6TZ8 | pdb_00006tz8

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 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1038/s41467-019-12199-1
  • Primary Citation 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). 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.


  • Organizational Affiliation
    • Division of Pediatric Infectious Diseases, Department of Pediatrics, Duke University Medical Center, Durham, NC, 27710, USA. praveen.juvvadi@duke.edu.

Macromolecule Content 

  • Total Structure Weight: 159.03 kDa 
  • Atom Count: 10,282 
  • Modeled Residue Count: 1,315 
  • Deposited Residue Count: 1,374 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase 2B catalytic subunit A1
A, D
390Cryptococcus neoformans H99Mutation(s): 0 
Gene Names: CNA1CNAG_04796
EC: 3.1.3.16
UniProt
Find proteins for O42773 (Cryptococcus neoformans (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487))
Explore O42773 
Go to UniProtKB:  O42773
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO42773
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Calcineurin subunit B
B, E
175Cryptococcus neoformans H99Mutation(s): 0 
Gene Names: CNAG_00888
UniProt
Find proteins for J9VL81 (Cryptococcus neoformans (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487))
Explore J9VL81 
Go to UniProtKB:  J9VL81
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ9VL81
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
FK506-binding protein 1
C, F
122Cryptococcus neoformans H99Mutation(s): 2 
Gene Names: FRR1CNAG_03682
EC: 5.2.1.8
UniProt
Find proteins for O94746 (Cryptococcus neoformans (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487))
Explore O94746 
Go to UniProtKB:  O94746
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO94746
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FK5
(Subject of Investigation/LOI)

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
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
ZN

Query on ZN



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

Query on FE



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

Query on CA



Download:Ideal Coordinates CCD File
K [auth B]
L [auth B]
M [auth B]
N [auth B]
S [auth E]
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free:  0.243 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
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

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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
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description