+Open data
-Basic information
Entry | Database: PDB / ID: 7b56 | ||||||
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Title | Crystal structure of CaMKII-actinin complex bound to AMPPNP | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / CaMKII / actinin / dendritic spine | ||||||
Function / homology | Function and homology information regulation of synaptic vesicle docking / actin filament uncapping / FATZ binding / titin Z domain binding / HSF1-dependent transactivation / glutamatergic postsynaptic density / Interferon gamma signaling / Ion transport by P-type ATPases / phospholipase C-activating angiotensin-activated signaling pathway / positive regulation of endocytic recycling ...regulation of synaptic vesicle docking / actin filament uncapping / FATZ binding / titin Z domain binding / HSF1-dependent transactivation / glutamatergic postsynaptic density / Interferon gamma signaling / Ion transport by P-type ATPases / phospholipase C-activating angiotensin-activated signaling pathway / positive regulation of endocytic recycling / Unblocking of NMDA receptors, glutamate binding and activation / peptidyl-threonine autophosphorylation / positive regulation of potassium ion transmembrane transporter activity / RAF activation / negative regulation of potassium ion transmembrane transporter activity / regulation of endocannabinoid signaling pathway / neurotransmitter receptor transport to plasma membrane / : / calcium- and calmodulin-dependent protein kinase complex / Trafficking of AMPA receptors / Ca2+ pathway / RAF/MAP kinase cascade / positive regulation of cation channel activity / Ca2+/calmodulin-dependent protein kinase / negative regulation of protein localization to cell surface / LIM domain binding / regulation of neurotransmitter secretion / postsynaptic actin cytoskeleton / microspike assembly / regulation of neuron migration / dendritic spine development / calcium-dependent protein serine/threonine kinase activity / positive regulation of potassium ion transport / Ion homeostasis / muscle cell development / positive regulation of calcium ion transport / focal adhesion assembly / negative regulation of hydrolase activity / postsynaptic neurotransmitter receptor diffusion trapping / Striated Muscle Contraction / presynaptic cytosol / Assembly and cell surface presentation of NMDA receptors / GTPase activating protein binding / cardiac muscle cell development / Nephrin family interactions / dendrite morphogenesis / postsynaptic specialization membrane / NMDA selective glutamate receptor signaling pathway / regulation of mitochondrial membrane permeability involved in apoptotic process / calcium/calmodulin-dependent protein kinase activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / structural constituent of muscle / postsynaptic cytosol / sarcomere organization / cortical actin cytoskeleton / positive regulation of cardiac muscle cell apoptotic process / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / pseudopodium / regulation of neuronal synaptic plasticity / negative regulation of potassium ion transport / Long-term potentiation / cellular response to interferon-beta / regulation of protein localization to plasma membrane / postsynaptic density, intracellular component / glutamate receptor binding / titin binding / phosphatidylinositol-4,5-bisphosphate binding / cytoskeletal protein binding / Ras activation upon Ca2+ influx through NMDA receptor / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / regulation of membrane potential / platelet alpha granule lumen / nuclear receptor coactivator activity / filopodium / protein localization to plasma membrane / response to ischemia / cell projection / actin filament / positive regulation of receptor signaling pathway via JAK-STAT / postsynaptic density membrane / Schaffer collateral - CA1 synapse / G1/S transition of mitotic cell cycle / Z disc / actin filament binding / integrin binding / cell junction / calcium ion transport / Platelet degranulation / peptidyl-serine phosphorylation / RAF/MAP kinase cascade / actin cytoskeleton organization / regulation of apoptotic process / transmembrane transporter binding / dendritic spine / calmodulin binding / postsynaptic density / cytoskeleton / cell adhesion Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Zhu, J. / Gold, M. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of CaMKII-actinin complex bound to MES 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 | 7b56.cif.gz | 216.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b56.ent.gz | 140.9 KB | Display | PDB format |
PDBx/mmJSON format | 7b56.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7b56_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7b56_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7b56_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 7b56_validation.cif.gz | 31.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/7b56 ftp://data.pdbj.org/pub/pdb/validation_reports/b5/7b56 | HTTPS FTP |
-Related structure data
Related structure data | 7b55C 2vz6S S: Starting model for refinement C: citing same article (ref.) |
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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, 444 molecules
#3: Chemical | ChemComp-ANP / |
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#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-MES / |
#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: 2.45 Å3/Da / Density % sol: 49.85 % |
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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: 1.45→92 Å / Num. obs: 77065 / % possible obs: 100 % / Redundancy: 12.1 % / Biso Wilson estimate: 22.55 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.016 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.45→1.47 Å / Num. unique obs: 3786 / CC1/2: 0.825 / Rpim(I) all: 0.522 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VZ6 Resolution: 1.45→52.77 Å / SU ML: 0.1456 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.2221 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: 30.22 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→52.77 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: 15.1121581365 Å / Origin y: -5.04463431322 Å / Origin z: -2.5044161769 Å
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Refinement TLS group | Selection details: all |