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Yorodumi- PDB-7uiq: Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7uiq | |||||||||
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Title | Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and Tiam1 | |||||||||
Components |
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Keywords | TRANSFERASE / CaMKII / Kinase / Human / CAMK2A | |||||||||
Function / homology | Function and homology information positive regulation of Schwann cell chemotaxis / brain-derived neurotrophic factor receptor signaling pathway / RAC3 GTPase cycle / regulation of non-canonical Wnt signaling pathway / RAC2 GTPase cycle / regulation of dopaminergic neuron differentiation / CDC42 GTPase cycle / EPH-ephrin mediated repulsion of cells / RHOA GTPase cycle / EPHB-mediated forward signaling ...positive regulation of Schwann cell chemotaxis / brain-derived neurotrophic factor receptor signaling pathway / RAC3 GTPase cycle / regulation of non-canonical Wnt signaling pathway / RAC2 GTPase cycle / regulation of dopaminergic neuron differentiation / CDC42 GTPase cycle / EPH-ephrin mediated repulsion of cells / RHOA GTPase cycle / EPHB-mediated forward signaling / peptidyl-threonine autophosphorylation / NRAGE signals death through JNK / regulation of endocannabinoid signaling pathway / calcium- and calmodulin-dependent protein kinase complex / extrinsic component of postsynaptic density membrane / RAC1 GTPase cycle / kinocilium / G alpha (12/13) signalling events / NMDA selective glutamate receptor signaling pathway / regulation of neuron migration / Ca2+/calmodulin-dependent protein kinase / regulation of epithelial to mesenchymal transition / 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 / positive regulation of calcium ion transport / Trafficking of AMPA receptors / negative regulation of hydrolase activity / Assembly and cell surface presentation of NMDA receptors / protein localization to membrane / cardiac muscle hypertrophy / activation of GTPase activity / calmodulin-dependent protein kinase activity / regulation of postsynapse organization / regulation of mitochondrial membrane permeability involved in apoptotic process / main axon / neuron projection extension / CaMK IV-mediated phosphorylation of CREB / regulation of neuronal synaptic plasticity / positive regulation of axonogenesis / small GTPase-mediated signal transduction / regulation of GTPase activity / Rac protein signal transduction / Negative regulation of NMDA receptor-mediated neuronal transmission / pericentriolar material / positive regulation of cardiac muscle cell apoptotic process / Unblocking of NMDA receptors, glutamate binding and activation / 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 / ephrin receptor signaling pathway / cellular response to interferon-beta / axonal growth cone / Ion homeostasis / somatodendritic compartment / Ras activation upon Ca2+ influx through NMDA receptor / ephrin receptor binding / cell-matrix adhesion / guanyl-nucleotide exchange factor activity / regulation of ERK1 and ERK2 cascade / response to ischemia / angiotensin-activated signaling pathway / phospholipid binding / G1/S transition of mitotic cell cycle / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of neuron projection development / receptor tyrosine kinase binding / ruffle membrane / kinase binding / 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 / cell-cell junction / cell migration / Signaling by BRAF and RAF1 fusions / Ca2+ pathway / positive regulation of NF-kappaB transcription factor activity / kinase activity / microtubule binding / RAF/MAP kinase cascade / protein-containing complex assembly / peptidyl-serine phosphorylation / dendritic spine / postsynaptic density / protein autophosphorylation / calmodulin binding / neuron projection / positive regulation of cell migration Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.11 Å | |||||||||
Authors | Ozden, C. / Stratton, M.M. / Garman, S.C. | |||||||||
Funding support | 1items
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Citation | Journal: Cell Rep / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uiq.cif.gz | 123.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uiq.ent.gz | 93.5 KB | Display | PDB format |
PDBx/mmJSON format | 7uiq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ui/7uiq ftp://data.pdbj.org/pub/pdb/validation_reports/ui/7uiq | HTTPS FTP |
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-Related structure data
Related structure data | 6x5gC 6x5qC 7kl0C 7kl1C 7uirC 7uisC 7ujpC 7ujqC 7ujrC 7ujsC 7ujtC 6vzkS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 1
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.) Homo sapiens (human) / Gene: CAMK2A, CAMKA, KIAA0968 / Production host: Escherichia coli BL21(DE3) (bacteria) 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.) Mus musculus (house mouse) / References: UniProt: Q60610 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.57 Å3/Da / Density % sol: 65.54 % |
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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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Apr 22, 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: 3.11→50 Å / Num. obs: 16346 / % possible obs: 93.4 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.266 / Rpim(I) all: 0.134 / Rrim(I) all: 0.3 / Χ2: 2.527 / Net I/σ(I): 3.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 6VZK Resolution: 3.11→31.54 Å / Cor.coef. Fo:Fc: 0.829 / Cor.coef. Fo:Fc free: 0.742 / SU B: 29.732 / SU ML: 0.488 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.535 / 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: 156.38 Å2 / Biso mean: 30.655 Å2 / Biso min: 6.58 Å2
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Refinement step | Cycle: final / Resolution: 3.11→31.54 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5
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LS refinement shell | Resolution: 3.115→3.196 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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