[English] 日本語
![](img/lk-miru.gif)
- PDB-3pvb: Crystal structure of (73-244)RIa:C holoenzyme of cAMP-dependent P... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3pvb | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of (73-244)RIa:C holoenzyme of cAMP-dependent Protein kinase | ||||||
![]() | (cAMP-dependent protein kinase ...) x 2 | ||||||
![]() | TRANSFERASE / Kinase / RIa Holoenzyme / Tetrameric Protein Kinase A | ||||||
Function / homology | ![]() : / 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 ...: / 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 / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Regulation of insulin secretion / Factors involved in megakaryocyte development and platelet production / 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 / PKA activation / 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 / nucleotide-activated protein kinase complex / Hedgehog 'off' state / 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 inhibitor activity / cAMP-dependent protein kinase / cellular response to cold / cardiac muscle cell proliferation / 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 / Vasopressin regulates renal water homeostasis via Aquaporins / sarcomere organization / cellular response to glucagon stimulus / protein kinase A regulatory subunit binding / negative regulation of activated T cell proliferation / plasma membrane raft / protein kinase A catalytic subunit binding / axoneme / immunological synapse / mesoderm formation / sperm flagellum / negative regulation of smoothened signaling pathway / regulation of proteasomal protein catabolic process / cAMP binding / 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 / multivesicular body / positive regulation of protein export from nucleus / acrosomal vesicle / neural tube closure / cellular response to glucose stimulus / regulation of protein phosphorylation / 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 / negative regulation of gene expression / protein serine kinase activity Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Boettcher, A.J. / Wu, J. / Kim, C. / Yang, J. / Bruystens, J. / Cheung, N. / Pennypacker, J.K. / Blumenthal, D.A. / Kornev, A.P. / Taylor, S.S. | ||||||
![]() | ![]() Title: Crystal structure of (73-244)RIa:C holoenzyme of cAMP-dependent Protein kinase Authors: Boettcher, A.J. / Wu, J. / Kim, C. / Yang, J. / Bruystens, J. / Cheung, N. / Pennypacker, J.K. / Blumenthal, D.A. / Kornev, A.P. / Taylor, S.S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 116.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 87.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 777.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 812.5 KB | Display | |
Data in XML | ![]() | 18.5 KB | Display | |
Data in CIF | ![]() | 25 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2qcsS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | one molecule per asymmetrical unit |
-
Components
-CAMP-dependent protein kinase ... , 2 types, 2 molecules AB
#1: Protein | Mass: 40432.891 Da / Num. of mol.: 1 / Fragment: unp residues 7-351 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Protein | Mass: 17909.275 Da / Num. of mol.: 1 / Fragment: unp residues 85-244 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 4 types, 19 molecules ![](data/chem/img/ANP.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ANP / | ||||
---|---|---|---|---|---|
#4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.86 Å3/Da / Density % sol: 74.7 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: The RIa(73-244):C complex was crystallized in 0.1M MES pH 6.0 and 12% PEG 20,000 by using a Douglas Instruments Oryx8 crystallography robot as 1:1 protein solution:crystallizing solution, ...Details: The RIa(73-244):C complex was crystallized in 0.1M MES pH 6.0 and 12% PEG 20,000 by using a Douglas Instruments Oryx8 crystallography robot as 1:1 protein solution:crystallizing solution, VAPOR DIFFUSION, SITTING DROP, temperature 298.0 K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 2, 2009 |
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: 3.3→50 Å / Num. obs: 27860 / % possible obs: 97.1 % / Observed criterion σ(F): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 3.3→3.39 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1797 / % possible all: 93.7 |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: pdb entry 2QCS Resolution: 3.3→50 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→50 Å
| ||||||||||||||||||||
Refine LS restraints |
|