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- PDB-1pic: PHOSPHATIDYLINOSITOL 3-KINASE, P85-ALPHA SUBUNIT: C-TERMINAL SH2 ... -

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Basic information

Entry
Database: PDB / ID: 1pic
TitlePHOSPHATIDYLINOSITOL 3-KINASE, P85-ALPHA SUBUNIT: C-TERMINAL SH2 DOMAIN COMPLEXED WITH A TYR751 PHOSPHOPEPTIDE FROM THE PDGF RECEPTOR, NMR, MINIMIZED MEAN STRUCTURE
Components
  • BETA-PLATELET-DERIVED GROWTH FACTOR RECEPTOR
  • PHOSPHATIDYLINOSITOL 3-KINASE
KeywordsCOMPLEX (PHOSPHOTRANSFERASE/RECEPTOR) / PHOSPHOTRANSFERASE / SH2 DOMAIN / SIGNAL TRANSDUCTION / PHOSPHOINOSITIDE 3-KINASE / COMPLEX (PHOSPHOTRANSFERASE-RECEPTOR) / COMPLEX (PHOSPHOTRANSFERASE-RECEPTOR) complex
Function / homology
Function and homology information


perinuclear endoplasmic reticulum membrane / regulation of toll-like receptor 4 signaling pathway / phosphatidylinositol kinase activity / phosphatidylinositol 3-kinase regulator activity / positive regulation of focal adhesion disassembly / IRS-mediated signalling / phosphatidylinositol 3-kinase activator activity / 1-phosphatidylinositol-3-kinase regulator activity / positive regulation of endoplasmic reticulum unfolded protein response / interleukin-18-mediated signaling pathway ...perinuclear endoplasmic reticulum membrane / regulation of toll-like receptor 4 signaling pathway / phosphatidylinositol kinase activity / phosphatidylinositol 3-kinase regulator activity / positive regulation of focal adhesion disassembly / IRS-mediated signalling / phosphatidylinositol 3-kinase activator activity / 1-phosphatidylinositol-3-kinase regulator activity / positive regulation of endoplasmic reticulum unfolded protein response / interleukin-18-mediated signaling pathway / myeloid leukocyte migration / phosphatidylinositol 3-kinase complex / T follicular helper cell differentiation / PI3K events in ERBB4 signaling / phosphatidylinositol 3-kinase regulatory subunit binding / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / cis-Golgi network / Activated NTRK3 signals through PI3K / ErbB-3 class receptor binding / transmembrane receptor protein tyrosine kinase adaptor activity / Signaling by cytosolic FGFR1 fusion mutants / Co-stimulation by ICOS / RHOD GTPase cycle / RHOF GTPase cycle / phosphatidylinositol 3-kinase complex, class IA / kinase activator activity / Nephrin family interactions / Signaling by LTK in cancer / positive regulation of leukocyte migration / Signaling by LTK / MET activates PI3K/AKT signaling / PI3K/AKT activation / negative regulation of stress fiber assembly / RND1 GTPase cycle / positive regulation of filopodium assembly / RND2 GTPase cycle / RND3 GTPase cycle / insulin binding / growth hormone receptor signaling pathway / Signaling by ALK / RHOV GTPase cycle / PI-3K cascade:FGFR3 / RHOB GTPase cycle / natural killer cell mediated cytotoxicity / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / GP1b-IX-V activation signalling / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / RHOC GTPase cycle / RHOJ GTPase cycle / intracellular glucose homeostasis / phosphatidylinositol phosphate biosynthetic process / negative regulation of osteoclast differentiation / Synthesis of PIPs at the plasma membrane / RHOU GTPase cycle / CDC42 GTPase cycle / RET signaling / PI3K events in ERBB2 signaling / insulin receptor substrate binding / T cell differentiation / Interleukin-3, Interleukin-5 and GM-CSF signaling / extrinsic apoptotic signaling pathway via death domain receptors / PI3K Cascade / RHOG GTPase cycle / negative regulation of cell-matrix adhesion / CD28 dependent PI3K/Akt signaling / RHOA GTPase cycle / RAC2 GTPase cycle / Role of LAT2/NTAL/LAB on calcium mobilization / RAC3 GTPase cycle / Interleukin receptor SHC signaling / GAB1 signalosome / Role of phospholipids in phagocytosis / enzyme-substrate adaptor activity / phosphatidylinositol 3-kinase binding / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / Signaling by FGFR4 in disease / positive regulation of lamellipodium assembly / Signaling by FLT3 ITD and TKD mutants / GPVI-mediated activation cascade / Signaling by FGFR3 in disease / Tie2 Signaling / insulin-like growth factor receptor binding / Signaling by FGFR2 in disease / RAC1 GTPase cycle / Signaling by FLT3 fusion proteins / FLT3 Signaling / phosphotyrosine residue binding / Signaling by FGFR1 in disease / Interleukin-7 signaling / Downstream signal transduction / substrate adhesion-dependent cell spreading / B cell differentiation / osteoclast differentiation / insulin-like growth factor receptor signaling pathway / response to endoplasmic reticulum stress / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers
Similarity search - Function
Phosphatidylinositol 3-kinase regulatory subunit alpha, SH3 domain / PIK3R1, inter-SH2 domain / PI3K p85 subunit, C-terminal SH2 domain / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases ...Phosphatidylinositol 3-kinase regulatory subunit alpha, SH3 domain / PIK3R1, inter-SH2 domain / PI3K p85 subunit, C-terminal SH2 domain / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / SH2 domain / SHC Adaptor Protein / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphatidylinositol 3-kinase regulatory subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsBreeze, A.L. / Kara, B.V. / Barratt, D.G. / Anderson, M. / Smith, J.C. / Luke, R.W. / Best, J.R. / Cartlidge, S.A.
CitationJournal: EMBO J. / Year: 1996
Title: Structure of a specific peptide complex of the carboxy-terminal SH2 domain from the p85 alpha subunit of phosphatidylinositol 3-kinase.
Authors: Breeze, A.L. / Kara, B.V. / Barratt, D.G. / Anderson, M. / Smith, J.C. / Luke, R.W. / Best, J.R. / Cartlidge, S.A.
History
DepositionJun 23, 1997Processing site: BNL
Revision 1.0Sep 17, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / 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.process_site / _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: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHATIDYLINOSITOL 3-KINASE
B: BETA-PLATELET-DERIVED GROWTH FACTOR RECEPTOR


Theoretical massNumber of molelcules
Total (without water)13,3402
Polymers13,3402
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)1 / 100
Representative

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Components

#1: Protein PHOSPHATIDYLINOSITOL 3-KINASE


Mass: 12612.094 Da / Num. of mol.: 1
Fragment: C-TERMINAL SH2 DOMAIN, RESIDUES 617 - 724 OF P85-ALPHA REGULATORY SUBUNIT
Source method: isolated from a genetically manipulated source
Details: CONTAINS AN N-TERMINAL EXTENSION (GSPI) DERIVED FROM THE RECOMBINANT EXPRESSION VECTOR
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): W3110 (CGSC 6564) / References: UniProt: P27986, phosphatidylinositol 3-kinase
#2: Protein/peptide BETA-PLATELET-DERIVED GROWTH FACTOR RECEPTOR


Mass: 727.805 Da / Num. of mol.: 1 / Fragment: ACETYL-PTYR-VAL-PRO-MET-LEU, RESIDUES 751 - 755
Source method: isolated from a genetically manipulated source
Details: TYROSINE-PHOSPHORYLATED PEPTIDE INCORPORATES AN N-TERMINAL ACETYL GROUP
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: THE STRUCTURE WAS DETERMINED BY TRIPLE-RESONANCE NMR ON 13C,15N-LABELLED SH2 DOMAIN COMBINED WITH ISOTOPE-FILTERED 1H-NMR FOR THE UNLABELLED BOUND PEPTIDE.

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Sample preparation

Sample conditionspH: 6.8 / Temperature: 296 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY6001
Varian UNITYVarianUNITY7502

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformers calculated total number: 100 / Conformers submitted total number: 1

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