+Open data
-Basic information
Entry | Database: PDB / ID: 4orb | ||||||
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Title | Crystal structure of mouse calcineurin | ||||||
Components |
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Keywords | HYDROLASE/METAL BINDING PROTEIN / Calmodulin-binding / HYDROLASE-METAL BINDING PROTEIN complex | ||||||
Function / homology | Function and homology information negative regulation of chromatin binding / Activation of BAD and translocation to mitochondria / : / CLEC7A (Dectin-1) induces NFAT activation / calcium-dependent protein serine/threonine phosphatase activity / Calcineurin activates NFAT / cellular response to xenobiotic stimulus => GO:0071466 / positive regulation of cardiac muscle hypertrophy in response to stress / calmodulin-dependent protein phosphatase activity / calcineurin complex ...negative regulation of chromatin binding / Activation of BAD and translocation to mitochondria / : / CLEC7A (Dectin-1) induces NFAT activation / calcium-dependent protein serine/threonine phosphatase activity / Calcineurin activates NFAT / cellular response to xenobiotic stimulus => GO:0071466 / positive regulation of cardiac muscle hypertrophy in response to stress / calmodulin-dependent protein phosphatase activity / calcineurin complex / positive regulation of connective tissue replacement / negative regulation of dendrite morphogenesis / calcineurin-mediated signaling / Ca2+ pathway / slit diaphragm / FCERI mediated Ca+2 mobilization / : / peptidyl-serine dephosphorylation / lung epithelial cell differentiation / calcineurin-NFAT signaling cascade / transition between fast and slow fiber / myelination in peripheral nervous system / cardiac muscle hypertrophy in response to stress / negative regulation of miRNA processing / cyclosporin A binding / branching involved in blood vessel morphogenesis / protein serine/threonine phosphatase activity / postsynaptic modulation of chemical synaptic transmission / protein-serine/threonine phosphatase / positive regulation of cardiac muscle hypertrophy / dephosphorylation / positive regulation of endocytosis / phosphoprotein phosphatase activity / positive regulation of cell adhesion / protein localization to nucleus / epithelial to mesenchymal transition / phosphatase binding / negative regulation of insulin secretion / multicellular organismal response to stress / skeletal muscle fiber development / Schwann cell development / response to amphetamine / protein dephosphorylation / excitatory postsynaptic potential / cellular response to glucose stimulus / calcium-mediated signaling / positive regulation of DNA-binding transcription factor activity / response to calcium ion / modulation of chemical synaptic transmission / brain development / Schaffer collateral - CA1 synapse / G1/S transition of mitotic cell cycle / cytoplasmic side of plasma membrane / sarcolemma / Z disc / protein import into nucleus / calcium ion transport / ATPase binding / heart development / postsynapse / dendritic spine / calmodulin binding / protein dimerization activity / positive regulation of cell migration / protein domain specific binding / negative regulation of gene expression / glutamatergic synapse / synapse / calcium ion binding / positive regulation of gene expression / protein-containing complex binding / enzyme binding / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.108 Å | ||||||
Authors | Ma, L. / Li, S.J. / Wang, J. / Wu, J.W. / Wang, Z.X. | ||||||
Citation | Journal: To be Published Title: Cooperative autoinhibition and multi-level activation mechanisms of calcineurin Authors: Li, S.J. / Ma, L. / Wang, J. / Lu, C. / Wang, J. / Wu, J.W. / Wang, Z.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4orb.cif.gz | 237.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4orb.ent.gz | 188.9 KB | Display | PDB format |
PDBx/mmJSON format | 4orb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4orb_validation.pdf.gz | 443.3 KB | Display | wwPDB validaton report |
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Full document | 4orb_full_validation.pdf.gz | 451.4 KB | Display | |
Data in XML | 4orb_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 4orb_validation.cif.gz | 28.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/4orb ftp://data.pdbj.org/pub/pdb/validation_reports/or/4orb | HTTPS FTP |
-Related structure data
Related structure data | 4or9C 4oraC 4orcC 1auiS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-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 AB
#1: Protein | Mass: 58754.734 Da / Num. of mol.: 1 / Fragment: catalytic subunit Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Calna, Ppp3ca / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P63328, protein-serine/threonine phosphatase |
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#2: Protein | Mass: 19322.904 Da / Num. of mol.: 1 / Fragment: regulatory subunit Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cnb, Ppp3r1 / Plasmid: pACYCDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q63810 |
-Non-polymers , 4 types, 21 molecules
#3: Chemical | ChemComp-ZN / | ||
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#4: Chemical | ChemComp-FE / | ||
#5: Chemical | ChemComp-CA / #6: Water | ChemComp-HOH / | |
-Details
Sequence details | AMINO ACIDS (447-456) ARE MISSING BECAUSE THIS SEQUENCE CORRESPOND |
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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: 2.96 Å3/Da / Density % sol: 58.39 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: 100mM MES, pH 6.1, 18% PEG3350, 8% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 21, 2010 |
Radiation | Monochromator: rotated-inclined double-crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→40 Å / Num. all: 17090 / Num. obs: 17038 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Biso Wilson estimate: 61.1 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 4 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 2.273 / Num. unique all: 1587 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AUI Resolution: 3.108→39.691 Å / SU ML: 0.42 / σ(F): 1.35 / Phase error: 22.86 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.512 Å2 / ksol: 0.377 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.108→39.691 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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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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