8USO | pdb_00008uso

Full-length human CaMKII delta holoenzyme

• PDB DOI: https://doi.org/10.2210/pdb8USO/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-10-28 Released: 2024-03-27 
• Deposition Author(s): Ozden, C., Abromson, N.L., Tomchick, D.R., Stratton, M.M., Garman, S.C.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.213 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Models: experimental

Literature

A domain-swapped CaMKII conformation facilitates linker-mediated allosteric regulation.

Nguyen, B.V., Ozden, C., Dong, K., Koc, O.C., Torres-Ocampo, A.P., Dziedzic, N., Flaherty, D., Huang, J., Sankara, S., Abromson, N.L., Tomchick, D.R., Fissore, R.A., Chen, J., Garman, S.C., Stratton, M.M.

(2025) Nat Commun 16: 8461-8461

• PubMed: 41006217 
• DOI: https://doi.org/10.1038/s41467-025-63249-w
• Primary Citation of Related Structures:  
  8USO


• PubMed Abstract: 
  

  Memory formation, fertilization, and cardiac function rely on precise Ca ²⁺ signaling and subsequent Ca ²⁺ /calmodulin-dependent protein kinase II (CaMKII) activation. Ca ²⁺ sensitivity of the four CaMKII paralogs in mammals is linked to the length of the variable linker region that undergoes extensive alternative splicing. In this study, we determine that the position of charged residues within the linker modulates the Ca ²⁺ /CaM sensitivity. We present an X-ray crystal structure of the full-length CaMKIIδ holoenzyme consisting of domain-swapped dimers within a dodecameric complex, revealing potential contacts for cooperativity and allostery. Based on molecular dynamics (MD) simulations, small-angle X-ray scattering (SAXS) measurements, and live-cell imaging, we propose a model where the domain-swapped conformation positions the charges of the linker region to drive an interaction with the regulatory segment that modulates the degree of autoinhibition. Our findings provide a framework for understanding allosteric regulation of CaMKII by the linker region in Ca ²⁺ -sensitive cells.

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Organizational Affiliation: 
• Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, USA.
Chemistry-Biology Interface Training Program, University of Massachusetts, Amherst, MA, USA.
Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA.
Department of Chemistry, University of Massachusetts, Amherst, MA, USA.
Biotechnology Training Program, University of Massachusetts, Amherst, MA, USA.
Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA.
Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D6  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 153.83 kDa 
• Atom Count: 10,781 
• Modeled Residue Count: 1,307 
• Deposited Residue Count: 1,350 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
calcium/calmodulin-dependent protein kinase	A, B, C	450	Homo sapiens	Mutation(s): 1  Gene Names: CAMK2D EC: 2.7.11.17
UniProt & NIH Common Fund Data Resources
Find proteins for D6R938 (Homo sapiens) Explore D6R938  Go to UniProtKB:  D6R938
GTEx:  ENSG00000145349

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLI	D [auth A], E [auth B], F [auth C]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.213 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 4₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.984	α = 90
b = 174.984	β = 90
c = 140.416	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-27 
Deposition Author(s): Ozden, C., Abromson, N.L., Tomchick, D.R., Stratton, M.M., Garman, S.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	183180

Revision History  

• Version 1.0: 2024-03-27
  Type: Initial release
  
• Version 1.1: 2025-10-08
  Changes: Database references, Structure summary