Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 163.21 kDa 
• Atom Count: 11185 
• Residue Count: 1401 
• 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, Tolypocladium inflatum
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• 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.

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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 

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

• PubMed: 12218175 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE/THREONINE PROTEIN PHOSPHATASE 2B CATALYTIC SUBUNIT, ALPHA ISOFORM	A, E	372	Homo sapiens	Mutation(s): 0  Gene Names: CNA ALPHA, PPP3CA, CALNA, CNA EC: 3.1.3.16
Find proteins for Q08209 (Homo sapiens) Explore Q08209  Go to UniProtKB:  Q08209
NIH Common Fund Data Resources
PHAROS  Q08209 GTEx  ENSG00000138814

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CALCINEURIN B SUBUNIT ISOFORM 1	B, F	169	Homo sapiens	Mutation(s): 0  Gene Names: CNB, PPP3R1, CNA2
Find proteins for P63098 (Homo sapiens) Explore P63098  Go to UniProtKB:  P63098
NIH Common Fund Data Resources
PHAROS  P63098 GTEx  ENSG00000221823

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
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) Explore P62937  Go to UniProtKB:  P62937
NIH Common Fund Data Resources
PHAROS  P62937 GTEx  ENSG00000196262

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
CYCLOSPORIN A	D, H	11	Tolypocladium inflatum	Mutation(s): 0

Small Molecules

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

Modified Residues  5 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ABA	D,H	L-PEPTIDE LINKING	C4 H9 N O2		ALA
BMT	D,H	L-PEPTIDE LINKING	C10 H19 N O3		THR
MLE	D,H	L-PEPTIDE LINKING	C7 H15 N O2		LEU
MVA	D,H	L-PEPTIDE LINKING	C6 H13 N O2		VAL
SAR	D,H	PEPTIDE LINKING	C3 H7 N O2		GLY

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
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: 2.80 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 = 108.657	α = 90
b = 108.657	β = 90
c = 316.59	γ = 90

Software Package:

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

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
  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