regulation of synaptic vesicle docking / glutamatergic postsynaptic density / HSF1-dependent transactivation / RAF activation / Ion transport by P-type ATPases / peptidyl-threonine autophosphorylation / regulation of endocannabinoid signaling pathway / neurotransmitter receptor transport to plasma membrane / : / calcium- and calmodulin-dependent protein kinase complex ...regulation of synaptic vesicle docking / glutamatergic postsynaptic density / HSF1-dependent transactivation / RAF activation / Ion transport by P-type ATPases / peptidyl-threonine autophosphorylation / regulation of endocannabinoid signaling pathway / neurotransmitter receptor transport to plasma membrane / : / calcium- and calmodulin-dependent protein kinase complex / Interferon gamma signaling / Ca2+/calmodulin-dependent protein kinase / regulation of neurotransmitter secretion / regulation of neuron migration / dendritic spine development / calcium-dependent protein serine/threonine kinase activity / Trafficking of AMPA receptors / positive regulation of calcium ion transport / Ca2+ pathway / negative regulation of hydrolase activity / postsynaptic neurotransmitter receptor diffusion trapping / presynaptic cytosol / GTPase activating protein binding / RAF/MAP kinase cascade / dendrite morphogenesis / postsynaptic specialization membrane / NMDA selective glutamate receptor signaling pathway / regulation of mitochondrial membrane permeability involved in apoptotic process / calcium/calmodulin-dependent protein kinase activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / postsynaptic cytosol / Ion homeostasis / positive regulation of cardiac muscle cell apoptotic process / regulation of neuronal synaptic plasticity / cellular response to interferon-beta / Unblocking of NMDA receptors, glutamate binding and activation / regulation of protein localization to plasma membrane / glutamate receptor binding / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / response to ischemia / angiotensin-activated signaling pathway / positive regulation of receptor signaling pathway via JAK-STAT / Schaffer collateral - CA1 synapse / G1/S transition of mitotic cell cycle / cellular response to type II interferon / calcium ion transport / kinase activity / dendritic spine / calmodulin binding / postsynaptic density / neuron projection / protein phosphorylation / axon / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / glutamatergic synapse / synapse / dendrite / protein homodimerization activity / mitochondrion / ATP binding / identical protein binding / metal ion binding / cytoplasm / cytosol Similarity search - Function
Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. ...Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily Similarity search - Domain/homology
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)
R01NS081248
United States
Citation
Journal: Nat Commun / Year: 2017 Title: The CaMKII holoenzyme structure in activation-competent conformations. Authors: Janette B Myers / Vincent Zaegel / Steven J Coultrap / Adam P Miller / K Ulrich Bayer / Steve L Reichow / Abstract: The Ca/calmodulin-dependent protein kinase II (CaMKII) assembles into large 12-meric holoenzymes, which is thought to enable regulatory processes required for synaptic plasticity underlying learning, ...The Ca/calmodulin-dependent protein kinase II (CaMKII) assembles into large 12-meric holoenzymes, which is thought to enable regulatory processes required for synaptic plasticity underlying learning, memory and cognition. Here we used single particle electron microscopy (EM) to determine a pseudoatomic model of the CaMKIIα holoenzyme in an extended and activation-competent conformation. The holoenzyme is organized by a rigid central hub complex, while positioning of the kinase domains is highly flexible, revealing dynamic holoenzymes ranging from 15-35 nm in diameter. While most kinase domains are ordered independently, ∼20% appear to form dimers and <3% are consistent with a compact conformation. An additional level of plasticity is revealed by a small fraction of bona-fide 14-mers (<4%) that may enable subunit exchange. Biochemical and cellular FRET studies confirm that the extended state of CaMKIIα resolved by EM is the predominant form of the holoenzyme, even under molecular crowding conditions.
History
Deposition
Dec 9, 2016
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Header (metadata) release
Dec 28, 2016
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Map release
Jun 21, 2017
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Update
Mar 13, 2024
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Current status
Mar 13, 2024
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Download / File: emd_8514.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
CaMKII holoenzyme structure resolved by negative stain EM.
Voxel size
X=Y=Z: 4.37 Å
Density
Contour Level
By AUTHOR: 0.12 / Movie #1: 0.12
Minimum - Maximum
-1.1835607 - 0.77028763
Average (Standard dev.)
0.0003138977 (±0.025755277)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
0
0
0
Dimensions
128
128
128
Spacing
128
128
128
Cell
A=B=C: 559.36 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
4.37
4.37
4.37
M x/y/z
128
128
128
origin x/y/z
0.000
0.000
0.000
length x/y/z
559.360
559.360
559.360
α/β/γ
90.000
90.000
90.000
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
128
128
128
D min/max/mean
-1.184
0.770
0.000
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Supplemental data
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Sample components
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Entire : Calcium-calmodulin dependent kinase II alpha
Entire
Name: Calcium-calmodulin dependent kinase II alpha
Components
Complex: Calcium-calmodulin dependent kinase II alpha
Protein or peptide: Calcium/calmodulin-dependent protein kinase type II subunit alpha
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Supramolecule #1: Calcium-calmodulin dependent kinase II alpha
Supramolecule
Name: Calcium-calmodulin dependent kinase II alpha / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Full-length CaMKII alpha wild type
Source (natural)
Organism: Rattus norvegicus (Norway rat)
Molecular weight
Theoretical: 620 KDa
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Macromolecule #1: Calcium/calmodulin-dependent protein kinase type II subunit alpha
Macromolecule
Name: Calcium/calmodulin-dependent protein kinase type II subunit alpha type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO / EC number: Ca2+/calmodulin-dependent protein kinase
Number classes used: 1 / Applied symmetry - Point group: D6 (2x6 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) Details: Only modeled the unstructured linker region, residues 300-345. The rest came from two other, previously published structures, namely 5IG3 and 2VZ6 Number images used: 2000
Initial angle assignment
Type: RANDOM ASSIGNMENT / Software - Name: EMAN (ver. 2.12)
Final angle assignment
Type: OTHER / Software - Name: RELION (ver. 1.4)
Final 3D classification
Number classes: 6 / Software - Name: RELION (ver. 1.4)
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