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Yorodumi- PDB-2jzi: Structure of Calmodulin complexed with the Calmodulin Binding Dom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jzi | ||||||
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Title | Structure of Calmodulin complexed with the Calmodulin Binding Domain of Calcineurin | ||||||
Components |
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Keywords | METAL BINDING PROTEIN / Calcium binding protein / Acetylation / Methylation / Phosphoprotein / Ubl conjugation / Alternative splicing / Calmodulin-binding / Hydrolase / Iron / Metal-binding / Nucleus / Protein phosphatase / Zinc | ||||||
Function / homology | Function and homology information negative regulation of angiotensin-activated signaling pathway / regulation of cell proliferation involved in kidney morphogenesis / positive regulation of glomerulus development / negative regulation of calcium ion import across plasma membrane / protein serine/threonine phosphatase complex / 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 / calmodulin-dependent protein phosphatase activity ...negative regulation of angiotensin-activated signaling pathway / regulation of cell proliferation involved in kidney morphogenesis / positive regulation of glomerulus development / negative regulation of calcium ion import across plasma membrane / protein serine/threonine phosphatase complex / 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 / calmodulin-dependent protein phosphatase activity / slit diaphragm / calcineurin complex / positive regulation of connective tissue replacement / negative regulation of dendrite morphogenesis / calcineurin-mediated signaling / peptidyl-serine dephosphorylation / calcineurin-NFAT signaling cascade / skeletal muscle tissue regeneration / renal filtration / : / positive regulation of calcineurin-NFAT signaling cascade / establishment of protein localization to mitochondrial membrane / transition between fast and slow fiber / type 3 metabotropic glutamate receptor binding / cardiac muscle hypertrophy in response to stress / positive regulation of osteoclast differentiation / dendrite morphogenesis / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / regulation of synaptic vesicle endocytosis / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / cyclosporin A binding / regulation of synaptic vesicle exocytosis / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / negative regulation of calcium ion export across plasma membrane / myosin phosphatase activity / organelle localization by membrane tethering / protein serine/threonine phosphatase activity / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / autophagosome membrane docking / extrinsic component of plasma membrane / response to corticosterone / postsynaptic modulation of chemical synaptic transmission / positive regulation of endocytosis / protein-serine/threonine phosphatase / positive regulation of activated T cell proliferation / positive regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Phase 0 - rapid depolarisation / protein phosphatase activator activity / RHO GTPases activate PAKs / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / Long-term potentiation / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / adenylate cyclase binding / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / detection of calcium ion / positive regulation of cell adhesion / negative regulation of ryanodine-sensitive calcium-release channel activity / negative regulation of insulin secretion / Smooth Muscle Contraction / RHO GTPases activate IQGAPs / epidermis development / regulation of cardiac muscle contraction / multicellular organismal response to stress / calcium channel inhibitor activity / cellular response to interferon-beta / positive regulation of DNA binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / positive regulation of osteoblast differentiation / Protein methylation / enzyme regulator activity / skeletal muscle fiber development / voltage-gated potassium channel complex / phosphatidylinositol 3-kinase binding / Activation of AMPK downstream of NMDARs / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / distance geometry | ||||||
Authors | Chyan, C. / Huang, J. / Irene, D. / Lin, T. | ||||||
Citation | Journal: To be Published Title: Structure of Calmodulin complexed with the Calmodulin Binding Domain of Calcineurin Authors: Chyan, C. / Huang, J. / Irene, D. / Lin, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jzi.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2jzi.ent.gz | 904 KB | Display | PDB format |
PDBx/mmJSON format | 2jzi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jz/2jzi ftp://data.pdbj.org/pub/pdb/validation_reports/jz/2jzi | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 16721.350 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P62158, UniProt: P0DP23*PLUS |
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#2: Protein/peptide | Mass: 2820.496 Da / Num. of mol.: 1 Fragment: UNP residues 391-414, Calmodulin_binding_domain_of_Calcineurin Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPP3CA, CALNA, CNA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: Q08209, protein-serine/threonine phosphatase |
#3: Chemical | ChemComp-CA / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1 mM [U-99% 13C; U-99% 15N] Calmodulin, 1 mM [U-99% 13C; U-99% 15N] Calmodulin binding domain of Calcineurin, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||
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Sample |
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Sample conditions | pH: 6.5 / Temperature: 310 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: distance geometry / Software ordinal: 1 | ||||||||||||
NMR constraints | Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 284 / Protein phi angle constraints total count: 142 / Protein psi angle constraints total count: 142 | ||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||
NMR ensemble | Average torsion angle constraint violation: 0 ° Conformer selection criteria: back calculated data agree with experimental NOESY spectrum Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 0 ° / Representative conformer: 1 / Torsion angle constraint violation method: TALOS |