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- PDB-2pld: NUCLEAR MAGNETIC RESONANCE STRUCTURE OF AN SH2 DOMAIN OF PHOSPHOL... -

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Entry
Database: PDB / ID: 2pld
TitleNUCLEAR MAGNETIC RESONANCE STRUCTURE OF AN SH2 DOMAIN OF PHOSPHOLIPASE C-GAMMA1 COMPLEXED WITH A HIGH AFFINITY BINDING PEPTIDE
Components
  • PHOSPHOLIPASE C GAMMA-1, C-TERMINAL SH2 DOMAIN
  • PHOSPHOPEPTIDE FROM PDGF
KeywordsPHOSPHORIC DIESTER HYDROLASE
Function / homology
Function and homology information


platelet-derived growth factor receptor activity / cell migration involved in coronary angiogenesis / metanephric glomerular mesangial cell proliferation involved in metanephros development / platelet activating factor receptor activity / positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway / smooth muscle cell chemotaxis / calcium-dependent phospholipase C activity / metanephric glomerular capillary formation / cell migration involved in vasculogenesis / aorta morphogenesis ...platelet-derived growth factor receptor activity / cell migration involved in coronary angiogenesis / metanephric glomerular mesangial cell proliferation involved in metanephros development / platelet activating factor receptor activity / positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway / smooth muscle cell chemotaxis / calcium-dependent phospholipase C activity / metanephric glomerular capillary formation / cell migration involved in vasculogenesis / aorta morphogenesis / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / smooth muscle adaptation / platelet-derived growth factor binding / phosphoinositide phospholipase C / vascular endothelial growth factor binding / retina vasculature development in camera-type eye / phosphatidylinositol metabolic process / cardiac myofibril assembly / Signaling by PDGF / COP9 signalosome / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / positive regulation of chemotaxis / phospholipase C activator activity / platelet-derived growth factor receptor binding / phospholipid catabolic process / positive regulation of DNA biosynthetic process / positive regulation of smooth muscle cell migration / phosphatidylinositol-mediated signaling / positive regulation of calcium ion import / platelet-derived growth factor receptor-beta signaling pathway / platelet-derived growth factor receptor signaling pathway / positive regulation of epithelial cell migration / cellular response to vascular endothelial growth factor stimulus / ruffle / release of sequestered calcium ion into cytosol / positive regulation of MAP kinase activity / Downstream signal transduction / positive regulation of mitotic nuclear division / cellular response to epidermal growth factor stimulus / GTPase activator activity / positive regulation of calcium-mediated signaling / lysosomal lumen / cell surface receptor protein tyrosine kinase signaling pathway / guanyl-nucleotide exchange factor activity / cell chemotaxis / regulation of actin cytoskeleton organization / positive regulation of smooth muscle cell proliferation / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / epidermal growth factor receptor signaling pathway / ruffle membrane / positive regulation of reactive oxygen species metabolic process / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / lamellipodium / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein autophosphorylation / protein tyrosine kinase activity / cytoplasmic vesicle / angiogenesis / in utero embryonic development / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of ERK1 and ERK2 cascade / protein kinase activity / positive regulation of cell migration / apical plasma membrane / signaling receptor binding / focal adhesion / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / calcium ion binding / protein kinase binding / enzyme binding / Golgi apparatus / signal transduction / ATP binding / nucleus / membrane / plasma membrane / cytoplasm
Similarity search - Function
Platelet-derived growth factor receptor beta / 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 ...Platelet-derived growth factor receptor beta / 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 / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / SH2 domain / SHC Adaptor Protein / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / PH domain / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / : / SH3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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 / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Immunoglobulin subtype / Immunoglobulin / PH-like domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1 / Platelet-derived growth factor receptor beta
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodSOLUTION NMR
AuthorsPascal, S.M. / Singer, A.U. / Gish, G. / Yamazaki, T. / Shoelson, S.E. / Pawson, T. / Kay, L.E. / Forman-Kay, J.D.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1994
Title: Nuclear magnetic resonance structure of an SH2 domain of phospholipase C-gamma 1 complexed with a high affinity binding peptide.
Authors: Pascal, S.M. / Singer, A.U. / Gish, G. / Yamazaki, T. / Shoelson, S.E. / Pawson, T. / Kay, L.E. / Forman-Kay, J.D.
History
DepositionAug 19, 1994Processing site: BNL
Revision 1.0Jan 26, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 30, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHOLIPASE C GAMMA-1, C-TERMINAL SH2 DOMAIN
B: PHOSPHOPEPTIDE FROM PDGF


Theoretical massNumber of molelcules
Total (without water)13,7562
Polymers13,7562
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Atom site foot note1: RESIDUES A 1 - A 10, A 99 - A 105, B 1 - B 2, AND B 11 - B 12 ARE DISORDERED IN SOLUTION; THEREFORE, COORDINATES DISPLAY LARGE RMSD VALUES FOR THESE ATOMS.
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

#1: Protein PHOSPHOLIPASE C GAMMA-1, C-TERMINAL SH2 DOMAIN


Mass: 12275.924 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle)
References: UniProt: P08487, phosphoinositide phospholipase C
#2: Protein/peptide PHOSPHOPEPTIDE FROM PDGF


Mass: 1480.532 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P09619
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR softwareName: X-PLOR / Developer: BRUNGER / Classification: refinement
NMR ensembleConformers submitted total number: 1

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