7URW | pdb_00007urw

Tetradecameric hub domain of CaMKII beta


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 
    0.300 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.255 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.257 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Ca2+/CaM dependent protein kinase II (CaMKII) alpha and CaMKII beta hub domains adopt distinct oligomeric states and stabilities.

Ozden, C.MacManus, S.Adafia, R.Samkutty, A.Torres-Ocampo, A.P.Garman, S.C.Stratton, M.M.

(2024) Protein Sci 33: e4960-e4960

  • DOI: https://doi.org/10.1002/pro.4960
  • Primary Citation of Related Structures:  
    7URW, 7URZ

  • PubMed Abstract: 

    Ca 2+ /calmodulin-dependent protein kinase II (CaMKII) is a multidomain serine/threonine kinase that plays important roles in the brain, heart, muscle tissue, and eggs/sperm. The N-terminal kinase and regulatory domain is connected by a flexible linker to the C-terminal hub domain. The hub domain drives the oligomeric organization of CaMKII, assembling the kinase domains into high local concentration. Previous structural studies have shown multiple stoichiometries of the holoenzyme as well as the hub domain alone. Here, we report a comprehensive study of the hub domain stoichiometry and stability in solution. We solved two crystal structures of the CaMKIIβ hub domain that show 14-mer (3.1 Å) and 16-mer (3.4 Å) assemblies. Both crystal structures were determined from crystals grown in the same drop, which suggests that CaMKII oligomers with different stoichiometries likely coexist. To further interrogate hub stability, we employed mass photometry and temperature denaturation studies of CaMKIIβ and CaMKIIα hubs, which highlight major differences between these highly similar domains. We created a dimeric CaMKIIβ hub unit using rational mutagenesis, which is significantly less stable than the oligomer. Both hub domains populate an intermediate during unfolding. We found that multiple CaMKIIβ hub stoichiometries are present in solution and that larger oligomers are more stable. CaMKIIα had a narrower distribution of molecular weight and was distinctly more stable than CaMKIIβ.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Calcium/calmodulin-dependent protein kinase type II subunit beta137Homo sapiensMutation(s): 0 
Gene Names: CAMK2BCAM2CAMK2CAMKB
EC: 2.7.11.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q13554 (Homo sapiens)
Explore Q13554 
Go to UniProtKB:  Q13554
PHAROS:  Q13554
GTEx:  ENSG00000058404 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13554
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free:  0.300 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.255 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.257 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.236α = 90
b = 183.189β = 90
c = 108.37γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHASERphasing

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 StatesR01123157

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-11
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.2: 2025-10-08
    Changes: Database references, Structure summary