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- PDB-8syg: Cryo-EM structure of tetradecameric hub domain of CaMKII alpha -

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Basic information

Entry
Database: PDB / ID: 8syg
TitleCryo-EM structure of tetradecameric hub domain of CaMKII alpha
ComponentsVenus-tagged CaMKII Alpha Association Domain
KeywordsSIGNALING PROTEIN / High-order oligomer / Protein Kinase / Signaling / Memory
Function / homology
Function and homology information


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 / regulation of neuron migration / Ca2+/calmodulin-dependent protein kinase / regulation of neurotransmitter secretion / calcium-dependent protein serine/threonine kinase activity / dendritic spine development / Trafficking of AMPA receptors / Ca2+ pathway / positive regulation of calcium ion transport / presynaptic cytosol / negative regulation of hydrolase activity / postsynaptic neurotransmitter receptor diffusion trapping / postsynaptic specialization membrane / GTPase activating protein binding / RAF/MAP kinase cascade / dendrite morphogenesis / NMDA selective glutamate receptor signaling pathway / regulation of mitochondrial membrane permeability involved in apoptotic process / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / postsynaptic cytosol / calmodulin-dependent protein kinase activity / Ion homeostasis / positive regulation of cardiac muscle cell apoptotic process / regulation of neuronal synaptic plasticity / Unblocking of NMDA receptors, glutamate binding and activation / cellular response to interferon-beta / regulation of protein localization to plasma membrane / glutamate receptor binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / bioluminescence / generation of precursor metabolites and energy / response to ischemia / angiotensin-activated signaling pathway / positive regulation of receptor signaling pathway via JAK-STAT / Schaffer collateral - CA1 synapse / cellular response to type II interferon / G1/S transition of mitotic cell cycle / calcium ion transport / kinase activity / dendritic spine / postsynaptic density / calmodulin binding / neuron projection / axon / protein phosphorylation / 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 / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic 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
Calcium/calmodulin-dependent protein kinase type II subunit alpha / Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Rattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsChien, C.-T. / Chiu, W. / Khan, S.
Funding support United States, 1items
OrganizationGrant numberCountry
Other governmentU24 GM129541 United States
CitationJournal: To Be Published
Title: Hub stability in the calcium calmodulin dependent protein kinase II
Authors: Chien, C.-T. / Puhl, H. / Vogel, S.S. / Molloy, J. / Chiu, W. / Khan, S.
History
DepositionMay 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Venus-tagged CaMKII Alpha Association Domain
A: Venus-tagged CaMKII Alpha Association Domain
C: Venus-tagged CaMKII Alpha Association Domain
D: Venus-tagged CaMKII Alpha Association Domain
E: Venus-tagged CaMKII Alpha Association Domain
F: Venus-tagged CaMKII Alpha Association Domain
G: Venus-tagged CaMKII Alpha Association Domain
H: Venus-tagged CaMKII Alpha Association Domain
I: Venus-tagged CaMKII Alpha Association Domain
J: Venus-tagged CaMKII Alpha Association Domain
K: Venus-tagged CaMKII Alpha Association Domain
L: Venus-tagged CaMKII Alpha Association Domain
M: Venus-tagged CaMKII Alpha Association Domain
N: Venus-tagged CaMKII Alpha Association Domain


Theoretical massNumber of molelcules
Total (without water)642,28614
Polymers642,28614
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, 2-stack ring with mirror symmetry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Venus-tagged CaMKII Alpha Association Domain


Mass: 45877.539 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Rattus norvegicus (Norway rat)
Gene: Camk2a / Production host: Escherichia coli (E. coli)
References: UniProt: P42212, UniProt: P11275, Ca2+/calmodulin-dependent protein kinase

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Venus-tagged CaMKII Alpha Association Domain / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 20 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 205902 / Symmetry type: POINT

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