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- PDB-4l1l: Rat PKC C2 domain bound to CD -

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Basic information

Entry
Database: PDB / ID: 4l1l
TitleRat PKC C2 domain bound to CD
ComponentsProtein kinase C alpha type
KeywordsTRANSFERASE / PROTEIN KINASE PKC
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 / histone H3T6 kinase activity / positive regulation of dense core granule biogenesis / 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 response to osmotic stress / regulation of muscle contraction / 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 / muscle cell cellular homeostasis / regulation of synaptic vesicle exocytosis / 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 blood vessel endothelial cell migration / positive regulation of bone resorption / 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 / response to reactive oxygen species / response to interleukin-1 / post-translational protein modification / positive regulation of mitotic cell cycle / intrinsic apoptotic signaling pathway / neutrophil chemotaxis / positive regulation of endothelial cell migration / 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 / intracellular calcium ion homeostasis / response to organic cyclic compound / response to peptide hormone / response to toxic substance / 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 / positive regulation of ERK1 and ERK2 cascade / learning or memory / 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 / dendrite / neuronal cell body / 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) / C2 domain / Protein kinase C conserved region 2 (CalB) / Zinc finger phorbol-ester/DAG-type signature. ...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) / C2 domain / Protein kinase C conserved region 2 (CalB) / Zinc finger phorbol-ester/DAG-type signature. / C2 domain / C2 domain profile. / 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 / 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 / SAD / Resolution: 1.6 Å
AuthorsMorales, K.M. / Yang, Y. / Long, Z. / Li, P. / Taylor, A.B. / Hart, P.J. / Igumenova, T.I.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Cd(2+) as a ca(2+) surrogate in protein-membrane interactions: isostructural but not isofunctional.
Authors: Morales, K.A. / Yang, Y. / Long, Z. / Li, P. / Taylor, A.B. / Hart, P.J. / Igumenova, T.I.
History
DepositionJun 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Feb 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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _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

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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)17,39512
Polymers16,2401
Non-polymers1,15511
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.224, 58.224, 88.539
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-429-

HOH

21A-478-

HOH

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Components

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


Mass: 16240.451 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 155-293
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pkca, Prkca / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / References: UniProt: P05696, protein kinase C
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.67 Å3/Da / Density % sol: 53.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.25
Details: 0.25 M Lithium Sulfate, 20% PEG 3350, pH 5.25, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.6→44.27 Å / Num. obs: 43697 / % possible obs: 98.6 % / Redundancy: 20 % / Biso Wilson estimate: 20.02 Å2 / Rsym value: 0.098 / Net I/σ(I): 22.4
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 17.8 % / Mean I/σ(I) obs: 7.2 / Num. unique all: 3157 / Rsym value: 0.397 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.6→43.816 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 1.7 / Phase error: 17.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1953 2000 8.67 %random
Rwork0.1568 ---
obs0.16 43697 98.5 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.09 Å2
Refinement stepCycle: LAST / Resolution: 1.6→43.816 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1133 0 31 141 1305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011224
X-RAY DIFFRACTIONf_angle_d1.2251664
X-RAY DIFFRACTIONf_dihedral_angle_d13.911480
X-RAY DIFFRACTIONf_chiral_restr0.087171
X-RAY DIFFRACTIONf_plane_restr0.007214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5995-1.61980.28661290.2041299X-RAY DIFFRACTION85
1.6198-1.64110.22971340.15511380X-RAY DIFFRACTION96
1.6411-1.66360.20661400.13971533X-RAY DIFFRACTION98
1.6636-1.68730.2241320.13731407X-RAY DIFFRACTION97
1.6873-1.71250.19921460.14061552X-RAY DIFFRACTION98
1.7125-1.73930.16761320.12941422X-RAY DIFFRACTION98
1.7393-1.76780.17221520.12481506X-RAY DIFFRACTION98
1.7678-1.79830.2031340.11991424X-RAY DIFFRACTION99
1.7983-1.8310.18111440.13211508X-RAY DIFFRACTION98
1.831-1.86620.21181420.13581474X-RAY DIFFRACTION99
1.8662-1.90430.20311420.13181451X-RAY DIFFRACTION99
1.9043-1.94570.16691460.12991527X-RAY DIFFRACTION99
1.9457-1.9910.19711360.12311433X-RAY DIFFRACTION99
1.991-2.04070.15651460.13191509X-RAY DIFFRACTION99
2.0407-2.09590.17171400.13091516X-RAY DIFFRACTION99
2.0959-2.15760.19831440.14471459X-RAY DIFFRACTION99
2.1576-2.22720.21781440.14091494X-RAY DIFFRACTION100
2.2272-2.30680.17861440.14961514X-RAY DIFFRACTION100
2.3068-2.39920.22351360.15691518X-RAY DIFFRACTION100
2.3992-2.50840.19491440.15361451X-RAY DIFFRACTION100
2.5084-2.64060.20461380.17221515X-RAY DIFFRACTION100
2.6406-2.8060.221420.17551488X-RAY DIFFRACTION100
2.806-3.02260.20191520.1751502X-RAY DIFFRACTION100
3.0226-3.32670.17781380.16291500X-RAY DIFFRACTION100
3.3267-3.80790.19021440.16281501X-RAY DIFFRACTION100
3.8079-4.79650.1921350.15641524X-RAY DIFFRACTION100
4.7965-43.83250.19731310.18661503X-RAY DIFFRACTION100

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