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- PDB-6mm8: Catalytic subunit of cAMP-dependent protein kinase A in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6mm8 | ||||||
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Title | Catalytic subunit of cAMP-dependent protein kinase A in complex with RyR2 K2879A, S2813D phosphomimetic (2699-2904) crystal form 2 | ||||||
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![]() | PROTEIN BINDING / Kinase / complex / ion channel / enzyme | ||||||
Function / homology | ![]() 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 / suramin binding / establishment of protein localization to endoplasmic reticulum ...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 / suramin binding / establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / PKA activation / Purkinje myocyte to ventricular cardiac muscle cell signaling / 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 / organic cyclic compound binding / 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 / regulation of AV node cell action potential / Recruitment of NuMA to mitotic centrosomes / calcium-induced calcium release activity / Anchoring of the basal body to the plasma membrane / MAPK6/MAPK4 signaling / GLI3 is processed to GLI3R by the proteasome / AURKA Activation by TPX2 / 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 / Mitochondrial protein degradation / 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 / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cellular response to parathyroid hormone stimulus / response to muscle activity / calcium ion transport into cytosol / calcium ion transmembrane import into cytosol / response to caffeine / A band / response to redox state / cAMP-dependent protein kinase / cellular response to cold / 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 / 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 / plasma membrane raft / protein kinase A catalytic subunit binding / axoneme / positive regulation of the force of heart contraction / response to magnesium ion / : / mesoderm formation / detection of calcium ion / smooth endoplasmic reticulum / sperm flagellum / 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 / monoatomic ion transmembrane transport / regulation of synaptic transmission, glutamatergic / positive regulation of gluconeogenesis / extrinsic component of cytoplasmic side of plasma membrane / sperm midpiece / negative regulation of TORC1 signaling / protein kinase A signaling / sarcoplasmic reticulum membrane / calcium channel complex / cellular response to epinephrine stimulus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | van Petegem, F. / Haji-Ghassemi, O. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 144.4 KB | Display | ![]() |
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PDB format | ![]() | 107.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 27.6 KB | Display | |
Data in CIF | ![]() | 40.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6mm5C ![]() 6mm6C ![]() 6mm7SC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules CD
#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.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 24285.613 Da / Num. of mol.: 1 / Fragment: residues 2699-2904 / Mutation: K2879A, S2813D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 6 types, 513 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/ANP.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/ANP.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-PEG / | ||||||||
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#4: Chemical | #5: Chemical | ChemComp-ANP / | #6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-CL / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.98 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.15 M HEPES pH 7.5, 15% (w/v) PEG 20k, and 25% (v/v) ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 30, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.85→35 Å / Num. obs: 58151 / % possible obs: 96.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.038 / Rrim(I) all: 0.074 / Χ2: 0.995 / Net I/σ(I): 6.5 / Num. measured all: 219079 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6MM7 Resolution: 1.85→33.95 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.189 / SU ML: 0.092 / SU R Cruickshank DPI: 0.1365 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.132 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: 104.48 Å2 / Biso mean: 26.447 Å2 / Biso min: 9.58 Å2
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Refinement step | Cycle: final / Resolution: 1.85→33.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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