+Open data
-Basic information
Entry | Database: PDB / ID: 3ll8 | ||||||
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Title | Crystal Structure of Calcineurin in Complex with AKAP79 Peptide | ||||||
Components |
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Keywords | Hydrolase/calcium binding protein / protein-peptide docking / protein targeting / calcineurin / AKAP79 / beta-augmentation / Calmodulin-binding / Membrane / Hydrolase / Iron / Metal-binding / Nucleus / Phosphoprotein / Protein phosphatase / Lipoprotein / Myristate / Hydrolase-calcium binding protein complex | ||||||
Function / homology | Function and homology information positive regulation of endosome to plasma membrane protein transport / postsynaptic recycling endosome membrane / 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 endosome to plasma membrane protein transport / postsynaptic recycling endosome membrane / 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 / postsynaptic recycling endosome / 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 / ROBO receptors bind AKAP5 / 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 / GABA receptor binding / positive regulation of calcineurin-NFAT signaling cascade / myelination in peripheral nervous system / regulation of protein kinase A signaling / negative regulation of adenylate cyclase activity / protein phosphatase 2B binding / Trafficking of AMPA receptors / cardiac muscle hypertrophy in response to stress / positive regulation of osteoclast differentiation / regulation of postsynaptic neurotransmitter receptor internalization / parallel fiber to Purkinje cell synapse / dendrite morphogenesis / beta-2 adrenergic receptor binding / protein kinase A binding / CLEC7A (Dectin-1) induces NFAT activation / cyclosporin A binding / myosin phosphatase activity / extrinsic component of plasma membrane / branching involved in blood vessel morphogenesis / protein serine/threonine phosphatase activity / postsynaptic modulation of chemical synaptic transmission / protein-serine/threonine phosphatase / dephosphorylation / positive regulation of activated T cell proliferation / protein kinase A regulatory subunit binding / positive regulation of endocytosis / Calcineurin activates NFAT / adenylate cyclase binding / excitatory synapse / positive regulation of cell adhesion / DARPP-32 events / Activation of BAD and translocation to mitochondria / epidermis development / epithelial to mesenchymal transition / phosphatase binding / negative regulation of insulin secretion / glutamate receptor binding / positive regulation of osteoblast differentiation / multicellular organismal response to stress / skeletal muscle fiber development / keratinocyte differentiation / dendrite membrane / response to amphetamine / T cell activation / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / positive regulation of protein localization to plasma membrane / hippocampal mossy fiber to CA3 synapse / protein dephosphorylation / FCERI mediated Ca+2 mobilization / excitatory postsynaptic potential / positive regulation of long-term synaptic potentiation / 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 / cytoplasmic side of plasma membrane / sarcolemma / Z disc / SH3 domain binding / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / protein import into nucleus / calcium ion transport / ATPase binding / Ca2+ pathway / heart development / scaffold protein binding / chemical synaptic transmission / postsynapse / dendritic spine / molecular adaptor activity Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Li, H. / Hogan, P.G. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2012 Title: Balanced interactions of calcineurin with AKAP79 regulate Ca(2+)-calcineurin-NFAT signaling. Authors: Li, H. / Pink, M.D. / Murphy, J.G. / Stein, A. / Dell'acqua, M.L. / Hogan, P.G. #1: Journal: Nature / Year: 1995 Title: Crystal structures of human calcineurin and the human FKBP12-FK506-calcineurin complex Authors: Kissinger, C.R. / Parge, H.E. / Knighton, D.R. / Lewis, C.T. / Pelletier, L.A. / Tempczyk, A. / Kalish, V.J. / Tucker, K.D. / Showalter, R.E. / Moomaw, E.W. / Gastinel, L.N. / Habuka, N. / ...Authors: Kissinger, C.R. / Parge, H.E. / Knighton, D.R. / Lewis, C.T. / Pelletier, L.A. / Tempczyk, A. / Kalish, V.J. / Tucker, K.D. / Showalter, R.E. / Moomaw, E.W. / Gastinel, L.N. / Habuka, N. / Chen, X. / Maldonado, F. / Barker, J.E. / Bacquet, R. / Villafranca, J.E. #2: Journal: J.Mol.Biol. / Year: 2007 Title: Structure of calcineurin in complex with PVIVIT peptide: portrait of a low-affinity signalling interaction Authors: Li, H. / Zhang, L. / Rao, A. / Harrison, S.C. / Hogan, P.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ll8.cif.gz | 234.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ll8.ent.gz | 184.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ll8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ll8_validation.pdf.gz | 473.3 KB | Display | wwPDB validaton report |
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Full document | 3ll8_full_validation.pdf.gz | 489.8 KB | Display | |
Data in XML | 3ll8_validation.xml.gz | 44.7 KB | Display | |
Data in CIF | 3ll8_validation.cif.gz | 64.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ll/3ll8 ftp://data.pdbj.org/pub/pdb/validation_reports/ll/3ll8 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
-Protein/peptide , 1 types, 1 molecules E
#1: Protein/peptide | Mass: 1214.362 Da / Num. of mol.: 1 / Fragment: UNP residues 336-346 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P24588 |
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-Protein , 2 types, 4 molecules ACBD
#2: Protein | Mass: 41259.223 Da / Num. of mol.: 2 / Fragment: UNP residues 14-370 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPP3CA, CALNA, CNA / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q08209, protein-serine/threonine phosphatase #3: Protein | Mass: 17623.979 Da / Num. of mol.: 2 / Fragment: UNP residues 16-170 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPP3R1, CNA2, CNB / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63098 |
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-Non-polymers , 5 types, 597 molecules
#4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-CA / #8: Water | ChemComp-HOH / | |
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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: 2.58 Å3/Da / Density % sol: 52.4 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 20,000 MgSO4 CaCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9789 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2008 / Details: 74MB unbinned | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Cryo-Cooled Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. obs: 80437 / % possible obs: 95.7 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 9.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→43.15 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0 / SU B: 3.812 / SU ML: 0.107 / SU R Cruickshank DPI: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.29 Å2
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Refinement step | Cycle: LAST / Resolution: 2→43.15 Å
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LS refinement shell | Resolution: 2→2.06 Å / Total num. of bins used: 20
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