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Yorodumi- PDB-6mm5: Catalytic subunit of cAMP-dependent protein kinase A in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mm5 | ||||||
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Title | Catalytic subunit of cAMP-dependent protein kinase A in complex with RyR2 peptide (2799-2810) | ||||||
Components |
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Keywords | TRANSFERASE/PROTEIN BINDING / Kinase / complex / ion channel / enzyme / PROTEIN BINDING / TRANSFERASE-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information manganese ion transmembrane transport / 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 / Mitochondrial protein degradation / suramin binding ...manganese ion transmembrane transport / 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 / Mitochondrial protein degradation / suramin binding / establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / PKA activation / regulation of SA node cell action potential / regulation of atrial cardiac muscle cell action potential / left ventricular cardiac muscle tissue morphogenesis / Vasopressin regulates renal water homeostasis via Aquaporins / Regulation of insulin secretion / GPER1 signaling / organic cyclic compound binding / Hedgehog 'off' state / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / regulation of AV node cell action potential / 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 / calcium-induced calcium release activity / sarcoplasmic reticulum calcium ion transport / 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 / RET signaling / Stimuli-sensing channels / Ion homeostasis / ventricular cardiac muscle cell action potential / regulation of ventricular cardiac muscle cell action potential / positive regulation of sequestering of calcium ion / VEGFA-VEGFR2 Pathway / embryonic heart tube morphogenesis / cardiac muscle hypertrophy / regulation of cellular respiration / regulation of protein processing / ryanodine-sensitive calcium-release channel activity / protein localization to lipid droplet / regulation of bicellular tight junction assembly / response to muscle activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cellular response to parathyroid hormone stimulus / calcium ion transport into cytosol / regulation of cardiac muscle contraction by calcium ion signaling / calcium ion transmembrane import into cytosol / response to caffeine / A band / response to redox state / cAMP-dependent protein kinase / cellular response to cold / sperm capacitation / regulation of osteoblast differentiation / cAMP-dependent protein kinase activity / ciliary base / cAMP-dependent protein kinase complex / negative regulation of glycolytic process through fructose-6-phosphate / AMP-activated protein kinase activity / positive regulation of heart rate / postsynaptic modulation of chemical synaptic transmission / negative regulation of cytosolic calcium ion concentration / cellular response to caffeine / cellular response to glucagon stimulus / protein kinase A regulatory subunit binding / intracellularly gated calcium channel activity / axoneme / protein kinase A catalytic subunit binding / plasma membrane raft / positive regulation of the force of heart contraction / response to magnesium ion / : / mesoderm formation / detection of calcium ion / sperm flagellum / smooth endoplasmic reticulum / regulation of cardiac muscle contraction / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / negative regulation of smoothened signaling pathway / striated muscle contraction / regulation of proteasomal protein catabolic process / release of sequestered calcium ion into cytosol / positive regulation of gluconeogenesis / cardiac muscle contraction / regulation of synaptic transmission, glutamatergic / extrinsic component of cytoplasmic side of plasma membrane / monoatomic ion transmembrane transport / sperm midpiece / negative regulation of TORC1 signaling Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | van Petegem, F. / Haji-Ghassemi, O. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Mol.Cell / Year: 2019 Title: cAMP-dependent protein kinase A in complex with RyR2 peptide (2799-2810) Authors: Haji-Ghassemi, O. / Yuchi, Z. / van Petegem, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mm5.cif.gz | 97.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mm5.ent.gz | 69 KB | Display | PDB format |
PDBx/mmJSON format | 6mm5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mm/6mm5 ftp://data.pdbj.org/pub/pdb/validation_reports/mm/6mm5 | HTTPS FTP |
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-Related structure data
Related structure data | 6mm6C 6mm7C 6mm8C 3o7lS 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
-Protein / Protein/peptide , 2 types, 2 molecules EC
#1: Protein | Mass: 39598.191 Da / Num. of mol.: 1 / Fragment: residues 16-351 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/peptide | Mass: 1497.681 Da / Num. of mol.: 1 / Fragment: residues 2799-2810 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: E9Q401 |
-Non-polymers , 4 types, 217 molecules
#3: Chemical | ChemComp-MG / |
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#4: Chemical | ChemComp-ANP / |
#5: Chemical | ChemComp-EDO / |
#6: 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: 2.46 Å3/Da / Density % sol: 50.06 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M trimethylamine N-oxide, 0.1 M tris-HCl, 20% (w/v) PEG monomethyl ether 2K 25% (v/V) ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 13, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→35 Å / Num. obs: 30237 / % possible obs: 99.5 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.027 / Rrim(I) all: 0.063 / Χ2: 0.92 / Net I/σ(I): 6.4 / Num. measured all: 157735 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3O7L Resolution: 1.95→32.95 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.575 / SU ML: 0.126 / SU R Cruickshank DPI: 0.1583 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.149 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 106.24 Å2 / Biso mean: 42.882 Å2 / Biso min: 26.31 Å2
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Refinement step | Cycle: final / Resolution: 1.95→32.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.949→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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