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Yorodumi- PDB-4dfy: Crystal structure of R194A mutant of cAMP-dependent protein kinas... -
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-Basic information
Entry | Database: PDB / ID: 4dfy | ||||||
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Title | Crystal structure of R194A mutant of cAMP-dependent protein kinase with unphosphorylated activation loop | ||||||
Components | cAMP-dependent protein kinase catalytic subunit alphaCAMP-dependent pathway | ||||||
Keywords | TRANSFERASE / protein kinase fold / Serine/Threonine kinase activity / cAMP-dependent protein kinase regulatory subunit / PKI / phosphorylation | ||||||
Function / homology | Function and homology information spontaneous exocytosis of neurotransmitter / HDL assembly / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of meiotic cell cycle / DARPP-32 events / Rap1 signalling / PKA activation / Vasopressin regulates renal water homeostasis via Aquaporins / Regulation of insulin secretion ...spontaneous exocytosis of neurotransmitter / HDL assembly / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of meiotic cell cycle / DARPP-32 events / Rap1 signalling / PKA activation / Vasopressin regulates renal water homeostasis via Aquaporins / Regulation of insulin secretion / GPER1 signaling / Hedgehog 'off' state / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / MAPK6/MAPK4 signaling / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / GLI3 is processed to GLI3R by the proteasome / AURKA Activation by TPX2 / Factors involved in megakaryocyte development and platelet production / CD209 (DC-SIGN) signaling / Regulation of PLK1 Activity at G2/M Transition / Interleukin-3, Interleukin-5 and GM-CSF signaling / RET signaling / Ion homeostasis / VEGFA-VEGFR2 Pathway / nucleotide-activated protein kinase complex / regulation of cellular respiration / regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cAMP-dependent protein kinase / cellular response to cold / sperm capacitation / regulation of osteoblast differentiation / cAMP-dependent protein kinase activity / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / postsynaptic modulation of chemical synaptic transmission / cellular response to glucagon stimulus / protein kinase A regulatory subunit binding / axoneme / plasma membrane raft / mesoderm formation / sperm flagellum / regulation of proteasomal protein catabolic process / negative regulation of smoothened signaling pathway / protein kinase A signaling / positive regulation of gluconeogenesis / regulation of synaptic transmission, glutamatergic / negative regulation of TORC1 signaling / sperm midpiece / protein export from nucleus / protein serine/threonine/tyrosine kinase activity / acrosomal vesicle / positive regulation of protein export from nucleus / neural tube closure / cellular response to glucose stimulus / modulation of chemical synaptic transmission / neuromuscular junction / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / mRNA processing / small GTPase binding / presynapse / cellular response to heat / manganese ion binding / postsynapse / peptidyl-serine phosphorylation / dendritic spine / regulation of cell cycle / protein kinase activity / nuclear speck / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / positive regulation of cell population proliferation / protein-containing complex binding / protein kinase binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / magnesium ion binding / protein-containing complex / mitochondrion / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.997 Å | ||||||
Authors | Steichen, J.M. / Kuchinskas, M. / Yang, J. / Taylor, S.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Structural basis for the regulation of protein kinase a by activation loop phosphorylation. Authors: Steichen, J.M. / Kuchinskas, M. / Keshwani, M.M. / Yang, J. / Adams, J.A. / Taylor, S.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dfy.cif.gz | 264.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dfy.ent.gz | 215.6 KB | Display | PDB format |
PDBx/mmJSON format | 4dfy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/4dfy ftp://data.pdbj.org/pub/pdb/validation_reports/df/4dfy | HTTPS FTP |
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-Related structure data
Related structure data | 1rdqS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 1 / Auth seq-ID: 14 - 350 / Label seq-ID: 35 - 371
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-Components
#1: Protein | Mass: 42793.766 Da / Num. of mol.: 2 / Mutation: R194A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prkaca, Pkaca / Production host: Escherichia coli (E. coli) / References: UniProt: P05132, cAMP-dependent protein kinase #2: 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: 2.69 Å3/Da / Density % sol: 54.26 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM Tris, 800 mM sodium formate, 10% PEG 8000, 10% PEG 1000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2008 |
Radiation | Monochromator: 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: 2.997→50 Å / Num. all: 18985 / Num. obs: 18017 / % possible obs: 94.9 % / Observed criterion σ(F): 2 / Net I/σ(I): 28.1 |
Reflection shell | Resolution: 2.997→3.11 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 1121 / Rsym value: 0.332 / % possible all: 59.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RDQ Resolution: 2.997→47.52 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.917 / SU B: 61.726 / SU ML: 0.471 / Cross valid method: THROUGHOUT / ESU R Free: 0.484 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 104.574 Å2
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Refinement step | Cycle: LAST / Resolution: 2.997→47.52 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2455 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.997→3.074 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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