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- PDB-2wh0: Recognition of an intrachain tandem 14-3-3 binding site within pr... -

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Basic information

Entry
Database: PDB / ID: 2wh0
TitleRecognition of an intrachain tandem 14-3-3 binding site within protein kinase C epsilon
Components
  • 14-3-3 PROTEIN ZETA/DELTA
  • PROTEIN KINASE C EPSILON TYPE, NPKC-EPSILON
KeywordsSIGNALING PROTEIN / TANDEM BINDING / PHOSPHOPROTEIN / 14-3-3 / CYTOPLASM / ACETYLATION / PKC EPSILON
Function / homology
Function and homology information


ethanol binding / TRAM-dependent toll-like receptor 4 signaling pathway / negative regulation of sodium ion transmembrane transport / toxin catabolic process / DAG and IP3 signaling / positive regulation of lipid catabolic process / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / calcium,diacylglycerol-dependent serine/threonine kinase activity / protein kinase C / diacylglycerol-dependent serine/threonine kinase activity ...ethanol binding / TRAM-dependent toll-like receptor 4 signaling pathway / negative regulation of sodium ion transmembrane transport / toxin catabolic process / DAG and IP3 signaling / positive regulation of lipid catabolic process / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / calcium,diacylglycerol-dependent serine/threonine kinase activity / protein kinase C / diacylglycerol-dependent serine/threonine kinase activity / synaptic target recognition / Golgi reassembly / mucus secretion / Effects of PIP2 hydrolysis / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / regulation of insulin secretion involved in cellular response to glucose stimulus / respiratory system process / regulation of synapse maturation / tube formation / macrophage activation involved in immune response / intermediate filament cytoskeleton / regulation of release of sequestered calcium ion into cytosol / Rap1 signalling / cellular response to ethanol / positive regulation of fibroblast migration / positive regulation of cell-substrate adhesion / negative regulation of protein localization to nucleus / insulin secretion / positive regulation of mucus secretion / response to morphine / KSRP (KHSRP) binds and destabilizes mRNA / synaptic transmission, GABAergic / positive regulation of actin filament polymerization / positive regulation of wound healing / GP1b-IX-V activation signalling / cell-substrate adhesion / positive regulation of cytokinesis / signaling receptor activator activity / Fc-gamma receptor signaling pathway involved in phagocytosis / locomotory exploration behavior / Regulation of localization of FOXO transcription factors / Interleukin-3, Interleukin-5 and GM-CSF signaling / positive regulation of epithelial cell migration / actin monomer binding / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / Role of phospholipids in phagocytosis / xenobiotic catabolic process / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / regulation of ERK1 and ERK2 cascade / cellular response to glucose starvation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / 14-3-3 protein binding / negative regulation of protein ubiquitination / Transcriptional and post-translational regulation of MITF-M expression and activity / ERK1 and ERK2 cascade / SHC1 events in ERBB2 signaling / protein sequestering activity / negative regulation of innate immune response / lipopolysaccharide-mediated signaling pathway / hippocampal mossy fiber to CA3 synapse / enzyme activator activity / positive regulation of superoxide anion generation / positive regulation of synaptic transmission, GABAergic / cell periphery / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / establishment of localization in cell / positive regulation of protein localization to plasma membrane / Deactivation of the beta-catenin transactivating complex / lung development / Negative regulation of NOTCH4 signaling / regulation of protein stability / positive regulation of insulin secretion / G alpha (z) signalling events / MAPK cascade / intracellular protein localization / cellular response to prostaglandin E stimulus / melanosome / peptidyl-serine phosphorylation / angiogenesis / DNA-binding transcription factor binding / cellular response to hypoxia / vesicle / blood microparticle / transmembrane transporter binding / positive regulation of canonical NF-kappaB signal transduction / protein kinase activity / positive regulation of MAPK cascade / intracellular signal transduction / protein phosphorylation / cadherin binding / protein domain specific binding / cell division / protein serine kinase activity
Similarity search - Function
Protein kinase C, epsilon / Novel protein kinase C epsilon, catalytic domain / Protein kinase C, delta/epsilon/eta/theta types / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / 14-3-3 domain / Phorbol esters/diacylglycerol binding domain (C1 domain) / Delta-Endotoxin; domain 1 / Zinc finger phorbol-ester/DAG-type signature. ...Protein kinase C, epsilon / Novel protein kinase C epsilon, catalytic domain / Protein kinase C, delta/epsilon/eta/theta types / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / 14-3-3 domain / Phorbol esters/diacylglycerol binding domain (C1 domain) / Delta-Endotoxin; domain 1 / 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 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / 14-3-3 protein zeta/delta / Protein kinase C epsilon type
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsKostelecky, B. / Saurin, A.T. / Purkiss, A. / Parker, P.J. / McDonald, N.Q.
CitationJournal: Embo Rep. / Year: 2009
Title: Recognition of an Intra-Chain Tandem 14-3-3 Binding Site within Pkc Epsilon.
Authors: Kostelecky, B. / Saurin, A.T. / Purkiss, A. / Parker, P.J. / Mcdonald, N.Q.
History
DepositionApr 28, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3 PROTEIN ZETA/DELTA
B: 14-3-3 PROTEIN ZETA/DELTA
C: 14-3-3 PROTEIN ZETA/DELTA
D: 14-3-3 PROTEIN ZETA/DELTA
Q: PROTEIN KINASE C EPSILON TYPE, NPKC-EPSILON
R: PROTEIN KINASE C EPSILON TYPE, NPKC-EPSILON
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,7568
Polymers118,5666
Non-polymers1902
Water1,15364
1
A: 14-3-3 PROTEIN ZETA/DELTA
B: 14-3-3 PROTEIN ZETA/DELTA
Q: PROTEIN KINASE C EPSILON TYPE, NPKC-EPSILON
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4334
Polymers59,2833
Non-polymers1501
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-20.45 kcal/mol
Surface area20590 Å2
MethodPISA
2
C: 14-3-3 PROTEIN ZETA/DELTA
D: 14-3-3 PROTEIN ZETA/DELTA
R: PROTEIN KINASE C EPSILON TYPE, NPKC-EPSILON
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3234
Polymers59,2833
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-33.8 kcal/mol
Surface area21250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.130, 78.160, 108.520
Angle α, β, γ (deg.)90.00, 90.10, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.994832, -0.101326, -0.006474), (-0.101381, 0.987854, 0.117757), (-0.005537, 0.117805, -0.993021)67.6781, -0.59923, 65.4697
2given(0.999803, 0.019824, -0.001291), (0.019829, -0.999796, 0.00378), (-0.001216, -0.003805, -0.999992)-39.6941, 10.0708, 54.3752
3given(-0.996404, 0.084209, 0.0094), (-0.084678, -0.985668, -0.145905), (-0.003022, -0.146177, 0.989254)105.66, 20.6159, 13.6988

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Components

#1: Protein
14-3-3 PROTEIN ZETA/DELTA / 14-3-3 ZETA / KCIP-1 / PROTEIN KINASE C INHIBITOR PROTEIN 1


Mass: 27777.092 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PACYC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63104
#2: Protein/peptide PROTEIN KINASE C EPSILON TYPE, NPKC-EPSILON / PKCEV3


Mass: 3728.884 Da / Num. of mol.: 2 / Fragment: PKC EPSILON V3-DERIVED PEPTIDE, RESIDUES 342-372 / Source method: obtained synthetically / Details: SYNTHETIC FRAGMENT OF PKC EPSILON V3 REGION / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q02156, protein kinase C
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.58 Å3/Da / Density % sol: 52.3 % / Description: NONE
Crystal growpH: 7.4
Details: 16 MG/ML PROTEIN 9% (W/V) POLYETHYLENE GLYCOL 3350, 25 MM CALCIUM ACETATE, 25 MM SODIUM FLUORIDE, pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 13, 2008 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.441
ReflectionResolution: 2.25→24.5 Å / Num. obs: 56277 / % possible obs: 99.4 % / Observed criterion σ(I): 3.9 / Redundancy: 4.9 % / Biso Wilson estimate: 39.6 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.4
Reflection shellResolution: 2.25→2.45 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.9 / % possible all: 82.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QJB

1qjb


Resolution: 2.25→24.46 Å / σ(F): 1.99 / Phase error: 37.54 / Stereochemistry target values: TWIN_LSQ_F / Details: TWINNED REFINEMENT
RfactorNum. reflection% reflection
Rfree0.235 2000 3.5 %
Rwork0.181 --
obs0.183 56277 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.57 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 34.93 Å2
Baniso -1Baniso -2Baniso -3
1--3.3597 Å20 Å2-1.0192 Å2
2--13.3635 Å2-0 Å2
3----10.0038 Å2
Refinement stepCycle: LAST / Resolution: 2.25→24.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6805 0 8 64 6877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056901
X-RAY DIFFRACTIONf_angle_d0.8839347
X-RAY DIFFRACTIONf_dihedral_angle_d16.8942391
X-RAY DIFFRACTIONf_chiral_restr0.0571084
X-RAY DIFFRACTIONf_plane_restr0.0031202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.28880.3007960.24422549X-RAY DIFFRACTION98
2.2888-2.33040.2768980.2352672X-RAY DIFFRACTION98
2.3304-2.37520.2857990.24182716X-RAY DIFFRACTION98
2.3752-2.42360.2118980.22682694X-RAY DIFFRACTION98
2.4236-2.47620.2895990.21972712X-RAY DIFFRACTION98
2.4762-2.53380.2973990.2282742X-RAY DIFFRACTION98
2.5338-2.59710.2897990.22122692X-RAY DIFFRACTION98
2.5971-2.66720.2968990.21332696X-RAY DIFFRACTION98
2.6672-2.74560.2657980.20252723X-RAY DIFFRACTION98
2.7456-2.83410.25931000.19542721X-RAY DIFFRACTION98
2.8341-2.93520.29041020.19572732X-RAY DIFFRACTION98
2.9352-3.05250.2899980.19532705X-RAY DIFFRACTION98
3.0525-3.19120.24991050.1862719X-RAY DIFFRACTION98
3.1912-3.3590.23091010.19042726X-RAY DIFFRACTION98
3.359-3.56890.25831020.17842728X-RAY DIFFRACTION98
3.5689-3.84350.20431060.16062720X-RAY DIFFRACTION98
3.8435-4.22850.1849980.13912769X-RAY DIFFRACTION98
4.2285-4.83620.2032970.13512744X-RAY DIFFRACTION98
4.8362-6.07770.22891030.18152746X-RAY DIFFRACTION98
6.0777-24.46540.1691990.1642775X-RAY DIFFRACTION98

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