6TZ8

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.199 

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:  

  • 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) subu ...

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein phosphatase 2B catalytic subunit A1
A, D
390Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487)Mutation(s): 0 
Gene Names: CNA1
EC: 3.1.3.16
Find proteins for O42773 (Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487))
Go to UniProtKB:  O42773
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Calcineurin subunit B
B, E
175Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487)Mutation(s): 0 
Find proteins for J9VL81 (Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487))
Go to UniProtKB:  J9VL81
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
FK506-binding protein 1
C, F
122Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487)Mutation(s): 2 
Gene Names: FRR1
EC: 5.2.1.8
Find proteins for O94746 (Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487))
Go to UniProtKB:  O94746
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FK5
Query on FK5

Download SDF File 
Download CCD File 
C, F
8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN
K506
C44 H69 N O12
QJJXYPPXXYFBGM-LFZNUXCKSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

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Download CCD File 
B, E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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Download CCD File 
A, D
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 118.720α = 90.00
b = 120.700β = 90.00
c = 134.960γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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