+Open data
-Basic information
Entry | Database: PDB / ID: 7b57 | ||||||
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Title | Crystal structure of CaMKII-actinin complex bound to ADP | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / CaMKII / actinin / dendritic spine | ||||||
Function / homology | Function and homology information regulation of synaptic vesicle docking / glutamatergic postsynaptic density / actin filament uncapping / FATZ binding / titin Z domain binding / HSF1-dependent transactivation / Interferon gamma signaling / phospholipase C-activating angiotensin-activated signaling pathway / Ion transport by P-type ATPases / positive regulation of endocytic recycling ...regulation of synaptic vesicle docking / glutamatergic postsynaptic density / actin filament uncapping / FATZ binding / titin Z domain binding / HSF1-dependent transactivation / Interferon gamma signaling / phospholipase C-activating angiotensin-activated signaling pathway / Ion transport by P-type ATPases / positive regulation of endocytic recycling / Unblocking of NMDA receptors, glutamate binding and activation / peptidyl-threonine autophosphorylation / positive regulation of potassium ion transmembrane transporter activity / regulation of endocannabinoid signaling pathway / negative regulation of potassium ion transmembrane transporter activity / Trafficking of AMPA receptors / calcium- and calmodulin-dependent protein kinase complex / RAF activation / calmodulin dependent kinase signaling pathway / Ca2+ pathway / RAF/MAP kinase cascade / calcium-dependent protein serine/threonine kinase activity / NMDA selective glutamate receptor signaling pathway / regulation of neuron migration / Ca2+/calmodulin-dependent protein kinase / positive regulation of cation channel activity / LIM domain binding / negative regulation of protein localization to cell surface / regulation of neurotransmitter secretion / microspike assembly / postsynaptic actin cytoskeleton / dendritic spine development / muscle cell development / positive regulation of potassium ion transport / Ion homeostasis / positive regulation of calcium ion transport / postsynaptic neurotransmitter receptor diffusion trapping / postsynaptic specialization membrane / presynaptic cytosol / focal adhesion assembly / Striated Muscle Contraction / negative regulation of hydrolase activity / Assembly and cell surface presentation of NMDA receptors / calmodulin-dependent protein kinase activity / cardiac muscle cell development / Nephrin family interactions / GTPase activating protein binding / dendrite morphogenesis / regulation of mitochondrial membrane permeability involved in apoptotic process / structural constituent of muscle / sarcomere organization / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / postsynaptic cytosol / regulation of neuronal synaptic plasticity / cortical actin cytoskeleton / Negative regulation of NMDA receptor-mediated neuronal transmission / positive regulation of cardiac muscle cell apoptotic process / Unblocking of NMDA receptors, glutamate binding and activation / pseudopodium / postsynaptic density, intracellular component / negative regulation of potassium ion transport / Long-term potentiation / glutamate receptor binding / cellular response to interferon-beta / regulation of protein localization to plasma membrane / titin binding / phosphatidylinositol-4,5-bisphosphate binding / cytoskeletal protein binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / Ras activation upon Ca2+ influx through NMDA receptor / regulation of membrane potential / nuclear receptor coactivator activity / platelet alpha granule lumen / filopodium / cell projection / actin filament / response to ischemia / protein localization to plasma membrane / angiotensin-activated signaling pathway / postsynaptic density membrane / G1/S transition of mitotic cell cycle / positive regulation of receptor signaling pathway via JAK-STAT / Schaffer collateral - CA1 synapse / Z disc / cellular response to type II interferon / calcium ion transport / actin filament binding / integrin binding / Platelet degranulation / cell junction / kinase activity / actin cytoskeleton organization / RAF/MAP kinase cascade / peptidyl-serine phosphorylation / regulation of apoptotic process / transmembrane transporter binding / dendritic spine / postsynaptic density / cytoskeleton Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Zhu, J. / Gold, M. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of CaMKII-actinin complex bound to ADP Authors: Zhu, J. / Gold, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7b57.cif.gz | 200.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b57.ent.gz | 129.5 KB | Display | PDB format |
PDBx/mmJSON format | 7b57.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/7b57 ftp://data.pdbj.org/pub/pdb/validation_reports/b5/7b57 | HTTPS FTP |
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-Related structure data
Related structure data | 2vz6S 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
-Protein , 2 types, 2 molecules BA
#1: Protein | Mass: 35903.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Camk2a / Production host: Escherichia coli (E. coli) References: UniProt: P11798, Ca2+/calmodulin-dependent protein kinase |
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#2: Protein | Mass: 7903.778 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACTN2 / Production host: Escherichia coli (E. coli) / References: UniProt: P35609 |
-Non-polymers , 4 types, 305 molecules
#3: Chemical | ChemComp-MG / |
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#4: Chemical | ChemComp-MES / |
#5: Chemical | ChemComp-ADP / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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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: 2.48 Å3/Da / Density % sol: 50.32 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.1 M MES pH 6.0, 20% w/v PEG4000, 0.2 M Lithium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9119 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 1, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9119 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→56.53 Å / Num. obs: 32429 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 35.29 Å2 / CC1/2: 0.967 / Rpim(I) all: 0.059 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.95→2 Å / Num. unique obs: 32429 / CC1/2: 0.487 / Rpim(I) all: 0.96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VZ6 Resolution: 1.95→56.53 Å / SU ML: 0.2495 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.4573 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→56.53 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 15.652585022 Å / Origin y: -5.02192391369 Å / Origin z: -2.79543889655 Å
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Refinement TLS group | Selection details: all |