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- PDB-5u6y: Pseudo-atomic model of the CaMKIIa holoenzyme. -

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Basic information

Entry
Database: PDB / ID: 5u6y
TitlePseudo-atomic model of the CaMKIIa holoenzyme.
ComponentsCalcium/calmodulin-dependent protein kinase type II subunit alpha
KeywordsTRANSFERASE / Calcium/calmodulin-dependent kinase II (CaMKII) / cell signaling / calcium / calmodulin (CaM) / long-term potentiation (LTP) / long-term depression (LTD) / synaptic plasticity / cooperativity / electron microscopy (EM) / single particle reconstruction / intrinsic disorder
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 / dendritic spine development / calcium-dependent protein serine/threonine kinase activity / Trafficking of AMPA receptors / positive regulation of calcium ion transport / Ca2+ pathway / presynaptic cytosol / negative regulation of hydrolase activity / postsynaptic neurotransmitter receptor diffusion trapping / postsynaptic specialization membrane / GTPase activating protein binding / RAF/MAP kinase cascade / NMDA selective glutamate receptor signaling pathway / dendrite morphogenesis / regulation of mitochondrial membrane permeability involved in apoptotic process / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / calcium/calmodulin-dependent protein kinase activity / postsynaptic cytosol / 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 / 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 / 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. ...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. / 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
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / negative staining / Resolution: 20 Å
AuthorsMyers, J. / Reichow, S.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS081248 United States
CitationJournal: 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
DepositionDec 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Data collection / Category: em_image_scans / pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 8, 2017Group: Derived calculations / Category: pdbx_struct_assembly
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.name
Revision 1.4Dec 18, 2019Group: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_validate_close_contact / struct_conn
Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Assembly

Deposited unit
A: Calcium/calmodulin-dependent protein kinase type II subunit alpha
B: Calcium/calmodulin-dependent protein kinase type II subunit alpha
C: Calcium/calmodulin-dependent protein kinase type II subunit alpha
D: Calcium/calmodulin-dependent protein kinase type II subunit alpha
E: Calcium/calmodulin-dependent protein kinase type II subunit alpha
F: Calcium/calmodulin-dependent protein kinase type II subunit alpha
G: Calcium/calmodulin-dependent protein kinase type II subunit alpha
H: Calcium/calmodulin-dependent protein kinase type II subunit alpha
I: Calcium/calmodulin-dependent protein kinase type II subunit alpha
J: Calcium/calmodulin-dependent protein kinase type II subunit alpha
K: Calcium/calmodulin-dependent protein kinase type II subunit alpha
L: Calcium/calmodulin-dependent protein kinase type II subunit alpha


Theoretical massNumber of molelcules
Total (without water)627,37812
Polymers627,37812
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area28350 Å2
ΔGint-220 kcal/mol
Surface area287170 Å2

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Components

#1: Protein
Calcium/calmodulin-dependent protein kinase type II subunit alpha / CaMK-II subunit alpha


Mass: 52281.535 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Camk2a / Plasmid: pFastBac1 / Production host: Spodoptera frugiperda (fall armyworm)
References: 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: Calcium-calmodulin dependent kinase II alpha / Type: COMPLEX / Details: Full-length CaMKII alpha wild type / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.62 MDa / Experimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Plasmid: pFastBac1
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPES1
2120 mMKCl1
30.5 mMEGTA1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO / Details: 100 nM complex
EM stainingType: NEGATIVE / Details: 0.75% (wt/vol) uranyl formate / Material: Uranyl Formate
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Ted Pella

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Electron microscopy imaging

MicroscopyModel: FEI TECNAI 12
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 49000 X
Image recordingAverage exposure time: 1 sec. / Electron dose: 20 e/Å2 / Film or detector model: FEI EAGLE (2k x 2k)

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Processing

EM software
IDNameVersionCategoryDetails
1EMAN2.12particle selectionHand picked
4EMAN2.12CTF correction
7UCSF Chimera1.11.2model fitting
10EMAN2.12initial Euler assignment
11RELION1.4final Euler assignment
12RELION1.4classification
13RELION1.43D reconstruction
CTF correctionDetails: Performed in EMAN2 / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 16616
SymmetryPoint symmetry: D6 (2x6 fold dihedral)
3D reconstructionResolution: 20 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2000
Details: Only modeled the unstructured linker region, residues 300-345. The rest came from two other, previously published structures, namely 5IG3 and 2VZ6
Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Target criteria: Correlation Coefficient
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDAccession codeInitial refinement model-IDPdb chain residue range
151G3

51g3

51G31345-472
22VZ6

2vz6

2VZ6213-300

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