Crystal structure of human CaMKII-alpha (CAMK2A)kinase domain

Experimental Data Snapshot

  • Resolution: 2.55 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.214 

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Characterization of CaMKII alpha holoenzyme stability.

Torres-Ocampo, A.P.Ozden, C.Hommer, A.Gardella, A.Lapinskas, E.Samkutty, A.Esposito, E.Garman, S.C.Stratton, M.M.

(2020) Protein Sci 29: 1524-1534

  • DOI: https://doi.org/10.1002/pro.3869
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Ca 2+ /calmodulin-dependent protein kinase II (CaMKII) is a Ser/Thr kinase necessary for long-term memory formation and other Ca 2+ -dependent signaling cascades such as fertilization. Here, we investigated the stability of CaMKIIα using a combination of differential scanning calorimetry (DSC), X-ray crystallography, and mass photometry (MP). The kinase domain has a low thermal stability (apparent T m = 36°C), which is slightly stabilized by ATP/MgCl 2 binding (apparent T m = 40°C) and significantly stabilized by regulatory segment binding (apparent T m = 60°C). We crystallized the kinase domain of CaMKII bound to p-coumaric acid in the active site. This structure reveals solvent-exposed hydrophobic residues in the substrate-binding pocket, which are normally buried in the autoinhibited structure when the regulatory segment is present. This likely accounts for the large stabilization that we observe in DSC measurements comparing the kinase alone with the kinase plus regulatory segment. The hub domain alone is extremely stable (apparent T m  ~ 90°C), and the holoenzyme structure has multiple unfolding transitions ranging from ~60°C to 100°C. Using MP, we compared a CaMKIIα holoenzyme with different variable linker regions and determined that the dissociation of both these holoenzymes occurs at a higher concentration (is less stable) compared with the hub domain alone. We conclude that within the context of the holoenzyme structure, the kinase domain is stabilized, whereas the hub domain is destabilized. These data support a model where domains within the holoenzyme interact.

  • Organizational Affiliation

    Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Calcium/calmodulin-dependent protein kinase type II subunit alpha268Homo sapiensMutation(s): 2 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UQM7 (Homo sapiens)
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Go to UniProtKB:  Q9UQM7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UQM7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on HC4

Download Ideal Coordinates CCD File 
C9 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.55 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.147α = 90
b = 56.928β = 90
c = 97.461γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5R01GM123157

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-22
    Type: Initial release
  • Version 1.1: 2020-06-10
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description