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- PDB-2k2j: NMR solution structure of the split PH domain from Phospholipase ... -

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Basic information

Entry
Database: PDB / ID: 2k2j
TitleNMR solution structure of the split PH domain from Phospholipase C gamma 2
Components1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma-2
KeywordsHYDROLASE / SIGNALING PROTEIN / two sheeted beta barrel / C-terminal helix / Calcium / Lipid degradation / Phosphoprotein / Polymorphism / SH2 domain / SH3 domain / Transducer
Function / homology
Function and homology information


follicular B cell differentiation / inositol trisphosphate biosynthetic process / regulation of calcineurin-NFAT signaling cascade / positive regulation of dendritic cell cytokine production / antifungal innate immune response / phosphoinositide phospholipase C / positive regulation of interleukin-23 production / phosphorylation-dependent protein binding / phospholipid catabolic process / cellular response to lectin ...follicular B cell differentiation / inositol trisphosphate biosynthetic process / regulation of calcineurin-NFAT signaling cascade / positive regulation of dendritic cell cytokine production / antifungal innate immune response / phosphoinositide phospholipase C / positive regulation of interleukin-23 production / phosphorylation-dependent protein binding / phospholipid catabolic process / cellular response to lectin / positive regulation of I-kappaB phosphorylation / response to yeast / positive regulation of cell cycle G1/S phase transition / phosphatidylinositol metabolic process / Toll Like Receptor 4 (TLR4) Cascade / cell activation / positive regulation of phagocytosis, engulfment / positive regulation of neuroinflammatory response / phosphatidylinositol phospholipase C activity / Erythropoietin activates Phospholipase C gamma (PLCG) / phospholipase C activity / programmed cell death / phosphatidylinositol biosynthetic process / macrophage activation involved in immune response / cellular response to lipid / negative regulation of programmed cell death / regulation of canonical NF-kappaB signal transduction / positive regulation of macrophage cytokine production / positive regulation of reactive oxygen species biosynthetic process / toll-like receptor signaling pathway / positive regulation of NLRP3 inflammasome complex assembly / intracellular vesicle / positive regulation of epithelial cell migration / Dectin-2 family / Synthesis of IP3 and IP4 in the cytosol / Fc-epsilon receptor signaling pathway / stimulatory C-type lectin receptor signaling pathway / phosphatidylinositol-mediated signaling / positive regulation of interleukin-10 production / positive regulation of receptor internalization / regulation of lipid metabolic process / Generation of second messenger molecules / response to axon injury / positive regulation of type I interferon production / Role of phospholipids in phagocytosis / positive regulation of calcium-mediated signaling / release of sequestered calcium ion into cytosol / lipopolysaccharide-mediated signaling pathway / GPVI-mediated activation cascade / cellular response to calcium ion / positive regulation of interleukin-2 production / positive regulation of interleukin-12 production / phosphotyrosine residue binding / FCERI mediated Ca+2 mobilization / B cell differentiation / protein tyrosine kinase binding / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / calcium-mediated signaling / FCERI mediated MAPK activation / B cell receptor signaling pathway / platelet activation / CLEC7A (Dectin-1) signaling / Wnt signaling pathway / ruffle membrane / positive regulation of DNA-binding transcription factor activity / positive regulation of interleukin-6 production / Signaling by CSF1 (M-CSF) in myeloid cells / positive regulation of tumor necrosis factor production / positive regulation of peptidyl-tyrosine phosphorylation / DAP12 signaling / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / scaffold protein binding / Potential therapeutics for SARS / positive regulation of MAPK cascade / intracellular signal transduction / membrane raft / positive regulation of gene expression / protein kinase binding / perinuclear region of cytoplasm / extracellular exosome / plasma membrane / cytosol / cytoplasm
Similarity search - Function
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-2, SH3 domain / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase gamma / PLC-gamma, C-terminal SH2 domain / PLC-gamma, N-terminal SH2 domain / Pleckstrin homology domain / Phosphoinositide phospholipase C family / Phospholipase C, phosphatidylinositol-specific, Y domain / Phosphatidylinositol-specific phospholipase C, Y domain / Phosphatidylinositol-specific phospholipase Y-box domain profile. / Phospholipase C, catalytic domain (part); domain Y ...1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-2, SH3 domain / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase gamma / PLC-gamma, C-terminal SH2 domain / PLC-gamma, N-terminal SH2 domain / Pleckstrin homology domain / Phosphoinositide phospholipase C family / Phospholipase C, phosphatidylinositol-specific, Y domain / Phosphatidylinositol-specific phospholipase C, Y domain / Phosphatidylinositol-specific phospholipase Y-box domain profile. / Phospholipase C, catalytic domain (part); domain Y / Phosphatidylinositol-specific phospholipase C, X domain / Phosphatidylinositol-specific phospholipase C, X domain / Phospholipase C, catalytic domain (part); domain X / Phosphatidylinositol-specific phospholipase X-box domain profile. / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand domain pair / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsHarris, R. / Bunney, T.D. / Katan, M. / Driscoll, P.C.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Rac Regulates Its Effector Phospholipase C{gamma}2 through Interaction with a Split Pleckstrin Homology Domain.
Authors: Walliser, C. / Retlich, M. / Harris, R. / Everett, K.L. / Josephs, M.B. / Vatter, P. / Esposito, D. / Driscoll, P.C. / Katan, M. / Gierschik, P. / Bunney, T.D.
History
DepositionApr 2, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_spectrometer ...pdbx_database_status / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma-2


Theoretical massNumber of molelcules
Total (without water)14,2471
Polymers14,2471
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 10020 structures for lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma-2 / Phosphoinositide phospholipase C / PLC-gamma-2 / Phospholipase C-gamma-2 / PLC-IV


Mass: 14246.834 Da / Num. of mol.: 1 / Fragment: PH domains (UNP residues 471-514 and 850-913)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLCG2 / Production host: Escherichia coli (E. coli)
References: UniProt: P16885, phosphoinositide phospholipase C

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-edited NOESY
1223D 13C-edited NOESY
1323D 13C-edited aromatic NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8-1.0 mM [U-15N] split PH domain from Phospholipase C gamma 2, 90% H2O, 10% D2O90% H2O/10% D2O
20.8-1.0 mM [U-13C; U-15N] split PH domain from Phospholipase C gamma 2, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMsplit PH domain from Phospholipase C gamma 2[U-15N]1
0.8 mMsplit PH domain from Phospholipase C gamma 2[U-13C; U-15N]2
Sample conditionsIonic strength: 150mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian InovaVarianINOVA6001
Varian UnityPlusVarianUNITYPLUS5002
Bruker AvanceBrukerAVANCE7003
Varian InovaVarianINOVA8004

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Processing

NMR softwareName: CNS / Developer: Brunger A. T. et.al. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Ab initio simulated annealing protocol within the CNS program, with PARALLHDGv5.3 force field and PROLSQ non-bonded energy function. This protocol adopts a mixture of Cartesian molecular ...Details: Ab initio simulated annealing protocol within the CNS program, with PARALLHDGv5.3 force field and PROLSQ non-bonded energy function. This protocol adopts a mixture of Cartesian molecular dynamics and torsion angle dynamics simulated annealing.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 20 structures for lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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