5NIN

Crystal Structure of AKAP79 calmodulin binding domain peptide in complex with Ca2+/Calmodulin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report



Literature

Molecular basis of AKAP79 regulation by calmodulin.

Patel, N.Stengel, F.Aebersold, R.Gold, M.G.

(2017) Nat Commun 8: 1681-1681

  • DOI: 10.1038/s41467-017-01715-w
  • Primary Citation of Related Structures:  
    5NIN

  • PubMed Abstract: 
  • AKAP79/150 is essential for coordinating second messenger-responsive enzymes in processes including synaptic long-term depression. Ca 2+ directly regulates AKAP79 through its effector calmodulin (CaM), but the molecular basis of this regulati ...

    AKAP79/150 is essential for coordinating second messenger-responsive enzymes in processes including synaptic long-term depression. Ca 2+ directly regulates AKAP79 through its effector calmodulin (CaM), but the molecular basis of this regulation was previously unknown. Here, we report that CaM recognizes a '1-4-7-8' pattern of hydrophobic amino acids starting at Trp79 in AKAP79. Cross-linking coupled to mass spectrometry assisted mapping of the interaction site. Removal of the CaM-binding sequence in AKAP79 prevents formation of a Ca 2+ -sensitive interface between AKAP79 and calcineurin, and increases resting cellular PKA phosphorylation. We determined a crystal structure of CaM bound to a peptide encompassing its binding site in AKAP79. CaM adopts a highly compact conformation in which its open Ca 2+ -activated C-lobe and closed N-lobe cooperate to recognize a mixed α/3 10 helix in AKAP79. The structure guided a bioinformatic screen to identify potential sites in other proteins that may employ similar motifs for interaction with CaM.


    Organizational Affiliation

    Department of Neuroscience, Physiology & Pharmacology, University College London, Gower Street, London, WC1E 6BT, UK. m.gold@ucl.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Calmodulin AB149Homo sapiensMutation(s): 0 
Gene Names: 
CALM1CALMCAMCAM1CALM2CAM2CAMBCALM3CALML2CAM3...
CALM1CALMCAMCAM1CALM2CAM2CAMBCALM3CALML2CAM3CAMCCAMIII

Find proteins for P0DP23 (Homo sapiens)
Explore P0DP23 
Go to UniProtKB:  P0DP23
NIH Common Fund Data Resources
PHAROS:  P0DP23
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
A-kinase anchor protein 5 CD16Homo sapiensMutation(s): 0 
Gene Names: AKAP5AKAP79
Find proteins for P24588 (Homo sapiens)
Explore P24588 
Go to UniProtKB:  P24588
NIH Common Fund Data Resources
PHAROS:  P24588
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.46α = 90
b = 76.46β = 90
c = 128.99γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-03-24 
  • Released Date: 2017-12-06 
  • Deposition Author(s): Gold, M.G., Patel, N.

Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom104194/Z/14/Z
Royal SocietyUnited Kingdom104194/Z/14/Z
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/N015274/1

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release