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- PDB-8uko: cAMP-dependent protein kinase A catalytic domain in complex with ... -

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Basic information

Entry
Database: PDB / ID: 8uko
TitlecAMP-dependent protein kinase A catalytic domain in complex with voltage gated calcium channel peptide ternary complex 2
Components
  • ARG-GLY-PHE-LEU-ARG-SER-ALA-SER-LEU-GLY-ARG-ARG-ALA-SER-PHE-HIS-LEU
  • cAMP-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)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 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
E: cAMP-dependent protein kinase catalytic subunit alpha
C: ARG-GLY-PHE-LEU-ARG-SER-ALA-SER-LEU-GLY-ARG-ARG-ALA-SER-PHE-HIS-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0895
Polymers41,5342
Non-polymers5553
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-26 kcal/mol
Surface area15790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.036, 118.036, 58.008
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

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


Mass: 39598.191 Da / Num. of mol.: 1
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/peptide ARG-GLY-PHE-LEU-ARG-SER-ALA-SER-LEU-GLY-ARG-ARG-ALA-SER-PHE-HIS-LEU


Mass: 1936.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.32 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M Succinic Acid pH 7.0, 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.89→35 Å / Num. obs: 9121 / % possible obs: 99.9 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.03 / Rrim(I) all: 0.065 / Net I/σ(I): 7.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.89-2.964.61.1246150.3420.7140.5831.2711.124100
2.96-3.034.70.926030.5410.8380.4741.0391.07899.8
3.03-3.114.60.7885960.5480.8410.410.8911.0899.8
3.11-3.250.4945970.790.9390.2430.5521.04799.8
3.2-3.314.90.4335950.840.9560.2170.4861.078100
3.31-3.434.80.2856130.9190.9790.1440.3211.002100
3.43-3.564.70.1946190.9530.9880.10.221.026100
3.56-3.734.50.1355780.9760.9940.0710.1531.039100
3.73-3.924.70.0936100.990.9970.0480.1051.006100
3.92-4.174.90.0636120.9960.9990.0310.070.891100
4.17-4.494.90.0526110.9960.9990.0260.0580.92100
4.49-4.944.60.046110.99810.0210.0460.89899.8
4.94-5.654.80.0356030.9980.9990.0180.0390.743100
5.65-7.114.70.0346220.99810.0170.0380.78199.7
7.11-354.60.0236360.99910.0120.0260.78799.2

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Processing

Software
NameVersionClassification
PHENIX1.20rc1_4392refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.89→32.56 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 27.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2593 441 5.41 %
Rwork0.2104 --
obs0.2132 8149 89.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.89→32.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2781 0 33 8 2822
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022886
X-RAY DIFFRACTIONf_angle_d0.4323926
X-RAY DIFFRACTIONf_dihedral_angle_d13.6071009
X-RAY DIFFRACTIONf_chiral_restr0.039425
X-RAY DIFFRACTIONf_plane_restr0.003499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-3.310.3432850.28851967X-RAY DIFFRACTION68
3.31-4.160.28161500.21462873X-RAY DIFFRACTION100
4.17-32.560.23472060.18432868X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 24.6034 Å / Origin y: -2.1396 Å / Origin z: 16.9813 Å
111213212223313233
T0.2127 Å20.178 Å2-0.0947 Å2--0.2245 Å20.0059 Å2--0.1212 Å2
L0.155 °20.0002 °20.0359 °2-0.0647 °20.0183 °2--0.0664 °2
S-0.1514 Å °-0.121 Å °0.357 Å °0.2313 Å °-0.0162 Å °-0.0679 Å °-0.2783 Å °0.0454 Å °-0.142 Å °
Refinement TLS groupSelection details: all

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