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- PDB-1fu5: NMR STRUCTURE OF THE N-SH2 DOMAIN OF THE P85 SUBUNIT OF PI3-KINAS... -

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Entry
Database: PDB / ID: 1fu5
TitleNMR STRUCTURE OF THE N-SH2 DOMAIN OF THE P85 SUBUNIT OF PI3-KINASE COMPLEXED TO A DOUBLY PHOSPHORYLATED PEPTIDE DERIVED FROM POLYOMAVIRUS MIDDLE T ANTIGEN
Components
  • DOUBLY PHOSPHORYLATED MIDDLE T ANTIGEN
  • PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY ALPHA SUBUNIT
KeywordsPEPTIDE BINDING PROTEIN / protein-peptide complex
Function / homology
Function and homology information


PI3K events in ERBB4 signaling / Costimulation by the CD28 family / CD28 dependent PI3K/Akt signaling / MET activates PI3K/AKT signaling / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / Interleukin receptor SHC signaling / Tie2 Signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / FLT3 Signaling / GAB1 signalosome ...PI3K events in ERBB4 signaling / Costimulation by the CD28 family / CD28 dependent PI3K/Akt signaling / MET activates PI3K/AKT signaling / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / Interleukin receptor SHC signaling / Tie2 Signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / FLT3 Signaling / GAB1 signalosome / PI3K events in ERBB2 signaling / PI-3K cascade:FGFR1 / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / RHOJ GTPase cycle / IRS-mediated signalling / Interleukin-7 signaling / Synthesis of PIPs at the plasma membrane / Downstream TCR signaling / GP1b-IX-V activation signalling / RND1 GTPase cycle / Signaling by LTK / PI3K/AKT activation / PI-3K cascade:FGFR2 / Regulation of signaling by CBL / RND2 GTPase cycle / RHOF GTPase cycle / PI3K Cascade / VEGFA-VEGFR2 Pathway / Signaling by SCF-KIT / Role of LAT2/NTAL/LAB on calcium mobilization / RHOB GTPase cycle / RHOD GTPase cycle / RND3 GTPase cycle / CDC42 GTPase cycle / GPVI-mediated activation cascade / PIP3 activates AKT signaling / Downstream signal transduction / Signaling by ALK / Role of phospholipids in phagocytosis / RHOU GTPase cycle / RHOV GTPase cycle / RAC2 GTPase cycle / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / DAP12 signaling / RHOG GTPase cycle / RAC1 GTPase cycle / RET signaling / RHOA GTPase cycle / Extra-nuclear estrogen signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / perinuclear endoplasmic reticulum membrane / response to yeast / regulation of toll-like receptor 4 signaling pathway / negative regulation of muscle cell apoptotic process / phosphatidylinositol metabolic process / phosphatidylinositol 3-kinase regulator activity / positive regulation of focal adhesion disassembly / response to fructose / interleukin-18-mediated signaling pathway / myeloid leukocyte migration / response to fatty acid / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase regulatory subunit binding / neurotrophin TRKA receptor binding / response to growth factor / cis-Golgi network / ErbB-3 class receptor binding / kinase activator activity / negative regulation of cell adhesion / regulation of stress fiber assembly / platelet-derived growth factor receptor binding / positive regulation of endoplasmic reticulum unfolded protein response / phosphatidylinositol 3-kinase complex, class IA / G alpha (q) signalling events / phosphatidylinositol 3-kinase complex / positive regulation of synapse assembly / RAF/MAP kinase cascade / response to iron(II) ion / positive regulation of leukocyte migration / positive regulation of filopodium assembly / growth hormone receptor signaling pathway / negative regulation of stress fiber assembly / cellular response to fatty acid / insulin binding / natural killer cell mediated cytotoxicity / 1-phosphatidylinositol-3-kinase activity / negative regulation of heart rate / negative regulation of cell-matrix adhesion / negative regulation of cell-cell adhesion / response to dexamethasone / intracellular glucose homeostasis / negative regulation of osteoclast differentiation / response to testosterone / phosphatidylinositol phosphate biosynthetic process / insulin receptor substrate binding / extrinsic apoptotic signaling pathway via death domain receptors / host cell membrane / response to amino acid / regulation of protein localization to plasma membrane
Similarity search - Function
Small/middle T-antigen / Small/middle T-antigen superfamily / T-antigen specific domain / 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 ...Small/middle T-antigen / Small/middle T-antigen superfamily / T-antigen specific domain / 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 / DnaJ molecular chaperone homology domain / Chaperone J-domain superfamily / DnaJ domain / Rho GTPase activation protein / SH2 domain / SHC Adaptor Protein / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Middle T antigen / Middle T antigen / Phosphatidylinositol 3-kinase regulatory subunit alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / The structures were energy minimized with MSI DISCOVER.
AuthorsWeber, T. / Schaffhausen, B. / Liu, Y. / Guenther, U.L.
CitationJournal: Biochemistry / Year: 2000
Title: NMR structure of the N-SH2 of the p85 subunit of phosphoinositide 3-kinase complexed to a doubly phosphorylated peptide reveals a second phosphotyrosine binding site.
Authors: Weber, T. / Schaffhausen, B. / Liu, Y. / Gunther, U.L.
History
DepositionSep 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 13, 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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Assembly

Deposited unit
A: PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY ALPHA SUBUNIT
B: DOUBLY PHOSPHORYLATED MIDDLE T ANTIGEN


Theoretical massNumber of molelcules
Total (without water)14,9332
Polymers14,9332
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 / 110structures with favorable non-bond energy
RepresentativeModel #1lowest energy

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Components

#1: Protein PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY ALPHA SUBUNIT / PI3-KINASE P85-ALPHA SUBUNIT / PTDINS-3-KINASE P85-ALPHA / PI3K


Mass: 12870.384 Da / Num. of mol.: 1
Fragment: RESIDUES 321 TO 431 OF P85, N-SH2 (SRC HOMOLOGY 2) DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: Q63787
#2: Protein/peptide DOUBLY PHOSPHORYLATED MIDDLE T ANTIGEN / MT PEPTIDE


Mass: 2063.089 Da / Num. of mol.: 1
Fragment: RESIDUES 312 TO 326 OF MT ANTIGEN, Y315 AND Y322 PHOSPHORYLATED
Source method: obtained synthetically
Details: MT peptide was synthesized by the Tufts Protein Chemistry Facility
References: UniProt: P03076, UniProt: P03077*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 13C-separated NOESY
1313D 15N-separated NOESY
14113C{F1}-filtered 2D-NOESY
NMR detailsText: NOESY assignments were obtained by a semi-automatic procedure employing a program from Pristovsek [Pristovsek, P. & Kidric, J. (1997) Biopol. 42, 671-679)]. Initial calculations included only ...Text: NOESY assignments were obtained by a semi-automatic procedure employing a program from Pristovsek [Pristovsek, P. & Kidric, J. (1997) Biopol. 42, 671-679)]. Initial calculations included only intramolecular constraints. The observed NOEs derived from 13C{F1}-filtered 2D-NOESY spectra were incorporated into the structure calculation when the protein fold was already correct.

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Sample preparation

DetailsContents: 0.15mM N-SH2 15N, 13C; MT peptide; 0.1mM KCl; 95% H2O, 5% D2O
Solvent system: 100% H2O
Sample conditionsIonic strength: 0.1mM / pH: 6.8 / Pressure: 1 bar / Temperature: 305 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameDeveloperClassification
NMRLABUlrich Guenther, Christian Ludwig and Heinz Rueterjansprocessing
ProntoM. Kjaerdata analysis
nmr2stP. Pristovsekdata analysis
DYANAP. Guentertstructure solution
DiscoverMSIrefinement
RefinementMethod: The structures were energy minimized with MSI DISCOVER.
Software ordinal: 1 / Details: The structure with the lowest energy is presented
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 110 / Conformers submitted total number: 1

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