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- PDB-6x5q: Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain a... -
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Basic information
Entry | Database: PDB / ID: 6x5q | ||||||
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Title | Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and GluA1 | ||||||
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![]() | TRANSFERASE / CaMKII / Kinase / Human / CAMK2A | ||||||
Function / homology | ![]() Activation of AMPA receptors / peptidyl-threonine autophosphorylation / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / calcium- and calmodulin-dependent protein kinase complex / regulation of endocannabinoid signaling pathway / axonal spine / Trafficking of GluR2-containing AMPA receptors / positive regulation of membrane potential / Ca2+/calmodulin-dependent protein kinase / cellular response to ammonium ion ...Activation of AMPA receptors / peptidyl-threonine autophosphorylation / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / calcium- and calmodulin-dependent protein kinase complex / regulation of endocannabinoid signaling pathway / axonal spine / Trafficking of GluR2-containing AMPA receptors / positive regulation of membrane potential / Ca2+/calmodulin-dependent protein kinase / cellular response to ammonium ion / dendritic spine development / negative regulation of hydrolase activity / regulation of neurotransmitter secretion / neuron spine / myosin V binding / Synaptic adhesion-like molecules / Cargo concentration in the ER / Trafficking of AMPA receptors / response to arsenic-containing substance / regulation of neuron migration / positive regulation of calcium ion transport / cellular response to dsRNA / glutamate receptor activity / calcium/calmodulin-dependent protein kinase activity / dendritic spine membrane / Assembly and cell surface presentation of NMDA receptors / long-term synaptic depression / COPII-mediated vesicle transport / regulation of mitochondrial membrane permeability involved in apoptotic process / beta-2 adrenergic receptor binding / cellular response to peptide hormone stimulus / CaMK IV-mediated phosphorylation of CREB / neuronal cell body membrane / protein kinase A binding / cellular response to amine stimulus / spinal cord development / perisynaptic space / Phase 0 - rapid depolarisation / AMPA glutamate receptor activity / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / response to lithium ion / Ion transport by P-type ATPases / AMPA glutamate receptor complex / Long-term potentiation / adenylate cyclase binding / Regulation of MECP2 expression and activity / immunoglobulin binding / excitatory synapse / response to electrical stimulus / regulation of receptor recycling / regulation of neuronal synaptic plasticity / G-protein alpha-subunit binding / HSF1-dependent transactivation / glutamate receptor binding / long-term memory / postsynaptic density, intracellular component / neuronal action potential / regulation of protein localization to plasma membrane / cellular response to interferon-beta / positive regulation of cardiac muscle cell apoptotic process / response to fungicide / Ion homeostasis / synapse assembly / cellular response to brain-derived neurotrophic factor stimulus / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / endoplasmic reticulum-Golgi intermediate compartment membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / Ras activation upon Ca2+ influx through NMDA receptor / synaptic membrane / response to ischemia / dendritic shaft / angiotensin-activated signaling pathway / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / response to cocaine / synaptic transmission, glutamatergic / positive regulation of receptor signaling pathway via JAK-STAT / PDZ domain binding / cellular response to amino acid stimulus / neuromuscular junction / RAF activation / ER to Golgi transport vesicle membrane / G1/S transition of mitotic cell cycle / positive regulation of NF-kappaB transcription factor activity / postsynaptic density membrane / modulation of chemical synaptic transmission / recycling endosome / cerebral cortex development / receptor internalization / cellular response to type II interferon / small GTPase binding / long-term synaptic potentiation / endocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / 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 Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ozden, C. / Stratton, M.M. / Garman, S.C. | ||||||
![]() | ![]() Title: CaMKII binds both substrates and activators at the active site. Authors: Ozden, C. / Sloutsky, R. / Mitsugi, T. / Santos, N. / Agnello, E. / Gaubitz, C. / Foster, J. / Lapinskas, E. / Esposito, E.A. / Saneyoshi, T. / Kelch, B.A. / Garman, S.C. / Hayashi, Y. / Stratton, M.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.6 KB | Display | ![]() |
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PDB format | ![]() | 52 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437 KB | Display | ![]() |
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Full document | ![]() | 437.2 KB | Display | |
Data in XML | ![]() | 12.9 KB | Display | |
Data in CIF | ![]() | 17.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6x5gC ![]() 7kl0C ![]() 7kl1C ![]() 7uiqC ![]() 7uirC ![]() 7uisC ![]() 7ujpC ![]() 7ujqC ![]() 7ujrC ![]() 7ujsC ![]() 7ujtC ![]() 6vzkS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() References: UniProt: Q9UQM7, Ca2+/calmodulin-dependent protein kinase | ||||
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#2: Protein/peptide | Mass: 2323.780 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.69 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Tris, 28% w/v PEG 4000 |
-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: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Jan 29, 2020 / 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: 2.1→50 Å / Num. obs: 15265 / % possible obs: 96.9 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.091 / Rrim(I) all: 0.202 / Χ2: 0.746 / Net I/σ(I): 3.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6VZK Resolution: 2.14→39.32 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.892 / SU B: 5.435 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.281 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 58.49 Å2 / Biso mean: 15.884 Å2 / Biso min: 1.6 Å2
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Refinement step | Cycle: final / Resolution: 2.14→39.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.104→2.159 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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