[English] 日本語
Yorodumi- PDB-1j3h: Crystal structure of apoenzyme cAMP-dependent protein kinase cata... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j3h | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of apoenzyme cAMP-dependent protein kinase catalytic subunit | ||||||
Components | cAMP-dependent protein kinase, alpha-catalytic subunit | ||||||
Keywords | TRANSFERASE / apoenzyme / cAMP-dependent protein kinase / catalytic subunit / open conformation / preformed active site | ||||||
Function / homology | Function and homology information spontaneous exocytosis of neurotransmitter / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of meiotic cell cycle / HDL assembly / DARPP-32 events / Rap1 signalling / PKA activation / Vasopressin regulates renal water homeostasis via Aquaporins / Regulation of insulin secretion ...spontaneous exocytosis of neurotransmitter / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of meiotic cell cycle / HDL assembly / 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 / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / MAPK6/MAPK4 signaling / GLI3 is processed to GLI3R by the proteasome / AURKA Activation by TPX2 / Factors involved in megakaryocyte development and platelet production / Regulation of PLK1 Activity at G2/M Transition / Interleukin-3, Interleukin-5 and GM-CSF signaling / CD209 (DC-SIGN) signaling / Mitochondrial protein degradation / RET signaling / Ion homeostasis / VEGFA-VEGFR2 Pathway / 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 / regulation of osteoblast differentiation / sperm capacitation / cAMP-dependent protein kinase activity / ciliary base / negative regulation of glycolytic process through fructose-6-phosphate / 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 / plasma membrane raft / axoneme / mesoderm formation / sperm flagellum / negative regulation of smoothened signaling pathway / regulation of proteasomal protein catabolic process / regulation of synaptic transmission, glutamatergic / positive regulation of gluconeogenesis / sperm midpiece / negative regulation of TORC1 signaling / protein kinase A signaling / protein serine/threonine/tyrosine kinase activity / protein export from nucleus / positive regulation of protein export from nucleus / acrosomal vesicle / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Akamine, P. / Madhusudan / Wu, J. / Xuong, N.H. / Ten Eyck, L.F. / Taylor, S.S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Dynamic Features of cAMP-dependent Protein Kinase Revealed by Apoenzyme Crystal Structure Authors: Akamine, P. / Madhusudan / Wu, J. / Xuong, N.-H. / Ten Eyck, L.F. / Taylor, S.S. #1: Journal: Nat.Struct.Biol. / Year: 2002 Title: Crystal structure of a transition state mimic of the catalytic subunit of cAMP-dependent protein kinase Authors: Madhusudan / Akamine, P. / Xuong, N.H. / Taylor, S.S. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1993 Title: Structure of the mammalian catalytic subunit of cAMP-dependent protein kinase and an inhibitor peptide displays an open conformation Authors: Karlsson, R. / Zheng, J. / Xuong, N. / Taylor, S.S. / Sowadski, J.M. #3: Journal: Protein Sci. / Year: 1993 Title: Crystal structures of the myristylated catalytic subunit of cAMP-dependent protein kinase reveal open and closed conformations Authors: Zheng, J. / Knighton, D.R. / Xuong, N.H. / Taylor, S.S. / Sowadski, J.M. / Ten Eyck, L.F. #4: Journal: Biochemistry / Year: 1993 Title: Crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with MgATP and peptide inhibitor Authors: Zheng, J. / Knighton, D.R. / Ten Eyck, L.F. / Karlsson, R. / Xuong, N. / Taylor, S.S. / Sowadski, J.M. #5: Journal: Structure / Year: 1997 Title: A binary complex of the catalytic subunit of cAMP-dependent protein kinase and adenosine further defines conformational flexibility Authors: Narayana, N. / Cox, S. / Nguyen-huu, X. / Ten Eyck, L.F. / Taylor, S.S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1j3h.cif.gz | 138.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1j3h.ent.gz | 107.5 KB | Display | PDB format |
PDBx/mmJSON format | 1j3h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j3h_validation.pdf.gz | 457.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1j3h_full_validation.pdf.gz | 471 KB | Display | |
Data in XML | 1j3h_validation.xml.gz | 26.2 KB | Display | |
Data in CIF | 1j3h_validation.cif.gz | 34.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/1j3h ftp://data.pdbj.org/pub/pdb/validation_reports/j3/1j3h | HTTPS FTP |
-Related structure data
Related structure data | 1ctpS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 40733.434 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pRSETb / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P05132, EC: 2.7.1.37 #2: Chemical | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Tris-hydrogen chloride, MPD, Bicine, ammonium acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 97 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 4, 1999 |
Radiation | Monochromator: 58CM LONG, PT-COATED, FUSED SILICA, VERTICAL FOCUSMIRROR, CYCLINDRICALLY BENT TRIANGULAR SI(111) ASYMMETRIC CUT, HORIZONTAL FOCUS MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→19.96 Å / Num. obs: 18822 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.055 / Rsym value: 0.055 |
Reflection shell | Resolution: 2.8→2.9 Å / Rsym value: 0.49 / % possible all: 82.8 |
Reflection | *PLUS Highest resolution: 2.9 Å / Num. obs: 18800 / Num. measured all: 102700 |
Reflection shell | *PLUS % possible obs: 82.8 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 2.5 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CTP Resolution: 2.9→19.96 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→19.96 Å
| |||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|