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Yorodumi- PDB-4ae9: Structure and function of the Human Sperm-Specific Isoform of Pro... -
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-Basic information
Entry | Database: PDB / ID: 4ae9 | ||||||
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Title | Structure and function of the Human Sperm-Specific Isoform of Protein Kinase A (PKA) Catalytic Subunit C alpha 2 | ||||||
Components | CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT ALPHA | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / ROBO receptors bind AKAP5 / HDL assembly / mitochondrial protein catabolic process / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / regulation of protein binding / nucleotide-activated protein kinase complex / high-density lipoprotein particle assembly / Rap1 signalling ...PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / ROBO receptors bind AKAP5 / HDL assembly / mitochondrial protein catabolic process / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / regulation of protein binding / nucleotide-activated protein kinase complex / high-density lipoprotein particle assembly / Rap1 signalling / renal water homeostasis / regulation of protein processing / 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 / cellular response to cold / Loss of phosphorylation of MECP2 at T308 / regulation of osteoblast differentiation / CREB1 phosphorylation through the activation of Adenylate Cyclase / sperm capacitation / PKA activation / 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 / cellular response to glucagon stimulus / Triglyceride catabolism / protein kinase A regulatory subunit binding / plasma membrane raft / PKA activation in glucagon signalling / : / Regulation of MECP2 expression and activity / mesoderm formation / RET signaling / DARPP-32 events / Interleukin-3, Interleukin-5 and GM-CSF signaling / regulation of cardiac muscle contraction / regulation of cardiac conduction / sperm flagellum / 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 / 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 / positive regulation of gluconeogenesis / Recruitment of mitotic centrosome proteins and complexes / sperm midpiece / negative regulation of TORC1 signaling / Mitochondrial protein degradation / Recruitment of NuMA to mitotic centrosomes / protein kinase A signaling / calcium channel complex / Anchoring of the basal body to the plasma membrane / cellular response to epinephrine stimulus / regulation of cytosolic calcium ion concentration / protein serine/threonine/tyrosine kinase activity / protein export from nucleus / regulation of heart rate / CD209 (DC-SIGN) signaling / AURKA Activation by TPX2 / FCGR3A-mediated IL10 synthesis / positive regulation of protein export from nucleus / acrosomal vesicle / neural tube closure / Regulation of insulin secretion / cellular response to glucose stimulus / Degradation of GLI1 by the proteasome / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / neuromuscular junction / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / mRNA processing / cytokine-mediated signaling pathway / Vasopressin regulates renal water homeostasis via Aquaporins / VEGFA-VEGFR2 Pathway / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / Regulation of PLK1 Activity at G2/M Transition / cellular response to heat / Factors involved in megakaryocyte development and platelet production / manganese ion binding / peptidyl-serine phosphorylation / dendritic spine / regulation of cell cycle / protein kinase activity / nuclear speck / mitochondrial matrix / protein domain specific binding / protein phosphorylation Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Hereng, T.H. / Backe, P.H. / Kahmann, J. / Scheich, C. / Bjoras, M. / Skalhegg, B.S. / Rosendal, K.R. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2012 Title: Structure and Function of the Human Sperm-Specific Isoform of Protein Kinase a (Pka) Catalytic Subunit Calpha2 Authors: Hereng, T.H. / Backe, P.H. / Kahmann, J. / Scheich, C. / Bjoras, M. / Skalhegg, B.S. / Rosendal, K.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ae9.cif.gz | 152.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ae9.ent.gz | 120.3 KB | Display | PDB format |
PDBx/mmJSON format | 4ae9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ae9_validation.pdf.gz | 438.7 KB | Display | wwPDB validaton report |
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Full document | 4ae9_full_validation.pdf.gz | 450.2 KB | Display | |
Data in XML | 4ae9_validation.xml.gz | 30.5 KB | Display | |
Data in CIF | 4ae9_validation.cif.gz | 43 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/4ae9 ftp://data.pdbj.org/pub/pdb/validation_reports/ae/4ae9 | HTTPS FTP |
-Related structure data
Related structure data | 4ae6C 1smhS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 40118.668 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell: SPERMATOZOA / Plasmid: PET24 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA PLYSS / References: UniProt: P17612, cAMP-dependent protein kinase #2: Water | ChemComp-HOH / | Sequence details | THE PROTEIN CORRESPOND | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.42 % / Description: NONE |
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Crystal grow | Details: 20 % PEG 3350, 0.2 M POTASSIUM ACETATE, 5 % POLYPROPYLENE GLYCOL P400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97558 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97558 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→71.02 Å / Num. obs: 34845 / % possible obs: 97 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.3→7.27 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 4.5 / % possible all: 98.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SMH Resolution: 2.3→71.02 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.878 / SU B: 6.947 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.361 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.467 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→71.02 Å
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