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- PDB-1a0n: NMR STUDY OF THE SH3 DOMAIN FROM FYN PROTO-ONCOGENE TYROSINE KINA... -

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Basic information

Entry
Database: PDB / ID: 1a0n
TitleNMR STUDY OF THE SH3 DOMAIN FROM FYN PROTO-ONCOGENE TYROSINE KINASE COMPLEXED WITH THE SYNTHETIC PEPTIDE P2L CORRESPONDING TO RESIDUES 91-104 OF THE P85 SUBUNIT OF PI3-KINASE, FAMILY OF 25 STRUCTURES
Components
  • FYN
  • PRO-PRO-ARG-PRO-LEU-PRO-VAL-ALA-PRO-GLY-SER-SER-LYS-THR
KeywordsCOMPLEX (PHOSPHOTRANSFERASE/PEPTIDE) / COMPLEX (PHOSPHOTRANSFERASE-PEPTIDE) / SH3 DOMAIN / POLYPROLINE-BINDING / COMPLEX (PHOSPHOTRANSFERASE-PEPTIDE) complex
Function / homology
Function and homology information


negative regulation of hydrogen peroxide biosynthetic process / response to singlet oxygen / Reelin signalling pathway / perinuclear endoplasmic reticulum membrane / perinuclear endoplasmic reticulum / regulation of toll-like receptor 4 signaling pathway / NTRK2 activates RAC1 / growth factor receptor binding / phosphatidylinositol kinase activity / regulation of glutamate receptor signaling pathway ...negative regulation of hydrogen peroxide biosynthetic process / response to singlet oxygen / Reelin signalling pathway / perinuclear endoplasmic reticulum membrane / perinuclear endoplasmic reticulum / regulation of toll-like receptor 4 signaling pathway / NTRK2 activates RAC1 / growth factor receptor binding / phosphatidylinositol kinase activity / regulation of glutamate receptor signaling pathway / heart process / Activated NTRK2 signals through FYN / 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 / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / interleukin-18-mediated signaling pathway / myeloid leukocyte migration / regulation of calcium ion import across plasma membrane / phosphatidylinositol 3-kinase complex / T follicular helper cell differentiation / reelin-mediated signaling pathway / PI3K events in ERBB4 signaling / phosphatidylinositol 3-kinase regulatory subunit binding / neurotrophin TRKA receptor binding / Platelet Adhesion to exposed collagen / positive regulation of protein localization to membrane / cellular response to L-glutamate / Activated NTRK2 signals through PI3K / G protein-coupled glutamate receptor signaling pathway / CRMPs in Sema3A signaling / cis-Golgi network / Activated NTRK3 signals through PI3K / FLT3 signaling through SRC family kinases / ErbB-3 class receptor binding / activated T cell proliferation / transmembrane receptor protein tyrosine kinase adaptor activity / Signaling by cytosolic FGFR1 fusion mutants / type 5 metabotropic glutamate receptor binding / Co-stimulation by ICOS / RHOD GTPase cycle / Nef and signal transduction / negative regulation of dendritic spine maintenance / RHOF GTPase cycle / feeding behavior / phosphatidylinositol 3-kinase complex, class IA / Co-stimulation by CD28 / kinase activator activity / Nephrin family interactions / natural killer cell activation / DCC mediated attractive signaling / EPH-Ephrin signaling / Signaling by LTK in cancer / positive regulation of leukocyte migration / Ephrin signaling / Signaling by LTK / dendritic spine maintenance / CD28 dependent Vav1 pathway / 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 / dendrite morphogenesis / growth hormone receptor signaling pathway / tau-protein kinase activity / Regulation of KIT signaling / Signaling by ALK / leukocyte migration / phospholipase activator activity / RHOV GTPase cycle / PI-3K cascade:FGFR3 / RHOB GTPase cycle / natural killer cell mediated cytotoxicity / Co-inhibition by CTLA4 / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / GP1b-IX-V activation signalling / EPHA-mediated growth cone collapse / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / Dectin-2 family / RHOC GTPase cycle / RHOJ GTPase cycle / stimulatory C-type lectin receptor signaling pathway / intracellular glucose homeostasis / phosphatidylinositol phosphate biosynthetic process / negative regulation of osteoclast differentiation / Fc-gamma receptor signaling pathway involved in phagocytosis / phospholipase binding / Synthesis of PIPs at the plasma membrane / PECAM1 interactions / response to amyloid-beta / RHOU GTPase cycle
Similarity search - Function
: / Fyn/Yrk, SH3 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 ...: / Fyn/Yrk, SH3 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 / Rho GTPase activation protein / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Tyrosine-protein kinase Fyn / Phosphatidylinositol 3-kinase regulatory subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsRenzoni, D.A. / Pugh, D.J.R. / Siligardi, G. / Das, P. / Morton, C.J. / Rossi, C. / Waterfield, M.D. / Campbell, I.D. / Ladbury, J.E.
Citation
Journal: Biochemistry / Year: 1996
Title: Structural and thermodynamic characterization of the interaction of the SH3 domain from Fyn with the proline-rich binding site on the p85 subunit of PI3-kinase.
Authors: Renzoni, D.A. / Pugh, D.J. / Siligardi, G. / Das, P. / Morton, C.J. / Rossi, C. / Waterfield, M.D. / Campbell, I.D. / Ladbury, J.E.
#1: Journal: Structure / Year: 1996
Title: Solution Structure and Peptide Binding of the SH3 Domain from Human Fyn
Authors: Morton, C.J. / Pugh, D.J. / Brown, E.L. / Kahmann, J.D. / Renzoni, D.A. / Campbell, I.D.
History
DepositionDec 5, 1997Processing site: BNL
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 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_ref_seq_dif
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_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PRO-PRO-ARG-PRO-LEU-PRO-VAL-ALA-PRO-GLY-SER-SER-LYS-THR
B: FYN


Theoretical massNumber of molelcules
Total (without water)9,1042
Polymers9,1042
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)25 / 50
Representative

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Components

#1: Protein/peptide PRO-PRO-ARG-PRO-LEU-PRO-VAL-ALA-PRO-GLY-SER-SER-LYS-THR / P2L


Mass: 1405.640 Da / Num. of mol.: 1 / Fragment: P85 SUBUNIT OF PI3-KINASE, RESIDUES 91 - 104
Source method: isolated from a genetically manipulated source
References: UniProt: P27986
#2: Protein FYN


Mass: 7698.238 Da / Num. of mol.: 1 / Fragment: SH3 DOMAIN, RESIDUES 82 - 148 / Mutation: N-TERMINAL GS FROM EXPRESSION SYSTEM
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P06241, EC: 2.7.1.112

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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
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR softwareName: X-PLOR / Version: 3.1 / Developer: BRUNGER / Classification: refinement
NMR ensembleConformers calculated total number: 50 / Conformers submitted total number: 25

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