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- PDB-1dsy: C2 DOMAIN FROM PROTEIN KINASE C (ALPHA) COMPLEXED WITH CA2+ AND P... -

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Basic information

Entry
Database: PDB / ID: 1dsy
TitleC2 DOMAIN FROM PROTEIN KINASE C (ALPHA) COMPLEXED WITH CA2+ AND PHOSPHATIDYLSERINE
ComponentsPROTEIN KINASE C, ALPHA TYPE
KeywordsTRANSFERASE / CALCIUM++ / PHOSPHOLIPID BINDING PROTEIN / CALCIUM-BINDING PROTEIN / PHOSPHATIDYLSERINE / PROTEIN KINASE C
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 / RET signaling / protein kinase C signaling / ooplasm / histone H3T6 kinase activity / 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 / induction of positive chemotaxis / regulation of the force of heart contraction / 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 / intercalated disc / peptidyl-threonine phosphorylation / positive regulation of exocytosis / 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 / apical part of cell / positive regulation of inflammatory response / 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 / positive regulation of cell migration / ciliary basal body / signaling receptor binding / negative regulation of cell population proliferation / axon / 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 / 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
PHOSPHATE ION / 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE / Protein kinase C alpha type
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsVerdaguer, N. / Corbalan-Garcia, S. / Ochoa, W.F. / Fita, I. / Gomez-Fernandez, J.C.
CitationJournal: EMBO J. / Year: 1999
Title: Ca(2+) bridges the C2 membrane-binding domain of protein kinase Calpha directly to phosphatidylserine.
Authors: Verdaguer, N. / Corbalan-Garcia, S. / Ochoa, W.F. / Fita, I. / Gomez-Fernandez, J.C.
History
DepositionJan 10, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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.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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN KINASE C, ALPHA TYPE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8715
Polymers16,2401
Non-polymers6314
Water70339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.8, 58.8, 91.7
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein PROTEIN KINASE C, ALPHA TYPE


Mass: 16240.451 Da / Num. of mol.: 1 / Fragment: CALCIUM/PHOSPHOLIPID BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P05696, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-PSF / 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE / PHOSPHATIDYLSERINE


Mass: 455.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34NO10P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.82 Å3/Da / Density % sol: 56.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG8K, POTASSIUM PHOSPHATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal
*PLUS
Density % sol: 50 %
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14-8 mg/mlprotein1drop
225 mMcalcium chloride1drop
32 mMDCPS1drop
425 mM1dropCaCl2
520 %PEG80001reservoir
650 mMpotassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 25, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 5950 / Num. obs: 5610 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 36.9 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 9.4
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.281 / Num. unique all: 562 / % possible all: 95.1
Reflection
*PLUS
Num. measured all: 17072
Reflection shell
*PLUS
% possible obs: 95.1 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.6→18 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2327 416 random
Rwork0.1947 --
all-5969 -
obs-5432 -
Refinement stepCycle: LAST / Resolution: 2.6→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1109 0 32 39 1180
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d1.667
X-RAY DIFFRACTIONc_angle_d2.899
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.233 / Rfactor Rwork: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.4

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