5B8I | pdb_00005b8i

Crystal structure of Calcineurin A and Calcineurin B in complex with FKBP12 and FK506 from Coccidioides immitis RS

• PDB DOI: https://doi.org/10.2210/pdb5B8I/pdb

• Classification: HYDROLASE
• Organism(s): Coccidioides immitis RS
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2015-05-03 Released: 2015-05-20 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID), Fox III, D., Dranow, D.M., Lorimer, D.D., Edwards, T.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.172 (Depositor), 0.173 (DCC) 
• R-Value Work: 
  0.145 (Depositor), 0.146 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Starting Model: experimental

Literature

Harnessing calcineurin-FK506-FKBP12 crystal structures from invasive fungal pathogens to develop antifungal agents.

Juvvadi, P.R., Fox 3rd, D., Bobay, B.G., Hoy, M.J., Gobeil, S.M.C., Venters, R.A., Chang, Z., Lin, J.J., Averette, A.F., Cole, D.C., Barrington, B.C., Wheaton, J.D., Ciofani, M., Trzoss, M., Li, X., Lee, S.C., Chen, Y.L., Mutz, M., Spicer, L.D., Schumacher, M.A., Heitman, J., Steinbach, W.J.

(2019) Nat Commun 10: 4275-4275

• PubMed: 31537789 
• DOI: https://doi.org/10.1038/s41467-019-12199-1
• Primary Citation Related Structures: 
  5B8I, 6TZ6, 6TZ7, 6TZ8


• PubMed Abstract: 
  

  Calcineurin is important for fungal virulence and a potential antifungal target, but compounds targeting calcineurin, such as FK506, are immunosuppressive. Here we report the crystal structures of calcineurin catalytic (CnA) and regulatory (CnB) subunits complexed with FK506 and the FK506-binding protein (FKBP12) from human fungal pathogens (Aspergillus fumigatus, Candida albicans, Cryptococcus neoformans and Coccidioides immitis). Fungal calcineurin complexes are similar to the mammalian complex, but comparison of fungal and human FKBP12 (hFKBP12) reveals conformational differences in the 40s and 80s loops. NMR analysis, molecular dynamic simulations, and mutations of the A. fumigatus CnA/CnB-FK506-FKBP12-complex identify a Phe88 residue, not conserved in hFKBP12, as critical for binding and inhibition of fungal calcineurin. These differences enable us to develop a less immunosuppressive FK506 analog, APX879, with an acetohydrazine substitution of the C22-carbonyl of FK506. APX879 exhibits reduced immunosuppressive activity and retains broad-spectrum antifungal activity and efficacy in a murine model of invasive fungal infection.

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Organizational Affiliation: 
• Division of Pediatric Infectious Diseases, Department of Pediatrics, Duke University Medical Center, Durham, NC, 27710, USA. [e-mail].
Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA, 98110, USA.
UCB Pharma., 7869 NE Day Road West, Bainbridge Island, WA, 98110, USA.
Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA.
Duke University NMR Center, Duke University Medical Center, Durham, NC, 27710, USA.
Department of Biochemistry, Duke University, Durham, NC, 27710, USA.
Department of Radiology, Duke University, Durham, NC, 27710, USA.
Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, USA.
Division of Pediatric Infectious Diseases, Department of Pediatrics, Duke University Medical Center, Durham, NC, 27710, USA.
Department of Immunology, Duke University Medical Center, Durham, NC, 27710, USA.
Amplyx Pharmaceuticals, 3210 Merryfield Row, San Diego, CA, 92121, USA.
Forge Therapeutics, Inc., 10578 Science Center Drive, San Diego, CA, 92121, USA.
South Texas Center for Emerging Infectious Diseases, Department of Biology, The University of Texas at San Antonio, San Antonio, TX, 78249, USA.
Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, 10617, Taiwan.
Genentech Inc., 1 DNA Way, San Francisco, CA, 94080, USA.
Division of Pediatric Infectious Diseases, Department of Pediatrics, Duke University Medical Center, Durham, NC, 27710, USA. [e-mail].
Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 81.22 kDa 
• Atom Count: 6,073 
• Modeled Residue Count: 649 
• Deposited Residue Count: 691 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein phosphatase	A	390	Coccidioides immitis RS	Mutation(s): 0  Gene Names: CIMG_06667 EC: 3.1.3.16
UniProt
Find proteins for J3K8M7 (Coccidioides immitis (strain RS)) Explore J3K8M7  Go to UniProtKB:  J3K8M7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcineurin subunit B, variant	B	171	Coccidioides immitis RS	Mutation(s): 0  Gene Names: CIMG_02704
UniProt
Find proteins for A0A0D8JSK0 (Coccidioides immitis (strain RS)) Explore A0A0D8JSK0  Go to UniProtKB:  A0A0D8JSK0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidylprolyl isomerase	C	130	Coccidioides immitis RS	Mutation(s): 0  Gene Names: CIMG_08666 EC: 5.2.1.8
UniProt
Find proteins for J3K5Z5 (Coccidioides immitis (strain RS)) Explore J3K5Z5  Go to UniProtKB:  J3K5Z5

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FK5	T [auth C]	8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN C44 H69 N O12 QJJXYPPXXYFBGM-LFZNUXCKSA-N
MES	F [auth A], G [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], R [auth B], S [auth B], U [auth C], V [auth C], W [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FE	E [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
CA	N [auth B], O [auth B], P [auth B], Q [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.172 (Depositor), 0.173 (DCC) 
• R-Value Work:  0.145 (Depositor), 0.146 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35B8I

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.67	α = 90
b = 154.63	β = 90
c = 64.75	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-20 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID), Fox III, D., Dranow, D.M., Lorimer, D.D., Edwards, T.E.

Revision History  

• Version 1.0: 2015-05-20
  Type: Initial release
  
• Version 1.1: 2016-08-10
  Changes: Data collection
• Version 1.2: 2017-11-01
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2018-01-31
  Changes: Database references
• Version 1.4: 2019-09-18
  Changes: Data collection, Database references, Structure summary
• Version 1.5: 2019-11-13
  Changes: Database references
• Version 1.6: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description