[English] 日本語
Yorodumi- PDB-6mm6: Catalytic subunit of cAMP-dependent protein kinase A in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mm6 | ||||||
---|---|---|---|---|---|---|---|
Title | Catalytic subunit of cAMP-dependent protein kinase A in complex with RyR2 phosphorylation domain (2699-2904) | ||||||
Components |
| ||||||
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 / 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 / GPER1 signaling / organic cyclic compound binding / 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 / AURKA Activation by TPX2 / MAPK6/MAPK4 signaling / GLI3 is processed to GLI3R by the proteasome / 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 / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / response to muscle activity / calcium ion transport into cytosol / response to caffeine / A band / response to redox state / cAMP-dependent protein kinase / calcium ion transmembrane import into cytosol / 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 / plasma membrane raft / intracellularly gated calcium channel activity / protein kinase A catalytic subunit binding / axoneme / positive regulation of the force of heart contraction / extrinsic component of cytoplasmic side of plasma membrane / response to magnesium ion / mesoderm formation / detection of calcium ion / sperm flagellum / smooth endoplasmic reticulum / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / striated muscle contraction / regulation of proteasomal protein catabolic process / negative regulation of smoothened signaling pathway / positive regulation of gluconeogenesis / sperm midpiece / monoatomic ion transmembrane transport / negative regulation of TORC1 signaling / regulation of synaptic transmission, glutamatergic / regulation of cytosolic calcium ion concentration / sarcoplasmic reticulum membrane / calcium channel complex / cellular response to epinephrine stimulus / protein kinase A signaling Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å | ||||||
Authors | van Petegem, F. / Haji-Ghassemi, O. | ||||||
Funding support | Canada, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6mm6.cif.gz | 447.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6mm6.ent.gz | 366.1 KB | Display | PDB format |
PDBx/mmJSON format | 6mm6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mm/6mm6 ftp://data.pdbj.org/pub/pdb/validation_reports/mm/6mm6 | HTTPS FTP |
---|
-Related structure data
Related structure data | 6mm5SC 6mm7C 6mm8C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
-Protein , 2 types, 4 molecules CEFD
#1: Protein | Mass: 39598.191 Da / Num. of mol.: 2 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 #2: Protein | Mass: 24257.604 Da / Num. of mol.: 2 / Fragment: residues 2699-2904 / Mutation: K2879A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ryr2 / Production host: Escherichia coli (E. coli) / References: UniProt: E9Q401 |
---|
-Non-polymers , 6 types, 373 molecules
#3: Chemical | ChemComp-ACT / | ||||||||
---|---|---|---|---|---|---|---|---|---|
#4: Chemical | #5: Chemical | ChemComp-PGE / | #6: Chemical | #7: Chemical | ChemComp-EDO / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.9 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.05M HEPES, 0.05 M KCl, 0.01M MgCl2, 15% (w/v) PEG 6K, and 25% (v/v) ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 8, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.39→35 Å / Num. obs: 56090 / % possible obs: 98.5 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.108 / Rrim(I) all: 0.161 / Χ2: 1.011 / Net I/σ(I): 5.2 / Num. measured all: 123858 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 2.2 %
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6MM5 Resolution: 2.39→34.87 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.892 / SU B: 22.792 / SU ML: 0.253 / SU R Cruickshank DPI: 0.3972 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.397 / ESU R Free: 0.264 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.21 Å2 / Biso mean: 38.839 Å2 / Biso min: 15.45 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.39→34.87 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.393→2.455 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|