6TZ8

Crystal structure of Cryptococcus neoformans Calceineurin A, Calcineurin B, and FKBP12 with FK-506


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.1 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:  
    6TZ7, 6TZ6, 6TZ8, 5B8I

  • 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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase 2B catalytic subunit A1A, D390Cryptococcus neoformans var. grubii H99Mutation(s): 0 
Gene Names: CNA1CNAG_04796
EC: 3.1.3.16
Find proteins for O42773 (Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487))
Explore O42773 
Go to UniProtKB:  O42773
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Calcineurin subunit BB, E175Cryptococcus neoformans var. grubii H99Mutation(s): 0 
Gene Names: CNAG_00888
Find proteins for J9VL81 (Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487))
Explore J9VL81 
Go to UniProtKB:  J9VL81
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
FK506-binding protein 1C, F122Cryptococcus neoformans var. grubii H99Mutation(s): 2 
Gene Names: FRR1CNAG_03682
EC: 5.2.1.8
Find proteins for O94746 (Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487))
Explore O94746 
Go to UniProtKB:  O94746
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FK5
Query on FK5

Download Ideal Coordinates CCD File 
O [auth C], W [auth F]8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN
C44 H69 N O12
QJJXYPPXXYFBGM-LFZNUXCKSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A], J [auth A], P [auth D]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

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

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

Download Ideal Coordinates CCD File 
K [auth B], L [auth B], M [auth B], N [auth B], S [auth E], T [auth E], U [auth E], V [auth E]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.72α = 90
b = 120.7β = 90
c = 134.96γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2019-10-02
    Changes: Data collection, Database references