[English] 日本語
Yorodumi- PDB-4q5u: Structure of calmodulin bound to its recognition site from calcineurin -
+Open data
-Basic information
Entry | Database: PDB / ID: 4q5u | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of calmodulin bound to its recognition site from calcineurin | ||||||
Components |
| ||||||
Keywords | CALCIUM BINDING PROTEIN/PROTEIN BINDING / EF hand / CALCIUM BINDING PROTEIN-PROTEIN BINDING complex | ||||||
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 / calcineurin complex / positive regulation of connective tissue replacement / negative regulation of dendrite morphogenesis / calcineurin-mediated signaling / slit diaphragm / peptidyl-serine dephosphorylation / calcineurin-NFAT signaling cascade / renal filtration / skeletal muscle tissue regeneration / : / transition between fast and slow fiber / positive regulation of calcineurin-NFAT signaling cascade / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / positive regulation of osteoclast differentiation / cardiac muscle hypertrophy in response to stress / CaM pathway / Cam-PDE 1 activation / dendrite morphogenesis / Sodium/Calcium exchangers / regulation of synaptic vesicle endocytosis / Calmodulin induced events / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / 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 / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / cyclosporin A binding / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / regulation of synaptic vesicle exocytosis / myosin phosphatase activity / CLEC7A (Dectin-1) induces NFAT activation / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / Activation of RAC1 downstream of NMDARs / postsynaptic modulation of chemical synaptic transmission / extrinsic component of plasma membrane / response to corticosterone / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / nitric-oxide synthase binding / positive regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of activated T cell proliferation / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / protein phosphatase activator activity / RHO GTPases activate PAKs / positive regulation of endocytosis / positive regulation of phosphoprotein phosphatase activity / Ion transport by P-type ATPases / Long-term potentiation / Uptake and function of anthrax toxins / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / adenylate cyclase binding / catalytic complex / positive regulation of cell adhesion / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / epidermis development / RHO GTPases activate IQGAPs / 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 / negative regulation of insulin secretion / Protein methylation / multicellular organismal response to stress / positive regulation of osteoblast differentiation / phosphatidylinositol 3-kinase binding / eNOS activation / skeletal muscle fiber development / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / enzyme regulator activity / dephosphorylation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Guo, H. / Dunlap, T.B. / Creamer, T.P. / Vander Kooi, C.W. | ||||||
Citation | Journal: Biochemistry / Year: 2014 Title: Stoichiometry of the calcineurin regulatory domain-calmodulin complex. Authors: Dunlap, T.B. / Guo, H.F. / Cook, E.C. / Holbrook, E. / Rumi-Masante, J. / Lester, T.E. / Colbert, C.L. / Vander Kooi, C.W. / Creamer, T.P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4q5u.cif.gz | 86.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4q5u.ent.gz | 65 KB | Display | PDB format |
PDBx/mmJSON format | 4q5u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4q5u_validation.pdf.gz | 428 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4q5u_full_validation.pdf.gz | 431.2 KB | Display | |
Data in XML | 4q5u_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 4q5u_validation.cif.gz | 12.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q5/4q5u ftp://data.pdbj.org/pub/pdb/validation_reports/q5/4q5u | HTTPS FTP |
-Related structure data
Related structure data | 2w73S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 16852.545 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII Plasmid: pETCaMI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62158, UniProt: P0DP23*PLUS | ||
---|---|---|---|
#2: Protein/peptide | Mass: 2820.496 Da / Num. of mol.: 1 / Fragment: calmodulin-binding domain (UNP residues 391-414) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q08209 | ||
#3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.11 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 3:1 10 mg/ml protein to mother liquor (24% PEG1000, 20% glycerol), final volume 200 nL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 2011 |
Radiation | Monochromator: Rosenbaum-Rock double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→19.12 Å / Num. obs: 15779 / % possible obs: 91.1 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 3.4 / % possible all: 69.6 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2W73 Resolution: 1.95→19.12 Å / SU ML: 0.17 / σ(F): 1.38 / Phase error: 30.04 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→19.12 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|