2P6B

Crystal Structure of Human Calcineurin in Complex with PVIVIT Peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of calcineurin in complex with PVIVIT peptide: Portrait of a low-affinity signalling interaction

Li, H.Zhang, L.Rao, A.Harrison, S.C.Hogan, P.G.

(2007) J Mol Biol 369: 1296-1306

  • DOI: 10.1016/j.jmb.2007.04.032
  • Primary Citation of Related Structures:  
    2P6B

  • PubMed Abstract: 
  • The protein phosphatase calcineurin recognizes a wide assortment of substrates and controls diverse developmental and physiological pathways in eukaryotic cells. Dephosphorylation of the transcription factor NFAT and certain other calcineurin substra ...

    The protein phosphatase calcineurin recognizes a wide assortment of substrates and controls diverse developmental and physiological pathways in eukaryotic cells. Dephosphorylation of the transcription factor NFAT and certain other calcineurin substrates depends on docking of calcineurin at a PxIxIT consensus site. We describe here the structural basis for recognition of the PxIxIT sequence by calcineurin. We demonstrate that the high-affinity peptide ligand PVIVIT adds as a beta-strand to the edge of a beta-sheet of calcineurin; that short peptide segments containing the PxIxIT consensus sequence suffice for calcineurin-substrate docking; and that sequence variations within the PxIxIT core modulate the K(d) of the interaction within the physiological range 1 microM to 1 mM. Calcineurin can adapt to a wide variety of substrates, because recognition requires only a PxIxIT sequence and because variation within the core PxIxIT sequence can fine-tune the affinity to match the physiological signalling requirements of individual substrates.


    Related Citations: 
    • Crystal Structures of Human Calcineurin and the Human FKBP12-FK506-Calcineurin Complex
      Kissinger, C.R., Parge, H.E., Knighton, D.R., Lewis, C.T., Pelletier, L.A., Tempczyk, A., Kalish, V.J., Tucker, K.D., Showalter, R.E., Moomaw, E.W., Gastinel, L.N., Habuka, N., Chen, X., Maldonado, F., Barker, J.E.
      (1995) Nature 378: 641
    • X-ray Structure of Calcineurin Inhibited by the Immunophilin-immunosuppressant FKBP12-FK506 Complex
      Griffith, J.P., Kim, J.L., Kim, E.E., Sintchak, M.D., Thomson, J.A., Fitzgibbon, M.J., Fleming, M.A., Caron, P.R., Hsiao, K., Navia, M.A.
      (1995) Cell 82: 507
    • Affinity-driven Peptide Selection of an NFAT Inhibitor More Selective Than Cyclosporin A
      Aramburu, J., Yaffe, M.B., Lopez-Rodriguez, C., Cantley, L.C., Hogan, P.G., Rao, A.
      (1999) Science 285: 2129
    • Structural Delineation of the Calcineurin-NFAT Interaction and Its Parallels to PP1 Targeting Interactions
      Li, H., Rao, A., Hogan, P.G.
      (2004) J Mol Biol 342: 1659

    Organizational Affiliation

    The CBR Institute, for Biomedical Research, 200 Longwood Avenue, Boston, MA 02115, USA.



Macromolecules
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PVIVIT 14-mer PeptideE15N/AMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Calmodulin-dependent calcineurin A subunit alpha isoformAC383Homo sapiensMutation(s): 0 
Gene Names: PPP3CACALNACNA
EC: 3.1.3.16
Find proteins for Q08209 (Homo sapiens)
Explore Q08209 
Go to UniProtKB:  Q08209
NIH Common Fund Data Resources
PHAROS  Q08209
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Calcineurin subunit B isoform 1BD156Homo sapiensMutation(s): 0 
Gene Names: PPP3R1CNA2CNB
Find proteins for P63098 (Homo sapiens)
Explore P63098 
Go to UniProtKB:  P63098
NIH Common Fund Data Resources
PHAROS  P63098
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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

Download CCD File 
A, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download CCD File 
A, C
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.104α = 90
b = 89.155β = 90
c = 157.685γ = 90
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
DENZOdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-05
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description