5B8I

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


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

  • DOI: 10.1038/s41467-019-12199-1
  • Primary Citation of 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) ...

    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.


    Related Citations: 
    • Harnessing calcineurin-FK506-FKBP12 crystal structures from invasive fungal pathogens to develop antifungal agents
      Juvvadi, P.R., Fox III, D., Bobay, B.G., Hoy, M.J., Gobeil, S.M., 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., Mutz, M., Spicer, L.D., Schumacher, M.A., Heitman, J., Steinbach, W.J.
      (2019) Nat Commun --: --

    Organizational Affiliation

    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, USA. bill.steinbach@duke.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein phosphataseA390Coccidioides immitis RSMutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ3K8M7
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Calcineurin subunit B, variantB171Coccidioides immitis RSMutation(s): 0 
Gene Names: CIMG_02704
UniProt
Find proteins for A0A0D8JSK0 (Coccidioides immitis (strain RS))
Explore A0A0D8JSK0 
Go to UniProtKB:  A0A0D8JSK0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0D8JSK0
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidylprolyl isomeraseC130Coccidioides immitis RSMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ3K5Z5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FK5
Query on FK5

Download Ideal Coordinates CCD File 
T [auth C]8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN
C44 H69 N O12
QJJXYPPXXYFBGM-LFZNUXCKSA-N
 Ligand Interaction
MES
Query on MES

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
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
 Ligand Interaction
FE
Query on FE

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

Download Ideal Coordinates CCD File 
N [auth B],
O [auth B],
P [auth B],
Q [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.67α = 90
b = 154.63β = 90
c = 64.75γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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