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- PDB-8ukn: APO and AMP-PNP bound cAMP-dependent protein kinase A catalytic domain -

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Basic information

Entry
Database: PDB / ID: 8ukn
TitleAPO and AMP-PNP bound cAMP-dependent protein kinase A catalytic domain
ComponentscAMP-dependent protein kinase catalytic subunit alpha
KeywordsTRANSFERASE / Protein Kinase / Complex / Ion Channel / Voltage gated calcium channel / Cardiac channel / Stress signaling
Function / homology
Function and homology information


PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / HDL assembly / DARPP-32 events / Rap1 signalling / PKA activation / Regulation of insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / GPER1 signaling / Hedgehog 'off' state ...PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / HDL assembly / DARPP-32 events / Rap1 signalling / PKA activation / Regulation of insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / 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 / Factors involved in megakaryocyte development and platelet production / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Regulation of PLK1 Activity at G2/M Transition / Interleukin-3, Interleukin-5 and GM-CSF signaling / CD209 (DC-SIGN) signaling / RET signaling / Mitochondrial protein degradation / Ion homeostasis / VEGFA-VEGFR2 Pathway / cAMP-dependent protein kinase / regulation of protein processing / cAMP-dependent protein kinase activity / protein localization to lipid droplet / cAMP-dependent protein kinase complex / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cellular response to cold / regulation of osteoblast differentiation / sperm capacitation / ciliary base / negative regulation of glycolytic process through fructose-6-phosphate / protein kinase A regulatory subunit binding / mesoderm formation / cAMP/PKA signal transduction / sperm flagellum / plasma membrane raft / axoneme / postsynaptic modulation of chemical synaptic transmission / negative regulation of TORC1 signaling / regulation of proteasomal protein catabolic process / sperm midpiece / positive regulation of gluconeogenesis / protein serine/threonine/tyrosine kinase activity / cellular response to glucagon stimulus / protein export from nucleus / acrosomal vesicle / positive regulation of protein export from nucleus / negative regulation of smoothened signaling pathway / neural tube closure / positive regulation of cholesterol biosynthetic process / modulation of chemical synaptic transmission / cellular response to glucose stimulus / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / neuromuscular junction / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / mRNA processing / peptidyl-serine phosphorylation / manganese ion binding / cellular response to heat / postsynapse / protein kinase activity / regulation of cell cycle / nuclear speck / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / magnesium ion binding / mitochondrion / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. ...cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsHaji-Ghassemi, O. / Van Petegem, F.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-153305 Canada
Canada Foundation for Innovation Canada
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Crystallographic, kinetic, and calorimetric investigation of PKA interactions with L-type calcium channels and Rad GTPase.
Authors: Yoo, R. / Haji-Ghassemi, O. / Bader, M. / Xu, J. / McFarlane, C. / Van Petegem, F.
History
DepositionOct 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2025Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: cAMP-dependent protein kinase catalytic subunit alpha
D: cAMP-dependent protein kinase catalytic subunit alpha
F: cAMP-dependent protein kinase catalytic subunit alpha
H: cAMP-dependent protein kinase catalytic subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,2816
Polymers158,7134
Non-polymers5682
Water2,450136
1
C: cAMP-dependent protein kinase catalytic subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7402
Polymers39,6781
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
D: cAMP-dependent protein kinase catalytic subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1842
Polymers39,6781
Non-polymers5061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
F: cAMP-dependent protein kinase catalytic subunit alpha


Theoretical massNumber of molelcules
Total (without water)39,6781
Polymers39,6781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
H: cAMP-dependent protein kinase catalytic subunit alpha


Theoretical massNumber of molelcules
Total (without water)39,6781
Polymers39,6781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.818, 139.828, 107.414
Angle α, β, γ (deg.)90.00, 102.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
cAMP-dependent protein kinase catalytic subunit alpha / PKA C-alpha


Mass: 39678.172 Da / Num. of mol.: 4
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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 277.115 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 10% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.75→35 Å / Num. obs: 44968 / % possible obs: 97.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.045 / Rrim(I) all: 0.089 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.75-2.813.30.46226310.830.9520.2970.5530.97985.1
2.81-2.883.60.40829470.8880.970.2480.480.97697
2.88-2.963.80.33330740.9360.9830.1960.3880.98699
2.96-3.053.80.26530270.9610.990.1560.3090.9498.9
3.05-3.153.80.22830010.9630.9910.1350.2660.98198.1
3.15-3.263.70.18730490.9760.9940.1130.220.95798.1
3.26-3.393.60.15129200.9790.9950.0930.1780.97795.4
3.39-3.543.90.11530360.990.9970.0670.1340.99999.1
3.54-3.733.80.08830520.9940.9990.0510.1020.98398.8
3.73-3.963.80.06830230.9940.9990.040.080.98998.4
3.96-4.273.60.05229650.9960.9990.0310.0610.92296.4
4.27-4.73.90.04530690.9970.9990.0260.0530.94399.2
4.7-5.383.70.04230380.9980.9990.0250.0490.89798
5.38-6.773.90.04530440.9970.9990.0260.0520.85598.2
6.77-353.70.03930920.9970.9990.0230.0461.02197.8

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Processing

Software
NameVersionClassification
PHENIX1.20rc1_4392refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→34.96 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.232 1908 5.04 %
Rwork0.1953 --
obs0.1971 37832 81.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→34.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10587 0 35 136 10758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410887
X-RAY DIFFRACTIONf_angle_d0.62714741
X-RAY DIFFRACTIONf_dihedral_angle_d14.0963984
X-RAY DIFFRACTIONf_chiral_restr0.0451581
X-RAY DIFFRACTIONf_plane_restr0.0051862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.820.2923740.241203X-RAY DIFFRACTION39
2.82-2.890.2694810.25511726X-RAY DIFFRACTION55
2.89-2.980.30631020.24161930X-RAY DIFFRACTION62
2.98-3.070.35441220.26792070X-RAY DIFFRACTION67
3.08-3.180.31221280.2572305X-RAY DIFFRACTION74
3.18-3.310.28541330.24192444X-RAY DIFFRACTION78
3.31-3.460.28341330.24092709X-RAY DIFFRACTION85
3.46-3.650.28541520.22333005X-RAY DIFFRACTION96
3.65-3.870.22441710.19283090X-RAY DIFFRACTION98
3.87-4.170.21751550.17772999X-RAY DIFFRACTION96
4.17-4.590.16821510.15153126X-RAY DIFFRACTION99
4.59-5.250.18651490.15353132X-RAY DIFFRACTION99
5.25-6.610.23031670.18723085X-RAY DIFFRACTION98
6.61-34.960.19131900.17683100X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 9.047 Å / Origin y: -10.0791 Å / Origin z: 36.4005 Å
111213212223313233
T0.188 Å20.0254 Å20.0491 Å2-0.2702 Å2-0.0103 Å2--0.2175 Å2
L0.0642 °20.062 °20.15 °2-0.5783 °2-0.084 °2--0.157 °2
S-0.0257 Å °0.0051 Å °-0.0353 Å °-0.1447 Å °0.0738 Å °0.0499 Å °0.0343 Å °0.0141 Å °-0.0366 Å °
Refinement TLS groupSelection details: all

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