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- PDB-2fjl: Solution Structure of the Split PH domain in Phospholipase C-gamma1 -

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Basic information

Entry
Database: PDB / ID: 2fjl
TitleSolution Structure of the Split PH domain in Phospholipase C-gamma1
Components1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma 1
KeywordsHYDROLASE / beta-barrel
Function / homology
Function and homology information


PECAM1 interactions / EGFR interacts with phospholipase C-gamma / Activated NTRK2 signals through PLCG1 / Activated NTRK3 signals through PLCG1 / phosphatidylinositol catabolic process / Phospholipase C-mediated cascade: FGFR1 / Phospholipase C-mediated cascade; FGFR3 / Phospholipase C-mediated cascade; FGFR4 / Phospholipase C-mediated cascade; FGFR2 / ISG15 antiviral mechanism ...PECAM1 interactions / EGFR interacts with phospholipase C-gamma / Activated NTRK2 signals through PLCG1 / Activated NTRK3 signals through PLCG1 / phosphatidylinositol catabolic process / Phospholipase C-mediated cascade: FGFR1 / Phospholipase C-mediated cascade; FGFR3 / Phospholipase C-mediated cascade; FGFR4 / Phospholipase C-mediated cascade; FGFR2 / ISG15 antiviral mechanism / Downstream signal transduction / Signaling by ALK / Generation of second messenger molecules / Role of phospholipids in phagocytosis / DAP12 signaling / FCERI mediated Ca+2 mobilization / VEGFR2 mediated cell proliferation / calcium-dependent phospholipase C activity / inositol trisphosphate biosynthetic process / RET signaling / Synthesis of IP3 and IP4 in the cytosol / response to curcumin / inositol trisphosphate metabolic process / phosphoinositide phospholipase C / FCERI mediated MAPK activation / response to gravity / phosphatidylinositol metabolic process / COP9 signalosome / phospholipase C activity / neurotrophin TRKA receptor binding / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / clathrin-coated vesicle / positive regulation of vascular endothelial cell proliferation / phosphatidylinositol-mediated signaling / positive regulation of epithelial cell migration / positive regulation of endothelial cell apoptotic process / positive regulation of blood vessel endothelial cell migration / glutamate receptor binding / ruffle / release of sequestered calcium ion into cytosol / cellular response to epidermal growth factor stimulus / positive regulation of release of sequestered calcium ion into cytosol / guanyl-nucleotide exchange factor activity / cell projection / phosphoprotein binding / insulin receptor binding / modulation of chemical synaptic transmission / calcium-mediated signaling / Schaffer collateral - CA1 synapse / receptor tyrosine kinase binding / response to hydrogen peroxide / epidermal growth factor receptor signaling pathway / ruffle membrane / positive regulation of angiogenesis / calcium ion transport / cell-cell junction / cell migration / lamellipodium / T cell receptor signaling pathway / in utero embryonic development / calcium ion binding / protein kinase binding / glutamatergic synapse / plasma membrane / cytosol / cytoplasm
Similarity search - Function
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1, SH3 domain / PLCG EF-hand motif 1 / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase gamma / PLC-gamma, C-terminal SH2 domain / PLC-gamma, N-terminal SH2 domain / PLCG EF-hand motif 2 / Phosphoinositide phospholipase C family / Phospholipase C, phosphatidylinositol-specific, Y domain / Phosphatidylinositol-specific phospholipase C, Y domain / Phosphatidylinositol-specific phospholipase Y-box domain profile. ...1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1, SH3 domain / PLCG EF-hand motif 1 / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase gamma / PLC-gamma, C-terminal SH2 domain / PLC-gamma, N-terminal SH2 domain / PLCG EF-hand motif 2 / 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 / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / 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 / SH2 domain superfamily / Src homology 3 domains / EF-Hand 1, calcium-binding site / SH3-like domain superfamily / EF-hand calcium-binding domain. / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing
AuthorsWen, W. / Zhang, M.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structural Characterization of the Split Pleckstrin Homology Domain in Phospholipase C-{gamma}1 and Its Interaction with TRPC3
Authors: Wen, W. / Yan, J. / Zhang, M.
History
DepositionJan 3, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)16,9161
Polymers16,9161
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma 1 / Phosphoinositide phospholipase C / PLC-gamma-1 / Phospholipase C-gamma-1 / PLC-II / PLC-148


Mass: 16915.568 Da / Num. of mol.: 1 / Fragment: the Split PH2 domain, residuse 1-35 and 112-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET32a / Production host: Escherichia coli (E. coli)
References: UniProt: P10686, 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-separated NOESY
122HN(CA)CB, CBCA(CO)NH
1333D 13C-separated NOESY
1442D NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0mM of the PHN-PHC tandem U-15N; 50mM potassium phosphate; 90% H2O, 10% D2O90% H2O/10% D2O
21.0mM of the PHN-PHC tandem U-15N,13C; 50mM potassium phosphate; 90% H2O, 10% D2O90% H2O/10% D2O
31.0mM of the PHN-PHC tandem U-15N,13C; 50mM potassium phosphate; 100% D2O100% D2O
41.0mM of the PHN-PHC tandem; 50mM potassium phosphate; 100% D2O100% D2O
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA5002

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Processing

NMR softwareName: CNS / Version: 1.1 / Developer: Brunger / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 2145 restraints, 2023 are NOE-derived distance constraints, 60 dihedral angle restraints,62 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 15

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