Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 163213.11 
• Atom Count: 11185 
• Residue Count: 1434 
• Unique protein chains: 4

1M63

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

• DOI: 10.2210/pdb1M63/pdb

• Classification: HYDROLASE/ISOMERASE/IMMUNOSUPPRESSANT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21


• Deposited: 2002-07-12 Released: 2002-09-25 
• Deposition Author(s): Huai, Q., Kim, H.-Y., Liu, Y., Zhao, Y., Mondragon, A., Liu, J.O., Ke, H.

---

Experimental Data Snapshot

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

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

• PubMed: 12218175 
• 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 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
Molecule	Chains	Sequence Length	Organism	Details
SERINE/THREONINE PROTEIN PHOSPHATASE 2B CATALYTIC SUBUNIT, ALPHA ISOFORM	A, E	372	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
CALCINEURIN B SUBUNIT ISOFORM 1	B, F	169	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A	C, G	165	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
CYCLOSPORIN A	D, H	11	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A, E	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	B, F	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
FE	A, E	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Biologically Interesting Molecules 1 Unique
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000142	D,H	Cyclosporin A	Cyclic peptide / Immunosuppressant		--

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 = 108.657	α = 90.00
b = 108.657	β = 90.00
c = 316.590	γ = 90.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
CNS	refinement
DENZO	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-07-12 
• Released Date: 2002-09-25 
• Deposition Author(s): Huai, Q., Kim, H.-Y., Liu, Y., Zhao, Y., Mondragon, A., Liu, J.O., Ke, H.

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