4F0Z

Crystal Structure of Calcineurin in Complex with the Calcineurin-Inhibiting Domain of the African Swine Fever Virus Protein A238L


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The molecular mechanism of substrate engagement and immunosuppressant inhibition of calcineurin.

Grigoriu, S.Bond, R.Cossio, P.Chen, J.A.Ly, N.Hummer, G.Page, R.Cyert, M.S.Peti, W.

(2013) PLoS Biol 11: e1001492-e1001492

  • DOI: https://doi.org/10.1371/journal.pbio.1001492
  • Primary Citation of Related Structures:  
    4F0Z

  • PubMed Abstract: 

    Ser/thr phosphatases dephosphorylate their targets with high specificity, yet the structural and sequence determinants of phosphosite recognition are poorly understood. Calcineurin (CN) is a conserved Ca(2+)/calmodulin-dependent ser/thr phosphatase and the target of immunosuppressants, FK506 and cyclosporin A (CSA). To investigate CN substrate recognition we used X-ray crystallography, biochemistry, modeling, and in vivo experiments to study A238L, a viral protein inhibitor of CN. We show that A238L competitively inhibits CN by occupying a critical substrate recognition site, while leaving the catalytic center fully accessible. Critically, the 1.7 Å structure of the A238L-CN complex reveals how CN recognizes residues in A238L that are analogous to a substrate motif, "LxVP." The structure enabled modeling of a peptide substrate bound to CN, which predicts substrate interactions beyond the catalytic center. Finally, this study establishes that "LxVP" sequences and immunosuppressants bind to the identical site on CN. Thus, FK506, CSA, and A238L all prevent "LxVP"-mediated substrate recognition by CN, highlighting the importance of this interaction for substrate dephosphorylation. Collectively, this work presents the first integrated structural model for substrate selection and dephosphorylation by CN and lays the groundwork for structure-based development of new CN inhibitors.


  • Organizational Affiliation

    Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, Rhode Island, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform372Homo sapiensMutation(s): 0 
Gene Names: PPP3CACALNACNA
EC: 3.1.3.16
UniProt & NIH Common Fund Data Resources
Find proteins for Q08209 (Homo sapiens)
Explore Q08209 
Go to UniProtKB:  Q08209
PHAROS:  Q08209
GTEx:  ENSG00000138814 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08209
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Calcineurin subunit B type 1170Homo sapiensMutation(s): 0 
Gene Names: PPP3R1CNA2CNB
EC: 3.1.3.16
UniProt & NIH Common Fund Data Resources
Find proteins for P63098 (Homo sapiens)
Explore P63098 
Go to UniProtKB:  P63098
PHAROS:  P63098
GTEx:  ENSG00000221823 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63098
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ankyrin repeat domain-containing protein A238L43African swine fever virus Malawi LIL 20/1Mutation(s): 0 
Gene Names: 5ELMal-047Ordered Locus Name: Mal-047 ORF Name: 5EL
UniProt
Find proteins for O36972 (African swine fever virus (isolate Tick/Malawi/Lil 20-1/1983))
Explore O36972 
Go to UniProtKB:  O36972
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO36972
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
L [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
H [auth B],
I [auth B],
J [auth B],
K [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.691α = 90
b = 48.976β = 104.37
c = 82.442γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
PHENIXmodel building
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-06
    Type: Initial release
  • Version 1.1: 2013-03-27
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description