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- PDB-9o7v: Crystal Structure of the RIb:C Heterodimer of PKA -

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Basic information

Entry
Database: PDB / ID: 9o7v
TitleCrystal Structure of the RIb:C Heterodimer of PKA
Components
  • cAMP-dependent protein kinase catalytic subunit alpha
  • cAMP-dependent protein kinase type I-beta regulatory subunit
KeywordsTRANSFERASE / cAMP-dependent protein kinase / regulatory subunit / N3A motif / allosteric crosstalk
Function / homology
Function and homology information


positive regulation of fear response / cAMP-dependent protein kinase regulator activity / 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 ...positive regulation of fear response / cAMP-dependent protein kinase regulator activity / 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 / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Hedgehog 'off' state / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / MAPK6/MAPK4 signaling / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / GLI3 is processed to GLI3R by the proteasome / AURKA Activation by TPX2 / Factors involved in megakaryocyte development and platelet production / Interleukin-3, Interleukin-5 and GM-CSF signaling / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Regulation of PLK1 Activity at G2/M Transition / CD209 (DC-SIGN) signaling / RET signaling / Mitochondrial protein degradation / VEGFA-VEGFR2 Pathway / Ion homeostasis / regulation of synaptic vesicle cycle / negative regulation of cAMP/PKA signal transduction / cAMP-dependent protein kinase inhibitor activity / 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 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / regulation of osteoblast differentiation / cellular response to cold / sperm capacitation / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / intracellular potassium ion homeostasis / mesoderm formation / cAMP/PKA signal transduction / plasma membrane raft / axoneme / PKA activation in glucagon signalling / DARPP-32 events / positive regulation of excitatory postsynaptic potential / sperm flagellum / postsynaptic modulation of chemical synaptic transmission / cAMP binding / Hedgehog 'off' state / negative regulation of TORC1 signaling / sperm midpiece / regulation of proteasomal protein catabolic process / multivesicular body / positive regulation of gluconeogenesis / protein serine/threonine/tyrosine kinase activity / cellular response to glucagon stimulus / acrosomal vesicle / FCGR3A-mediated IL10 synthesis / protein export from nucleus / positive regulation of phagocytosis / hippocampal mossy fiber to CA3 synapse / positive regulation of protein export from nucleus / positive regulation of long-term synaptic potentiation / negative regulation of smoothened signaling pathway / neural tube closure / neuromuscular junction / cellular response to glucose stimulus / positive regulation of cholesterol biosynthetic process / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / modulation of chemical synaptic transmission / peptidyl-serine phosphorylation / Schaffer collateral - CA1 synapse / mRNA processing / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / manganese ion binding / cellular response to heat / Factors involved in megakaryocyte development and platelet production / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / learning or memory / protein kinase activity / postsynapse / regulation of cell cycle / nuclear speck
Similarity search - Function
RIbeta, dimerization/docking domain / cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / : / Cyclic nucleotide-binding domain signature 2. / cAMP-dependent protein kinase catalytic subunit / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site ...RIbeta, dimerization/docking domain / cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / : / Cyclic nucleotide-binding domain signature 2. / cAMP-dependent protein kinase catalytic subunit / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / RmlC-like jelly roll fold / 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
cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase type I-beta regulatory subunit
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsWu, J. / Ilouz, R. / Taylor, S.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorGM130389 United States
CitationJournal: Protein Sci. / Year: 2025
Title: N3A motifs in RI beta mediate allosteric crosstalk between cAMP and ATP in PKA activation.
Authors: Wu, J. / Bruystens, J.G.H. / Sahoo, P. / Bubis, J. / Maillard, R.A. / Taylor, S.S. / Ilouz, R.
History
DepositionApr 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: cAMP-dependent protein kinase catalytic subunit alpha
B: cAMP-dependent protein kinase type I-beta regulatory subunit


Theoretical massNumber of molelcules
Total (without water)83,7882
Polymers83,7882
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-11 kcal/mol
Surface area27610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.497, 103.497, 313.382
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 40657.316 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 cAMP-dependent protein kinase type I-beta regulatory subunit


Mass: 43130.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAR1B / Production host: Escherichia coli (E. coli) / References: UniProt: P31321
Has ligand of interestN
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: 2.89 Å3/Da / Density % sol: 57.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 1.4M ammonium sulfate and 0.1M sodium acetate at pH 5.3.

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: under liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.7→50 Å / Num. obs: 11338 / % possible obs: 99.5 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 30.8
Reflection shellResolution: 3.7→3.78 Å / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 8.4 / Num. unique obs: 638 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.7_650refinement
SCALEPACKdata scaling
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.7→46.371 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2931 537 4.76 %
Rwork0.2313 --
obs0.2343 11271 99.5 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 82.261 Å2 / ksol: 0.311 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-13.5577 Å20 Å2-0 Å2
2--13.5577 Å20 Å2
3----27.1155 Å2
Refinement stepCycle: LAST / Resolution: 3.7→46.371 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4902 0 0 0 4902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135012
X-RAY DIFFRACTIONf_angle_d2.0526785
X-RAY DIFFRACTIONf_dihedral_angle_d16.4271849
X-RAY DIFFRACTIONf_chiral_restr0.108738
X-RAY DIFFRACTIONf_plane_restr0.01876
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7-4.07280.30671210.26852594X-RAY DIFFRACTION99
4.0728-4.66160.27631340.21252611X-RAY DIFFRACTION100
4.6616-5.87130.28321440.23612669X-RAY DIFFRACTION100
5.8713-46.370.30191380.2252860X-RAY DIFFRACTION99

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