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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-8514 | |||||||||
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Title | 3D reconstruction of the CaMKIIa holoenzyme. | |||||||||
![]() | CaMKII holoenzyme structure resolved by negative stain EM.![]() | |||||||||
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![]() | Calcium/calmodulin-dependent kinase II (CaMKII) / ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Function / homology | ![]() 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 / calcium- and calmodulin-dependent protein kinase complex / calmodulin dependent kinase signaling pathway / Interferon gamma signaling ...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 / calcium- and calmodulin-dependent protein kinase complex / calmodulin dependent kinase signaling pathway / Interferon gamma signaling / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Myers J / Reichow SL | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 7.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.8 KB 13.8 KB | Display Display | ![]() |
Images | ![]() | 30.8 KB | ||
Filedesc metadata | ![]() | 6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5u6yMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | CaMKII holoenzyme structure resolved by negative stain EM. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.37 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Calcium-calmodulin dependent kinase II alpha
Entire | Name: Calcium-calmodulin dependent kinase II alpha |
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Components |
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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 |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 620 KDa |
-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: ![]() |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 52.281535 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MYQLFEELGK GAFSVVRRCV KVLAGQEYAA KIINTKKLSA RDHQKLEREA RICRLLKHPN IVRLHDSISE EGHHYLIFDL VTGGELFED IVAREYYSEA DASHCIQQIL EAVLHCHQMG VVHRDLKPEN LLLASKLKGA AVKLADFGLA IEVEGEQQAW F GFAGTPGY ...String: MYQLFEELGK GAFSVVRRCV KVLAGQEYAA KIINTKKLSA RDHQKLEREA RICRLLKHPN IVRLHDSISE EGHHYLIFDL VTGGELFED IVAREYYSEA DASHCIQQIL EAVLHCHQMG VVHRDLKPEN LLLASKLKGA AVKLADFGLA IEVEGEQQAW F GFAGTPGY LSPEVLRKDP YGKPVDLWAC GVILYILLVG YPPFWDEDQH RLYQQIKAGA YDFPSPEWDT VTPEAKDLIN KM LTINPSK RITAAEALKH PWISHRSTVA SCMHRQETVD CLKKFNARRK LKGAILTTML ATRNFSGGKS GGNKKSDGVK ESS ESTNTT IEDEDTKVRK QEIIKVTEQL IEAISNGDFE SYTKMCDPGM TAFEPEALGN LVEGLDFHRF YFENLWSRNS KPVH TTILN PHIHLMGDES ACIAYIRITQ YLDAGGIPRT AQSEETRVWH RRDGKWQIVH FHRSGA UniProtKB: ![]() |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 Component:
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Staining | Type: NEGATIVE / Material: Uranyl Formate / Details: 0.75% (wt/vol) uranyl formate | ||||||||||||
Grid | Model: Ted Pella / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. | ||||||||||||
Details | 100 nM complex |
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Electron microscopy
Microscope | FEI TECNAI 12 |
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Electron beam | Acceleration voltage: 120 kV / Electron source: TUNGSTEN HAIRPIN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: FEI EAGLE (2k x 2k) / Average exposure time: 1.0 sec. / Average electron dose: 20.0 e/Å2 |
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Image processing
Particle selection | Number selected: 16616 |
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Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
Initial angle assignment | Type: RANDOM ASSIGNMENT / Software - Name: EMAN (ver. 2.12) |
Final 3D classification | Number classes: 6 / Software - Name: RELION (ver. 1.4) |
Final angle assignment | Type: OTHER / Software - Name: RELION (ver. 1.4) |
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: D6 (2x6 fold dihedral![]() 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 |
-Atomic model buiding 1
Initial model |
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Refinement | Protocol: RIGID BODY FIT / Target criteria: Correlation Coefficient | ||||||
Output model | ![]() PDB-5u6y: |