+Open data
-Basic information
Entry | Database: PDB / ID: 5sve | ||||||
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Title | Structure of Calcineurin in complex with NFATc1 LxVP peptide | ||||||
Components |
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Keywords | HYDROLASE / protein binding | ||||||
Function / homology | Function and homology information skeletal muscle adaptation / 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 / positive regulation of saliva secretion / positive regulation of cardiac muscle hypertrophy in response to stress ...skeletal muscle adaptation / 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 / positive regulation of saliva secretion / positive regulation of cardiac muscle hypertrophy in response to stress / positive regulation of calcium ion import across plasma membrane / negative regulation of vascular associated smooth muscle cell differentiation / calmodulin-dependent protein phosphatase activity / calcineurin complex / positive regulation of connective tissue replacement / negative regulation of dendrite morphogenesis / calcineurin-mediated signaling / slit diaphragm / protein serine/threonine phosphatase complex / mononuclear cell differentiation / peptidyl-serine dephosphorylation / renal filtration / lung epithelial cell differentiation / calcineurin-NFAT signaling cascade / skeletal muscle tissue regeneration / regulation of synaptic vesicle cycle / transition between fast and slow fiber / positive regulation of calcineurin-NFAT signaling cascade / pulmonary valve morphogenesis / myelination in peripheral nervous system / cardiac muscle hypertrophy in response to stress / positive regulation of osteoclast differentiation / regulation of postsynaptic neurotransmitter receptor internalization / aortic valve morphogenesis / response to muscle activity / parallel fiber to Purkinje cell synapse / dendrite morphogenesis / CLEC7A (Dectin-1) induces NFAT activation / cyclosporin A binding / myosin phosphatase activity / extrinsic component of plasma membrane / branching involved in blood vessel morphogenesis / positive regulation of DNA biosynthetic process / protein serine/threonine phosphatase activity / FK506 binding / postsynaptic modulation of chemical synaptic transmission / mitogen-activated protein kinase p38 binding / protein-serine/threonine phosphatase / negative regulation of Wnt signaling pathway / dephosphorylation / positive regulation of activated T cell proliferation / positive regulation of endocytosis / Calcineurin activates NFAT / positive regulation of cell adhesion / DARPP-32 events / sarcoplasm / Activation of BAD and translocation to mitochondria / epidermis development / epithelial to mesenchymal transition / phosphatase binding / negative regulation of insulin secretion / positive regulation of osteoblast differentiation / multicellular organismal response to stress / skeletal muscle fiber development / keratinocyte differentiation / cellular response to transforming growth factor beta stimulus / response to amphetamine / T cell activation / hippocampal mossy fiber to CA3 synapse / protein dephosphorylation / FCERI mediated Ca+2 mobilization / excitatory postsynaptic potential / cellular response to glucose stimulus / wound healing / response to calcium ion / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / G1/S transition of mitotic cell cycle / sarcolemma / transcription coactivator binding / Z disc / protein import into nucleus / calcium ion transport / sequence-specific double-stranded DNA binding / cellular response to tumor necrosis factor / ATPase binding / Ca2+ pathway / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / nucleic acid binding / RNA polymerase II-specific DNA-binding transcription factor binding / postsynapse / dendritic spine / calmodulin binding / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / nuclear body / positive regulation of cell migration / intracellular signal transduction Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.596 Å | ||||||
Authors | Sheftic, S.R. / Page, R. / Peti, W. | ||||||
Funding support | United States, 1items
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Citation | Journal: Sci Rep / Year: 2016 Title: Investigating the human Calcineurin Interaction Network using the pi LxVP SLiM. Authors: Sheftic, S.R. / Page, R. / Peti, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5sve.cif.gz | 123.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5sve.ent.gz | 92.8 KB | Display | PDB format |
PDBx/mmJSON format | 5sve.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sv/5sve ftp://data.pdbj.org/pub/pdb/validation_reports/sv/5sve | HTTPS FTP |
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-Related structure data
Related structure data | 4f0zS 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: 42659.852 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPP3CA, CALNA, CNA / Production host: Escherichia coli (E. coli) References: UniProt: Q08209, protein-serine/threonine phosphatase |
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#2: Protein | Mass: 19322.904 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPP3R1, CNA2, CNB / Production host: Escherichia coli (E. coli) / References: UniProt: P63098 |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 2187.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O95644*PLUS |
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-Non-polymers , 4 types, 59 molecules
#4: Chemical | ChemComp-FE / | ||
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#5: Chemical | ChemComp-ZN / | ||
#6: Chemical | ChemComp-CA / #7: 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: 2.67 Å3/Da / Density % sol: 53.88 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES pH 7.0 15% Peg 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 4, 2016 |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→39.04 Å / Num. obs: 21785 / % possible obs: 99.6 % / Redundancy: 7.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.115 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 2.6→2.71 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.805 / Mean I/σ(I) obs: 1.7 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4F0Z Resolution: 2.596→39.035 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.36
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.596→39.035 Å
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Refine LS restraints |
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LS refinement shell |
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