+Open data
-Basic information
Entry | Database: PDB / ID: 4or9 | ||||||
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Title | Crystal structure of human calcineurin | ||||||
Components |
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Keywords | HYDROLASE/METAL BINDING PROTEIN / Calmodulin-binding / HYDROLASE-METAL BINDING PROTEIN complex | ||||||
Function / homology | Function and homology information calcium-dependent protein serine/threonine phosphatase regulator activity / negative regulation of calcium ion import across plasma membrane / calcium-dependent protein serine/threonine phosphatase activity / negative regulation of signaling / locomotion involved in locomotory behavior / positive regulation of calcium ion import across plasma membrane / calmodulin-dependent protein phosphatase activity / positive regulation of lysosome organization / calcineurin complex / calcineurin-mediated signaling ...calcium-dependent protein serine/threonine phosphatase regulator activity / negative regulation of calcium ion import across plasma membrane / calcium-dependent protein serine/threonine phosphatase activity / negative regulation of signaling / locomotion involved in locomotory behavior / positive regulation of calcium ion import across plasma membrane / calmodulin-dependent protein phosphatase activity / positive regulation of lysosome organization / calcineurin complex / calcineurin-mediated signaling / negative regulation of T cell mediated cytotoxicity / protein serine/threonine phosphatase complex / ROBO receptors bind AKAP5 / lymphangiogenesis / lung epithelial cell differentiation / calcineurin-NFAT signaling cascade / regulation of synaptic vesicle cycle / positive regulation of calcineurin-NFAT signaling cascade / calcium-ion regulated exocytosis / myelination in peripheral nervous system / protein phosphatase 2B binding / axon extension / regulation of postsynaptic neurotransmitter receptor internalization / parallel fiber to Purkinje cell synapse / regulation of synaptic vesicle endocytosis / CLEC7A (Dectin-1) induces NFAT activation / cyclosporin A binding / myosin phosphatase activity / branching involved in blood vessel morphogenesis / protein serine/threonine phosphatase activity / postsynaptic modulation of chemical synaptic transmission / protein-serine/threonine phosphatase / dephosphorylation / T cell homeostasis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of insulin secretion / Calcineurin activates NFAT / DARPP-32 events / T cell differentiation / Activation of BAD and translocation to mitochondria / epithelial to mesenchymal transition / phosphatase binding / skeletal muscle fiber development / T cell proliferation / T-tubule / T cell activation / hippocampal mossy fiber to CA3 synapse / protein dephosphorylation / FCERI mediated Ca+2 mobilization / learning / response to cytokine / regulation of synaptic plasticity / Schaffer collateral - CA1 synapse / T cell mediated cytotoxicity / sarcolemma / memory / Z disc / positive regulation of protein localization to nucleus / protein import into nucleus / Ca2+ pathway / heart development / postsynapse / calmodulin binding / protein dimerization activity / protein domain specific binding / protein phosphorylation / glutamatergic synapse / calcium ion binding / positive regulation of DNA-templated transcription / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å | ||||||
Authors | 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 | 4or9.cif.gz | 255.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4or9.ent.gz | 204.2 KB | Display | PDB format |
PDBx/mmJSON format | 4or9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4or9_validation.pdf.gz | 437.5 KB | Display | wwPDB validaton report |
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Full document | 4or9_full_validation.pdf.gz | 442.4 KB | Display | |
Data in XML | 4or9_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 4or9_validation.cif.gz | 34.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/4or9 ftp://data.pdbj.org/pub/pdb/validation_reports/or/4or9 | HTTPS FTP |
-Related structure data
Related structure data | 4oraC 4orbC 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: 61264.473 Da / Num. of mol.: 1 / Fragment: catalytic subunit Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CALNA2, CALNB, CNA2, PPP3CB / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P16298, 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.) Homo sapiens (human) / Gene: CNA2, CNB, PPP3R1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63098 |
-Non-polymers , 4 types, 257 molecules
#3: Chemical | ChemComp-FE / | ||
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#4: Chemical | ChemComp-ZN / | ||
#5: Chemical | ChemComp-CA / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.48 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 100mM MES, pH 5.8, 7% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 5, 2012 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→50 Å / Num. all: 51079 / Num. obs: 50855 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 18.6 % / Biso Wilson estimate: 40.7 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 28.8 |
Reflection shell | Resolution: 2.23→2.31 Å / Redundancy: 17.7 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 9.842 / Num. unique all: 4998 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AUI Resolution: 2.23→47.782 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 21.39 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.692 Å2 / ksol: 0.334 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.23→47.782 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: 18
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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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