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- PDB-6c0u: Crystal structure of cAMP-dependent protein kinase Calpha subunit... -

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Basic information

Entry
Database: PDB / ID: 6c0u
TitleCrystal structure of cAMP-dependent protein kinase Calpha subunit bound with N46
ComponentscAMP-dependent protein kinase catalytic subunit alpha
Keywordstransferase/transferase inhibitor / Serine/threonine protein kinase (EC 2.7.11.11) / TRANSFERASE / transferase-transferase inhibitor complex
Function / homology
Function and homology information


cAMP/PKA signal transduction / PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / ROBO receptors bind AKAP5 / channel activator activity / HDL assembly / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / mitochondrial protein catabolic process / nucleotide-activated protein kinase complex / cell communication by electrical coupling involved in cardiac conduction ...cAMP/PKA signal transduction / PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / ROBO receptors bind AKAP5 / channel activator activity / HDL assembly / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / mitochondrial protein catabolic process / nucleotide-activated protein kinase complex / cell communication by electrical coupling involved in cardiac conduction / high-density lipoprotein particle assembly / Rap1 signalling / regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cellular response to cold / cAMP-dependent protein kinase / regulation of osteoblast differentiation / Loss of phosphorylation of MECP2 at T308 / cAMP-dependent protein kinase activity / sperm capacitation / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of glycolytic process through fructose-6-phosphate / PKA activation / ciliary base / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / negative regulation of interleukin-2 production / postsynaptic modulation of chemical synaptic transmission / 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 / Interleukin-3, Interleukin-5 and GM-CSF signaling / DARPP-32 events / regulation of cardiac muscle contraction / regulation of cardiac conduction / sperm flagellum / regulation of macroautophagy / renal water homeostasis / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Hedgehog 'off' state / regulation of proteasomal protein catabolic process / negative regulation of smoothened signaling pathway / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Ion homeostasis / Recruitment of mitotic centrosome proteins and complexes / positive regulation of gluconeogenesis / sperm midpiece / negative regulation of TORC1 signaling / Recruitment of NuMA to mitotic centrosomes / cellular response to glucagon stimulus / Anchoring of the basal body to the plasma membrane / calcium channel complex / cellular response to epinephrine stimulus / Mitochondrial protein degradation / protein serine/threonine/tyrosine kinase activity / protein kinase A signaling / protein export from nucleus / CD209 (DC-SIGN) signaling / positive regulation of calcium-mediated signaling / regulation of heart rate / AURKA Activation by TPX2 / FCGR3A-mediated IL10 synthesis / acrosomal vesicle / positive regulation of protein export from nucleus / 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 / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cytokine-mediated signaling pathway / VEGFA-VEGFR2 Pathway / mRNA processing / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / Regulation of PLK1 Activity at G2/M Transition / manganese ion binding / Factors involved in megakaryocyte development and platelet production / cellular response to heat / peptidyl-serine phosphorylation / dendritic spine / regulation of cell cycle / protein kinase activity / nuclear speck / mitochondrial matrix / protein phosphorylation / protein domain specific binding
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. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-EE4 / PHOSPHATE ION / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsQin, L. / Sankaran, B. / Kim, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM090161-08 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural basis for selective inhibition of human PKG I alpha by the balanol-like compound N46.
Authors: Qin, L. / Sankaran, B. / Aminzai, S. / Casteel, D.E. / Kim, C.
History
DepositionJan 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cAMP-dependent protein kinase catalytic subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9806
Polymers41,0911
Non-polymers8895
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.494, 120.494, 80.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 41090.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKACA, PKACA / Plasmid: pet15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P17612, cAMP-dependent protein kinase
#2: Chemical ChemComp-EE4 / N-[(3R,4R)-4-{[4-(2-fluoro-3-methoxy-6-propoxybenzene-1-carbonyl)benzene-1-carbonyl]amino}pyrrolidin-3-yl]-1H-indazole-5-carboxamide


Mass: 559.588 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H30FN5O5
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
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: 4.09 Å3/Da / Density % sol: 69.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 16% (w/v) PEG8000, 0.04 M potassium phosphate (monobasic), 20% (v/v) glycerol

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→48.3 Å / Num. obs: 20021 / % possible obs: 100 % / Redundancy: 9.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Net I/σ(I): 21.5
Reflection shellResolution: 2.65→2.78 Å / CC1/2: 0.753

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BX6

1bx6


Resolution: 2.65→43.833 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2432 2021 10.11 %
Rwork0.2077 --
obs0.2113 19997 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→43.833 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2684 0 58 34 2776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022810
X-RAY DIFFRACTIONf_angle_d0.5443819
X-RAY DIFFRACTIONf_dihedral_angle_d4.4931626
X-RAY DIFFRACTIONf_chiral_restr0.041409
X-RAY DIFFRACTIONf_plane_restr0.005489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6502-2.71650.35971420.28961265X-RAY DIFFRACTION100
2.7165-2.78990.33251440.27631288X-RAY DIFFRACTION100
2.7899-2.8720.32251410.26741261X-RAY DIFFRACTION100
2.872-2.96470.28661420.25351262X-RAY DIFFRACTION100
2.9647-3.07060.27761420.23811275X-RAY DIFFRACTION100
3.0706-3.19350.26361430.23271272X-RAY DIFFRACTION100
3.1935-3.33880.26961430.23531261X-RAY DIFFRACTION100
3.3388-3.51480.23411430.21851286X-RAY DIFFRACTION100
3.5148-3.73490.23361460.20761281X-RAY DIFFRACTION100
3.7349-4.02310.2051430.19041289X-RAY DIFFRACTION100
4.0231-4.42760.24721420.18031271X-RAY DIFFRACTION100
4.4276-5.06740.2261430.17871304X-RAY DIFFRACTION100
5.0674-6.38130.24761490.20821304X-RAY DIFFRACTION100
6.3813-43.83890.21041580.19481357X-RAY DIFFRACTION100

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