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

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Basic information

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


response to antipsychotic drug / spontaneous exocytosis of neurotransmitter / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of meiotic cell cycle / HDL assembly / DARPP-32 events / Rap1 signalling / PKA activation / Vasopressin regulates renal water homeostasis via Aquaporins ...response to antipsychotic drug / spontaneous exocytosis of neurotransmitter / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of meiotic cell cycle / HDL assembly / DARPP-32 events / Rap1 signalling / PKA activation / Vasopressin regulates renal water homeostasis via Aquaporins / Regulation of insulin secretion / GPER1 signaling / 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 / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / MAPK6/MAPK4 signaling / GLI3 is processed to GLI3R by the proteasome / AURKA Activation by TPX2 / Factors involved in megakaryocyte development and platelet production / cAMP-dependent protein kinase regulator activity / Regulation of PLK1 Activity at G2/M Transition / Interleukin-3, Interleukin-5 and GM-CSF signaling / CD209 (DC-SIGN) signaling / Mitochondrial protein degradation / RET signaling / Ion homeostasis / VEGFA-VEGFR2 Pathway / 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 / cAMP-dependent protein kinase / cellular response to cold / regulation of osteoblast differentiation / sperm capacitation / cAMP-dependent protein kinase activity / ciliary base / negative regulation of glycolytic process through fructose-6-phosphate / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / postsynaptic modulation of chemical synaptic transmission / cellular response to glucagon stimulus / protein kinase A regulatory subunit binding / plasma membrane raft / protein kinase A catalytic subunit binding / axoneme / mesoderm formation / sperm flagellum / negative regulation of smoothened signaling pathway / regulation of proteasomal protein catabolic process / cAMP binding / regulation of synaptic transmission, glutamatergic / positive regulation of gluconeogenesis / sperm midpiece / negative regulation of TORC1 signaling / protein kinase A signaling / protein serine/threonine/tyrosine kinase activity / protein export from nucleus / positive regulation of protein export from nucleus / acrosomal vesicle / fatty acid metabolic process / dendritic shaft / learning / 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 / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / neuronal cell body / glutamatergic synapse / ubiquitin protein ligase binding / dendrite / positive regulation of cell population proliferation / protein-containing complex binding / protein kinase binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II
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
cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase type II-beta regulatory subunit
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 12, 2012Group: Database references / Derived calculations
Revision 1.2Feb 27, 2013Group: Source and taxonomy

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: cAMP-dependent protein kinase catalytic subunit alpha
B: cAMP-dependent protein kinase type II-beta regulatory subunit
F: cAMP-dependent protein kinase catalytic subunit alpha
E: cAMP-dependent protein kinase type II-beta regulatory subunit


Theoretical massNumber of molelcules
Total (without water)174,0224
Polymers174,0224
Non-polymers00
Water6,431357
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: cAMP-dependent protein kinase catalytic subunit alpha
B: cAMP-dependent protein kinase type II-beta regulatory subunit


Theoretical massNumber of molelcules
Total (without water)87,0112
Polymers87,0112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-12 kcal/mol
Surface area28390 Å2
MethodPISA
3
F: cAMP-dependent protein kinase catalytic subunit alpha
E: cAMP-dependent protein kinase type II-beta regulatory subunit


Theoretical massNumber of molelcules
Total (without water)87,0112
Polymers87,0112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-12 kcal/mol
Surface area28390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.962, 213.277, 61.625
Angle α, β, γ (deg.)90.00, 90.41, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain C and (resseq 14:138 or resseq 140:196 or resseq 198:337 or resseq 339:350 )
211chain F and (resseq 14:138 or resseq 140:196 or resseq 198:337 or resseq 339:350 )
112chain B and (resseq 104:121 or resseq 130:324 or resseq 337:393 )
212chain E and (resseq 104:121 or resseq 130:324 or resseq 337:393 )

NCS ensembles :
ID
1
2

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Components

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


Mass: 40817.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pkaca, Prkaca, rCG_51506 / Production host: Escherichia coli (E. coli) / References: UniProt: P05132, cAMP-dependent protein kinase
#2: Protein cAMP-dependent protein kinase type II-beta regulatory subunit


Mass: 46193.969 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O

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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: 2.87 Å3/Da / Density % sol: 57.13 %
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

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: 2.3→20 Å / Num. all: 96666 / Num. obs: 82530 / % possible obs: 95 % / 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: 2.3→19.899 Å / SU ML: 0.32 / σ(F): 1.36 / Phase error: 24.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2346 4116 4.99 %5%
Rwork0.2259 ---
obs0.2263 82530 95.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.662 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.2063 Å2-0 Å20.3532 Å2
2--0.4822 Å20 Å2
3----0.2274 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9838 0 0 357 10195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110040
X-RAY DIFFRACTIONf_angle_d1.29413530
X-RAY DIFFRACTIONf_dihedral_angle_d14.2973780
X-RAY DIFFRACTIONf_chiral_restr0.091456
X-RAY DIFFRACTIONf_plane_restr0.0051740
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11C2756X-RAY DIFFRACTIONPOSITIONAL
12F2756X-RAY DIFFRACTIONPOSITIONAL0.003
21B2131X-RAY DIFFRACTIONPOSITIONAL
22E2131X-RAY DIFFRACTIONPOSITIONAL0
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.38210.31134230.28437692X-RAY DIFFRACTION94
2.3821-2.47730.27243950.26727971X-RAY DIFFRACTION97
2.4773-2.58980.26424220.26617975X-RAY DIFFRACTION97
2.5898-2.7260.31723870.2768030X-RAY DIFFRACTION97
2.726-2.89630.26664190.25898050X-RAY DIFFRACTION98
2.8963-3.11920.27524450.25338000X-RAY DIFFRACTION98
3.1192-3.43160.24924310.23867973X-RAY DIFFRACTION97
3.4316-3.92490.20623960.21457678X-RAY DIFFRACTION93
3.9249-4.93250.18234040.17767475X-RAY DIFFRACTION91
4.9325-19.89950.20793940.19597570X-RAY DIFFRACTION91

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