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- PDB-8t6k: Cryo-EM structure of tetradecameric CaMKII beta holoenzyme T287A ... -

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Basic information

Entry
Database: PDB / ID: 8t6k
TitleCryo-EM structure of tetradecameric CaMKII beta holoenzyme T287A T306A T307A
ComponentsVenus-tagged CaMKII Beta Holoenzyme mutant
KeywordsSIGNALING PROTEIN / High-order oligomer / Protein Kinase / Signaling / Memory
Function / homology
Function and homology information


regulation of synaptic transmission, cholinergic / activation of meiosis involved in egg activation / cell projection morphogenesis / HSF1-dependent transactivation / RAF activation / Ion transport by P-type ATPases / hippocampal neuron apoptotic process / calcium- and calmodulin-dependent protein kinase complex / cellular response to homocysteine / Interferon gamma signaling ...regulation of synaptic transmission, cholinergic / activation of meiosis involved in egg activation / cell projection morphogenesis / HSF1-dependent transactivation / RAF activation / Ion transport by P-type ATPases / hippocampal neuron apoptotic process / calcium- and calmodulin-dependent protein kinase complex / cellular response to homocysteine / Interferon gamma signaling / positive regulation of synapse maturation / regulation of neuron migration / Ca2+/calmodulin-dependent protein kinase / structural constituent of postsynaptic actin cytoskeleton / regulation of synapse maturation / positive regulation of dendritic spine morphogenesis / calcium-dependent protein serine/threonine kinase activity / Trafficking of AMPA receptors / RAF/MAP kinase cascade / calmodulin-dependent protein kinase activity / response to psychosocial stress / Ion homeostasis / phospholipase binding / neuromuscular process controlling balance / Unblocking of NMDA receptors, glutamate binding and activation / regulation of protein localization to plasma membrane / spindle midzone / response to cadmium ion / sarcoplasmic reticulum membrane / bioluminescence / generation of precursor metabolites and energy / long-term synaptic potentiation / positive regulation of apoptotic signaling pathway / apoptotic signaling pathway / regulation of long-term neuronal synaptic plasticity / positive regulation of neuron projection development / G1/S transition of mitotic cell cycle / calcium ion transport / nervous system development / perikaryon / peptidyl-serine phosphorylation / protein autophosphorylation / postsynaptic density / cell differentiation / calmodulin binding / neuron projection / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / glutamatergic synapse / dendrite / protein kinase binding / protein homodimerization activity / ATP binding / identical protein 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 beta / Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Rattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 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
DepositionJun 16, 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

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Assembly

Deposited unit
A: Venus-tagged CaMKII Beta Holoenzyme mutant
B: Venus-tagged CaMKII Beta Holoenzyme mutant
C: Venus-tagged CaMKII Beta Holoenzyme mutant
D: Venus-tagged CaMKII Beta Holoenzyme mutant
E: Venus-tagged CaMKII Beta Holoenzyme mutant
F: Venus-tagged CaMKII Beta Holoenzyme mutant
G: Venus-tagged CaMKII Beta Holoenzyme mutant
H: Venus-tagged CaMKII Beta Holoenzyme mutant
I: Venus-tagged CaMKII Beta Holoenzyme mutant
J: Venus-tagged CaMKII Beta Holoenzyme mutant
K: Venus-tagged CaMKII Beta Holoenzyme mutant
L: Venus-tagged CaMKII Beta Holoenzyme mutant
M: Venus-tagged CaMKII Beta Holoenzyme mutant
N: Venus-tagged CaMKII Beta Holoenzyme mutant


Theoretical massNumber of molelcules
Total (without water)1,271,85614
Polymers1,271,85614
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Venus-tagged CaMKII Beta Holoenzyme mutant


Mass: 90846.859 Da / Num. of mol.: 14 / Mutation: T287A T306A T307A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Rattus norvegicus (Norway rat)
Gene: GFP, Camk2b / Production host: Escherichia coli (E. coli) / References: UniProt: P42212, UniProt: P08413

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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 Beta Holoenzyme T287A T306A T307A / 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: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D7 (2x7 fold dihedral)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 138904 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 40.27 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005215498
ELECTRON MICROSCOPYf_angle_d0.686621042
ELECTRON MICROSCOPYf_chiral_restr0.04852240
ELECTRON MICROSCOPYf_plane_restr0.00532800
ELECTRON MICROSCOPYf_dihedral_angle_d20.98829240

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