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- PDB-4din: Novel Localization and Quaternary Structure of the PKA RI beta Ho... -

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Basic information

Entry
Database: PDB / ID: 4din
TitleNovel Localization and Quaternary Structure of the PKA RI beta Holoenzyme
Components
  • cAMP-dependent protein kinase catalytic subunit alpha
  • cAMP-dependent protein kinase type I-beta regulatory subunit
KeywordsTransferase/Transport Protein / isoform diversity / RIb2:C2 tetrameric complex / Transferase-Transport Protein complex
Function / homology
Function and homology information


positive regulation of fear response / cAMP-dependent protein kinase regulator activity / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / HDL assembly / DARPP-32 events / Rap1 signalling / PKA activation / Regulation of insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins ...positive regulation of fear response / cAMP-dependent protein kinase regulator activity / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / HDL assembly / DARPP-32 events / Rap1 signalling / PKA activation / Regulation of insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / 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 / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Regulation of PLK1 Activity at G2/M Transition / Interleukin-3, Interleukin-5 and GM-CSF signaling / CD209 (DC-SIGN) signaling / RET signaling / Mitochondrial protein degradation / VEGFA-VEGFR2 Pathway / Ion homeostasis / regulation of synaptic vesicle cycle / negative regulation of cAMP/PKA signal transduction / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / regulation of protein processing / intracellular potassium ion homeostasis / cAMP-dependent protein kinase activity / protein localization to lipid droplet / CREB1 phosphorylation through the activation of Adenylate Cyclase / cAMP-dependent protein kinase complex / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / PKA activation / regulation of osteoblast differentiation / cellular response to cold / sperm capacitation / ciliary base / negative regulation of glycolytic process through fructose-6-phosphate / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / mesoderm formation / sperm flagellum / cAMP/PKA signal transduction / plasma membrane raft / PKA activation in glucagon signalling / axoneme / DARPP-32 events / regulation of proteasomal protein catabolic process / positive regulation of excitatory postsynaptic potential / postsynaptic modulation of chemical synaptic transmission / cAMP binding / Hedgehog 'off' state / sperm midpiece / positive regulation of phagocytosis / negative regulation of TORC1 signaling / multivesicular body / positive regulation of gluconeogenesis / protein serine/threonine/tyrosine kinase activity / cellular response to glucagon stimulus / FCGR3A-mediated IL10 synthesis / protein export from nucleus / acrosomal vesicle / hippocampal mossy fiber to CA3 synapse / positive regulation of long-term synaptic potentiation / positive regulation of protein export from nucleus / negative regulation of smoothened signaling pathway / neural tube closure / cellular response to glucose stimulus / positive regulation of cholesterol biosynthetic process / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / modulation of chemical synaptic transmission / neuromuscular junction / positive regulation of insulin secretion / Schaffer collateral - CA1 synapse / adenylate cyclase-activating G protein-coupled receptor signaling pathway / mRNA processing / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / peptidyl-serine phosphorylation / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / manganese ion binding / cellular response to heat / Factors involved in megakaryocyte development and platelet production / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / learning or memory / postsynapse / protein kinase activity / regulation of cell cycle / nuclear speck
Similarity search - Function
RIbeta, dimerization/docking 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 ...RIbeta, dimerization/docking 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Jelly Rolls / 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 / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase type I-beta regulatory subunit
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.7 Å
AuthorsIlouz, R. / Bubis, J. / Wu, J. / Yim, Y.Y. / Deal, M.S. / Kornev, A.P. / Ma, Y. / Blumenthal, D.K. / Taylor, S.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Localization and quaternary structure of the PKA RI Beta holoenzyme
Authors: Ilouz, R. / Bubis, J. / Wu, J. / Yim, Y.Y. / Deal, M.S. / Kornev, A.P. / Ma, Y. / Blumenthal, D.K. / Taylor, S.S.
History
DepositionJan 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_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.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_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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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-beta regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,3445
Polymers83,7882
Non-polymers5563
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-34 kcal/mol
Surface area33370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.194, 172.194, 146.646
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

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


Mass: 40657.316 Da / Num. of mol.: 1
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-beta regulatory subunit


Mass: 43130.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAR1B / Production host: Escherichia coli (E. coli) / References: UniProt: P31321
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
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: 3.75 Å3/Da / Density % sol: 67.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 1.4 M ammonium sulfate, 0.1M Sodium Acetate pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 19, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.7→50 Å / Num. obs: 16198 / % possible obs: 96.1 % / Observed criterion σ(I): 2 / Redundancy: 9.3 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 11
Reflection shellResolution: 3.7→3.77 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2 / % possible all: 90

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
CNS1.3 with DEN refinementrefinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementStarting model: PDB entry 2QCS

2qcs


Resolution: 3.7→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 2517
RfactorNum. reflection% reflection
Rfree0.2926 495 3.5 %
Rwork0.211 9118 -
obs-9613 67.7 %
Solvent computationBsol: 143.399 Å2
Displacement parametersBiso max: 299.96 Å2 / Biso mean: 156.4891 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-44.269 Å2-0 Å20 Å2
2--44.269 Å20 Å2
3----88.539 Å2
Refinement stepCycle: LAST / Resolution: 3.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5393 0 33 0 5426
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_angle_d0.737
X-RAY DIFFRACTIONc_mcbond_it11.52115
X-RAY DIFFRACTIONc_scbond_it16.91520
X-RAY DIFFRACTIONc_mcangle_it17.81920
X-RAY DIFFRACTIONc_scangle_it23.63725
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.7-3.830.337220.367640642830.9
3.83-3.990.3238230.362453155440.2
3.99-4.170.381380.292157060843.8
4.17-4.390.3234440.246974278656.5
4.39-4.660.2953630.233791397669.4
4.66-5.020.2701630.1843983104674.6
5.02-5.530.3077580.20331068112679.7
5.53-6.320.3102490.24291167121684.9
6.32-7.960.2484560.18291279133592.3
7.96-500.2863790.18561459153898.3

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