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: 1.7 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1371/journal.pbio.1001492

  • 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 a ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
A
372Homo sapiensMutation(s): 0 
Gene Names: PPP3CA (CALNA, CNA)
EC: 3.1.3.16
Find proteins for Q08209 (Homo sapiens)
Go to Gene View: PPP3CA
Go to UniProtKB:  Q08209
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Calcineurin subunit B type 1
B
170Homo sapiensMutation(s): 0 
Gene Names: PPP3R1 (CNA2, CNB)
Find proteins for P63098 (Homo sapiens)
Go to Gene View: PPP3R1
Go to UniProtKB:  P63098
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ankyrin repeat domain-containing protein A238L
C
43African swine fever virusMutation(s): 0 
Gene Names: A238L
Find proteins for O36972 (African swine fever virus)
Go to UniProtKB:  O36972
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.157 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 72.691α = 90.00
b = 48.976β = 104.37
c = 82.442γ = 90.00
Software Package:
Software NamePurpose
CBASSdata collection
PHENIXmodel building
PHENIXphasing
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-06
    Type: Initial release
  • Version 1.1: 2013-03-27
    Type: Database references