+Open data
-Basic information
Entry | Database: PDB / ID: 4il1 | ||||||
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Title | Crystal Structure of the Rat Calcineurin | ||||||
Components | Calmodulin, Calcineurin subunit B type 1, Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | ||||||
Keywords | HYDROLASE / Calcium-binding protein / chimera protein / fusion protein / Protein phosphatase | ||||||
Function / homology | Function and homology information Activation of BAD and translocation to mitochondria / Calcineurin activates NFAT / CLEC7A (Dectin-1) induces NFAT activation / negative regulation of chromatin binding / FCERI mediated Ca+2 mobilization / : / calcium-dependent protein serine/threonine phosphatase activity / cellular response to xenobiotic stimulus => GO:0071466 / regulation of store-operated calcium channel activity / positive regulation of cardiac muscle hypertrophy in response to stress ...Activation of BAD and translocation to mitochondria / Calcineurin activates NFAT / CLEC7A (Dectin-1) induces NFAT activation / negative regulation of chromatin binding / FCERI mediated Ca+2 mobilization / : / calcium-dependent protein serine/threonine phosphatase activity / cellular response to xenobiotic stimulus => GO:0071466 / regulation of store-operated calcium channel activity / positive regulation of cardiac muscle hypertrophy in response to stress / calmodulin-dependent protein phosphatase activity / regulation of high voltage-gated calcium channel activity / calcineurin complex / positive regulation of connective tissue replacement / negative regulation of dendrite morphogenesis / calcineurin-mediated signaling / : / peptidyl-serine dephosphorylation / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / lung epithelial cell differentiation / calcineurin-NFAT signaling cascade / negative regulation of calcium ion-dependent exocytosis / : / myelination in peripheral nervous system / establishment of protein localization to mitochondrial membrane / transition between fast and slow fiber / type 3 metabotropic glutamate receptor binding / Ca2+ pathway / cardiac muscle hypertrophy in response to stress / establishment of protein localization to membrane / regulation of postsynaptic neurotransmitter receptor internalization / negative regulation of miRNA processing / parallel fiber to Purkinje cell synapse / regulation of synaptic vesicle endocytosis / negative regulation of high voltage-gated calcium channel activity / cyclosporin A binding / regulation of synaptic vesicle exocytosis / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / branching involved in blood vessel morphogenesis / protein serine/threonine phosphatase activity / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / postsynaptic modulation of chemical synaptic transmission / positive regulation of endocytosis / protein-serine/threonine phosphatase / positive regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of cardiac muscle hypertrophy / nitric-oxide synthase binding / protein phosphatase activator activity / phosphoprotein phosphatase activity / calcium channel regulator activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / adenylate cyclase binding / protein localization to nucleus / catalytic complex / detection of calcium ion / positive regulation of cell adhesion / negative regulation of ryanodine-sensitive calcium-release channel activity / epithelial to mesenchymal transition / negative regulation of insulin secretion / regulation of cardiac muscle contraction / multicellular organismal response to stress / phosphatase binding / calcium channel inhibitor activity / cellular response to interferon-beta / positive regulation of DNA binding / enzyme regulator activity / skeletal muscle fiber development / voltage-gated potassium channel complex / phosphatidylinositol 3-kinase binding / Schwann cell development / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / dephosphorylation / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / potassium ion transmembrane transport / sperm midpiece / response to amphetamine / calcium channel complex / excitatory postsynaptic potential / activation of adenylate cyclase activity / adenylate cyclase activator activity / regulation of heart rate / nitric-oxide synthase regulator activity / protein serine/threonine kinase activator activity / sarcomere / protein dephosphorylation / regulation of cytokinesis / positive regulation of nitric-oxide synthase activity / calcium-mediated signaling / spindle microtubule / cellular response to glucose stimulus Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Ye, Q. / Faucher, F. / Jia, Z. | ||||||
Citation | Journal: Cell Signal / Year: 2013 Title: Structural basis of calcineurin activation by calmodulin. Authors: Ye, Q. / Feng, Y. / Yin, Y. / Faucher, F. / Currie, M.A. / Rahman, M.N. / Jin, J. / Li, S. / Wei, Q. / Jia, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4il1.cif.gz | 448.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4il1.ent.gz | 358.6 KB | Display | PDB format |
PDBx/mmJSON format | 4il1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/il/4il1 ftp://data.pdbj.org/pub/pdb/validation_reports/il/4il1 | HTTPS FTP |
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-Related structure data
Related structure data | 1mf8S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0
NCS ensembles :
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-Components
#1: Protein | Mass: 92698.812 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) Gene: Calm, Calm1, Calm2, Calm3, Calna, Cam, Cam1, Cam2, Cam3, Camb, Camc, Ppp3ca, Cn a2, Cnb, Ppp3r1 Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P62161, UniProt: P63100, UniProt: P63329, UniProt: P0DP29*PLUS, protein-serine/threonine phosphatase #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | Sequence details | THE DEPOSITED PROTEIN SEQUENCE IS A CHIMERA PROTEIN: COMPOSED OF THREE PROTEINS WHICH ARE FUSED BY ...THE DEPOSITED PROTEIN SEQUENCE IS A CHIMERA PROTEIN: COMPOSED OF THREE PROTEINS WHICH ARE FUSED BY TWO GLYCINE LINKERS BETWEEN THEM. THE CLONING CONSTRUCT ORDER FOR THESE THREE PROTEINS IS CALMODULIN | |
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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: 2.8 Å3/Da / Density % sol: 56.05 % |
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Crystal grow | Temperature: 293 K / pH: 5.6 Details: PEG 3350, 1-Propanol, Citric acid, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.917 |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 6, 2009 / Details: SYNCHROTRON OPTICS |
Radiation | Monochromator: MONOCHROMATIC MACROMOLECULAR CRYSTALLOGRAPHY / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.917 Å / Relative weight: 1 |
Reflection | Resolution: 3→10 Å / Num. obs: 81046 / % possible obs: 99.6 % / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 3→3.1 Å / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MF8 Resolution: 3→10 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.869 / SU B: 17.535 / SU ML: 0.323 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.939 / ESU R Free: 0.385 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 61.91 Å2
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Refinement step | Cycle: LAST / Resolution: 3→10 Å
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Refine LS restraints |
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