1MF8 | pdb_00001mf8

Crystal Structure of human calcineurin complexed with cyclosporin A and human cyclophilin

• PDB DOI: https://doi.org/10.2210/pdb1MF8/pdb

• Classification: HYDROLASE/ISOMERASE/IMMUNOSUPPRESSANT
• Organism(s): Homo sapiens, Tolypocladium inflatum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-08-09 Released: 2002-10-16 
• Deposition Author(s): Jin, L., Harrison, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.300 (Depositor), 0.293 (DCC) 
• R-Value Work: 
  0.250 (Depositor), 0.257 (DCC) 
• R-Value Observed: 
  0.250 (Depositor) 

Starting Models: experimental

Literature

Crystal Structure of Human Calcineurin Complexed with Cyclosporin a and Human Cyclophilin

Jin, L., Harrison, S.C.

(2002) Proc Natl Acad Sci U S A 99: 13522

• PubMed: 12357034 
• DOI: https://doi.org/10.1073/pnas.212504399
• Primary Citation Related Structures: 
  1MF8


• PubMed Abstract: 
  

  Calcineurin (Cn), a Ca(2+)/calmodulin-dependent Ser/Thr protein phosphatase, is an important participant in signaling pathways that activate T cells. It is the target of the immunosuppressive drugs cyclosporin A (CsA) and FK506. These drugs bind proteins known as cyclophilin (Cyp) and FK506-binding protein, respectively, and the drug-protein complexes in turn inhibit Cn. We report the crystal structure of a Cyp/CsA/Cn ternary complex, determined to a resolution of 3.1 A. Residues 3-9 of CsA, particularly N-methyl leucines 4 and 6, and Trp-121 of Cyp form a composite surface for interaction with Cn. The hydrophobic interface buries two hydrogen bonds. The structure accounts clearly for the effects of mutations in Cn on CsA-resistance and for the way modifications of CsA alter immunosuppressive activity.

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Organizational Affiliation: 
• Department of Molecular and Cellular Biology, and Howard Hughes Medical Institute, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 81.61 kDa 
• Atom Count: 5,522 
• Modeled Residue Count: 691 
• Deposited Residue Count: 719 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CALMODULIN-DEPENDENT CALCINEURIN A SUBUNIT, ALPHA ISOFORM	A	373	Homo sapiens	Mutation(s): 0  EC: 3.1.3.16
UniProt & NIH Common Fund Data Resources
Find proteins for Q08209 (Homo sapiens) Explore Q08209  Go to UniProtKB:  Q08209
PHAROS:  Q08209 GTEx:  ENSG00000138814

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CALCINEURIN B SUBUNIT ISOFORM 1	B	170	Homo sapiens	Mutation(s): 0  EC: 3.1.3.16
UniProt & NIH Common Fund Data Resources
Find proteins for P63098 (Homo sapiens) Explore P63098  Go to UniProtKB:  P63098
PHAROS:  P63098 GTEx:  ENSG00000221823

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A	C	165	Homo sapiens	Mutation(s): 0  EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P62937 (Homo sapiens) Explore P62937  Go to UniProtKB:  P62937
PHAROS:  P62937 GTEx:  ENSG00000196262

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CA	F [auth B], G [auth B], H [auth B], I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  5 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ABA	D	L-PEPTIDE LINKING	C4 H9 N O2		ALA
BMT	D	L-PEPTIDE LINKING	C10 H19 N O3		THR
DAL	D	D-PEPTIDE LINKING	C3 H7 N O2		--
MLE	D	L-PEPTIDE LINKING	C7 H15 N O2		LEU
MVA	D	L-PEPTIDE LINKING	C6 H13 N O2		VAL
SAR	D	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	Cyclosporin A	Cyclic peptide / Immunosuppressant

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.300 (Depositor), 0.293 (DCC) 
• R-Value Work:  0.250 (Depositor), 0.257 (DCC) 
• R-Value Observed: 0.250 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.949	α = 90
b = 108.334	β = 90
c = 112.841	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-10-16 
Deposition Author(s): Jin, L., Harrison, S.C.

Revision History  

• Version 1.0: 2002-10-16
  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: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary