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- PDB-3fjq: Crystal structure of cAMP-dependent protein kinase catalytic subu... -

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Basic information

Entry
Database: PDB / ID: 3fjq
TitleCrystal structure of cAMP-dependent protein kinase catalytic subunit alpha in complex with peptide inhibitor PKI alpha (6-25)
Components
  • cAMP-dependent protein kinase catalytic subunit alpha
  • cAMP-dependent protein kinase inhibitor alpha
KeywordsTRANSFERASE / nucleotide binding / protein kinase activity / protein serine/threonine kinase activity / cAMP-dependent protein kinase activity / protein binding / ATP binding / kinase activity / transferase activity / Alternative splicing / ATP-binding / cAMP / Cytoplasm / Kinase / Lipoprotein / Myristate / Nucleotide-binding / Nucleus / Phosphoprotein / Serine/threonine-protein kinase / Protein kinase inhibitor
Function / homology
Function and homology information


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 ...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 / AURKA Activation by TPX2 / MAPK6/MAPK4 signaling / GLI3 is processed to GLI3R by the proteasome / Factors involved in megakaryocyte development and platelet production / 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 / negative regulation of protein import into nucleus / 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 / regulation of proteasomal protein catabolic process / negative regulation of smoothened signaling pathway / positive regulation of gluconeogenesis / sperm midpiece / negative regulation of TORC1 signaling / regulation of synaptic transmission, glutamatergic / regulation of G2/M transition of mitotic cell cycle / protein kinase A signaling / protein serine/threonine/tyrosine kinase activity / protein export from nucleus / acrosomal vesicle / positive regulation of protein export from nucleus / neural tube closure / cellular response to glucose stimulus / modulation of chemical synaptic transmission / neuromuscular junction / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / small GTPase binding / mRNA processing / presynapse / manganese ion binding / cellular response to heat / peptidyl-serine phosphorylation / postsynapse / 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 / glutamatergic synapse / ubiquitin protein ligase binding / 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 / magnesium ion binding / protein-containing complex / mitochondrion / nucleoplasm / ATP binding / nucleus / plasma membrane
Similarity search - Function
cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsKim, C.
CitationJournal: Protein Sci. / Year: 2009
Title: Comparative surface geometry of the protein kinase family.
Authors: Thompson, E.E. / Kornev, A.P. / Kannan, N. / Kim, C. / Ten Eyck, L.F. / Taylor, S.S.
History
DepositionDec 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: cAMP-dependent protein kinase catalytic subunit alpha
I: cAMP-dependent protein kinase inhibitor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5015
Polymers42,8842
Non-polymers6173
Water7,098394
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-5.2 kcal/mol
Surface area15810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.517, 80.548, 97.622
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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/peptide cAMP-dependent protein kinase inhibitor alpha / cAMP-dependent protein kinase inhibitor / muscle/brain isoform / PKI-alpha


Mass: 2226.411 Da / Num. of mol.: 1 / Fragment: UNP residues 6-25
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pkia / Production host: Escherichia coli (E. coli) / References: UniProt: P63248
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.64 Å3/Da / Density % sol: 53.35 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein solution: 10mM MOPS buffer pH 7.0, 50 mM NaCl, 3mM MnCl2, 0.2 mM ATP. Well solution: 0.5 M (NH4)2SO4, 0.1 M HEPES, 10 % MPD, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / 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: 1.6→50 Å / Num. obs: 60216 / % possible obs: 99.49 % / Observed criterion σ(I): 2
Reflection shellResolution: 1.6→1.642 Å / Num. unique all: 4022 / % possible all: 96.54

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0 / SU B: 3.584 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.205 3040 5 %RANDOM
Rwork0.177 ---
obs0.179 60216 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 53.05 Å2 / Biso mean: 21.314 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å2-0 Å2-0 Å2
2--0.58 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2869 0 33 394 3296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222929
X-RAY DIFFRACTIONr_bond_other_d0.0010.021986
X-RAY DIFFRACTIONr_angle_refined_deg1.1281.9583977
X-RAY DIFFRACTIONr_angle_other_deg0.91634790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0735351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.95523.603136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.76115.032472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7481516
X-RAY DIFFRACTIONr_chiral_restr0.0650.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023239
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02642
X-RAY DIFFRACTIONr_nbd_refined0.2280.2573
X-RAY DIFFRACTIONr_nbd_other0.1930.22051
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21466
X-RAY DIFFRACTIONr_nbtor_other0.0780.21488
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2304
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0990.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1750.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1030.222
X-RAY DIFFRACTIONr_mcbond_it0.6521.52289
X-RAY DIFFRACTIONr_mcbond_other0.1641.5716
X-RAY DIFFRACTIONr_mcangle_it0.73322823
X-RAY DIFFRACTIONr_scbond_it1.24931414
X-RAY DIFFRACTIONr_scangle_it1.7864.51154
X-RAY DIFFRACTIONr_rigid_bond_restr0.6336287
X-RAY DIFFRACTIONr_sphericity_free2.6323396
X-RAY DIFFRACTIONr_sphericity_bonded0.80534842
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 224 -
Rwork0.253 4022 -
all-4246 -
obs--96.54 %

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