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Open data
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Basic information
Entry | Database: PDB / ID: 4il1 | ||||||
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Title | Crystal Structure of the Rat Calcineurin | ||||||
![]() | Calmodulin, Calcineurin subunit B type 1, Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | ||||||
![]() | HYDROLASE / Calcium-binding protein / chimera protein / fusion protein / Protein phosphatase | ||||||
Function / homology | ![]() 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 / : / transition between fast and slow fiber / establishment of protein localization to mitochondrial membrane / myelination in peripheral nervous system / 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 / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / regulation of synaptic vesicle exocytosis / branching involved in blood vessel morphogenesis / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / postsynaptic modulation of chemical synaptic transmission / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / nitric-oxide synthase binding / positive regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of cardiac muscle hypertrophy / protein phosphatase activator activity / positive regulation of endocytosis / positive regulation of phosphoprotein phosphatase activity / phosphoprotein phosphatase activity / adenylate cyclase binding / protein localization to nucleus / catalytic complex / positive regulation of cell adhesion / calcium channel regulator activity / detection of calcium ion / regulation of cardiac muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / epithelial to mesenchymal transition / phosphatase binding / calcium channel inhibitor activity / cellular response to interferon-beta / positive regulation of DNA binding / negative regulation of insulin secretion / multicellular organismal response to stress / phosphatidylinositol 3-kinase binding / Schwann cell development / skeletal muscle fiber development / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / enzyme regulator activity / dephosphorylation / positive regulation of protein dephosphorylation / regulation of calcium-mediated signaling / regulation of ryanodine-sensitive calcium-release channel activity / titin binding / potassium ion transmembrane transport / voltage-gated potassium channel complex / sperm midpiece / calcium channel complex / response to amphetamine / activation of adenylate cyclase activity / adenylate cyclase activator activity / nitric-oxide synthase regulator activity / excitatory postsynaptic potential / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / protein dephosphorylation / regulation of cytokinesis / positive regulation of nitric-oxide synthase activity / calcium-mediated signaling / cellular response to glucose stimulus / positive regulation of receptor signaling pathway via JAK-STAT Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ye, Q. / Faucher, F. / Jia, Z. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 448.3 KB | Display | ![]() |
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PDB format | ![]() | 358.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.2 KB | Display | ![]() |
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Full document | ![]() | 485.8 KB | Display | |
Data in XML | ![]() | 44.3 KB | Display | |
Data in CIF | ![]() | 66.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1mf8S 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _
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.) ![]() ![]() Gene: Calm, Calm1, Calm2, Calm3, Calna, Cam, Cam1, Cam2, Cam3, Camb, Camc, Ppp3ca, Cn a2, Cnb, Ppp3r1 Plasmid: pET21a / Production host: ![]() ![]() 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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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