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Yorodumi- PDB-1jlu: Crystal Structure of the Catalytic Subunit of cAMP-dependent Prot... -
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-Basic information
Entry | Database: PDB / ID: 1jlu | ||||||
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Title | Crystal Structure of the Catalytic Subunit of cAMP-dependent Protein Kinase Complexed with a Phosphorylated Substrate Peptide and Detergent | ||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Protein kinase-phosphorylated substrate complex / transferase-transferase inhibitor complex | ||||||
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 / negative regulation of catalytic activity / Factors involved in megakaryocyte development and platelet production / CD209 (DC-SIGN) signaling / negative regulation of cAMP-dependent protein kinase activity / 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 inhibitor activity / 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 / negative regulation of protein import into nucleus / postsynaptic modulation of chemical synaptic transmission / cellular response to glucagon stimulus / protein kinase A regulatory subunit binding / axoneme / protein kinase A catalytic subunit binding / 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 / regulation of G2/M transition of mitotic cell cycle / 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 / negative regulation of protein kinase activity / 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 / centrosome / protein serine/threonine kinase activity / 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 Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Madhusudan / Trafny, E.A. / Xuong, N.-H. / Adams, J.A. / Ten Eyck, L.F. / Taylor, S.S. / Sowadski, J.M. | ||||||
Citation | Journal: Protein Sci. / Year: 1994 Title: cAMP-dependent protein kinase: crystallographic insights into substrate recognition and phosphotransfer. Authors: Madhusudan / Trafny, E.A. / Xuong, N.H. / Adams, J.A. / Ten Eyck, L.F. / Taylor, S.S. / Sowadski, J.M. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1993 Title: 2.0 A Refined Crystal Structure of the Catalytic Subunit of cAMP-dependent Protein Kinase Complexed with a Peptide Inhibitor and Detergent Authors: Knighton, D.R. / Bell, S.M. / Zheng, J. / Ten Eyck, L.F. / Xuong, N. / Taylor, S.S. / Sowadski, J.M. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1993 Title: 2.2 A Refined Crystal Structure of the Catalytic Subunit of cAMP-dependent Protein Kinase Complexed with MnATP and a Peptide Inhibitor Authors: Zheng, J. / Trafny, E.A. / Knighton, D.R. / Xuong, N. / Taylor, S.S. / Ten Eyck, L.F. / Sowadski, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jlu.cif.gz | 90.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jlu.ent.gz | 65.2 KB | Display | PDB format |
PDBx/mmJSON format | 1jlu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jl/1jlu ftp://data.pdbj.org/pub/pdb/validation_reports/jl/1jlu | HTTPS FTP |
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-Related structure data
Related structure data | 1jbpC 1atpS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 40657.316 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P05132, EC: 2.7.1.37 |
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#2: Protein/peptide | Mass: 2279.365 Da / Num. of mol.: 1 / Fragment: Residues 5-24 / Mutation: N20A, A21(SEP) / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Mus musculus (mouse). References: UniProt: P27776, UniProt: P61925*PLUS |
#3: Chemical | ChemComp-OCT / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.1 % | |||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Vapor diffusion, hanging drop, pH 8.0,277K, 10mM dithiothreitol, 8% Dow polyethylene glycol 400, methanol, Bicine, VAPOR DIFFUSION, HANGING DROP | |||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Zheng, J., (1992) Acta Crystallogr., B48, 241. / PH range low: 8.3 / PH range high: 8 | |||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jul 1, 1992 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→30 Å / Num. obs: 19924 / % possible obs: 90 % / Rsym value: 0.043 |
Reflection shell | Highest resolution: 2.25 Å |
Reflection | *PLUS Rmerge(I) obs: 0.043 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ATP Resolution: 2.25→30 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 2.25→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||
Refinement | *PLUS σ(F): 2 / Rfactor Rwork: 0.181 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |