6TZ7

Crystal Structure of Aspergillus fumigatus Calcineurin A, Calcineurin B, FKBP12 and FK506 (Tacrolimus)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

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Ligand Structure Quality Assessment 


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:  
    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 phosphatase 2B catalytic subunitA388Aspergillus fumigatus Af293Mutation(s): 0 
Gene Names: cnaAAFUA_5G09360
EC: 3.1.3.16
UniProt
Find proteins for Q4WUR1 (Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100))
Explore Q4WUR1 
Go to UniProtKB:  Q4WUR1
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Calcineurin Ca2+-binding regulatory subunit CnaBB174Aspergillus fumigatus Af293Mutation(s): 0 
Gene Names: AFUA_6G04540
UniProt
Find proteins for Q4WDF2 (Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100))
Explore Q4WDF2 
Go to UniProtKB:  Q4WDF2
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
FK506-binding protein 1AC127Aspergillus fumigatus Af293Mutation(s): 0 
Gene Names: fpr1AAFUA_6G12170
EC: 5.2.1.8
UniProt
Find proteins for Q4WLV6 (Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100))
Explore Q4WLV6 
Go to UniProtKB:  Q4WLV6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FK5 (Subject of Investigation/LOI)
Query on FK5

Download Ideal Coordinates CCD File 
L [auth C]8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN
C44 H69 N O12
QJJXYPPXXYFBGM-LFZNUXCKSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
F [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 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 
G [auth A], H [auth A]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 
I [auth B], J [auth B], K [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.24α = 90
b = 94.46β = 109.28
c = 69.83γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



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