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- PDB-4f0z: Crystal Structure of Calcineurin in Complex with the Calcineurin-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4f0z | ||||||
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Title | Crystal Structure of Calcineurin in Complex with the Calcineurin-Inhibiting Domain of the African Swine Fever Virus Protein A238L | ||||||
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![]() | hydrolase/protein binding / EF-hand / phosphatase / PxIxIT / LxVP / calcium signaling / transcription regulation / T-cell activation / Calcineurin inhibition / calmodulin / RCAN / NFAT / heart / nucleus / skeletal muscle / ion channels / hydrolase-protein binding complex | ||||||
Function / homology | ![]() : / : / negative regulation of angiotensin-activated signaling pathway / regulation of cell proliferation involved in kidney morphogenesis / calcium-dependent protein serine/threonine phosphatase regulator activity / positive regulation of glomerulus development / negative regulation of calcium ion import across plasma membrane / calcium-dependent protein serine/threonine phosphatase activity / negative regulation of signaling / protein serine/threonine phosphatase complex ...: / : / negative regulation of angiotensin-activated signaling pathway / regulation of cell proliferation involved in kidney morphogenesis / calcium-dependent protein serine/threonine phosphatase regulator activity / positive regulation of glomerulus development / negative regulation of calcium ion import across plasma membrane / calcium-dependent protein serine/threonine phosphatase activity / negative regulation of signaling / protein serine/threonine phosphatase complex / positive regulation of saliva secretion / positive regulation of cardiac muscle hypertrophy in response to stress / positive regulation of calcium ion import across plasma membrane / calmodulin-dependent protein phosphatase activity / calcineurin complex / positive regulation of connective tissue replacement / negative regulation of dendrite morphogenesis / calcineurin-mediated signaling / slit diaphragm / : / peptidyl-serine dephosphorylation / lung epithelial cell differentiation / calcineurin-NFAT signaling cascade / renal filtration / skeletal muscle tissue regeneration / regulation of synaptic vesicle cycle / transition between fast and slow fiber / positive regulation of calcineurin-NFAT signaling cascade / myelination in peripheral nervous system / cardiac muscle hypertrophy in response to stress / positive regulation of osteoclast differentiation / regulation of postsynaptic neurotransmitter receptor internalization / parallel fiber to Purkinje cell synapse / dendrite morphogenesis / cyclosporin A binding / myosin phosphatase activity / CLEC7A (Dectin-1) induces NFAT activation / branching involved in blood vessel morphogenesis / postsynaptic modulation of chemical synaptic transmission / extrinsic component of plasma membrane / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / positive regulation of activated T cell proliferation / positive regulation of endocytosis / Calcineurin activates NFAT / positive regulation of cell adhesion / DARPP-32 events / Activation of BAD and translocation to mitochondria / epidermis development / epithelial to mesenchymal transition / phosphatase binding / negative regulation of insulin secretion / multicellular organismal response to stress / positive regulation of osteoblast differentiation / skeletal muscle fiber development / dephosphorylation / keratinocyte differentiation / response to amphetamine / T cell activation / excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / FCERI mediated Ca+2 mobilization / protein dephosphorylation / cellular response to glucose stimulus / wound healing / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / sarcolemma / Z disc / response to calcium ion / G1/S transition of mitotic cell cycle / protein import into nucleus / calcium ion transport / Ca2+ pathway / heart development / ATPase binding / postsynapse / host cell cytoplasm / dendritic spine / protein dimerization activity / calmodulin binding / positive regulation of cell migration / protein domain specific binding / negative regulation of gene expression / glutamatergic synapse / calcium ion binding / host cell nucleus / protein-containing complex binding / positive regulation of gene expression / enzyme binding / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Grigoriu, S. / Peti, W. / Page, R. | ||||||
![]() | ![]() Title: The molecular mechanism of substrate engagement and immunosuppressant inhibition of calcineurin. Authors: Grigoriu, S. / Bond, R. / Cossio, P. / Chen, J.A. / Ly, N. / Hummer, G. / Page, R. / Cyert, M.S. / Peti, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 338.3 KB | Display | ![]() |
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PDB format | ![]() | 280.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.7 KB | Display | ![]() |
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Full document | ![]() | 459.5 KB | Display | |
Data in XML | ![]() | 26.5 KB | Display | |
Data in CIF | ![]() | 39 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1auiS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 42855.047 Da / Num. of mol.: 1 / Fragment: Calcineurin A Subunit Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q08209, protein-serine/threonine phosphatase |
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#2: Protein | Mass: 19322.904 Da / Num. of mol.: 1 / Fragment: Calcineurin B Subunit Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P63098, protein-serine/threonine phosphatase |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 5109.087 Da / Num. of mol.: 1 / Fragment: A238L CID (unp residues 200-239) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: Malawi (Lil 20-1) Gene: 5EL, Mal-047, Ordered Locus Name: Mal-047 ORF Name: 5EL Plasmid: pET-RP1B / Production host: ![]() ![]() |
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-Non-polymers , 3 types, 482 molecules ![](data/chem/img/GOL.gif)
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#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-CA / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.78 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.16 M ammonium citrate dibasic, 20% (w/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2011 / Details: Si-111 double crystal monochromator |
Radiation | Monochromator: Si-111 double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 62191 / Num. obs: 60590 / % possible obs: 97.4 % / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 1.7→1.73 Å / % possible all: 87.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1AUI Resolution: 1.7→47.313 Å / SU ML: 0.21 / σ(F): 0 / Phase error: 18.7 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.893 Å2 / ksol: 0.433 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.7→47.313 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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