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- PDB-3rdj: Rat PKC C2 domain Apo -

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Basic information

Entry
Database: PDB / ID: 3rdj
TitleRat PKC C2 domain Apo
ComponentsProtein kinase C alpha type
KeywordsTRANSFERASE / Protein Kinase PKC
Function / homology
Function and homology information


EGFR Transactivation by Gastrin / HuR (ELAVL1) binds and stabilizes mRNA / Acetylcholine regulates insulin secretion / Depolymerization of the Nuclear Lamina / Signaling by SCF-KIT / Regulation of KIT signaling / Calmodulin induced events / Disinhibition of SNARE formation / SHC1 events in ERBB2 signaling / Response to elevated platelet cytosolic Ca2+ ...EGFR Transactivation by Gastrin / HuR (ELAVL1) binds and stabilizes mRNA / Acetylcholine regulates insulin secretion / Depolymerization of the Nuclear Lamina / Signaling by SCF-KIT / Regulation of KIT signaling / Calmodulin induced events / Disinhibition of SNARE formation / SHC1 events in ERBB2 signaling / Response to elevated platelet cytosolic Ca2+ / Syndecan interactions / positive regulation of angiotensin-activated signaling pathway / response to phorbol 13-acetate 12-myristate / positive regulation of dense core granule biogenesis / cellular response to carbohydrate stimulus / cone photoreceptor outer segment / VEGFR2 mediated cell proliferation / calcium,diacylglycerol-dependent serine/threonine kinase activity / protein kinase C signaling / RET signaling / histone H3T6 kinase activity / ooplasm / central nervous system neuron axonogenesis / desmosome assembly / WNT5A-dependent internalization of FZD4 / RHO GTPases Activate NADPH Oxidases / protein kinase C / diacylglycerol-dependent serine/threonine kinase activity / regulation of platelet aggregation / negative regulation of glial cell apoptotic process / negative regulation of D-glucose import / positive regulation of macrophage differentiation / regulation of muscle contraction / regulation of the force of heart contraction / induction of positive chemotaxis / alphav-beta3 integrin-PKCalpha complex / positive regulation of lipopolysaccharide-mediated signaling pathway / positive regulation of bone resorption / positive regulation of synapse assembly / response to corticosterone / muscle cell cellular homeostasis / positive regulation of cardiac muscle hypertrophy / regulation of synaptic vesicle exocytosis / Trafficking of GluR2-containing AMPA receptors / positive regulation of exocytosis / intercalated disc / peptidyl-threonine phosphorylation / positive regulation of blood vessel endothelial cell migration / chondrocyte differentiation / response to mechanical stimulus / presynaptic cytosol / negative regulation of MAPK cascade / positive regulation of endothelial cell proliferation / neutrophil chemotaxis / positive regulation of smooth muscle cell proliferation / presynaptic modulation of chemical synaptic transmission / positive regulation of endothelial cell migration / positive regulation of cell adhesion / intrinsic apoptotic signaling pathway / negative regulation of insulin receptor signaling pathway / positive regulation of mitotic cell cycle / response to interleukin-1 / calyx of Held / response to reactive oxygen species / stem cell differentiation / establishment of protein localization / response to peptide hormone / mitochondrial membrane / response to toxic substance / integrin binding / positive regulation of angiogenesis / intracellular calcium ion homeostasis / positive regulation of inflammatory response / apical part of cell / response to estradiol / response to ethanol / angiogenesis / learning or memory / cell population proliferation / positive regulation of ERK1 and ERK2 cascade / protein kinase activity / cell adhesion / negative regulation of translation / intracellular signal transduction / ciliary basal body / positive regulation of cell migration / signaling receptor binding / axon / negative regulation of cell population proliferation / protein serine kinase activity / neuronal cell body / protein serine/threonine kinase activity / dendrite / lipid binding / perinuclear region of cytoplasm / enzyme binding / endoplasmic reticulum / protein-containing complex / mitochondrion / zinc ion binding
Similarity search - Function
Classical Protein Kinase C alpha, catalytic domain / Protein kinase C, alpha/beta/gamma types / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / C2 domain / Protein kinase C conserved region 2 (CalB) / Zinc finger phorbol-ester/DAG-type signature. / C2 domain ...Classical Protein Kinase C alpha, catalytic domain / Protein kinase C, alpha/beta/gamma types / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / C2 domain / Protein kinase C conserved region 2 (CalB) / Zinc finger phorbol-ester/DAG-type signature. / C2 domain / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C2 domain / C2 domain profile. / C1-like domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / C2 domain superfamily / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Protein kinase C alpha type
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLi, P.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Pb2+ as modulator of protein-membrane interactions.
Authors: Morales, K.A. / Lasagna, M. / Gribenko, A.V. / Yoon, Y. / Reinhart, G.D. / Lee, J.C. / Cho, W. / Li, P. / Igumenova, T.I.
History
DepositionApr 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein kinase C alpha type


Theoretical massNumber of molelcules
Total (without water)16,0451
Polymers16,0451
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.000, 58.000, 90.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Protein kinase C alpha type / PKC-A / PKC-alpha


Mass: 16045.253 Da / Num. of mol.: 1 / Fragment: UNP residues 156-292
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Prkca, Pkca / Production host: Escherichia coli (E. coli) / References: UniProt: P05696, protein kinase C
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.74 Å3/Da / Density % sol: 55.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 24, 2010
RadiationMonochromator: micromax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 14383 / Num. obs: 14022 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→1.97 Å / % possible all: 99.7

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Processing

Software
NameClassification
CrystalCleardata collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→25.11 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1438 10 %random
Rwork0.225 ---
all0.225 14383 --
obs0.225 14022 --
Solvent computationBsol: 53.3545 Å2
Displacement parametersBiso max: 99.52 Å2 / Biso mean: 38.2637 Å2 / Biso min: 13.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.089 Å2-0.082 Å20 Å2
2---0.089 Å20 Å2
3---0.178 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1129 0 0 107 1236
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.67
X-RAY DIFFRACTIONc_bond_d0.01

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