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- PDB-7uir: Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7uir | |||||||||
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Title | Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and Tiam1 in complex with ATP | |||||||||
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![]() | TRANSFERASE / CaMKII / Kinase / Human / CAMK2A | |||||||||
Function / homology | ![]() positive regulation of Schwann cell chemotaxis / brain-derived neurotrophic factor receptor signaling pathway / regulation of non-canonical Wnt signaling pathway / RAC3 GTPase cycle / RAC2 GTPase cycle / regulation of dopaminergic neuron differentiation / CDC42 GTPase cycle / EPH-ephrin mediated repulsion of cells / EPHB-mediated forward signaling / peptidyl-threonine autophosphorylation ...positive regulation of Schwann cell chemotaxis / brain-derived neurotrophic factor receptor signaling pathway / regulation of non-canonical Wnt signaling pathway / RAC3 GTPase cycle / RAC2 GTPase cycle / regulation of dopaminergic neuron differentiation / CDC42 GTPase cycle / EPH-ephrin mediated repulsion of cells / EPHB-mediated forward signaling / peptidyl-threonine autophosphorylation / NRAGE signals death through JNK / extrinsic component of postsynaptic density membrane / regulation of endocannabinoid signaling pathway / kinocilium / RAC1 GTPase cycle / RHOA GTPase cycle / calcium- and calmodulin-dependent protein kinase complex / G alpha (12/13) signalling events / regulation of neuron migration / Ca2+/calmodulin-dependent protein kinase / regulation of neurotransmitter secretion / positive regulation of dendritic spine morphogenesis / dendritic spine development / regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of modification of postsynaptic actin cytoskeleton / cell-cell contact zone / Trafficking of AMPA receptors / positive regulation of calcium ion transport / protein localization to membrane / negative regulation of hydrolase activity / cardiac muscle hypertrophy / Assembly and cell surface presentation of NMDA receptors / activation of GTPase activity / NMDA selective glutamate receptor signaling pathway / regulation of mitochondrial membrane permeability involved in apoptotic process / regulation of postsynapse organization / calmodulin-dependent protein kinase activity / neuron projection extension / CaMK IV-mediated phosphorylation of CREB / main axon / positive regulation of axonogenesis / small GTPase-mediated signal transduction / regulation of GTPase activity / pericentriolar material / positive regulation of cardiac muscle cell apoptotic process / Rac protein signal transduction / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / regulation of neuronal synaptic plasticity / Ion transport by P-type ATPases / Long-term potentiation / Regulation of MECP2 expression and activity / HSF1-dependent transactivation / ephrin receptor signaling pathway / cellular response to interferon-beta / glutamate receptor binding / axonal growth cone / Ion homeostasis / somatodendritic compartment / Ras activation upon Ca2+ influx through NMDA receptor / ephrin receptor binding / regulation of ERK1 and ERK2 cascade / guanyl-nucleotide exchange factor activity / cell-matrix adhesion / response to ischemia / angiotensin-activated signaling pathway / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT / receptor tyrosine kinase binding / phospholipid binding / ruffle membrane / positive regulation of neuron projection development / cellular response to type II interferon / G1/S transition of mitotic cell cycle / 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 / endocytic vesicle membrane / Interferon gamma signaling / Signaling by BRAF and RAF1 fusions / cell-cell junction / cell migration / Ca2+ pathway / kinase activity / positive regulation of NF-kappaB transcription factor activity / RAF/MAP kinase cascade / microtubule binding / peptidyl-serine phosphorylation / protein autophosphorylation / dendritic spine / postsynaptic density / calmodulin binding / positive regulation of cell migration / neuron projection / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ozden, C. / Stratton, M.M. / Garman, S.C. | |||||||||
Funding support | 1items
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![]() | ![]() 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 | ![]() | 129.3 KB | Display | ![]() |
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PDB format | ![]() | 96.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 21.7 KB | Display | |
Data in CIF | ![]() | 29 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6x5gC ![]() 6x5qC ![]() 7kl0C ![]() 7kl1C ![]() 7uiqC ![]() 7uisC ![]() 7ujpC ![]() 7ujqC ![]() 7ujrC ![]() 7ujsC ![]() 7ujtC ![]() 6vzkS C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
NCS oper:
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Components
#1: Protein | Mass: 30548.086 Da / Num. of mol.: 2 / Mutation: D135N, Q223K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9UQM7, Ca2+/calmodulin-dependent protein kinase #2: Protein/peptide | Mass: 2160.521 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #3: Chemical | ChemComp-EPE / | #4: Chemical | #5: Chemical | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.58 Å3/Da / Density % sol: 65.61 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES, 16% PEG 6000, 0.1% v/v Triton X-114 |
-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: Apr 23, 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: 3.1→50 Å / Num. obs: 16953 / % possible obs: 98 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.287 / Rpim(I) all: 0.131 / Rrim(I) all: 0.317 / Χ2: 3.446 / Net I/σ(I): 3.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 3.1→33.31 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.839 / SU B: 22.977 / SU ML: 0.376 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.456 / 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: 122.41 Å2 / Biso mean: 41.56 Å2 / Biso min: 14.05 Å2
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Refinement step | Cycle: final / Resolution: 3.1→33.31 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 3.103→3.183 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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