3LL8

Crystal Structure of Calcineurin in Complex with AKAP79 Peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Balanced interactions of calcineurin with AKAP79 regulate Ca(2+)-calcineurin-NFAT signaling.

Li, H.Pink, M.D.Murphy, J.G.Stein, A.Dell'acqua, M.L.Hogan, P.G.

(2012) Nat.Struct.Mol.Biol. 19: 337-345

  • DOI: 10.1038/nsmb.2238

  • PubMed Abstract: 
  • In hippocampal neurons, the scaffold protein AKAP79 recruits the phosphatase calcineurin to L-type Ca(2+) channels and couples Ca(2+) influx to activation of calcineurin and of its substrate, the transcription factor NFAT. Here we show that an IAIIIT ...

    In hippocampal neurons, the scaffold protein AKAP79 recruits the phosphatase calcineurin to L-type Ca(2+) channels and couples Ca(2+) influx to activation of calcineurin and of its substrate, the transcription factor NFAT. Here we show that an IAIIIT anchoring site in human AKAP79 binds the same surface of calcineurin as the PxIxIT recognition peptide of NFAT, albeit more strongly. A modest decrease in calcineurin-AKAP affinity due to an altered anchoring sequence is compatible with NFAT activation, whereas a further decrease impairs activation. Counterintuitively, increasing calcineurin-AKAP affinity increases recruitment of calcineurin to the scaffold but impairs NFAT activation; this is probably due to both slower release of active calcineurin from the scaffold and sequestration of active calcineurin by 'decoy' AKAP sites. We propose that calcineurin-AKAP79 scaffolding promotes NFAT signaling by balancing strong recruitment of calcineurin with its efficient release to communicate with NFAT.


    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.,Bacquet, R.,Villafranca, J.E.
      (1995) Nature 378: 641
    • 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


    Organizational Affiliation

    Immune Disease Institute and Program in Cellular and Molecular Medicine, Children's Hospital, Boston, Massachusetts, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AKAP79 peptide
E
11Homo sapiensGene Names: AKAP5 (AKAP79)
Find proteins for P24588 (Homo sapiens)
Go to Gene View: AKAP5
Go to UniProtKB:  P24588
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
A, C
357Homo sapiensGene 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: 3
MoleculeChainsSequence LengthOrganismDetails
Calcineurin subunit B type 1
B, D
155Homo sapiensGene Names: PPP3R1 (CNA2, CNB)
Find proteins for P63098 (Homo sapiens)
Go to Gene View: PPP3R1
Go to UniProtKB:  P63098
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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

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

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Download CCD File 
B, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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Download CCD File 
A, C
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 86.275α = 90.00
b = 89.699β = 90.00
c = 158.914γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
ADSCdata collection
PDB_EXTRACTdata extraction
REFMACrefinement
DENZOdata reduction
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-01-28 
  • Released Date: 2011-01-12 
  • Deposition Author(s): Li, H., Hogan, P.G.

Revision History 

  • Version 1.0: 2011-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-03-21
    Type: Database references
  • Version 1.3: 2017-11-01
    Type: Advisory, Refinement description