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Yorodumi- PDB-2y4v: CRYSTAL STRUCTURE OF HUMAN CALMODULIN IN COMPLEX WITH A DAP KINAS... -
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-Basic information
Entry | Database: PDB / ID: 2y4v | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN CALMODULIN IN COMPLEX WITH A DAP KINASE-1 MUTANT (W305Y) PEPTIDE | ||||||
Components |
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Keywords | METAL BINDING PROTEIN/TRANSFERASE / METAL BINDING PROTEIN-TRANSFERASE COMPLEX | ||||||
Function / homology | Function and homology information cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / defense response to tumor cell / Caspase activation via Dependence Receptors in the absence of ligand / calmodulin-dependent protein kinase activity ...cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / defense response to tumor cell / Caspase activation via Dependence Receptors in the absence of ligand / calmodulin-dependent protein kinase activity / CaM pathway / syntaxin-1 binding / 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 / regulation of synaptic vesicle exocytosis / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / 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 / response to corticosterone / 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 / regulation of NMDA receptor activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / 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 / extrinsic apoptotic signaling pathway via death domain receptors / DARPP-32 events / detection of calcium ion / Smooth Muscle Contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / RHO GTPases activate IQGAPs / cellular response to interferon-beta / regulation of cardiac muscle contraction / calcium channel inhibitor activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / positive regulation of DNA binding / Protein methylation / enzyme regulator activity / voltage-gated potassium channel complex / phosphatidylinositol 3-kinase binding / Activation of AMPK downstream of NMDARs / positive regulation of autophagy / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / positive regulation of protein autophosphorylation / sperm midpiece / response to amphetamine / calcium channel complex / activation of adenylate cyclase activity / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / protein serine/threonine kinase activator activity / nitric-oxide synthase regulator activity / sarcomere / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / regulation of cytokinesis / regulation of autophagy Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | de Diego, I. / Lehmann, F. / Wilmanns, M. | ||||||
Citation | Journal: To be Published Title: A Journey Through the Dap Kinase Architecture Authors: De Diego, I. / Kuper, J. / Lehmann, F. / Wilmanns, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y4v.cif.gz | 81.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y4v.ent.gz | 60.1 KB | Display | PDB format |
PDBx/mmJSON format | 2y4v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y4/2y4v ftp://data.pdbj.org/pub/pdb/validation_reports/y4/2y4v | HTTPS FTP |
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-Related structure data
Related structure data | 2y4pC 3zxtC 1yr5S 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 on special symmetry positions |
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-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) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: P62158, UniProt: P0DP23*PLUS | ||||
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#2: Protein/peptide | Mass: 2369.899 Da / Num. of mol.: 1 / Fragment: RESIDUES 302-320 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) References: UniProt: P53355, non-specific serine/threonine protein kinase | ||||
#3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.73 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 0.1 M HEPES PH 7.5, 25(W/V) PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.99989 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 1, 2009 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99989 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→23.59 Å / Num. obs: 14844 / % possible obs: 96.9 % / Observed criterion σ(I): 3.3 / Redundancy: 1.9 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 3.3 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1YR5 Resolution: 1.8→74.2 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.055 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1A-3A AND 78A-80A ARE DISORDERED AND REMOVED FROM MODEL.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.612 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→74.2 Å
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