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- PDB-3twy: RAT PKC C2 DOMAIN BOUND TO PB -

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Basic information

Entry
Database: PDB / ID: 3twy
TitleRAT PKC C2 DOMAIN BOUND TO PB
ComponentsProtein kinase C alpha type
KeywordsTRANSFERASE / PROTEIN KINASE PKC
Function / homology
Function and homology information


Acetylcholine regulates insulin secretion / response to phorbol 13-acetate 12-myristate / EGFR Transactivation by Gastrin / HuR (ELAVL1) binds and stabilizes mRNA / 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 ...Acetylcholine regulates insulin secretion / response to phorbol 13-acetate 12-myristate / EGFR Transactivation by Gastrin / HuR (ELAVL1) binds and stabilizes mRNA / 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 / cellular response to carbohydrate stimulus / positive regulation of dense core granule biogenesis / VEGFR2 mediated cell proliferation / cone photoreceptor outer segment / ooplasm / RET signaling / central nervous system neuron axonogenesis / desmosome assembly / WNT5A-dependent internalization of FZD4 / calcium,diacylglycerol-dependent serine/threonine kinase activity / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / protein kinase C / RHO GTPases Activate NADPH Oxidases / diacylglycerol-dependent serine/threonine kinase activity / negative regulation of glial cell apoptotic process / regulation of platelet aggregation / 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 / negative regulation of D-glucose import / positive regulation of lipopolysaccharide-mediated signaling pathway / positive regulation of synapse assembly / response to corticosterone / muscle cell cellular homeostasis / regulation of synaptic vesicle exocytosis / positive regulation of cardiac muscle hypertrophy / Trafficking of GluR2-containing AMPA receptors / positive regulation of exocytosis / intercalated disc / positive regulation of blood vessel endothelial cell migration / chondrocyte differentiation / negative regulation of MAPK cascade / positive regulation of bone resorption / presynaptic cytosol / response to mechanical stimulus / positive regulation of endothelial cell proliferation / neutrophil chemotaxis / presynaptic modulation of chemical synaptic transmission / positive regulation of endothelial cell migration / peptidyl-threonine phosphorylation / calyx of Held / negative regulation of insulin receptor signaling pathway / positive regulation of cell adhesion / response to interleukin-1 / positive regulation of mitotic cell cycle / post-translational protein modification / intrinsic apoptotic signaling pathway / response to reactive oxygen species / stem cell differentiation / positive regulation of smooth muscle cell proliferation / establishment of protein localization / mitochondrial membrane / : / response to peptide hormone / response to toxic substance / intracellular calcium ion homeostasis / positive regulation of inflammatory response / positive regulation of angiogenesis / integrin binding / apical part of cell / response to estradiol / angiogenesis / response to ethanol / learning or memory / histone H3T6 kinase activity / cell population proliferation / positive regulation of ERK1 and ERK2 cascade / protein kinase activity / negative regulation of translation / cell adhesion / intracellular signal transduction / ciliary basal body / positive regulation of cell migration / axon / signaling receptor binding / negative regulation of cell population proliferation / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / lipid binding / dendrite / perinuclear region of cytoplasm / enzyme binding / endoplasmic reticulum / protein-containing complex
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 / Zinc finger phorbol-ester/DAG-type signature. / Protein kinase C conserved region 2 (CalB) / 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 / Zinc finger phorbol-ester/DAG-type signature. / Protein kinase C conserved region 2 (CalB) / 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
LEAD (II) ION / Protein kinase C alpha type
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 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
DepositionSep 22, 2011Deposition site: RCSB / Processing site: RCSB
SupersessionNov 2, 2011ID: 3RDL
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.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_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_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

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Assembly

Deposited unit
A: Protein kinase C alpha type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8447
Polymers16,0451
Non-polymers7996
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.290, 58.290, 87.980
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: Pkca, Prkca / Production host: Escherichia coli (E. coli) / References: UniProt: P05696, protein kinase C
#2: Chemical ChemComp-PB / LEAD (II) ION


Mass: 207.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pb
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growpH: 7.5
Details: 20% PEG3350, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 25, 2009 / Details: MICROMAX
RadiationMonochromator: MICROMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.5→1.55 Å / % possible all: 93.2

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Processing

Software
NameClassification
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→19.08 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.219 5041 -RANDOM
Rwork0.204 ---
all0.204 53576 --
obs0.204 51491 96.1 %-
Solvent computationBsol: 51.42 Å2
Displacement parametersBiso mean: 22.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.581 Å20.02 Å20 Å2
2--0.581 Å20 Å2
3----1.163 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1129 0 22 204 1355
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.67

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