6TZ7

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.200 

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
A
388Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100)Mutation(s): 0 
Gene Names: cnaA
EC: 3.1.3.16
Find proteins for Q4WUR1 (Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100))
Go to UniProtKB:  Q4WUR1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Calcineurin Ca2+-binding regulatory subunit CnaB
B
174Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100)Mutation(s): 0 
Find proteins for Q4WDF2 (Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100))
Go to UniProtKB:  Q4WDF2
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
FK506-binding protein 1A
C
127Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100)Mutation(s): 0 
Gene Names: fpr1A
EC: 5.2.1.8
Find proteins for Q4WLV6 (Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100))
Go to UniProtKB:  Q4WLV6
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FK5
Query on FK5

Download SDF File 
Download CCD File 
C
8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN
K506
C44 H69 N O12
QJJXYPPXXYFBGM-LFZNUXCKSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 59.240α = 90.00
b = 94.460β = 109.28
c = 69.830γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
XDSdata reduction
PHASERphasing

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