5NIN

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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

  • PubMed Abstract: 
  • AKAP79/150 is essential for coordinating second messenger-responsive enzymes in processes including synaptic long-term depression. Ca2+ directly regulates AKAP79 through its effector calmodulin (CaM), but the molecular basis of this regulation was pr ...

    AKAP79/150 is essential for coordinating second messenger-responsive enzymes in processes including synaptic long-term depression. Ca2+ 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 Ca2+-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 Ca2+-activated C-lobe and closed N-lobe cooperate to recognize a mixed α/310 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Calmodulin
B, A
149Homo sapiensMutation(s): 0 
Gene Names: CALM1 (CALM, CAM, CAM1)
Find proteins for P0DP23 (Homo sapiens)
Go to Gene View: CALM1
Go to UniProtKB:  P0DP23
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
A-kinase anchor protein 5
C, D
16Homo sapiensMutation(s): 0 
Gene Names: AKAP5 (AKAP79)
Find proteins for P24588 (Homo sapiens)
Go to Gene View: AKAP5
Go to UniProtKB:  P24588
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, 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: 0.194 
  • R-Value Work: 0.164 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 76.460α = 90.00
b = 76.460β = 90.00
c = 128.990γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
iMOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



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