+Open data
-Basic information
Entry | Database: PDB / ID: 6vzk | ||||||
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Title | Crystal structure of human CaMKII-alpha (CAMK2A)kinase domain | ||||||
Components | Calcium/calmodulin-dependent protein kinase type II subunit alpha | ||||||
Keywords | TRANSFERASE / CaMKII / Kinase / Human / CAMK2A | ||||||
Function / homology | Function and homology information peptidyl-threonine autophosphorylation / regulation of endocannabinoid signaling pathway / calcium- and calmodulin-dependent protein kinase complex / regulation of neuron migration / Ca2+/calmodulin-dependent protein kinase / regulation of neurotransmitter secretion / dendritic spine development / positive regulation of calcium ion transport / Trafficking of AMPA receptors / Assembly and cell surface presentation of NMDA receptors ...peptidyl-threonine autophosphorylation / regulation of endocannabinoid signaling pathway / calcium- and calmodulin-dependent protein kinase complex / regulation of neuron migration / Ca2+/calmodulin-dependent protein kinase / regulation of neurotransmitter secretion / dendritic spine development / positive regulation of calcium ion transport / Trafficking of AMPA receptors / Assembly and cell surface presentation of NMDA receptors / negative regulation of hydrolase activity / calmodulin-dependent protein kinase activity / regulation of mitochondrial membrane permeability involved in apoptotic process / CaMK IV-mediated phosphorylation of CREB / regulation of neuronal synaptic plasticity / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of cardiac muscle cell apoptotic process / Phase 0 - rapid depolarisation / Long-term potentiation / Ion transport by P-type ATPases / Regulation of MECP2 expression and activity / HSF1-dependent transactivation / glutamate receptor binding / cellular response to interferon-beta / Ion homeostasis / Ras activation upon Ca2+ influx through NMDA receptor / response to ischemia / angiotensin-activated signaling pathway / G1/S transition of mitotic cell cycle / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT / cellular response to type II interferon / endocytic vesicle membrane / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / calcium ion transport / Interferon gamma signaling / Signaling by BRAF and RAF1 fusions / Ca2+ pathway / positive regulation of NF-kappaB transcription factor activity / kinase activity / RAF/MAP kinase cascade / peptidyl-serine phosphorylation / dendritic spine / protein autophosphorylation / postsynaptic density / calmodulin binding / neuron projection / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein homodimerization activity / mitochondrion / nucleoplasm / ATP binding / metal ion binding / nucleus / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å | ||||||
Authors | Ozden, C. / Stratton, M.M. / Garman, S.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Protein Sci. / Year: 2020 Title: Characterization of CaMKII alpha holoenzyme stability. Authors: Torres-Ocampo, A.P. / Ozden, C. / Hommer, A. / Gardella, A. / Lapinskas, E. / Samkutty, A. / Esposito, E. / Garman, S.C. / Stratton, M.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vzk.cif.gz | 67.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vzk.ent.gz | 47.1 KB | Display | PDB format |
PDBx/mmJSON format | 6vzk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vz/6vzk ftp://data.pdbj.org/pub/pdb/validation_reports/vz/6vzk | HTTPS FTP |
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-Related structure data
Related structure data | 3soaS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30548.086 Da / Num. of mol.: 1 / Mutation: D135N, Q223K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CAMK2A, CAMKA, KIAA0968 / Production host: Escherichia coli BL21 (bacteria) References: UniProt: Q9UQM7, Ca2+/calmodulin-dependent protein kinase |
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#2: Chemical | ChemComp-HC4 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.77 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 6000, 50 mM HEPES, 3-Aminobenzene-sulfonic acid, 5-Sulfosalicylic acid dihydrate, p-Coumaric acid, PIPES, Terephthalic acid, Vanillic acid |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: 100 K thorughout the collection / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Mar 9, 2019 / Details: Rigaku VariMax HF | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.55→50 Å / Num. obs: 8711 / % possible obs: 99.9 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.093 / Rrim(I) all: 0.215 / Χ2: 0.916 / Net I/σ(I): 3.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3SOA Resolution: 2.55→43.2 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.868 / SU B: 14.04 / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.348 / ESU R Free: 0.375 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 103 Å2 / Biso mean: 34.924 Å2 / Biso min: 16.51 Å2
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Refinement step | Cycle: final / Resolution: 2.55→43.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.552→2.618 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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