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- PDB-2eob: Solution structure of the second SH2 domain from rat PLC gamma-2 -

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Basic information

Entry
Database: PDB / ID: 2eob
TitleSolution structure of the second SH2 domain from rat PLC gamma-2
Components1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma 2
KeywordsHYDROLASE / sh2 / Phosphoinositide phospholipase C / PLC-gamma-2 / Phospholipase C-gamma-2 / PLC-IV / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Dectin-2 family / GPVI-mediated activation cascade / CLEC7A (Dectin-1) signaling / inositol trisphosphate biosynthetic process / Generation of second messenger molecules / Role of phospholipids in phagocytosis / Toll Like Receptor 4 (TLR4) Cascade / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / DAP12 signaling / FCERI mediated Ca+2 mobilization ...Dectin-2 family / GPVI-mediated activation cascade / CLEC7A (Dectin-1) signaling / inositol trisphosphate biosynthetic process / Generation of second messenger molecules / Role of phospholipids in phagocytosis / Toll Like Receptor 4 (TLR4) Cascade / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / DAP12 signaling / FCERI mediated Ca+2 mobilization / Synthesis of IP3 and IP4 in the cytosol / regulation of calcineurin-NFAT signaling cascade / activation of store-operated calcium channel activity / follicular B cell differentiation / response to yeast / positive regulation of dendritic cell cytokine production / phosphoinositide phospholipase C / positive regulation of macrophage cytokine production / antifungal innate immune response / FCERI mediated MAPK activation / cellular response to lectin / positive regulation of interleukin-23 production / phosphorylation-dependent protein binding / phosphatidylinositol metabolic process / positive regulation of cell cycle G1/S phase transition / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / cell activation / positive regulation of phagocytosis, engulfment / phosphatidylinositol biosynthetic process / macrophage activation involved in immune response / phospholipid catabolic process / cellular response to lipid / regulation of canonical NF-kappaB signal transduction / negative regulation of programmed cell death / positive regulation of neuroinflammatory response / toll-like receptor signaling pathway / response to ATP / stimulatory C-type lectin receptor signaling pathway / positive regulation of reactive oxygen species biosynthetic process / intracellular vesicle / phosphatidylinositol-mediated signaling / positive regulation of epithelial cell migration / lipopolysaccharide-mediated signaling pathway / positive regulation of intracellular signal transduction / positive regulation of interleukin-10 production / response to axon injury / B cell activation / positive regulation of NLRP3 inflammasome complex assembly / positive regulation of receptor internalization / regulation of lipid metabolic process / response to magnesium ion / positive regulation of interleukin-12 production / release of sequestered calcium ion into cytosol / B cell differentiation / positive regulation of calcium-mediated signaling / positive regulation of interleukin-2 production / positive regulation of type I interferon production / phosphotyrosine residue binding / cellular response to calcium ion / B cell receptor signaling pathway / protein tyrosine kinase binding / calcium-mediated signaling / positive regulation of interleukin-6 production / ruffle membrane / T cell receptor signaling pathway / positive regulation of tumor necrosis factor production / regulation of gene expression / positive regulation of cytosolic calcium ion concentration / response to lipopolysaccharide / scaffold protein binding / positive regulation of MAPK cascade / positive regulation of canonical NF-kappaB signal transduction / intracellular signal transduction / membrane raft / positive regulation of gene expression / protein kinase binding / perinuclear region of cytoplasm / 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 / : / : / PLCG EF-hand motif 1 / PLCG EF-hand motif 2 / Phosphoinositide phospholipase C family / Phospholipase C, phosphatidylinositol-specific, Y domain ...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 / : / : / PLCG EF-hand motif 1 / 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 / SH2 domain / SHC Adaptor Protein / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / PH domain profile. / C2 domain superfamily / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSano, R. / Hayashi, F. / Nagashima, T. / Yoshida, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the second SH2 domain from rat PLC gamma-2
Authors: Sano, R. / Hayashi, F. / Nagashima, T. / Yoshida, M. / Yokoyama, S.
History
DepositionMar 29, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)14,2821
Polymers14,2821
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)20 / 100structures with the least restraint violations, structures with the lowest energy, target function
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: 14282.141 Da / Num. of mol.: 1 / Fragment: SH2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Description: cell-free protein synthesis / Gene: Plcg2 / Plasmid: P051205-01
References: UniProt: P24135, phosphoinositide phospholipase C

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 0.71mM 13C, 15N-labeled protein; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA9001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe20030801Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.982Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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