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- PDB-3tnq: Structure and Allostery of the PKA RIIb Tetrameric Holoenzyme -

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Basic information

Entry
Database: PDB / ID: 3tnq
TitleStructure and Allostery of the PKA RIIb Tetrameric Holoenzyme
Components
  • Protein kinase, cAMP-dependent, catalytic, alpha
  • cAMP-dependent protein kinase type II-beta regulatory subunit
KeywordsTRANSFERASE / PKA RIIb tetrameric holoenzyme
Function / homology
Function and homology information


HDL assembly / Interleukin-3, Interleukin-5 and GM-CSF signaling / negative regulation of meiotic cell cycle process involved in oocyte maturation / Rap1 signalling / VEGFA-VEGFR2 Pathway / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / DARPP-32 events / GLI3 is processed to GLI3R by the proteasome / GPER1 signaling ...HDL assembly / Interleukin-3, Interleukin-5 and GM-CSF signaling / negative regulation of meiotic cell cycle process involved in oocyte maturation / Rap1 signalling / VEGFA-VEGFR2 Pathway / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / DARPP-32 events / GLI3 is processed to GLI3R by the proteasome / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / 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 / AURKA Activation by TPX2 / Mitochondrial protein degradation / Regulation of PLK1 Activity at G2/M Transition / MAPK6/MAPK4 signaling / PKA activation / Hedgehog 'off' state / RET signaling / Regulation of insulin secretion / spontaneous exocytosis of neurotransmitter / negative regulation of meiotic cell cycle / cAMP-dependent protein kinase regulator activity / regulation of cellular respiration / response to antipsychotic drug / nucleotide-activated protein kinase complex / dorsal/ventral neural tube patterning / germinal vesicle / regulation of protein processing / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / cAMP-dependent protein kinase inhibitor activity / cellular response to parathyroid hormone stimulus / protein localization to lipid droplet / histone H1-4S35 kinase activity / cAMP-dependent protein kinase / cAMP-dependent protein kinase activity / mesoderm formation / Ion homeostasis / regulation of bicellular tight junction assembly / cAMP-dependent protein kinase complex / cellular response to cold / interleukin-2-mediated signaling pathway / sperm capacitation / regulation of osteoblast differentiation / negative regulation of glycolytic process through fructose-6-phosphate / protein kinase A regulatory subunit binding / ciliary base / protein kinase A catalytic subunit binding / TORC1 signaling / intracellular potassium ion homeostasis / plasma membrane raft / cAMP/PKA signal transduction / neural tube closure / axoneme / sperm flagellum / postsynaptic modulation of chemical synaptic transmission / cAMP binding / negative regulation of cAMP/PKA signal transduction / regulation of synaptic transmission, glutamatergic / negative regulation of TORC1 signaling / protein export from nucleus / positive regulation of gluconeogenesis / protein serine/threonine/tyrosine kinase activity / cellular response to glucagon stimulus / cellular response to nutrient levels / fatty acid metabolic process / positive regulation of phagocytosis / positive regulation of protein export from nucleus / acrosomal vesicle / learning / regulation of proteasomal protein catabolic process / negative regulation of smoothened signaling pathway / dendritic shaft / peptidyl-serine phosphorylation / cellular response to glucose stimulus / neuromuscular junction / positive regulation of insulin secretion / positive regulation of cholesterol biosynthetic process / modulation of chemical synaptic transmission / small GTPase binding / mRNA processing / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / sperm midpiece / manganese ion binding / cellular response to heat / presynapse / adenylate cyclase-activating G protein-coupled receptor signaling pathway / dendritic spine / regulation of cell cycle / protein kinase activity / postsynapse / nuclear speck / protein domain specific binding / protein serine 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. / cAMP-dependent protein kinase catalytic subunit / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate 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. / 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 / Jelly Rolls / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Jelly Rolls / 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'-DIPHOSPHATE / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase type II-beta regulatory subunit
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.097 Å
AuthorsZhang, P. / Smith-Nguyen, E.V. / Keshwani, M.M. / Deal, M.S. / Kornev, A.P. / Taylor, S.S.
CitationJournal: Science / Year: 2012
Title: Structure and allostery of the PKA RIIbeta tetrameric holoenzyme
Authors: Zhang, P. / Smith-Nguyen, E.V. / Keshwani, M.M. / Deal, M.S. / Kornev, A.P. / Taylor, S.S.
History
DepositionSep 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Protein kinase, cAMP-dependent, catalytic, alpha
A: cAMP-dependent protein kinase type II-beta regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,5675
Polymers87,0912
Non-polymers4763
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-17 kcal/mol
Surface area28430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.819, 212.753, 61.951
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-391-

LYS

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Components

#1: Protein Protein kinase, cAMP-dependent, catalytic, alpha


Mass: 40817.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Prkaca, rCG_51506 / Production host: Escherichia coli (E. coli) / References: UniProt: A1L1M0, UniProt: P27791*PLUS
#2: Protein cAMP-dependent protein kinase type II-beta regulatory subunit


Mass: 46273.945 Da / Num. of mol.: 1 / Mutation: R230K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prkar2b / Production host: Escherichia coli (E. coli) / References: UniProt: P31324
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.91 Å3/Da / Density % sol: 57.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: The RII (R230K)2:C2 holoenzyme complex was crystallized at room temperature in 10% PEG8000, 8% ethylene glycol, pH7.5 HEPES buffer by using vapor diffusion at a 1:1 ratio of protein to ...Details: The RII (R230K)2:C2 holoenzyme complex was crystallized at room temperature in 10% PEG8000, 8% ethylene glycol, pH7.5 HEPES buffer by using vapor diffusion at a 1:1 ratio of protein to crystallization solution. VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.097→40 Å / Num. all: 18000 / Num. obs: 16119 / % possible obs: 90 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.097→38.836 Å / SU ML: 0.48 / σ(F): 1.35 / Phase error: 28.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2753 827 5.13 %5%
Rwork0.2313 ---
obs0.2335 16119 84.83 %-
all-18000 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20 Å2 / ksol: 0.268 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.6961 Å20 Å20 Å2
2--2.7226 Å2-0 Å2
3---4.8071 Å2
Refinement stepCycle: LAST / Resolution: 3.097→38.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4901 0 29 13 4943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0165041
X-RAY DIFFRACTIONf_angle_d1.5526811
X-RAY DIFFRACTIONf_dihedral_angle_d16.4751893
X-RAY DIFFRACTIONf_chiral_restr0.099728
X-RAY DIFFRACTIONf_plane_restr0.006868
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.097-3.29120.41031410.31442543X-RAY DIFFRACTION86
3.2912-3.54510.28611290.26372585X-RAY DIFFRACTION87
3.5451-3.90160.28951570.22532534X-RAY DIFFRACTION86
3.9016-4.46540.26981490.20942526X-RAY DIFFRACTION85
4.4654-5.62330.21861290.20012547X-RAY DIFFRACTION84
5.6233-38.83880.24281220.22032557X-RAY DIFFRACTION81

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