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- PDB-3gpe: Crystal Structure Analysis of PKC (alpha)-C2 domain complexed wit... -

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Basic information

Entry
Database: PDB / ID: 3gpe
TitleCrystal Structure Analysis of PKC (alpha)-C2 domain complexed with Ca2+ and PtdIns(4,5)P2
ComponentsProtein kinase C alpha type
KeywordsSIGNALING PROTEIN / CALCIUM/PHOSPHOLIPID BINDING DOMAIN / C2 domain / Phosphatidil serine / protein kinase / ATP-binding / Kinase / Metal-binding / Nucleotide-binding / Phorbol-ester binding / Phosphoprotein / Serine/threonine-protein kinase / Transferase / Zinc-finger
Function / homology
Function and homology information


Acetylcholine regulates insulin secretion / EGFR Transactivation by Gastrin / HuR (ELAVL1) binds and stabilizes mRNA / Depolymerization of the Nuclear Lamina / Signaling by SCF-KIT / Regulation of KIT signaling / Syndecan interactions / Calmodulin induced events / Disinhibition of SNARE formation / SHC1 events in ERBB2 signaling ...Acetylcholine regulates insulin secretion / EGFR Transactivation by Gastrin / HuR (ELAVL1) binds and stabilizes mRNA / Depolymerization of the Nuclear Lamina / Signaling by SCF-KIT / Regulation of KIT signaling / Syndecan interactions / Calmodulin induced events / Disinhibition of SNARE formation / SHC1 events in ERBB2 signaling / Response to elevated platelet cytosolic Ca2+ / positive regulation of angiotensin-activated signaling pathway / desmosome assembly / positive regulation of dense core granule biogenesis / histone H3T6 kinase activity / cone photoreceptor outer segment / regulation of receptor-mediated endocytosis / VEGFR2 mediated cell proliferation / calcium,diacylglycerol-dependent serine/threonine kinase activity / ooplasm / RET signaling / central nervous system neuron axonogenesis / WNT5A-dependent internalization of FZD4 / RHO GTPases Activate NADPH Oxidases / protein kinase C / cellular response to carbohydrate stimulus / negative regulation of glial cell apoptotic process / diacylglycerol-dependent serine/threonine kinase activity / regulation of platelet aggregation / regulation of muscle contraction / regulation of response to osmotic stress / positive regulation of macrophage differentiation / positive regulation of lipopolysaccharide-mediated signaling pathway / alphav-beta3 integrin-PKCalpha complex / regulation of the force of heart contraction / induction of positive chemotaxis / negative regulation of glucose import / presynaptic cytosol / positive regulation of synapse assembly / regulation of synaptic vesicle exocytosis / muscle cell cellular homeostasis / response to corticosterone / negative regulation of MAPK cascade / positive regulation of cardiac muscle hypertrophy / positive regulation of exocytosis / Trafficking of GluR2-containing AMPA receptors / calyx of Held / positive regulation of cell adhesion / intercalated disc / positive regulation of bone resorption / positive regulation of blood vessel endothelial cell migration / chondrocyte differentiation / response to mechanical stimulus / regulation of peptidyl-tyrosine phosphorylation / negative regulation of insulin receptor signaling pathway / presynaptic modulation of chemical synaptic transmission / positive regulation of endothelial cell proliferation / post-translational protein modification / positive regulation of mitotic cell cycle / response to interleukin-1 / intrinsic apoptotic signaling pathway / neutrophil chemotaxis / positive regulation of endothelial cell migration / response to reactive oxygen species / ciliary basal body / negative regulation of protein phosphorylation / stem cell differentiation / mitochondrial membrane / positive regulation of smooth muscle cell proliferation / peptidyl-threonine phosphorylation / establishment of protein localization / response to organic cyclic compound / response to toxic substance / response to peptide hormone / intracellular calcium ion homeostasis / positive regulation of inflammatory response / positive regulation of angiogenesis / integrin binding / presynapse / response to estradiol / apical part of cell / angiogenesis / response to ethanol / cell population proliferation / negative regulation of translation / learning or memory / positive regulation of ERK1 and ERK2 cascade / cell adhesion / protein kinase activity / intracellular signal transduction / positive regulation of cell migration / positive regulation of protein phosphorylation / axon / negative regulation of cell population proliferation / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / dendrite / lipid binding / perinuclear region of cytoplasm
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 / C2 domain / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / C2 domain / Protein kinase C conserved region 2 (CalB) ...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 / C2 domain / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / C2 domain / Protein kinase C conserved region 2 (CalB) / 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 / Chem-PT5 / Protein kinase C alpha type
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFerrer-Orta, C. / Querol-Audi, J. / Fita, I. / Verdaguer, N.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structural and mechanistic insights into the association of PKCalpha-C2 domain to PtdIns(4,5)P2.
Authors: Guerrero-Valero, M. / Ferrer-Orta, C. / Querol-Audi, J. / Marin-Vicente, C. / Fita, I. / Gomez-Fernandez, J.C. / Verdaguer, N. / Corbalan-Garcia, S.
History
DepositionMar 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)17,3086
Polymers16,0451
Non-polymers1,2625
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.848, 57.848, 90.479
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-alpha / PKC-A


Mass: 16045.253 Da / Num. of mol.: 1 / Fragment: C2 domain, UNP residues 156-292
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: NORWAY RAT / Gene: Prkca, Pkca / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P05696, protein kinase C
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-PT5 / [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate / Phosphatidylinositol 4,5-bisphosphate / PtdIns(4,5)P2 / Phosphatidylinositol 4,5-bisphosphate


Mass: 1047.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H85O19P3 / Comment: phospholipid*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.72 Å3/Da / Density % sol: 54.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 8000, 50mM potassium phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 96 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 14140 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Rsym value: 0.06 / Net I/σ(I): 13.3
Reflection shellResolution: 1.9→2 Å / Mean I/σ(I) obs: 1.6 / Rsym value: 0.464 / % possible all: 97.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.5.0066refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: C2 DOMAIN FROM PROTEIN KINASE C (ALPHA) COMPLEXED WITH CA2+ AND PHOSPHATIDYLSERINE

Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.875 / SU B: 9.532 / SU ML: 0.129 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2773 609 5 %RANDOM
Rwork0.24274 ---
obs0.24434 11566 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.343 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0.04 Å20 Å2
2---0.08 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1124 0 32 92 1248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0221180
X-RAY DIFFRACTIONr_angle_refined_deg0.7072.0071603
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4235136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.33224.3453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.42215218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.357158
X-RAY DIFFRACTIONr_chiral_restr0.0380.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021862
X-RAY DIFFRACTIONr_mcbond_it0.1311.5688
X-RAY DIFFRACTIONr_mcangle_it0.25921123
X-RAY DIFFRACTIONr_scbond_it0.3843492
X-RAY DIFFRACTIONr_scangle_it0.6414.5480
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 52 -
Rwork0.271 803 -
obs--98.62 %
Refinement TLS params.Method: refined / Origin x: 26.667 Å / Origin y: -13.927 Å / Origin z: 9.301 Å
111213212223313233
T0.0455 Å20.0358 Å20.0334 Å2-0.0303 Å20.0296 Å2--0.0308 Å2
L5.7297 °2-1.6464 °2-1.8974 °2-4.269 °22.297 °2--5.1862 °2
S0.4083 Å °0.3566 Å °0.3663 Å °-0.2308 Å °-0.1464 Å °-0.0635 Å °-0.3689 Å °-0.3045 Å °-0.2618 Å °

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