go to UniProtKB:  Q08209
PHAROS:  Q08209
GTEx:  ENSG00000138814 
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UniProt GroupQ08209
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CALCINEURIN B SUBUNIT ISOFORM 1
B, F
169Homo sapiensMutation(s): 0 
Gene Names: CNB
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Find proteins for P63098 (Homo sapiens)
Explore P63098 
Go to UniProtKB:  P63098
PHAROS:  P63098
GTEx:  ENSG00000221823 
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UniProt GroupP63098
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A
C, G
165Homo sapiensMutation(s): 0 
EC: 5.2.1.8
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Find proteins for P62937 (Homo sapiens)
Explore P62937 
Go to UniProtKB:  P62937
PHAROS:  P62937
GTEx:  ENSG00000196262 
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UniProt GroupP62937
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
CYCLOSPORIN A
D, H
11Tolypocladium inflatumMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
I [auth A],
O [auth E]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
FE
Query on FE

Download Ideal Coordinates CCD File 
J [auth A],
P [auth E]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
K [auth B]
L [auth B]
M [auth B]
N [auth B]
Q [auth F]
K [auth B],
L [auth B],
M [auth B],
N [auth B],
Q [auth F],
R [auth F],
S [auth F],
T [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  5 Unique
IDChains TypeFormula2D DiagramParent
ABA
Query on ABA
D, H
L-PEPTIDE LINKINGC4 H9 N O2ALA
BMT
Query on BMT
D, H
L-PEPTIDE LINKINGC10 H19 N O3THR
MLE
Query on MLE
D, H
L-PEPTIDE LINKINGC7 H15 N O2LEU
MVA
Query on MVA
D, H
L-PEPTIDE LINKINGC6 H13 N O2VAL
SAR
Query on SAR
D, H
PEPTIDE LINKINGC3 H7 N O2GLY
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.260 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.657α = 90
b = 108.657β = 90
c = 316.59γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-09-25
    Type: Initial release
  • Version 1.1: 2011-06-14
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-07-27
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 1.4: 2012-12-12
    Changes: Other
  • Version 1.5: 2017-11-01
    Changes: Derived calculations
  • Version 1.6: 2021-07-21
    Changes: Data collection, Derived calculations, Refinement description