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- PDB-6byr: Structures of the PKA RI alpha holoenzyme with the FLHCC driver J... -
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Basic information
Entry | Database: PDB / ID: 6byr | ||||||
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Title | Structures of the PKA RI alpha holoenzyme with the FLHCC driver J-PKAc alpha or native PKAc alpha | ||||||
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![]() | SIGNALING PROTEIN / Protein complex / PKA holoenzyme / Fibrolamellar Hepatocellular Carcinoma | ||||||
Function / homology | ![]() PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / : / ROBO receptors bind AKAP5 / sperm head / negative regulation of inclusion body assembly / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling ...PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / : / ROBO receptors bind AKAP5 / sperm head / negative regulation of inclusion body assembly / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / HDL assembly / mitochondrial protein catabolic process / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / PKA activation / regulation of protein binding / nucleotide-activated protein kinase complex / Hedgehog 'off' state / high-density lipoprotein particle assembly / Rap1 signalling / renal water homeostasis / regulation of protein processing / positive regulation of ATP-dependent activity / transcription regulator inhibitor activity / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cell communication by electrical coupling involved in cardiac conduction / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cellular response to cold / cardiac muscle cell proliferation / Loss of phosphorylation of MECP2 at T308 / regulation of osteoblast differentiation / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / 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 / Vasopressin regulates renal water homeostasis via Aquaporins / sarcomere organization / cellular response to glucagon stimulus / Triglyceride catabolism / protein kinase A regulatory subunit binding / negative regulation of activated T cell proliferation / plasma membrane raft / protein kinase A catalytic subunit binding / axoneme / PKA activation in glucagon signalling / ATPase activator activity / : / Regulation of MECP2 expression and activity / chaperone cofactor-dependent protein refolding / immunological synapse / HSF1-dependent transactivation / mesoderm formation / RET signaling / DARPP-32 events / response to unfolded protein / Interleukin-3, Interleukin-5 and GM-CSF signaling / regulation of cardiac muscle contraction / regulation of cardiac conduction / Regulation of HSF1-mediated heat shock response / sperm flagellum / Attenuation phase / regulation of macroautophagy / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Hedgehog 'off' state / negative regulation of smoothened signaling pathway / regulation of proteasomal protein catabolic process / regulation of cellular response to heat / cAMP binding / protein folding chaperone / Ion homeostasis / regulation of ryanodine-sensitive calcium-release channel activity / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / forebrain development / positive regulation of gluconeogenesis / Recruitment of mitotic centrosome proteins and complexes / sperm midpiece / negative regulation of TORC1 signaling / Recruitment of NuMA to mitotic centrosomes / protein kinase A signaling / Mitochondrial protein degradation / calcium channel complex / Anchoring of the basal body to the plasma membrane / cellular response to epinephrine stimulus / regulation of cytosolic calcium ion concentration / Hsp70 protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein serine/threonine/tyrosine kinase activity / protein export from nucleus / regulation of heart rate / CD209 (DC-SIGN) signaling / multivesicular body Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cao, B. / Lu, T.W. / Martinez Fiesco, J.A. / Tomasini, M. / Fan, L. / Simon, S.M. / Taylor, S.S. / Zhang, P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of the PKA RI alpha Holoenzyme with the FLHCC Driver J-PKAc alpha or Wild-Type PKAc alpha. Authors: Cao, B. / Lu, T.W. / Martinez Fiesco, J.A. / Tomasini, M. / Fan, L. / Simon, S.M. / Taylor, S.S. / Zhang, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 295.9 KB | Display | ![]() |
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PDB format | ![]() | 236.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 49.8 KB | Display | |
Data in CIF | ![]() | 65.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6bysC ![]() 2qcsS ![]() 4wb7S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 47591.945 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P25685, UniProt: P17612, cAMP-dependent protein kinase #2: Protein | Mass: 42816.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | #4: Chemical | ChemComp-MG / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.64 Å3/Da / Density % sol: 66.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 100 mM NaCl, 16-18% pentaerythritol propoxylate and 10% dimethyl sulfoxide |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jun 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.66→50 Å / Num. obs: 30877 / % possible obs: 100 % / Redundancy: 21.3 % / Rsym value: 0.135 / Net I/σ(I): 29.5 |
Reflection shell | Resolution: 3.66→3.79 Å / Redundancy: 22.2 % / Mean I/σ(I) obs: 8.7 / Num. unique obs: 3018 / Rsym value: 0.498 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2QCS and 4WB7 Resolution: 3.661→48.914 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.84
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.661→48.914 Å
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Refine LS restraints |
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LS refinement shell |
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