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- PDB-4x6r: An Isoform-specific Myristylation Switch Targets RIIb PKA Holoenz... -

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Basic information

Entry
Database: PDB / ID: 4x6r
TitleAn Isoform-specific Myristylation Switch Targets RIIb PKA Holoenzymes to Membranes
Components(cAMP-dependent protein kinase ...Protein kinase A) x 2
KeywordsTRANSFERASE / PKA / membrane binding / molecular switch
Function / homology
Function and homology information


sperm connecting piece / spontaneous exocytosis of neurotransmitter / HDL assembly / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of meiotic cell cycle / DARPP-32 events / Rap1 signalling / PKA activation / Vasopressin regulates renal water homeostasis via Aquaporins ...sperm connecting piece / spontaneous exocytosis of neurotransmitter / HDL assembly / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of meiotic cell cycle / DARPP-32 events / Rap1 signalling / PKA activation / Vasopressin regulates renal water homeostasis via Aquaporins / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Regulation of insulin secretion / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / 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 / 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 / PKA activation / Factors involved in megakaryocyte development and platelet production / CD209 (DC-SIGN) signaling / Regulation of PLK1 Activity at G2/M Transition / Interleukin-3, Interleukin-5 and GM-CSF signaling / RET signaling / Hedgehog 'off' state / Ion homeostasis / VEGFA-VEGFR2 Pathway / nucleotide-activated protein kinase complex / regulation of cellular respiration / 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 / sarcomere organization / cAMP-dependent protein kinase / cellular response to cold / cardiac muscle cell proliferation / sperm capacitation / regulation of osteoblast differentiation / 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 / protein kinase A regulatory subunit binding / axoneme / negative regulation of activated T cell proliferation / protein kinase A catalytic subunit binding / plasma membrane raft / immunological synapse / mesoderm formation / sperm flagellum / regulation of proteasomal protein catabolic process / negative regulation of smoothened signaling pathway / protein kinase A signaling / cAMP binding / positive regulation of gluconeogenesis / regulation of synaptic transmission, glutamatergic / negative regulation of TORC1 signaling / sperm midpiece / protein export from nucleus / protein serine/threonine/tyrosine kinase activity / multivesicular body / acrosomal vesicle / positive regulation of protein export from nucleus / neural tube closure / cellular response to glucose stimulus / regulation of protein phosphorylation / modulation of chemical synaptic transmission / neuromuscular junction / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / mRNA processing / small GTPase binding / presynapse / cellular response to heat / manganese ion binding / postsynapse / peptidyl-serine phosphorylation / dendritic spine / regulation of cell cycle / protein kinase activity / nuclear speck / protein domain specific binding / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity
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 / Jelly Rolls / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / RmlC-like jelly roll fold / Jelly Rolls / 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 / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / MYRISTIC ACID / cAMP-dependent protein kinase type I-alpha regulatory subunit / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsZhang, P. / Ye, F. / Bastidas, A.C. / Kornev, A.P. / Ginsberg, M.H. / Wu, J. / Taylor, S.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM034921 United States
CitationJournal: Structure / Year: 2015
Title: An Isoform-Specific Myristylation Switch Targets Type II PKA Holoenzymes to Membranes.
Authors: Zhang, P. / Ye, F. / Bastidas, A.C. / Kornev, A.P. / Wu, J. / Ginsberg, M.H. / Taylor, S.S.
History
DepositionDec 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Experimental preparation
Revision 1.2Sep 2, 2015Group: Database references
Revision 1.3Sep 16, 2015Group: Database references
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Jun 24, 2020Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,07115
Polymers73,3632
Non-polymers1,70813
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8010 Å2
ΔGint-103 kcal/mol
Surface area28960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.760, 125.760, 140.881
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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CAMP-dependent protein kinase ... , 2 types, 2 molecules AB

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


Mass: 40711.258 Da / Num. of mol.: 1 / Mutation: K7C
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-alpha regulatory subunit / CAMP-dependent pathway


Mass: 32652.068 Da / Num. of mol.: 1 / Mutation: R333K
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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Non-polymers , 7 types, 282 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE / Tris


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.3 Å3/Da / Density % sol: 71.41 %
Crystal growTemperature: 298 K / Method: batch mode
Details: Crystallization of RIb(91-379,R333K): myrC(K7C) heterodimer :RC heterodimer that was concentrated to 14 mg/mL and screened against different ammonium sulfate concentrations ranging from 0.8- ...Details: Crystallization of RIb(91-379,R333K): myrC(K7C) heterodimer :RC heterodimer that was concentrated to 14 mg/mL and screened against different ammonium sulfate concentrations ranging from 0.8-2.5 M in 0.1 M sodium citrate buffer and also varying the pH from 5.0-6.0 using the hanging drop vapor diffusion method. The crystal used for structure determination was obtained from a 4 uL drop containing 1:1 protein to well solution with the well solution containing 1.6 M ammonium sulfate and 0.1 M sodium citrate at pH 5.5

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Jul 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→63 Å / Num. obs: 48209 / % possible obs: 99.9 % / Redundancy: 4 % / Net I/σ(I): 3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.7_650)refinement
MOSFLMdata reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.4→62.88 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.6 / Phase error: 22.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.234 2575 5.07 %
Rwork0.184 --
obs0.186 -99.9 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.35 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.8891 Å20 Å20 Å2
2--1.8891 Å20 Å2
3----3.7782 Å2
Refinement stepCycle: LAST / Resolution: 2.4→62.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5145 0 101 269 5515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0225389
X-RAY DIFFRACTIONf_angle_d1.8577277
X-RAY DIFFRACTIONf_dihedral_angle_d17.8222029
X-RAY DIFFRACTIONf_chiral_restr0.133769
X-RAY DIFFRACTIONf_plane_restr0.01927
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.44620.29521370.22932681X-RAY DIFFRACTION100
2.4462-2.49620.3041400.23072615X-RAY DIFFRACTION100
2.4962-2.55040.30541490.23422673X-RAY DIFFRACTION100
2.5504-2.60980.24521260.22842636X-RAY DIFFRACTION100
2.6098-2.6750.31361450.22152660X-RAY DIFFRACTION100
2.675-2.74740.26351340.20882645X-RAY DIFFRACTION100
2.7474-2.82820.27881370.21662671X-RAY DIFFRACTION100
2.8282-2.91950.291460.20982654X-RAY DIFFRACTION100
2.9195-3.02380.26871320.20322661X-RAY DIFFRACTION100
3.0238-3.14490.25521510.20022683X-RAY DIFFRACTION100
3.1449-3.2880.24641280.19992646X-RAY DIFFRACTION100
3.288-3.46140.24971420.19632678X-RAY DIFFRACTION100
3.4614-3.67820.20811520.18232648X-RAY DIFFRACTION100
3.6782-3.96220.21561460.16162697X-RAY DIFFRACTION100
3.9622-4.36080.20231650.14632688X-RAY DIFFRACTION100
4.3608-4.99160.18721440.1432698X-RAY DIFFRACTION100
4.9916-6.2880.23041580.17922734X-RAY DIFFRACTION100
6.288-62.90160.2211430.18342841X-RAY DIFFRACTION100

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