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Yorodumi- PDB-4din: Novel Localization and Quaternary Structure of the PKA RI beta Ho... -
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-Basic information
Entry | Database: PDB / ID: 4din | ||||||
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Title | Novel Localization and Quaternary Structure of the PKA RI beta Holoenzyme | ||||||
Components |
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Keywords | Transferase/Transport Protein / isoform diversity / RIb2:C2 tetrameric complex / Transferase-Transport Protein complex | ||||||
Function / homology | Function and homology information positive regulation of fear response / 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 ...positive regulation of fear response / 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 / regulation of synaptic vesicle cycle / cAMP-dependent protein kinase regulator 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 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / 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 / protein kinase A catalytic subunit binding / plasma membrane raft / positive regulation of excitatory postsynaptic potential / PKA activation in glucagon signalling / mesoderm formation / DARPP-32 events / sperm flagellum / Hedgehog 'off' state / regulation of proteasomal protein catabolic process / negative regulation of smoothened signaling pathway / protein kinase A signaling / cAMP binding / positive regulation of gluconeogenesis / regulation of synaptic transmission, glutamatergic / negative regulation of TORC1 signaling / sperm midpiece / hippocampal mossy fiber to CA3 synapse / protein export from nucleus / protein serine/threonine/tyrosine kinase activity / multivesicular body / FCGR3A-mediated IL10 synthesis / acrosomal vesicle / positive regulation of protein export from nucleus / neural tube closure / positive regulation of long-term synaptic potentiation / cellular response to glucose stimulus / modulation of chemical synaptic transmission / neuromuscular junction / Schaffer collateral - CA1 synapse / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / mRNA processing / small GTPase binding / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / presynapse / cellular response to heat / manganese ion binding / Factors involved in megakaryocyte development and platelet production / postsynapse / peptidyl-serine phosphorylation / dendritic spine / learning or memory / regulation of cell cycle Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.7 Å | ||||||
Authors | Ilouz, R. / Bubis, J. / Wu, J. / Yim, Y.Y. / Deal, M.S. / Kornev, A.P. / Ma, Y. / Blumenthal, D.K. / Taylor, S.S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Localization and quaternary structure of the PKA RI Beta holoenzyme Authors: Ilouz, R. / Bubis, J. / Wu, J. / Yim, Y.Y. / Deal, M.S. / Kornev, A.P. / Ma, Y. / Blumenthal, D.K. / 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 | 4din.cif.gz | 140.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4din.ent.gz | 108.5 KB | Display | PDB format |
PDBx/mmJSON format | 4din.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/di/4din ftp://data.pdbj.org/pub/pdb/validation_reports/di/4din | HTTPS FTP |
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-Related structure data
Related structure data | 2qcsS 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
#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) / Gene: Prkaca, Pkaca / Production host: Escherichia coli (E. coli) / References: UniProt: P05132, cAMP-dependent protein kinase |
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#2: Protein | Mass: 43130.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAR1B / Production host: Escherichia coli (E. coli) / References: UniProt: P31321 |
#3: Chemical | ChemComp-ATP / |
#4: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.75 Å3/Da / Density % sol: 67.16 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.3 Details: 1.4 M ammonium sulfate, 0.1M Sodium Acetate pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-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: Oct 19, 2010 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.7→50 Å / Num. obs: 16198 / % possible obs: 96.1 % / Observed criterion σ(I): 2 / Redundancy: 9.3 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 11 |
Reflection shell | Resolution: 3.7→3.77 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2 / % possible all: 90 |
-Processing
Software |
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Refinement | Starting model: PDB entry 2QCS Resolution: 3.7→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 2517
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Solvent computation | Bsol: 143.399 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 299.96 Å2 / Biso mean: 156.4891 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: LAST / Resolution: 3.7→50 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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