+Open data
-Basic information
Entry | Database: PDB / ID: 7ury | ||||||
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Title | Tetradecameric hub domain of CaMKII beta | ||||||
Components | Calcium/calmodulin-dependent protein kinase type II subunit beta | ||||||
Keywords | TRANSFERASE / CaMKII / Kinase / Human / CAMK2B | ||||||
Function / homology | Function and homology information regulation of skeletal muscle adaptation / regulation of synapse structural plasticity / calcium- and calmodulin-dependent protein kinase complex / calcium-dependent protein serine/threonine kinase activity / regulation of dendritic spine development / positive regulation of synapse maturation / regulation of neuron migration / Ca2+/calmodulin-dependent protein kinase / positive regulation of dendritic spine morphogenesis / Trafficking of AMPA receptors ...regulation of skeletal muscle adaptation / regulation of synapse structural plasticity / calcium- and calmodulin-dependent protein kinase complex / calcium-dependent protein serine/threonine kinase activity / regulation of dendritic spine development / positive regulation of synapse maturation / regulation of neuron migration / Ca2+/calmodulin-dependent protein kinase / positive regulation of dendritic spine morphogenesis / Trafficking of AMPA receptors / Assembly and cell surface presentation of NMDA receptors / calmodulin-dependent protein kinase activity / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / CaMK IV-mediated phosphorylation of CREB / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / regulation of calcium ion transport / Long-term potentiation / Ion transport by P-type ATPases / Regulation of MECP2 expression and activity / HSF1-dependent transactivation / Ion homeostasis / sarcoplasmic reticulum membrane / Ras activation upon Ca2+ influx through NMDA receptor / regulation of long-term neuronal synaptic plasticity / RAF activation / positive regulation of neuron projection development / 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 / Interferon gamma signaling / Signaling by BRAF and RAF1 fusions / nervous system development / actin binding / RAF/MAP kinase cascade / peptidyl-serine phosphorylation / protein autophosphorylation / cell differentiation / calmodulin binding / neuron projection / protein phosphorylation / protein serine kinase activity / centrosome / synapse / signal transduction / protein homodimerization activity / nucleoplasm / ATP binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.64 Å | ||||||
Authors | Ozden, C. / Saha, S. / Samkutty, A. / Stratton, M.M. / Garman, S.C. / Perry, S.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Lab Chip / Year: 2023 Title: Polymer-based microfluidic device for on-chip counter-diffusive crystallization and in situ X-ray crystallography at room temperature. Authors: Saha, S. / Ozden, C. / Samkutty, A. / Russi, S. / Cohen, A. / Stratton, M.M. / Perry, S.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ury.cif.gz | 186.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ury.ent.gz | 147.7 KB | Display | PDB format |
PDBx/mmJSON format | 7ury.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ur/7ury ftp://data.pdbj.org/pub/pdb/validation_reports/ur/7ury | HTTPS FTP |
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-Related structure data
Related structure data | 7urwS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15588.548 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CAMK2B, CAM2, CAMK2, CAMKB / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q13554, Ca2+/calmodulin-dependent protein kinase #2: Chemical | ChemComp-MLT / Has ligand of interest | N | |
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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: 2.45 Å3/Da / Density % sol: 49.72 % |
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Crystal grow | Temperature: 293 K / Method: microfluidic / pH: 7 Details: 0.1 M imidazole pH 7, 0.15 M DL-Malic acid, 22% PEG methyl ether 550 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 26, 2021 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.64→50 Å / Num. obs: 28300 / % possible obs: 88.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.04 / Rrim(I) all: 0.083 / Χ2: 0.46 / Net I/σ(I): 4.4 / Num. measured all: 102591 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 7URW Resolution: 2.64→38.23 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.931 / SU B: 11.72 / SU ML: 0.241 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.338 / 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: 141.47 Å2 / Biso mean: 52.555 Å2 / Biso min: 26.9 Å2
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Refinement step | Cycle: final / Resolution: 2.64→38.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.64→2.707 Å / Rfactor Rfree error: 0
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