5SVE

Structure of Calcineurin in complex with NFATc1 LxVP peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.596 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Investigating the human Calcineurin Interaction Network using the pi LxVP SLiM.

Sheftic, S.R., Page, R., Peti, W.

(2016) Sci Rep 6: 38920-38920

  • DOI: 10.1038/srep38920

  • PubMed Abstract: 

    • Ser/thr phosphorylation is the primary reversible covalent modification of proteins in eukaryotes. As a consequence, it is the reciprocal actions of kinases and phosphatases that act as key molecular switches to fine tune cellular events. It has been ...

    Ser/thr phosphorylation is the primary reversible covalent modification of proteins in eukaryotes. As a consequence, it is the reciprocal actions of kinases and phosphatases that act as key molecular switches to fine tune cellular events. It has been well documented that ~400 human ser/thr kinases engage substrates via consensus phosphosite sequences. Strikingly, we know comparatively little about the mechanism by which ~40 human protein ser/thr phosphatases (PSPs) dephosphorylate ~15000 different substrates with high specificity. The identification of substrates of the essential PSP calcineurin (CN) has been exceptionally challenging and only a small fraction has been biochemically confirmed. It is now emerging that CN binds regulators and substrates via two short linear motifs (SLiMs), the well-studied PxIxIT SLiM and the LxVP SLiM, which remains controversial at the molecular level. Here we describe the crystal structure of CN in complex with its substrate NFATc1 and show that the LxVP SLiM is correctly defined as πɸLxVP. Bioinformatics studies using the πɸLxVP SLiM resulted in the identification of 567 potential CN substrates; a small subset was experimentally confirmed. This combined structural-bioinformatics approach provides a powerful method for dissecting the CN interaction network and for elucidating the role of CN in human health and disease.

    Organizational Affiliation: 

    Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI, 02912, USA.,Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, 02912, USA.,Department of Chemistry, Brown University, Providence, RI, 02912, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
A
370Homo 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
NFATc1 LxVP peptide
C
18Homo sapiensMutation(s): 0 
Gene Names: NFATC1 (NFAT2, NFATC)
Find proteins for O95644 (Homo sapiens)
Go to Gene View: NFATC1
Go to UniProtKB:  O95644
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA
Download SDF File 
Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE
Download SDF File 
Download CCD File 
A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.596 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.679α = 90.00
b = 106.046β = 90.00
c = 111.913γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01NS091336

Revision History 

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence
  • Version 1.2: 2019-12-18
    Type: Author supporting evidence