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- PDB-6bys: Structures of the PKA RI alpha holoenzyme with the FLHCC driver J... -

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Basic information

Entry
Database: PDB / ID: 6bys
TitleStructures of the PKA RI alpha holoenzyme with the FLHCC driver J-PKAc alpha or native PRKAc alpha
Components
  • cAMP-dependent protein kinase catalytic subunit alphaCAMP-dependent pathway
  • cAMP-dependent protein kinase type I-alpha regulatory subunitCAMP-dependent pathway
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / sperm connecting piece / ROBO receptors bind AKAP5 / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / HDL assembly ...PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / sperm connecting piece / ROBO receptors bind AKAP5 / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / HDL assembly / high-density lipoprotein particle assembly / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / PKA activation / regulation of protein binding / Hedgehog 'off' state / Rap1 signalling / nucleotide-activated protein kinase complex / renal water homeostasis / regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cAMP-dependent protein kinase inhibitor activity / cell communication by electrical coupling involved in cardiac conduction / sarcomere organization / cAMP-dependent protein kinase / cellular response to cold / cardiac muscle cell proliferation / Loss of phosphorylation of MECP2 at T308 / sperm capacitation / regulation of osteoblast differentiation / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / cAMP-dependent protein kinase activity / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / Vasopressin regulates renal water homeostasis via Aquaporins / postsynaptic modulation of chemical synaptic transmission / cellular response to glucagon stimulus / Triglyceride catabolism / protein kinase A regulatory subunit binding / axoneme / negative regulation of activated T cell proliferation / protein kinase A catalytic subunit binding / plasma membrane raft / PKA activation in glucagon signalling / : / Regulation of MECP2 expression and activity / immunological synapse / mesoderm formation / regulation of cardiac conduction / RET signaling / DARPP-32 events / Interleukin-3, Interleukin-5 and GM-CSF signaling / regulation of macroautophagy / sperm flagellum / regulation of cardiac muscle contraction / 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 / protein kinase A signaling / cAMP binding / positive regulation of gluconeogenesis / regulation of ryanodine-sensitive calcium-release channel activity / Ion homeostasis / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / negative regulation of TORC1 signaling / Recruitment of mitotic centrosome proteins and complexes / sperm midpiece / Recruitment of NuMA to mitotic centrosomes / cellular response to epinephrine stimulus / calcium channel complex / Anchoring of the basal body to the plasma membrane / regulation of cytosolic calcium ion concentration / regulation of heart rate / protein export from nucleus / protein serine/threonine/tyrosine kinase activity / CD209 (DC-SIGN) signaling / multivesicular body / AURKA Activation by TPX2 / FCGR3A-mediated IL10 synthesis / acrosomal vesicle / positive regulation of protein export from nucleus / Regulation of insulin secretion / neural tube closure / cellular response to glucose stimulus / Degradation of GLI1 by the proteasome / regulation of protein phosphorylation / 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 / Vasopressin regulates renal water homeostasis via Aquaporins
Similarity search - Function
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. / Cyclic nucleotide-binding domain signature 1. / cAMP-dependent protein kinase catalytic subunit / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding 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. / Cyclic nucleotide-binding domain signature 1. / cAMP-dependent protein kinase catalytic subunit / 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 type I-alpha regulatory subunit / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.75 Å
AuthorsCao, B. / Lu, T.W. / Martinez Fiesco, J.A. / Tomasini, M. / Fan, L. / Simon, S.M. / Taylor, S.S. / Zhang, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Structure / Year: 2019
Title: Structures of the PKA RI alpha Holoenzyme with the FLHCC Driver J-PKAc alpha or Wild-Type PKAc alpha.
Authors: Cao, B. / Lu, T.W. / Martinez Fiesco, J.A. / Tomasini, M. / Fan, L. / Simon, S.M. / Taylor, S.S. / Zhang, P.
History
DepositionDec 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: citation / pdbx_validate_close_contact / struct_conn
Item: _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cAMP-dependent protein kinase catalytic subunit alpha
B: cAMP-dependent protein kinase type I-alpha regulatory subunit
C: cAMP-dependent protein kinase catalytic subunit alpha
D: cAMP-dependent protein kinase type I-alpha regulatory subunit
E: cAMP-dependent protein kinase catalytic subunit alpha
F: cAMP-dependent protein kinase type I-alpha regulatory subunit
G: cAMP-dependent protein kinase catalytic subunit alpha
H: cAMP-dependent protein kinase type I-alpha regulatory subunit


Theoretical massNumber of molelcules
Total (without water)334,2958
Polymers334,2958
Non-polymers00
Water0
1
A: cAMP-dependent protein kinase catalytic subunit alpha
B: cAMP-dependent protein kinase type I-alpha regulatory subunit
G: cAMP-dependent protein kinase catalytic subunit alpha
H: cAMP-dependent protein kinase type I-alpha regulatory subunit


Theoretical massNumber of molelcules
Total (without water)167,1484
Polymers167,1484
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: cAMP-dependent protein kinase catalytic subunit alpha
D: cAMP-dependent protein kinase type I-alpha regulatory subunit
E: cAMP-dependent protein kinase catalytic subunit alpha
F: cAMP-dependent protein kinase type I-alpha regulatory subunit


Theoretical massNumber of molelcules
Total (without water)167,1484
Polymers167,1484
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: cAMP-dependent protein kinase catalytic subunit alpha
B: cAMP-dependent protein kinase type I-alpha regulatory subunit


Theoretical massNumber of molelcules
Total (without water)83,5742
Polymers83,5742
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-16 kcal/mol
Surface area29310 Å2
MethodPISA
4
C: cAMP-dependent protein kinase catalytic subunit alpha
D: cAMP-dependent protein kinase type I-alpha regulatory subunit


Theoretical massNumber of molelcules
Total (without water)83,5742
Polymers83,5742
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-17 kcal/mol
Surface area29170 Å2
MethodPISA
5
E: cAMP-dependent protein kinase catalytic subunit alpha
F: cAMP-dependent protein kinase type I-alpha regulatory subunit


Theoretical massNumber of molelcules
Total (without water)83,5742
Polymers83,5742
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-16 kcal/mol
Surface area29210 Å2
MethodPISA
6
G: cAMP-dependent protein kinase catalytic subunit alpha
H: cAMP-dependent protein kinase type I-alpha regulatory subunit


Theoretical massNumber of molelcules
Total (without water)83,5742
Polymers83,5742
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-16 kcal/mol
Surface area29310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.495, 186.161, 186.668
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 40757.352 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKACA, PKACA / Production host: Escherichia coli (E. coli) / References: UniProt: P17612, cAMP-dependent protein kinase
#2: Protein
cAMP-dependent protein kinase type I-alpha regulatory subunit / CAMP-dependent pathway


Mass: 42816.422 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: PRKAR1A / Production host: Escherichia coli (E. coli) / References: UniProt: P00514

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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: 3.65 Å3/Da / Density % sol: 66.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM HEPES sodium-MOPS (acid) pH 7.5, 90 mM NPS (30 mM sodium nitrate, 30 mM sodium phosphate dibasic, 30 mM ammonium sulfate), 40-42% Precipitant Mix 2 (40% ethylene glycol; 20% PEG 8000) ...Details: 100 mM HEPES sodium-MOPS (acid) pH 7.5, 90 mM NPS (30 mM sodium nitrate, 30 mM sodium phosphate dibasic, 30 mM ammonium sulfate), 40-42% Precipitant Mix 2 (40% ethylene glycol; 20% PEG 8000), 3% D-(+)-Glucose monohydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.75→50 Å / Num. obs: 24440 / % possible obs: 97.2 % / Redundancy: 6.7 % / Rsym value: 0.109 / Net I/σ(I): 16.3
Reflection shellResolution: 4.75→4.92 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1975 / Rsym value: 0.412 / % possible all: 80.5

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BYR

6byr


Resolution: 4.75→45.158 Å / SU ML: 0.63 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.03
RfactorNum. reflection% reflection
Rfree0.2554 1983 8.18 %
Rwork0.212 --
obs0.2156 24239 95.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 4.75→45.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20336 0 0 0 20336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01420792
X-RAY DIFFRACTIONf_angle_d1.5728060
X-RAY DIFFRACTIONf_dihedral_angle_d25.2987820
X-RAY DIFFRACTIONf_chiral_restr0.0792992
X-RAY DIFFRACTIONf_plane_restr0.0083624
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.7461-4.86460.36031010.29471095X-RAY DIFFRACTION67
4.8646-4.9960.34341200.28951380X-RAY DIFFRACTION85
4.996-5.14280.31121320.25631526X-RAY DIFFRACTION93
5.1428-5.30860.3331460.25551625X-RAY DIFFRACTION99
5.3086-5.4980.27781410.24271630X-RAY DIFFRACTION99
5.498-5.71770.28571450.26261627X-RAY DIFFRACTION99
5.7177-5.97740.29421490.25131636X-RAY DIFFRACTION99
5.9774-6.29170.31531440.241627X-RAY DIFFRACTION99
6.2917-6.68480.27351480.22021670X-RAY DIFFRACTION100
6.6848-7.1990.31941490.21371651X-RAY DIFFRACTION100
7.199-7.920.23991460.20231647X-RAY DIFFRACTION100
7.92-9.05790.2041510.18791700X-RAY DIFFRACTION100
9.0579-11.38180.20651500.16251690X-RAY DIFFRACTION100
11.3818-45.15990.2481610.21261752X-RAY DIFFRACTION98

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