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- PDB-1yrk: The C2 Domain of PKC is a new Phospho-Tyrosine Binding Domain -

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Basic information

Entry
Database: PDB / ID: 1yrk
TitleThe C2 Domain of PKC is a new Phospho-Tyrosine Binding Domain
Components
  • 13-residue peptide
  • Protein kinase C, delta type
KeywordsPROTEIN BINDING / C2 domain
Function / homology
Function and homology information


positive regulation of phospholipid scramblase activity / positive regulation of glucosylceramide catabolic process / positive regulation of sphingomyelin catabolic process / regulation of ceramide biosynthetic process / endolysosome / negative regulation of filopodium assembly / positive regulation of ceramide biosynthetic process / HuR (ELAVL1) binds and stabilizes mRNA / DAG and IP3 signaling / termination of signal transduction ...positive regulation of phospholipid scramblase activity / positive regulation of glucosylceramide catabolic process / positive regulation of sphingomyelin catabolic process / regulation of ceramide biosynthetic process / endolysosome / negative regulation of filopodium assembly / positive regulation of ceramide biosynthetic process / HuR (ELAVL1) binds and stabilizes mRNA / DAG and IP3 signaling / termination of signal transduction / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / calcium,diacylglycerol-dependent serine/threonine kinase activity / protein kinase C / diacylglycerol-dependent serine/threonine kinase activity / cellular response to hydroperoxide / negative regulation of glial cell apoptotic process / Effects of PIP2 hydrolysis / negative regulation of actin filament polymerization / activation of protein kinase activity / neutrophil activation / negative regulation of platelet aggregation / positive regulation of endodeoxyribonuclease activity / Calmodulin induced events / cellular response to fatty acid / intrinsic apoptotic signaling pathway in response to oxidative stress / Apoptotic cleavage of cellular proteins / Fc-gamma receptor signaling pathway involved in phagocytosis / B cell proliferation / immunoglobulin mediated immune response / insulin receptor substrate binding / cellular response to angiotensin / RHO GTPases Activate NADPH Oxidases / Role of phospholipids in phagocytosis / negative regulation of MAPK cascade / regulation of mRNA stability / peptidyl-threonine phosphorylation / negative regulation of insulin receptor signaling pathway / post-translational protein modification / SHC1 events in ERBB2 signaling / enzyme activator activity / VEGFR2 mediated cell proliferation / positive regulation of superoxide anion generation / positive regulation of apoptotic signaling pathway / cell chemotaxis / non-membrane spanning protein tyrosine kinase activity / regulation of actin cytoskeleton organization / non-specific protein-tyrosine kinase / CLEC7A (Dectin-1) signaling / negative regulation of inflammatory response / cellular response to hydrogen peroxide / positive regulation of protein import into nucleus / nuclear matrix / Interferon gamma signaling / G alpha (z) signalling events / cellular response to UV / cellular senescence / azurophil granule lumen / KEAP1-NFE2L2 pathway / cell-cell junction / peptidyl-serine phosphorylation / protein kinase activity / protein stabilization / intracellular signal transduction / defense response to bacterium / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / Neutrophil degranulation / protein kinase binding / perinuclear region of cytoplasm / enzyme binding / endoplasmic reticulum / signal transduction / mitochondrion / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Novel protein kinase C delta, catalytic domain / Protein kinase C, delta / Protein kinase C delta/epsilon/eta/theta, C2 domain / Protein kinase C, delta/epsilon/eta/theta 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. ...Novel protein kinase C delta, catalytic domain / Protein kinase C, delta / Protein kinase C delta/epsilon/eta/theta, C2 domain / Protein kinase C, delta/epsilon/eta/theta 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. / 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
ACETIC ACID / Protein kinase C delta type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBenes, C.H. / Wu, N. / Elia, A.E. / Dharia, T. / Cantley, L.C. / Soltoff, S.P.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2005
Title: The C2 domain of PKCdelta is a phosphotyrosine binding domain.
Authors: Benes, C.H. / Wu, N. / Elia, A.E. / Dharia, T. / Cantley, L.C. / Soltoff, S.P.
History
DepositionFeb 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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, delta type
B: 13-residue peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9933
Polymers15,9332
Non-polymers601
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-11 kcal/mol
Surface area8590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.272, 41.856, 88.463
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe protein is the monomeric form.

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Components

#1: Protein Protein kinase C, delta type / nPKC-delta


Mass: 14287.434 Da / Num. of mol.: 1 / Fragment: C2 domain, residues 1-123
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: Q05655
#2: Protein/peptide 13-residue peptide


Mass: 1645.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.57 Å3/Da / Density % sol: 52.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG4K, PEG200, potassium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.7→100 Å / Num. all: 15581 / Num. obs: 15254 / % possible obs: 97.9 % / Biso Wilson estimate: 9.5 Å2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→34.35 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 276148.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1043 6.8 %RANDOM
Rwork0.176 ---
obs0.176 15254 96.2 %-
all-15254 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.0499 Å2 / ksol: 0.364346 e/Å3
Displacement parametersBiso mean: 12.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--0.6 Å20 Å2
3----0.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.7→34.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1117 0 0 224 1341
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it1.652
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_scangle_it2.792.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.253 121 5.1 %
Rwork0.183 2257 -
obs--92.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PRO.PARAMPRO.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ACY.PARAM

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